tag:blogger.com,1999:blog-75836745115198088332024-03-19T06:21:08.108+00:00Rosa RubicondiorReligion, Creationism, evolution, science and politics from a centre-left atheist humanist. The blog religious frauds tell lies about.Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.comBlogger3272125tag:blogger.com,1999:blog-7583674511519808833.post-28543626338879566152024-03-18T23:15:00.001+00:002024-03-18T23:18:28.748+00:00Religion News - People Who Believe Absurdities Will Commit Atrocities!<div class="title-box" style="height: 900px; display: none">
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<div class="left-column" style="text-align: left; flex: 2">The blood sacrifice on which the Christian religion is founded</div>
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<a href="https://www.psychologytoday.com/us/blog/why-religion-is-natural-and-science-is-not/202311/why-religions-seem-to-involve-outlandish">Why Religions Seem to Involve Outlandish Beliefs | Psychology Today</a><br>
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It's axiomatic that people who can believe absurdities can be persuaded to commit atrocities.<br>
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One only need look at the history of just about every world religion to know that is especially true of people who hold to religious beliefs, yet most religious people will look at other religions and wonder how on Earth they can believe that nonsense, while having no understanding why others who look at their beliefs have the same thoughts.<br>
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How many devout Christians, for example, would find nothing strange in the belief that the sun was swallowed each evening by the goddess Isis, who then gave birth to it every morning or that ancient Celtic chiefs physically mated with the Earth goddess at Tara to unite the Irish people with the land they lived on?<br>
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Yet those same Christians have no difficulty believing that the blood sacrifice of an innocent person can atone for collective 'sins' inherited from ancient ancestors or that the dismembered bodies of ancient holy men can somehow persuade a god to change his perfect plans for their better one, or an omniscient, omnibenevolent god needs to be told about a wrong and why if should be righted, or a mind-reading god needs to be told their thoughts.<br>
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And a Moslem who believes the founder of their religion split the moon in half and flew to Heaven on a magic flying creature finds it incomprehensible that saying prayers to a painting of an ancient holy man or priest can change the direction of the universe, or that the prohibition on 'graven images' doesn't apply to gold-covered icons or depictions of a god nailed to a stick, worn by people who believe tiny images of a blood sacrifice or miniature instrument of torture worn around their neck protects them from evil spirits?<br>
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There are even people who believe the sun can be made to perform strange maneuvers in the sky while no-one else on Earth noticed it and without Earth itself needing to suddenly change its speed and direction of rotation or orbital path round the sun. Even the leaders of a major branch of Christianity, with a whole panel of expert scientific advisors, believe that really happened and continue to send people to Fatima where it is alleged to have happened - just one of the many equally implausible and evidence-free beliefs orthodox Catholics needs to hold. <br>
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Even coeliac suffering Catholics can believe a piece of wafer, when the right spells are cast over it, miraculously becomes the body of a dead god to be consumed in a cannibalistic ritual, while knowing they need to avoid eating it to avoid the consequences of gluten intolerance! That's a condition of belonging to a cultural group called 'Catholics'.<br>
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And in defence of those bizarre and irrational beliefs, people will be induced to go to war and 'ethnically cleanse' people who reject their ridiculous notions, that the faithful would also find ridiculous if they were part of someone else's religion.<br>
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So, what it is about religions and cults in general, that can induce otherwise sensible people who can even cross a busy road without responsible adult supervision, to hold to such bizarre beliefs with such conviction and apparently oblivious of their impossibility?<br>
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According to a book by philosopher, Neil Van Leeuwen, <a href="https://www.hup.harvard.edu/catalog.php?isbn=9780674290334">Religion as Make-Believe: A Theory of Belief, Imagination, and Group Identity</a>, the English word 'belief' can take two forms: one is a factual belief such as the belief that something that can be seen is really there - a pencil is on a table, a bus is at a bus stop, because they can be seen to be factual beliefs; and the other is 'groupish belief' where a claim is accepted as factual because the group believe it is. <br>
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Anyone can see a pencil on a table, or a bus is at a bus-stop, and will modify the belief if it is removed. <br>
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On the other hand, because the group believes Jesus rose from the dead and ascended bodily to Heaven, or because he was sacrificed to absolve us of 'sin', they really did happen, even though the believer never witnessed it. Heaven must be a real place and 'sin' must be something that needs to be absolved because the group believes them.<br>
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To modify those beliefs would be to leave the group and lose the group affiliation, and the cultural identity, that a shared belief conveys.<br>
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In other words, it's not the evidence that convinced the believe but the necessity to believe as a condition of group affiliation and cultural identity that is the 'evidence' on which belief is based.<br>
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It is the dilution of shared responsibility that makes the bizarre and irrational believable - 'every-one' else believes it so they must be right, no matter how stupid the belief is. <br>
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<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgm_QFl9zh2B0_3fONebvxd9Puj9Sjg4bkbKAnpc_48hzTqEahIa05Rrwhyphenhyphensr19n-52CyZYPFWjOY4NSUzEJJzuRBaRp9cg9KgWoaEDfxP-fTF0ov0o9tNzNXRgUKBIU9jZ1bzF4JgzKDPXXe1vflp_ADVcCyujmDcaoQjg-uCJRck0PFAAyOmN2ofI48HF/s1600/Srebrenica_massacre_memorial_gravestones_2009_1.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgm_QFl9zh2B0_3fONebvxd9Puj9Sjg4bkbKAnpc_48hzTqEahIa05Rrwhyphenhyphensr19n-52CyZYPFWjOY4NSUzEJJzuRBaRp9cg9KgWoaEDfxP-fTF0ov0o9tNzNXRgUKBIU9jZ1bzF4JgzKDPXXe1vflp_ADVcCyujmDcaoQjg-uCJRck0PFAAyOmN2ofI48HF/s1600/Srebrenica_massacre_memorial_gravestones_2009_1.jpg"/></a>
<div class="captionc">Bosniak Muslim men and boys - victims of Orthodox Christian fascists</div></div>And in the same way, dilution of shared responsibility makes an atrocity possible, and participating in it is a condition of group membership and cultural identity. So <a href="https://en.wikipedia.org/wiki/Srebrenica_massacre" target="_blank">massacring 8000 Bosniak men and boys in Srebrenica</a>, murdering Jews in the death camps or participating in the <a href="https://en.wikipedia.org/wiki/Armenian_genocide" target="_blank">Armenian</a> or <a href="https://en.wikipedia.org/wiki/Rwandan_genocide" target="_blank">Rwanda Genocides</a> (to name three recent faith-based atrocities) was what the group did, and to be in the group meant participation in the atrocity. If you're not with us, you're against us.<br>
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Driven by the bizarre religious beliefs of America evangelicals, fools were persuaded that the serial adulterer, habitual liar and head of a family crime syndicate with an acute narcissistic personality disorder, Donald Trump, was ordained by God to lead America out of the clutches of a cabal of Satanic Paedophiles. So, without the slightest evidence to support those beliefs, other than that others of the cult believed them, a mindless mob of manipulated idiots were prepared to launch an attempted coup d’etat with the intention of killing the Vice President and leading Democrats and handing over power to the loser in a democratic election.
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<a href="https://www.uottawa.ca/about-us/media/news/new-research-suggests-our-universe-has-no-dark-matter">New research suggests that our universe has no dark matter | About us</a><br>
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A leading theoretical physicist has questioned whether dark matter really exists.<br>
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Dark Matter is a placeholder for what appears to be mass without substance which suffuses the universe, observable only by the gravity it exerts and thought by mainstream cosmologists to account for 27% of the matter in the universe with 'ordinary' matter making up just 5%. The rest - 68% - being composed of dark energy, another placeholder for something theory says should be there to account for the expansion of the universe, but which we don't have a model for in the standard model of particles and related fields.<br>
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I don't pretend to understand this stuff, but I'll post it here by way of a rebuttal of creationist claims that scientists devise experiments to try to prove preconceptions and that peer-review is just to ensure conformity to scientific orthodoxy.<br>
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Besides, the HTML coding is the sort of challenge I enjoy.<br>
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In fact, science is about continued reassessment and revision with names made not by confirming preconceptions but by overthrowing established consensus or exposing flaws in it which require further investigation.
The leading theoretical physicist is Professor Rajendra Gupta of the Faculty of Science, University of Ottawa, Canada, who has just published a paper in <i>The Astrophysical Journal</i>. He has also authored an earlier paper which he believes shows the Universe to be about twice as old as the mainstream consensus believes it to be, so he can hardly be described as subscribing to some establishment orthodoxy. His work is explained in a University of Ottawa News release:
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<blockquote class="blockit"><span style="font-weight: normal">The current theoretical model for the composition of the universe is that it’s made of ‘normal matter,’ ‘dark energy’ and ‘dark matter.’ A new uOttawa study challenges this.</span><br>
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A University of Ottawa study published today challenges the current model of the universe by showing that, in fact, it has no room for dark matter.<br>
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In cosmology, the term “dark matter” describes all that appears not to interact with light or the electromagnetic field, or that can only be explained through gravitational force. We can’t see it, nor do we know what it’s made of, but it helps us understand how galaxies, planets and stars behave.<br>
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Rajendra Gupta, a physics professor at the Faculty of Science, used a combination of the <a href="https://doi.org/10.48550/arXiv.2201.11667" target="_blank">covarying coupling constants</a> (CCC) and “<a href="https://ui.adsabs.harvard.edu/abs/2017JAHH...20....2K/abstract" target="_blank">tired light</a>” (TL) theories (the CCC+TL model) to reach this conclusion. This model combines two ideas — about how the forces of nature decrease over cosmic time and about light losing energy when it travels a long distance. It’s been tested and has been shown to match up with several observations, such as about how galaxies are spread out and how light from the early universe has evolved.<br>
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This discovery challenges the prevailing understanding of the universe, which suggests that roughly 27% of it is composed of dark matter and less than 5% of ordinary matter, remaining being the dark energy. <br>
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<span>Challenging the need for dark matter in the universe</span><br>
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<div class="block"><p>The study's findings confirm that our previous work (“<a href="https://doi.org/10.1093/mnras/stad2032" target="_blank">JWST early Universe observations and ΛCDM</a>”) about the <a href="https://doi.org/10.1093/mnras/stad2032" target="_blank">age of the universe</a> being 26.7 billionyears has allowed us to discover that the universe does not require dark matter to exist. In standard cosmology, the accelerated expansion of the universe is said to be caused by dark energy but is in fact due to the weakening forces of nature as it expands, not due to dark energy.</p>
<p>There are several papers that question the existence of dark matter, but mine is the first one, to my knowledge, that eliminates its cosmological existence while being consistent with key cosmological observations that we have had time to confirm.</p>
<div class="creditl">Professor Rajendra Gupta<br>
Faculty of Science<br>
University of Ottawa, Canada.</div></div>
“Redshifts” refer to when light is shifted toward the red part of the spectrum. The researcher analyzed data from recent papers on the distribution of galaxies at low redshifts and the angular size of the sound horizon in the literature at high redshift.
By challenging the need for dark matter in the universe and providing evidence for a new cosmological model, this study opens up new avenues for exploring the fundamental properties of the universe.
The study, <a href="https://iopscience.iop.org/article/10.3847/1538-4357/ad1bc6" target="_blank">Testing CCC+TL Cosmology with Observed Baryon Acoustic Oscillation</a>, was published in the peer-reviewed Astrophysical Journal.
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The following extract from his open access paper is highly mathematical, so if you can understand it, you're better at higher maths than I could ever hope to be:<br>
<blockquote class="blockit"><span>Abstract</span><br>
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The primary purpose of this paper is to see how well a recently proposed new model fits (a) the position of the baryon acoustic oscillation (BAO) features observed in the large-scale distribution of galaxies and (b) the angular size measured for the sound horizon due to BAO imprinted in the cosmic microwave background (CMB) anisotropy. The new model is a hybrid model that combines the tired light (TL) theory with a variant of the ΛCDM model in which the cosmological constant is replaced with a covarying coupling constants' (CCC) parameter α. This model, dubbed the CCC+TL model, can fit the Type Ia supernovae Pantheon+ data as accurately as the ΛCDM model, and also fit the angular size of cosmic dawn galaxies observed by the James Webb Space Telescope, which is in tension with the ΛCDM model. The results we obtained are 151.0 (±5.1) Mpc for the absolute BAO scale at the current epoch, and the angular size of the sound horizon θ<sub class="small">sh</sub> = 0°60, matching Planck's observations at the surface of the last scattering when the baryon density is set to 100% of the matter density and ∣α∣ is increased by 5.6%. It remains to be seen if the new model is consistent with the CMB power spectrum, the Big Bang nucleosynthesis of light elements, and other critical observations.<br>
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<span>1. Introduction</span><br>
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One of the most important tests of a cosmological model is to reproduce in the galaxy distribution the signatures of the baryon acoustic oscillations (BAOs) resulting from the sound waves in the baryon–photon fluid at the time when photons and baryon decoupled, and radiation traveled freely in space. This radiation is observed as the cosmic microwave background (CMB). The BAO features are detected as tiny temperature fluctuations (anisotropies) in the highly isotropic CMB observations. These oscillations are believed to develop into large-scale structures as higher-density regions of perturbations become the nucleation points where galaxies form. Thus, the two features are expected to be correlated, and BAO could serve as a fundamental standard ruler to test cosmological models (Peebles & Yu <a class="newtooltip">1970</a>; Bond & Efstathiou <a class="newtooltip">1984</a>; Eisenstein & Hu <a class="newtooltip">1998</a>; Meiksin et al. <a class="newtooltip">1999</a>). The observation of BAO features at different redshifts endorses the propagation of primordial gravitational instability (Cole et al. <a class="newtooltip">2005</a>; Eisenstein et al. <a class="newtooltip">2005.1</a>; Fronenberg et al. <a class="newtooltip">2023</a>). Xu et al. (<a class="newtooltip">2023.1</a>) have recently established evidence for BAOs from galaxy–ellipticity correlations. Tully et al. (<a class="newtooltip">2023.2</a>) have presented remarkably strong evidence for the existence of an individual BAO signal at <i>z</i> = 0.068. Shao et al. (<a class="newtooltip">2023.48</a>) raised the possibility of using the angular scale of cosmic inhomogeneities as a new, model-independent way to constrain cosmological parameters.<br>
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Sutherland (<a class="newtooltip">2012</a>) succinctly stated, "...the observed BAO features support the standard cosmology in several independent ways: the existence of features supports the basic gravitational instability paradigm for structure formation; the relative weakness of the BAO feature supports the ∼1:5 ratio of baryons to dark matter, since baryon-dominated universe would have a BAO feature much stronger than observed; and the observed length-scale of the feature in redshift space is consistent with the concordance ΛCDM model derived from the CMB and other observations, with Ω<sub class="small">m</sub> ≈ 0.27 and H<sub class="small">0</sub> ≈ 70 km s<sup class="small">−1</sup> Mpc<sup class="small">−1</sup> (Komatsu et al. <a class="newtooltip">2011</a>)."<br>
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Weinberg et al. (<a class="newtooltip">2013</a>) have shown that BAO features in the matter power spectrum (galaxies), when combined with the tracer power spectrum (CMB), can effectively constrain the cosmological parameter and test a model. For our purpose, we are interested in the BAO measurements of angular separations θBAO of pairs of galaxies at different redshift values. Carvalho et al. (<a class="newtooltip">2016</a>) used 409,337 luminous red galaxies in the redshift range <i>z</i> = [0.440, 0.555] to estimate θ<sub class="small">BAO</sub>(<i>z</i>) at six redshift shells. Their work was extended to include observations that provided θ<sub class="small">BAO</sub> at <i>z</i> = 0.11 within <i>z</i> = [0.105, 0.115] (Carvalho et al. <a class="newtooltip">2021</a>), and at up to <i>z</i> = 0.65 (Lemos et al. <a class="newtooltip">2023.3</a>). We will use their data to explore if the recently proposed hybrid model (Gupta <a class="newtooltip">2023.4</a>) is consistent with features of the BAOs observed in the CMB and matter power spectra. This model comprises a modified ΛCDM model permitting the covariation of coupling constants (CCC) and includes the tired light (TL) phenomenon to partially account for the observed redshift. This two-parameter hybrid model, dubbed CCC+TL, was able to account for the bewildering observation by the James Webb Space Telescope (JWST) showing unexpected morphology of galaxies existent at cosmic dawn. The model parameters H<sub class="small">0</sub> and <i>α</i>, the latter determining the strength of the coupling constants' variation and replaces Λ of the standard model, are determined by fitting the Type Ia supernovae (Pantheon+) data (Brout et al. <a class="newtooltip">2022</a>; Scolnic et al. <a class="newtooltip">2022.1</a>).<br>
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The galaxies observed in the early Universe, some less than 500 million years after the Big Bang, appear to have shapes, structures, and masses similar to those in existence for billions of years (e.g., Naidu et al. <a class="newtooltip">2022.2</a>a, <a class="newtooltip">2022.3</a>b; Curtis-Lake et al. <a class="newtooltip">2023.5</a>; Hainline et al. <a class="newtooltip">2023.6</a>; Labbé et al. <a class="newtooltip">2023.7</a>; Robertson et al. <a class="newtooltip">2023.8</a>) but with angular sizes 1 order of magnitude smaller than expected for such galaxies (e.g., Finkelstein et al. <a class="newtooltip">2022.4</a>; Naidu et al. <a class="newtooltip">2022.2</a>a, <a class="newtooltip">2022.3</a>b; Yang et al. <a class="newtooltip">2022.7</a>; Adams et al. <a class="newtooltip">2023.9</a>; Atek et al. <a class="newtooltip">2023.10</a>b; Austin et al. <a class="newtooltip">2023.11</a>; Baggen et al. <a class="newtooltip">2023.12</a>; Chen et al. <a class="newtooltip">2023.13</a>b; Donnan et al. <a class="newtooltip">2023.14</a>; Ono et al. <a class="newtooltip">2023.15</a>; Tacchella et al. <a class="newtooltip">2023.16</a>a, <a class="newtooltip">2023.17</a>b; Wu et al. <a class="newtooltip">2023.18</a>). Attempts have been made to resolve the problem by modifying the star and galaxy formation models (e.g., Haslbauer et al. <a class="newtooltip">2022.8</a>; Inayoshi et al. <a class="newtooltip">2022.9</a>; Atek et al. <a class="newtooltip">2023.19</a>a; Kannan et al. <a class="newtooltip">2023.20</a>; Keller et al. <a class="newtooltip">2023.21</a>; Mason et al. <a class="newtooltip">2023.22</a>; McCaffrey et al. <a class="newtooltip">2023.23</a>; Mirocha & Furlanetto <a class="newtooltip">2023.24</a>; Regan <a class="newtooltip">2023.25</a>; Whitler et al. <a class="newtooltip">2023.26</a>a, <a class="newtooltip">2023.27</a>b; Yajima et al. <a class="newtooltip">2023.28</a>), such as by compressing time for the formation of Population III stars and galaxies more and more by considering the presence of primordial massive black hole seeds, and super-Eddington accretion rates in the early Universe (Ellis <a class="newtooltip">2022.10</a>; Larson et al. <a class="newtooltip">2022.11</a>; Brummel-Smith et al. <a class="newtooltip">2023.29</a>; Chantavat et al. <a class="newtooltip">2023.30</a>; Dolgov <a class="newtooltip">2023.31</a>; Maiolino et al. <a class="newtooltip">2023.32</a>; Reinoso et al. <a class="newtooltip">2023.33</a>). Other researchers (Boyett et al. <a class="newtooltip">2023.34</a>; Bunker et al. <a class="newtooltip">2023.35</a>; Dekel et al. <a class="newtooltip">2023.36</a>; Eilers et al. <a class="newtooltip">2023.37</a>; Haro et al. <a class="newtooltip">2023.38</a>; Long et al. <a class="newtooltip">2023.39</a>; Looser et al. <a class="newtooltip">2023.40</a>) are concerned if they provide satisfactory answers. Some even suggest looking for new physics (Chen et al. <a class="newtooltip">2023.41</a>a; Mauerhofer & Dayal <a class="newtooltip">2023.42</a>; Schneider et al. <a class="newtooltip">2023.43</a>). In the words of Garaldi et al. (<a class="newtooltip">2023.44</a>), "Cosmological simulations serve as invaluable tools for understanding the Universe. However, the technical complexity and substantial computational resources required to generate such simulations often limit their accessibility within the broader research community. Notable exceptions exist, but most are not suited for simultaneously studying the physics of galaxy formation and cosmic reionization during the first billion years of cosmic history." According to Xiao et al. (<a class="newtooltip">2023.45</a>), "Massive optically dark galaxies unveiled by JWST challenge galaxy formation models." (See also Greene et al. <a class="newtooltip">2023.46</a>; Katz et al. <a class="newtooltip">2023.47</a>; Ormerod et al. <a class="newtooltip">2024</a>.)<br>
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The CCC+TL model predicts the age of the Universe as 26.7 Gyr against the generally accepted value of 13.8 Gyr. This is of deep concern and needs the model validation against multiple observations, including BAOs, CMB, Big Bang nucleosynthesis (BBN), and globular cluster ages. Our focus here is on BAOs. This paper is organized to include the theoretical background in Section 2, results in Section 3, discussion in Section 4, and conclusions in Section 5.<br>
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<span>2. Theoretical Background</span><br>
<br>
<i>CCC Model</i>. The modified FLRW metric, incorporating the covarying coupling constant (CCC) concept, is (Gupta <a class="newtooltip">2023.4</a>) 1
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</mtable>
</math>
and the continuity equation is<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:4">
<mtext>(4)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mrow data-mjx-texclass="ORD">
<mover>
<mi>ε</mi>
<mo>˙</mo>
</mover>
</mrow>
<mo>+</mo>
<mn>3</mn>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mover>
<mi>a</mi>
<mo>˙</mo>
</mover>
</mrow>
<mi>a</mi>
</mfrac>
<mo stretchy="false">(</mo>
<mi>ε</mi>
<mo>+</mo>
<mi>p</mi>
<mo stretchy="false">)</mo>
<mo>=</mo>
<mo>−</mo>
<mi>α</mi>
<mo stretchy="false">(</mo>
<mi>ε</mi>
<mo>+</mo>
<mn>3</mn>
<mi>p</mi>
<mo stretchy="false">)</mo>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
<br>
Here <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>a</mi>
</math>
is the scale factor, G<sub class="small">0</sub> is the current value of the gravitational constant, c<sub class="small">0</sub> is the current value of the speed of light, <i>k</i> is the curvature constant, <i>α</i> is a constant defining the variation of the constant through a function <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mo>=</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>α</mi>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>t</mi>
<mo>−</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</math>
with time measured from the beginning of the Universe and t<sub class="small">0</sub> the current time, <i>ε</i> is the energy density of all the components, and <i>p</i> is their pressure. Using the function <i>f(t), c(t) = c<sub class="small">0</sub> f(t)</i> and <i>G = G<sub class="small">0</sub> f(t)<sup class="small">3</sup></i> in the CCC model. The solutions of this Equation (4) for matter (<i>p</i> = 0) and radiation (p = <i>ε</i>/3) are, respectively,
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:5">
<mtext>(5)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ε</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>m</mi>
</mrow>
</msub>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ε</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>m</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
</mrow>
</msup>
<mo>,</mo>
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">and</mi>
</mrow>
<mtext> </mtext>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ε</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
</mrow>
</msub>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ε</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>4</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>2</mn>
</mrow>
</msup>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
Defining the Hubble expansion parameter as <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>H</mi>
<mo>=</mo>
<mrow data-mjx-texclass="ORD">
<mover>
<mi>a</mi>
<mo>˙</mo>
</mover>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mi>a</mi>
</math>
, we may write Equation (2) for a flat Universe (<i>k</i> = 0) as<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:6">
<mtext>(6)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>H</mi>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mo>=</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>8</mn>
<mi>π</mi>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>G</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
<mrow>
<mn>3</mn>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msubsup>
</mrow>
</mfrac>
<mi>ε</mi>
<mo stretchy="false">⇒</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ε</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<mo>≡</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>3</mn>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msubsup>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
</mrow>
<mrow>
<mn>8</mn>
<mi>π</mi>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>G</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
This equation defines the critical density of the Universe in the CCC model. Using Equations (5) and (6), we may write<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:7">
<mtext>(7)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mi>H</mi>
<mo>=</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>m</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
</mrow>
</msup>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>4</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>2</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>−</mo>
<mi>α</mi>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
In this equation, relative matter density Ω<sub class="small">m,0</sub> = ε<sub class="small">m,0</sub>/ε<sub class="small">c,0</sub> and relative radiation density Ω<sub class="small">r,0</sub> = ε<sub class="small">r,0</sub>/ε<sub class="small">c,0</sub>. Since Ω<sub class="small">r,0</sub> ≪ Ω<sub class="small">m,0</sub>, and we do not have to worry about the dark energy density in the CCC model, Equation (7) simplifies to<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:8">
<mtext>(8)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mi>H</mi>
<mo>=</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
</mrow>
</msup>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>4</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>2</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>−</mo>
<mi>α</mi>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
Since the observations are made using redshift <i>z</i>, we have to see how the scale factor <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>a</mi>
</math>
relates to <i>z</i> in the CCC model. Along the spatial geodesic (<i>θ</i> and <i>ϕ</i> constant) between the observer and the source at a fixed time <i>t</i> using the modified FLRW metric (Equation (1))<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:9">
<mtext>(9)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>s</mi>
</mrow>
<mo>=</mo>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>r</mi>
</mrow>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math>
Thus, the proper distance for commoving coordinate <i>r</i> (since <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>a</mi>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>≡</mo>
<mn>1</mn>
<mo>=</mo>
<mi>f</mi>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</math>)
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:10">
<mtext>(10)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>p</mi>
</mrow>
</msub>
<mo>=</mo>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
</mrow>
</msubsup>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>r</mi>
</mrow>
<mo>=</mo>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mi>r</mi>
<mo stretchy="false">⇒</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>p</mi>
</mrow>
</msub>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>=</mo>
<mi>r</mi>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
Since light follows the null geodesic, Equation (1) yields for a light emitted by a source at a time t<sub class="small">e</sub> and detected by the observer at a time t<sub class="small">0</sub><br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:11">
<mtext>(11)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>e</mi>
</mrow>
</msub>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>t</mi>
</mrow>
<mrow>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
</mrow>
</mfrac>
<mo>=</mo>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
</mrow>
</msubsup>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>r</mi>
</mrow>
<mo>=</mo>
<mi>r</mi>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>p</mi>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo stretchy="false">)</mo>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
It can now be easily shown (e.g., Ryden 2017) that <i>a</i> = 1/(1 + <i>z</i>), i.e., the same as for the ΛCDM model.<br>
<br>
We now need to transpose <i>f(t)</i> to <i>f(z)</i>, as it is the latter that we will require in calculating the proper distance. Following Gupta's (<a class="newtooltip">2023.4</a>) Equations (24)–(27), we have<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:12">
<mtext>(12)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mtable columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>=</mo>
<mi>x</mi>
<mo>=</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>D</mi>
<mrow>
<mn>2</mn>
<mi>A</mi>
</mrow>
</mfrac>
<mo>+</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>D</mi>
<mrow>
<mn>2</mn>
<mi>A</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mo>+</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>C</mi>
<mrow>
<mn>3</mn>
<mi>A</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>3</mn>
</mrow>
</msup>
</mtd>
</mtr>
<mtr>
<mtd>
<mo>+</mo>
<mstyle scriptlevel="0">
<mspace width="0.167em"></mspace>
</mstyle>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>D</mi>
<mrow>
<mn>2</mn>
<mi>A</mi>
</mrow>
</mfrac>
<mo>−</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>D</mi>
<mrow>
<mn>2</mn>
<mi>A</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mo>+</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mi>C</mi>
<mrow>
<mn>3</mn>
<mi>A</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>3</mn>
</mrow>
</msup>
<mo>,</mo>
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">where</mi>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd>
<mi>A</mi>
<mo>=</mo>
<mn>1</mn>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mn>3</mn>
<mn>2</mn>
</mfrac>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mi>α</mi>
</mfrac>
<mo>=</mo>
<mn>1</mn>
<mo>−</mo>
<mi>C</mi>
<mo>,</mo>
</mstyle>
</mstyle>
</mtd>
</mtr>
<mtr>
<mtd>
<mi>D</mi>
<mo>=</mo>
<mo>−</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>,</mo>
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">and</mi>
</mrow>
<mtext> </mtext>
<mi>x</mi>
<mo>=</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mo>−</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mi>α</mi>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>t</mi>
<mo>−</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mn>2</mn>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
Since the scale factor <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>a</mi>
</math>
= 1/(1 + <i>z</i>), we have D = −[1/(1 + <i>z</i>)]<sup class="small">3/2</sup>. Thus, the above equation provides the function <i>f(<i>z</i>, H<sub class="small">0</sub>, α)</i> for the matter-dominated Universe. What about its expression in the radiation-dominated Universe? Since <i>z</i> ≫ 1 in such a Universe, i.e., <i>t</i> ≪ t<sub class="small">0</sub>, it is easy to see that <math xmlns="http://www.w3.org/1998/Math/MathML">
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mo>=</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>α</mi>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>t</mi>
<mo>−</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</math>
approaches a constant value. We can, therefore, use the same expression for <i>f(z)</i>, i.e., Equation (12) for all values of <i>z</i>.
We now need the expression for the proper distance d<sub class="small">p</sub>. Since <math xmlns="http://www.w3.org/1998/Math/MathML">
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>t</mi>
</mrow>
<mo>=</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>t</mi>
</mrow>
<mo>×</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>a</mi>
</mrow>
<mo>=</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mover>
<mi>a</mi>
<mo>˙</mo>
</mover>
</mrow>
</math>
, we may write Equation (10)<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:13">
<mtext>(13)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>p</mi>
</mrow>
</msub>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>e</mi>
</mrow>
</msub>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>t</mi>
</mrow>
<mrow>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
</mrow>
</mfrac>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>e</mi>
</mrow>
</msub>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>a</mi>
</mrow>
<mrow>
<mi>a</mi>
<mrow data-mjx-texclass="ORD">
<mover>
<mi>a</mi>
<mo>˙</mo>
</mover>
</mrow>
</mrow>
</mfrac>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>e</mi>
</mrow>
</msub>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>a</mi>
</mrow>
<mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>a</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mi>H</mi>
</mrow>
</mfrac>
<mo>,</mo>
</mstyle>
</mstyle>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
and since <i>a</i> = 1/(1 + <i>z</i>), <i>da = − dz/(1 + z)<sup class="small">2</sup> = −dza<sup class="small">2</sup></i>, we get, using Equation (8),<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:14">
<mtext>(14)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mtable columnalign="center" columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>p</mi>
</mrow>
</msub>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>z</mi>
</mrow>
<mi>H</mi>
</mfrac>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
</msubsup>
</mstyle>
</mtd>
</mtr>
<mtr>
<mtd>
<mo>×</mo>
<mstyle scriptlevel="0">
<mspace width="0.167em"></mspace>
</mstyle>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>z</mi>
</mrow>
<mrow>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
</mrow>
</msup>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>4</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>2</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>−</mo>
<mi>α</mi>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
We can now follow TL and CCC+TL models developed by Gupta (2023) for our computations in this work.
<i>Sound Horizon Distance and Angular Size.</i> Denoted as d<sub class="small">sh</sub>(t<sub class="small">ls</sub>), it represents the distance sound travels at the speed c<sub class="small">s</sub> (t) in the photon–baryon fluid from the Big Bang until such plasma cools down and disappears due to the formation of atoms, i.e., until the time of last scattering <i>t<sub class="small">ls</sub></i> corresponding to the redshift <i>z<sub class="small">ls</sub></i>. One may write the sound horizon distance (Durrer <a class="newtooltip">2021.2</a>), using the metric given by Equation (1) for the CCC+TL model, as<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:15">
<mtext>(15)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">sh</mi>
</mrow>
</mrow>
</msub>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>=</mo>
<mi>a</mi>
<mo stretchy="false">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
<mo stretchy="false">)</mo>
<mi>f</mi>
<mo stretchy="false">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
<mo stretchy="false">)</mo>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
</mrow>
</msubsup>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>s</mi>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>t</mi>
</mrow>
</mrow>
<mrow>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
The speed of sound in terms of the speed of light is given by (Durrer 2021)<br>
<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:16">
<mtext>(16)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right" columnspacing="" rowspacing="3pt">
<mtr>
<mtd>
<mtable columnalign="right center left" columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>s</mi>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
</mtd>
<mtd>
<mo>≈</mo>
</mtd>
<mtd>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
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<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msqrt>
<mn>3</mn>
</msqrt>
</mfrac>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
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<mn>1</mn>
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<mn>3</mn>
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<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>b</mi>
</mrow>
</msub>
</mrow>
<mrow>
<mn>4</mn>
<msub>
<mrow data-mjx-texclass="ORD">
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<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
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<mrow data-mjx-texclass="ORD">
<mi>r</mi>
</mrow>
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</mrow>
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<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
</mstyle>
</mtd>
</mtr>
<mtr>
<mtd></mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
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<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msqrt>
<mn>3</mn>
</msqrt>
</mfrac>
<msup>
<mrow data-mjx-texclass="ORD">
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<mn>3</mn>
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<mi mathvariant="normal">Ω</mi>
</mrow>
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<mi>b</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
</mrow>
<mrow>
<mn>4</mn>
<msub>
<mrow data-mjx-texclass="ORD">
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<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
</mrow>
</mfrac>
<mi>a</mi>
<mo stretchy="false">(</mo>
<mi>t</mi>
<mo stretchy="false">)</mo>
<mi>f</mi>
<mo stretchy="false">(</mo>
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</mstyle>
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<mo>−</mo>
<mn>1</mn>
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<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>,</mo>
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">or</mi>
</mrow>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:17">
<mtext>(17)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>s</mi>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<mi>z</mi>
<mo stretchy="false">)</mo>
<mo>≈</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msqrt>
<mn>3</mn>
</msqrt>
</mfrac>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>3</mn>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>b</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<mi>f</mi>
<mo stretchy="false">(</mo>
<mi>z</mi>
<mo stretchy="false">)</mo>
</mrow>
<mrow>
<mn>4</mn>
<msub>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo stretchy="false">)</mo>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>,</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
where Ω<sub class="small">b</sub> is the baryon density and Ω<sub class="small">r</sub> is the radiation density. Following Equations (13) and (14), we get<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:18">
<mtext>(18)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<mtable columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">sh</mi>
</mrow>
</mrow>
</msub>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>=</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mn>1</mn>
<mrow>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
</mrow>
</mfrac>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mo data-mjx-texclass="OP">∫</mo>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">∞</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">ls</mi>
</mrow>
</mrow>
</msub>
</mrow>
</msubsup>
</mstyle>
</mtd>
</mtr>
<mtr>
<mtd>
<mo>×</mo>
<mstyle scriptlevel="0">
<mspace width="0.167em"></mspace>
</mstyle>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>s</mi>
</mrow>
</msub>
<mo stretchy="false">(</mo>
<mi>z</mi>
<mo stretchy="false">)</mo>
<mrow data-mjx-texclass="ORD">
<mi>d</mi>
<mi>z</mi>
</mrow>
</mrow>
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<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>H</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo>+</mo>
<mi>α</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
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<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
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<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>1</mn>
</mrow>
</msup>
<mo>+</mo>
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<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="ORD">
<mi mathvariant="normal">Ω</mi>
</mrow>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>r</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
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<mrow data-mjx-texclass="INNER">
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<mn>1</mn>
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<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>4</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
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<mo>−</mo>
<mn>2</mn>
</mrow>
</msup>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>1</mn>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<mn>2</mn>
</mrow>
</msup>
<mo>−</mo>
<mi>α</mi>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
It is to be noted that the variation of the speed of light is already included in the Friedmann equations and all the expressions derived from it. In addition, we have dropped <i>f(t<sub class="small">ls</sub>)</i> in Equation (18), since we are observing dsh in today's distance unit when <i>f</i> = 1.
Next, we have to determine <i>z<sub class="small">ls</sub></i> in the CCC+TL model wherein the constants evolve as <i>c(t) = c<sub class="small">0</sub> f(t), G = G<sub class="small">0</sub> f(t)<sup class="small">3</sup>, h = h<sub class="small">0</sub> f(t)<sup class="small">2</sup></i>, and <i>k<sub class="small">B</sub> = k<sub class="small">B,0</sub> f(t)<sup class="small">2</sup></i>, and distance is measured using the speed of light (Gupta <a class="newtooltip">2022.12</a>a). How does the CMB Planck spectrum evolve with the redshift? We know that the frequency evolves as <i>ν = ν<sub class="small">0</sub>(1 + z), d ν = d ν<sub class="small">0</sub>(1 + z)</i>, and volume <i>V</i> evolves as<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:19">
<mtext>(19)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right" columnspacing="" rowspacing="3pt">
<mtr>
<mtd>
<mtable columnalign="right center left" columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<mi>V</mi>
</mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mi>a</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mi>f</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
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<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo>=</mo>
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<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
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<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
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<mi>c</mi>
</mrow>
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<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
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<mo>−</mo>
<mn>3</mn>
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<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
</mtd>
</mtr>
<mtr>
<mtd></mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
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<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<mi>f</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo>,</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
since <math xmlns="http://www.w3.org/1998/Math/MathML">
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo>=</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</math>
. The energy density of the CMB photons in the frequency range <i>ν</i> and <i>ν + d ν</i>, assuming it has the Planck spectrum, is given by<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:20">
<mtext>(20)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>u</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
<mi>d</mi>
<mi>ν</mi>
<mo>≡</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>8</mn>
<mi>π</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mtext> </mtext>
<mi>h</mi>
<mi>ν</mi>
<mtext> </mtext>
<mi>d</mi>
<mi>ν</mi>
</mrow>
<mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mspace width="0ex" height="2.5ex"></mspace>
<mo stretchy="false">[</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mstyle displaystyle="false" scriptlevel="0">
<mfrac>
<mrow>
<mi>h</mi>
<mi>ν</mi>
</mrow>
<mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>k</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>B</mi>
</mrow>
</msub>
<mi>T</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>−</mo>
<mn>1</mn>
<mspace width="0ex" height="2.5ex"></mspace>
<mo stretchy="false">]</mo>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
Therefore, the number density of photons<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:21">
<mtext>(21)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right center left" columnspacing="0em 0.278em" rowspacing="3pt">
<mtr>
<mtd></mtd>
<mtd></mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
<mo>=</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>u</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
<mi>d</mi>
<mi>ν</mi>
</mrow>
<mrow>
<mi>h</mi>
<mi>ν</mi>
</mrow>
</mfrac>
<mo>=</mo>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>8</mn>
<mi>π</mi>
<mtext> </mtext>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mtext> </mtext>
<mi>d</mi>
<mi>ν</mi>
</mrow>
<mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mspace width="0ex" height="2.5ex"></mspace>
<mo stretchy="false">[</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mstyle displaystyle="false" scriptlevel="0">
<mfrac>
<mrow>
<mi>h</mi>
<mi>ν</mi>
</mrow>
<mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>k</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>B</mi>
</mrow>
</msub>
<mi>T</mi>
</mrow>
</mfrac>
</mstyle>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>−</mo>
<mn>1</mn>
<mspace width="0ex" height="2.5ex"></mspace>
<mo stretchy="false">]</mo>
</mrow>
</mfrac>
<mo>.</mo>
</mstyle>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
The number of photons in a volume <i>V</i> is conserved, i.e.,<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:22">
<mtext>(22)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right" columnspacing="" rowspacing="3pt">
<mtr>
<mtd>
<mtable columnalign="right center left" columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
<mi>V</mi>
</mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</msub>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo stretchy="false">⇒</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<mi>f</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo>=</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</msub>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>V</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo>,</mo>
<mrow data-mjx-texclass="ORD">
<mi data-mjx-auto-op="false">or</mi>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
</mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
</msub>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mi>f</mi>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<mo>.</mo>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
We may now write<br>
<math xmlns="http://www.w3.org/1998/Math/MathML" display="block">
<mtable displaystyle="true">
<mlabeledtr>
<mtd id="mjx-eqn:23">
<mtext>(23)</mtext>
</mtd>
<mtd>
<mtable displaystyle="true" columnalign="right" columnspacing="" rowspacing="3pt">
<mtr>
<mtd>
<mtable columnalign="right center left" columnspacing="1em" rowspacing="4pt">
<mtr>
<mtd>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>n</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
</msub>
</mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>8</mn>
<mi>π</mi>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msubsup>
<mtext> </mtext>
<mi>d</mi>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
</mrow>
<mrow>
<msubsup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msubsup>
<mo stretchy="false">[</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>h</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>k</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>B</mi>
<mo>,</mo>
<mn>0</mn>
</mrow>
</msub>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>T</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>0</mn>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>−</mo>
<mn>1</mn>
<mo stretchy="false">]</mo>
</mrow>
</mfrac>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<mi>z</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>f</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<mo>,</mo>
</mstyle>
</mtd>
</mtr>
<mtr>
<mtd></mtd>
<mtd>
<mo>=</mo>
</mtd>
<mtd>
<mstyle displaystyle="true" scriptlevel="0">
<mfrac>
<mrow>
<mn>8</mn>
<mi>π</mi>
<mtext> </mtext>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>ν</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>2</mn>
</mrow>
</msup>
<mtext> </mtext>
<mi>d</mi>
<mi>ν</mi>
</mrow>
<mrow>
<msup>
<mrow data-mjx-texclass="ORD">
<mi>c</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mn>3</mn>
</mrow>
</msup>
<mo stretchy="false">[</mo>
<mi>exp</mi>
<mo data-mjx-texclass="NONE">⁡</mo>
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mi>h</mi>
<mi>ν</mi>
<mrow data-mjx-texclass="ORD">
<mo>/</mo>
</mrow>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>k</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>B</mi>
</mrow>
</msub>
<mi>T</mi>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
<mo>−</mo>
<mn>1</mn>
<mo stretchy="false">]</mo>
</mrow>
</mfrac>
<msup>
<mrow data-mjx-texclass="ORD">
<mrow data-mjx-texclass="INNER">
<mo data-mjx-texclass="OPEN">(</mo>
<mn>1</mn>
<mo>+</mo>
<msub>
<mrow data-mjx-texclass="ORD">
<mi>z</mi>
</mrow>
<mrow data-mjx-texclass="ORD">
<mi>t</mi>
</mrow>
</msub>
<mo data-mjx-texclass="CLOSE">)</mo>
</mrow>
</mrow>
<mrow data-mjx-texclass="ORD">
<mo>−</mo>
<mn>3</mn>
</mrow>
</msup>
<mo>,</mo>
</mstyle>
</mtd>
</mtr>
</mtable>
</mtd>
</mtr>
</mtable>
</mtd>
</mlabeledtr>
</mtable>
</math><br>
where T = T<sub class="small">0</sub>(1 + <i>z</i>). We can see that the CMB emission has the blackbody spectrum, but its intensity scales as
due to the TL effect. We can now determine <i>z<sub class="small">ls</sub></i> in the next section.<br>
<br>
<div class="creditl"><a href="https://iopscience.iop.org/article/10.3847/1538-4357/ad1bc6" target="_blank">Rajendra P. Gupta 2024<br>
Testing CCC+TL Cosmology with Observed Baryon Acoustic Oscillation Features<br>
<i>ApJ</i> <b>964</b> 55. doi: 10.3847/1538-4357/ad1bc6</a><br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by IOP Publishing. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
The point here is not to bamboozle anyone with (to me) incomprehensible maths, but to demonstrate the lie in the creationist claim that scientists design experiments to confirm preconceptions or to deliver paid-for results, and that the peer-review process is to ensure conformity to establishment dogma.<br>
<br>
In fact, science thrives on challenge and questioning and peer-review, as anyone who has ever read one will testify, it to ensure that the authors have established their findings with sufficient academic rigour, have constructed properly controlled experiments and eliminated possible sources of bias. Any editor of a scientific journal would positively welcome a paper that challenges establishment consensus because it is those papers that become well known in the specialty and so attract a high number of readers and citations.<br>
<br>
It's a characteristic of creationist frauds that they routinely accuse their opponents of things of which they themselves are guilty. The only people claiming to be scientists who deliver 'orthodox' conclusions are so-called 'creation scientists' who are required to swear an oath that they will only ever reach a particular conclusion as a condition of their employment. Any 'peer-review' of their work is to ensure compliance with that oath and conformity with creationist dogma before publication and payment.<br>
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-24843092622631162812024-03-16T13:01:00.003+00:002024-03-18T23:05:10.258+00:00Why Religious People Find Atheism and Science Hard To Understand - Study Shows Atheists Are Generally More Intelligent Than Religious People<div class="title-box" style="height: 700px; display: none">
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<a href="https://www.psychologytoday.com/us/blog/mr-personality/201312/why-are-religious-people-generally-less-intelligent">Why Are Religious People (Generally) Less Intelligent? | Psychology Today</a><br>
<br>
One of the frustrating things about trying to debate with religious people in the social media, especially fundamentalists and creationists, is that they seem to have difficulty understanding simple logic such as the idea that the only reason for belief is evidence or the fact that lots of people believe something doesn't affect the truth of the belief.<br>
<br>
There is also the impression (actually, it’s more than an impression, it seems to be a characteristic) that they think ignored evidence can be disregarded, so they will never read an article showing their beliefs to be wrong.<br>
<br>
They generally seem more easily fooled by, for example, believing that an internet source supports them, when it is almost a rule that a link to a science paper provided by a fundamentalist will always say the opposite to what they claim it says, or that the ridiculous parody of science they've been fed by a creationist disinformation site such as AnswersInGenesis.com that no sane person would believe, is actually what real scientists believe. They have simply swallowed a lie and didn't see any need to check.<br>
<br>
So, why do so many fundamentalists come across as limited in their ability to assimilate information and use it as the basis for opinions, other than an arrogant assumption that their beliefs must be true because they believe them, so no evidence is required and any contradictory evidence can be dismissed out of hand as 'wrong' or 'lies' or part of a giant conspiracy, and why do so many creationists came across as having the thinking ability of a toddler with a teleological view of the universe where even elementary particles are sentient and need to be told how to behave and which rules they must obey? <br>
<br>
A meta-analysis of 63 earlier studies showed a statistically significant negative correlation between IQ and religiosity.<br>
<br><a name='more'></a>
The 2013 report, by Miron Zuckerman and Jordan Silberman of Rochester University, NY, USA together with Judith A. Hall of Northeastern University, Boston, MA, USA, the body of which is annoyingly behind a paywall, was published in the journal <i>Personality and Social Psychology Review</i> and lists three possible reasons for this correlation. <br>
<br>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
A meta-analysis of 63 studies showed a significant negative association between intelligence and religiosity. The association was stronger for college students and the general population than for participants younger than college age; it was also stronger for religious beliefs than religious behavior. For college students and the general population, means of weighted and unweighted correlations between intelligence and the strength of religious beliefs ranged from −.20 to −.25 (mean r = −.24). Three possible interpretations were discussed. First, intelligent people are less likely to conform and, thus, are more likely to resist religious dogma. Second, intelligent people tend to adopt an analytic (as opposed to intuitive) thinking style, which has been shown to undermine religious beliefs. Third, several functions of religiosity, including compensatory control, self-regulation, self-enhancement, and secure attachment, are also conferred by intelligence. Intelligent people may therefore have less need for religious beliefs and practices.
</blockquote>
In summary, the three reasons the researchers identified are:
<ol class="dbl1 bold">
<li>Intelligent people are less likely to conform to religious dogma.</li>
<li>Intelligent people are analytical rather than intuitive and analytical thinking tends to undermine religious superstitions.</li>
<li>Intelligent people have less need for religion because their self-esteem and life-style needs are conferred by intelligence - which enhances understanding through learning.
</ol>
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Learning, especially learning science, is hard and takes effort; it is far easier to stick to simplistic views and pretend that faith is a better route to knowledge and understanding so you can pretend to know or understanding things better than those clever-dicky scientists. A low IQ also enhances the Dunning-Kruger effect where the ignoramus over-estimates his/her understanding and level of expertise, imagining themselves to be leaders in the field while have minimal knowledge of the subject.<br>
<br>
The paper was the subject of an article in <i>Psychology Today</i> by Tomas Chamorro-Premuzic Ph.D. who fleshes out those three reasons for the negative correlation between IQ and religiosity:<br>
<blockquote class="blockit">
<ol class="dbl1 bold">
<li>Intelligent people are generally more analytical and data-driven, and formal religions are the antithesis: They are empirically fluffy and their claims are often in direct contradiction with scientific evidence, unless they are interpreted metaphorically – but maybe intelligent people are not that keen on metaphor. Another way of putting it is that people with a high IQ are more likely to have faith in science, which isn’t religion’s best friends (yes, yes, I do know about Einstein’s quotes).</li>
<li>Intelligent people are less likely to conform, and, in most societies, religiosity is closer to the norm than atheism is. Although this interpretation is based on extrapolation, it still makes sense. First, smarter people tend to be less gullible. Second, in most societies, religious people outnumber atheists and agnostics — though global levels of religiosity have been declining, and there is substantial cultural variability in religiosity levels.</li>
<li>Intelligence and religiosity are “functionally equivalent,” which means that they fulfill the same psychological role. Although this intriguing argument contradicts points 1 and 2, it deserves serious consideration. Humans will always crave meaning. Religion – like science and logical reasoning – provides them with a comprehensive framework or system to make meaningful interpretations of the world. At times, religion and science are in conflict, but they can also act in concert, complementing each other to answer non-falsifiable and falsifiable questions, respectively. The authors conclude that some people satisfy their desire to find meaning via religion, whereas others do so via logical, analytical, or scientific reasoning – and IQ predicts whether you are in the former or latter group.</li>
</ol>
</blockquote>
If the correlation found by this meta-analysis is true, and there is no reason to think it might not be, then it goes a long way to explaining the behaviour and sheer stupidity of most of the fundamentalists you're likely to encounter in the social media. It could also explain why so many of them also hold far-right views, support Donald Trump and his Repugnicans, have fallen for the QAnon conspiracy theories, think COVID-19 was a hoax and are antivaxxers.<br>
<br>
The worry is that people who can believe absurdities can be persuaded to commit atrocities.
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-40715007783571603982024-03-15T19:57:00.009+00:002024-03-16T23:28:27.464+00:00Creationism in Crisis - From Where Did The Bible's Authors Get The Idea That Humans Are Materially Different To Other Animals? And Why Were They Wrong?<div class="title-box" style="height: 800px; display: none">
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<div class="left-column" style="text-align: left; flex: 2">Impression of a meeting of the Athenian Assembly on the Pnyx</div>
<div class="right-column" style="text-align: right; flex: 1">Artist unknown</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjkfjfzZGX-VOCVxD1EHDSn8VsdJDxMeVavAWjDoeXqdIaiKlc_dyIO70ZL6yhNrPfAQ50zijzJd9iDUPxtKfmwxHVqJAShhdd8H5eyKAmhzrxIE5MDfa2yp6ebcMR7xm_yEJA8HKrXAZ-LFfDhtZb58Kt8uHE-ODYDnaHGhqtMVhMjBqH1mNjDPblBB6J/s1600/6I-qS3S0zJz_ENkT5U4A0JCnZPb90R4_P6B9yfiqICY.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjkfjfzZGX-VOCVxD1EHDSn8VsdJDxMeVavAWjDoeXqdIaiKlc_dyIO70ZL6yhNrPfAQ50zijzJd9iDUPxtKfmwxHVqJAShhdd8H5eyKAmhzrxIE5MDfa2yp6ebcMR7xm_yEJA8HKrXAZ-LFfDhtZb58Kt8uHE-ODYDnaHGhqtMVhMjBqH1mNjDPblBB6J/s1600/6I-qS3S0zJz_ENkT5U4A0JCnZPb90R4_P6B9yfiqICY.webp"/></a></div>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIX7Bk6-q3VLPjf7tY9UAEyq1HsDH1eXjxe28px0n9Vf5Vlfnnu-t7D3ggsFuabVo4-iFS_gIMpyKGPO-uu1Cp6PnaXQ6HNlfsF9rGTyqN0xOxot22oGbSxHsKQy5mlMpgk5R-VlRuKTJdFMBQVo051ws-Zq26Bnle_iOUefFSgKu8uzxROKrT9hAMKn7p/s1600/19th-century-antique-vase-illustration-of-dionysus-and-three-figures.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIX7Bk6-q3VLPjf7tY9UAEyq1HsDH1eXjxe28px0n9Vf5Vlfnnu-t7D3ggsFuabVo4-iFS_gIMpyKGPO-uu1Cp6PnaXQ6HNlfsF9rGTyqN0xOxot22oGbSxHsKQy5mlMpgk5R-VlRuKTJdFMBQVo051ws-Zq26Bnle_iOUefFSgKu8uzxROKrT9hAMKn7p/s1600/19th-century-antique-vase-illustration-of-dionysus-and-three-figures.jpg"/></a>
<div class="captionc">Greek vase decoration - Dionysus and three figures.(Gods created in human image)</div>
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<a href="https://theconversation.com/friday-essay-from-political-bees-to-talking-pigs-how-ancient-thinkers-saw-the-human-animal-divide-218800">Friday essay: from political bees to talking pigs – how ancient thinkers saw the human-animal divide</a><br>
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It's a fundamental part of the Abrahamic religions and other religions that there is something materially different to humans, above and beyond the sort of difference that distinguishes one species from another. Biologically, of course, this is nonsense as any study of comparative anatomy and physiology will show. Humans are just another mammal, albeit with some highly evolved abilities that other species lack such as language, the ability to invent narrative, etc. The differences, as with the differences between any pair of related taxons is quantitative, not qualitative.<br>
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So, from where did religions and, especially the Abrahamic religions - Judaism, Christianity and Islam - get the idea of human exceptionalism from and why did they need to invent narratives to explain it, usually in terms of a special creation or a special closeness to gods - even a familial relationship or at least created in their image like children to their parents? In fact, as we will see, it’s much more likely that gods were created by humans in their image.<br>
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In the following article, reprinted from <i>The Conversation</i>, Professor Julia Kindt, Department of Classics and Ancient History, University of Sydney, SNW, Australia, explains the ideas origins in Ancient Greece and why it is wrong. Her article has been reformatted for stylistic purposes:
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<div class="convo"><a href="https://theconversation.com/uk"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtjgccyP-2wbUH2Pszt5rI3PWgttFGwpL9WZ_WWd6fpCQwbP8-oPCQljiwUUDw0VjsQame1hi9fdoaVNUUXb0A67wF5AIcrzI9bcME2uudgqtMVhobCp5liwk-xNkVT3cMfq-S1hjF6hfUfUc9hFjZwIAHaVGiHFJoonPnhldia8zGGFkCYcEfMOgDIg/s1600/logo-horizontal-en-df7faf4238d541b16db76bba081fdd73.png" width="33%"/></a><br>
<time datetime="2024-03-14T19:24:53Z">Published: March 14, 2024 7.24pm GMT</time><br><br>
<div class="title-box" style="background-image: url(https://images.theconversation.com/files/581424/original/file-20240312-18-f7g0up.jpg)"><div class="outlined-text" style="font-size: 50px; color: white"> Friday essay: from political bees to talking pigs – how ancient thinkers saw the human-animal divide</div>
<br><div class="credit">Shutterstock</div>
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<a href="https://theconversation.com/profiles/julia-kindt-223239">Julia Kindt</a>, <i><a href="https://theconversation.com/institutions/university-of-sydney-841">University of Sydney</a></i><br>
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What makes us human? What (if anything) sets us apart from all other creatures? Ever since Charles Darwin’s theory of evolution, the answer to these questions has pointed us back to our own animal nature.<br><br>
Yet the idea that, in one way or another, our humanity is entangled with the non-human has a much longer and more venerable history. In the West, it goes all the way back to Classical antiquity – to Greek and Roman views about humans and animals. <br><br>
The Greek philosopher Aristotle (384-322) first argued the human stands out from all other animals through the presence of <i>logos</i> (“speech” but also “reason”). Numerous Greek and Roman thinkers engaged in similar attempts to name what, exactly, sets humans apart. <br><br>
Who or what is man? The arguments these philosophers came up with verged from the obscure to the outright bizarre: The human alone has the capacity to have sex at all seasons and well into old age; the human alone can sit comfortably on his hip bones; the human alone has hands that can build altars to the gods and craft divine statues. No observation seemed too far-fetched or outlandish. <br><br>
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<a href="https://images.theconversation.com/files/581448/original/file-20240312-28-9lkgw1.jpg"><img alt="A painting of a bearded man, Aristotle." src="https://images.theconversation.com/files/581448/original/file-20240312-28-9lkgw1.jpg"></a>
<div class="captionc">Aristotle, as painted by Raphael.<br>
<br><div class="credit">Wikimedia Commons, <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></div></div>
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And yet, above all, the argument that animals lack logos continued to resonate. In classical antiquity it became powerful enough to coin the very word for animals in ancient Greek: <i>ta aloga</i> – “those without logos”. <br><br>
This position was taken up by the philosophical school of the Stoics and from there came to influence Christianity, with its view of man made in the image of God. <br><br>
The idea of an insurmountable gap between humans and other animals soon became the dominant paradigm, informing, for instance, the 18th century naturalist <a href="https://www.britannica.com/biography/Carolus-Linnaeus">Carl Linnaeus’s</a> influential classification of the human as <i>homo sapiens</i> (literally: the “wise”, or “rational man”). <br><br>
The practical implications of this idea cannot be underestimated. What has been termed “<a href="https://plato.stanford.edu/entries/moral-animal/">the moral status of animals</a>” – the question of whether they should be included in considerations of justice – has traditionally been linked to the question of whether they have logos. Because animals differ from humans in lacking both speech and reason (so this line of argument goes) they cannot themselves formulate moral positions. Therefore, they do not warrant inclusion in our moral considerations, or at least not in the same way as humans. <br><br>
Increasingly, of course, as many contemporary philosophers have pointed out, this idea seems too simple. <br><br>
New research in the behavioural sciences illustrates the at times astonishing capacities of certain animals: crows and otters using tools to crack open nuts or shells to make their contents available for consumption; octopuses lifting the lids to their tanks and successfully escaping to the ocean through pipes; bees optimising their flight path on repeated trips to a food source.<br>
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<a href="https://images.theconversation.com/files/581188/original/file-20240312-24-3u7e8f.jpg"><img alt="A pink octopus in a tank." src="https://images.theconversation.com/files/581188/original/file-20240312-24-3u7e8f.jpg"></a>
<div class="captionc">Octopus have lifted the lids of their tanks and escaped.<br>
<br><div class="credit"><a href="https://www.shutterstock.com/image-photo/dofleins-octopus-latin-enteroctopus-dofleini-tentacles-2278086727">Victor1153/shutterstock</a></div>
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But there is, in fact, a considerable body of evidence from the ancient Greek and Roman worlds showcasing the complex behaviours of different kinds of animals.<br><br>
Ancient authors like <a href="https://www.livius.org/articles/person/pliny-the-elder/">Pliny</a>, <a href="https://www.livius.org/sources/content/plutarch/">Plutarch</a>, <a href="https://oxfordre.com/classics/display/10.1093/acrefore/9780199381135.001.0001/acrefore-9780199381135-e-4570">Oppian</a>, <a href="https://www.oxfordreference.com/display/10.1093/oi/authority.20110803095353490">Aelian</a>,<a href="https://plato.stanford.edu/entries/porphyry/"> Porphyry</a>, <a href="https://www.oxfordreference.com/display/10.1093/oi/authority.20110803095431452">Athenaeus </a>and others have dedicated whole books or treatises to this topic, pushing back on the notion of animals as merely “dumb beasts”. <br><br>
Their views anticipated the modern debate by attributing animals not only with forms of reason; they also highlighted their capacity to suffer, to feel pain and to feel empathy towards each other and, occasionally, even towards members of the human species. <br><br>
Then there are the human-animal hybrid creatures of the Greek and Roman myths (more on this later) – the Sirens, the Sphinx, the Minotaur. All combine the body parts of human and animal. Individually and collectively they thus raise a fundamental yet potentially disturbing question: what if we are really, in part at least, animal?<br><br>
<span>Ancient animal-smarts</span><br><br>
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In <a href="https://www.goodreads.com/en/book/show/11879565">On the Nature of Animals</a> (late second/early third century CE), Aelian, a Roman author writing in Greek, described fish that helped their unfortunate mates when caught at sea, setting their backs against the trapped creature and “pushing with all their might to try to stop him from being hauled in”. <br><br>
He wrote, too, of dolphins that helped fisher-folk, pressing the fish in “on all sides” so they couldn’t escape. In return, they were rewarded for their labours by a share of the catch.<br><br>
He celebrated the clever design of beehives, observing:
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The first thing that they construct are the chambers of their kings, and they are spacious and above all the rest. Round them they put a barrier, as it were a wall or fence, thereby also enhancing their importance of the royal dwelling. <br><br>
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By parading animal-smarts in action these examples – of which there are hundreds - astonish, inform, and entertain at the same time – similar perhaps to the ubiquitous reels showing animals doing amazing things circulating in modern social media.<br><br>
Modern ethological studies variously observe animal behaviours which reverberate with Aelian’s examples.<br><br>
Pairs of <a href="https://www.sciencedaily.com/releases/2015/09/150925085344.htm">rabbit fish</a> have been shown to cooperate, with one partner standing on guard protecting the other one while feeding. Honeybees indeed build bigger cells for their queen that are set apart at the bottom of the hive separated by thicker walls. And <a href="https://www.pnas.org/post/podcast/cooperative-fishing-between-humans-and-dolphins">bottlenose dolphins</a> have been found to cooperate with humans in their efforts to capture fish. <br>
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<a href="https://images.theconversation.com/files/581193/original/file-20240312-16-rsj49.jpg"><img alt="Dolphins swimming over seagrass." src="https://images.theconversation.com/files/581193/original/file-20240312-16-rsj49.jpg"></a>
<div class="captionc">Bottlenose dolphins have been seen cooperating with humans while fishing.<br>
<br><div class="credit">Anita Kainrath/shutterstock</div>
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While not all of the ancient anecdotal evidence is confirmed by modern research, the overall thrust is clear: it deserves to be taken seriously and is part of the ancient conversation of what makes us human. <br><br>
<span>The power of storytelling</span><br><br>
Some Greek and Roman thinkers resorted to the medium of storytelling to articulate views that are essentially philosophical in nature. The Greek philosopher Plutarch’s treatise <a href="https://penelope.uchicago.edu/Thayer/E/Roman/Texts/Plutarch/Moralia/Gryllus*.html">Beasts are Rational</a> draws on the famous story from Homer’s Odyssey in which some of Odysseus’ comrades are turned into pigs by the sorceress Circe. <br>
<div class="readmore"><a href="https://theconversation.com/guide-to-the-classics-homers-odyssey-82911">Guide to the Classics: Homer's Odyssey</a></div>
Odysseus is eventually able to convince the sorceress to turn them back into human beings. In Plutarch’s rendering of the story he returns to Circe’s island to check whether there are any other Greeks turned animal – and finds a pig named Gryllus (“Grunter”).<br>
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<a href="https://images.theconversation.com/files/581192/original/file-20240312-26-tn9od0.jpg"><img alt="A painting of men with animal heads." src="https://images.theconversation.com/files/581192/original/file-20240312-26-tn9od0.jpg"></a>
<div class="captionc">Detail of a wine cup (kylix) depicting scenes from The Odyssey including men turned into animals, circa 560-550 BCE.<br>
<br><div class="credit"><a href="https://commons.wikimedia.org/wiki/File:Detail_view_-_Odysseus_men_turned_into_animals_by_Circe_receive_antidote_photo_by_Lucas_ancientartpodcast_flickr_cca2.0_8705662763_02d64d713e_o.jpg">Wikimedia Commons</a>, <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></div>
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Things take a turn for the unexpected when Grunter declines Odysseus’ offer of help. The reason? He prefers his animal to his human existence.<br><br>
Grunter sets out to make an impassioned, highly rational case, arguing all animals in one form or another, have reason. Individual species differ from each other merely in the extent of and kind of reason. And, yes, this includes even those animals that have come to serve as the epitome of dumbness: sheep and the ass. <br><br>
“Please note,” he adds, “that cases of dullness and stupidity in some animals are demonstrated by the cleverness and sharpness of others – as when you compare an ass and a sheep with a fox or a wolf or a bee.”<br><br>
Grunter is not afraid to push things even further: Don’t individual humans, too, differ from each other in cleverness and wit? Long before the arrival of evolutionary theory, the pig here points towards a gradual view of how certain features, skills, and capacities map onto a continuum of all living creatures (the human included). The implied conclusion: there is no insurmountable gap between the human and other animals.<br><br>
Grunter’s views are supported by others such as the speaking rooster of Lucian’s <a href="https://www.goodreads.com/en/book/show/11879565">The Dream or the Cock</a> (second century CE). Claiming to be the latest in a long line of previous incarnations that include (brace yourself) – the philosopher Pythagoras, the Cynic philosopher Crates, the Trojan hero Euphorbus, the Greek courtesan Aspasia, and several animals – this rooster-philosopher, too, prefers his animal to his human existence. <br><br>
Animals, the rooster argues, are content with the basics; humans, by contrast, over-complicate things because they can’t get enough and greedily strive for ever more. <br>
<div class="readmore"><a href="https://theconversation.com/guide-to-the-classics-darwins-the-descent-of-man-150-years-on-sex-race-and-our-lowly-ape-ancestry-155305">Guide to the classics: Darwin's The Descent of Man 150 years on — sex, race and our 'lowly' ape ancestry</a></div>
<span>Myths and hybrid monsters</span><br><br>
Myth is arguably the most influential genre of ancient storytelling. A set of malleable tales of great age and importance, myth constitutes a world apart, a medium just far enough removed from the intricacies (and banalities) of everyday life to allow for the exploration of fundamental questions concerning the human condition. And Greek myths often explore human entanglements with non-human animals in ways that reference the philosophical debate.<br><br>
The mythical figure of <a href="https://www.britannica.com/topic/Minotaur">the Minotaur</a> for example – a hybrid creature sporting the head of a bull and the body of a human male – does not seem to adhere to the norms and conventions applying to either of his composite identities. <br>
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<a href="https://images.theconversation.com/files/580856/original/file-20240310-28-ykqvft.jpg"><img alt="A painting of a minotaur." src="https://images.theconversation.com/files/580856/original/file-20240310-28-ykqvft.jpg"></a>
<div class="captionc">Tondo of a Minotaur, circa 515 BC.
<br><div class="credit"><a href="https://commons.wikimedia.org/wiki/File:Tondo_Minotaur_London_E4_MAN.jpg">Wikimedia Commons</a>, <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></div>
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His insatiable appetite for young humans sets him apart from accepted behaviour for both humans and cattle alike, identifying him as monstrous. <br><br>
But what are monsters for?<br><br>
This question also applies to another famous hybrid beast of the ancient world: the Theban sphinx. Perched high outside the gates of the city of Thebes, in the region of Boeotia in central Greece, this creature (half woman, half lion, often endowed with an extra set of wings) challenges all wishing to enter with the following riddle:
<blockquote class="blockit">
What is that which has one voice and yet becomes four-footed and two-footed and three-footed?<br><br>
</blockquote>
Many try and fail to name the right answer, paying for it with their lives. Until Oedipus comes along. He gives the correct answer and thus busts the beast, which dutifully throws itself to death. <br><br>
<div class="rpanel450plain" style="width: 350px"><a href="https://images.theconversation.com/files/581190/original/file-20240312-20-tc1s5x.jpg"><img src="https://images.theconversation.com/files/581190/original/file-20240312-20-tc1s5x.jpg"/></a>
<div class="captionc">Oedipus (on the right), the Sphinx (on the middle) and Hermes (on the left). Ancient Greek stamnos, ca. 440 BC.<br><br>
<div class="credit"><a href="https://commons.wikimedia.org/wiki/File:Oedipus_sphinx_Louvre_G417_n2.jpg" target="_blank">Wikimedia</a></div></div></div>
The creature in the riddle is, of course, the human: man first crawls on four legs, then walks on two, until in old age when a walking stick may serve as a third “leg”. And yet despite his clever wit, Oedipus is ultimately unable to use reason to his and the city’s advantage (a situation explored in depth in <a href="https://classics.mit.edu/Sophocles/oedipus.html">Sophocles’ famous tragedy Oedipus the King</a>).<br><br>
What is the point of the riddle of the Sphinx? This story poses the human as a question but also illustrates the limits of logos in gaining self-understanding. Oedipus can solve the beast’s riddle; yet the riddle of his own humanity remains unresolved until it is too late. Here, the monstrous figure holds up a mirror for the human to recognise himself. <br><br>
<span>Speaking animals</span><br><br>
Logos (in the sense of speech) also features prominently in the intervention of another iconic creature from classical antiquity: Xanthus, Achilles’ speaking horse. <br><br>
On the battlefields of Troy (featured in Homer’s Iliad) Xanthus reminds Achilles of his imminent death. In this way the horse seems to tease all those thinkers (ancient and modern) who have argued the human stands out from all other animals in his capacity to speak in complex sentences.<br>
<div class="readmore"><a href="https://theconversation.com/guide-to-the-classics-homers-iliad-80968">Guide to the classics: Homer's Iliad</a></div>
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<a href="https://images.theconversation.com/files/581226/original/file-20240312-30-tn9od0.jpg"><img alt="A painting of a Greek god with two horses." src="https://images.theconversation.com/files/581226/original/file-20240312-30-tn9od0.jpg"></a>
<div class="captionc">Automedon with the Horses of Achilles, painting by Henri Regnault, 1868.<br>
<br><div class="credit">Wikimedia Commons, <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></div>
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Xanthus’s voice resonates with that of numerous other speaking animals populating Greek and Roman literature, including the gnat of <a href="http://virgil.org/appendix/culex.htm">Pseudo-Virgil’s Culex</a>, the speaking eel in Oppian’s didactic poem <a href="https://www.loebclassics.com/view/oppian-halieutica_fishing/1928/pb_LCL219.279.xml">On Fishing</a>, and the whole chorus of animals speaking to us in ancient fables. <br><br>
Individually and as a group they raise a question: what if animals could speak to us in human language? What would they have to say to those humans prepared to listen? <br><br>
As it turns out in these stories, often nothing too flattering. In classical antiquity, speaking animals often use their special position to question or examine the human condition.<br><br>
Xanthus is a case in point. By reminding Achilles he is fated to die at Troy, the speaking horse reminds the Greek hero of an important aspect of the human condition: his own mortality and the fact that he, too, is ultimately subject to powers beyond human control.<br><br>
<span>The political bee</span><br><br>
In Greek and Roman accounts of honeybee politics we find a peculiar human habit with a surprisingly long history: the attribution of political qualities to honeybees. <br><br>
When we distinguish a “queen bee” from “workers” we are continuing a tradition that goes back to the ancient world (and possibly beyond). Aristotle names honeybees among the <i>zoa politika</i> (the “political animals”) – a category that includes wasps, ants, cranes, and, above all, the human.<br>
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<a href="https://images.theconversation.com/files/581201/original/file-20240312-24-r54i0o.jpg"><img alt="" src="https://images.theconversation.com/files/581201/original/file-20240312-24-r54i0o.jpg"></a>
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<br><div class="credit"><a href="https://commons.wikimedia.org/wiki/File:Day_85_-_Sweat_Bee_-_Lasioglossum_species,_Leesylvania_State_Park,_Woodbridge,_Virginia.jpg">Wikimedia Commons</a>, <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></div>
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He and others then set out to explore the intricacies of honeybee society. The ancient Greeks and Romans traditionally considered honeybees to inhabit a monarchy. In line with the gender realities of the ancient world, they imagined this monarchy to be led by a king or male leader. <br><br>
Does the bee monarch have a stinger? If not, how does he assert his power and leadership? And what does the presence of the obviously unproductive drones in the hive say about the distribution of labour in a community? These are the kind of questions that resonated among Greek and Roman thinkers.<br><br>
Honeybee society thus provided a perfect microcosm to study a set of questions that concerned human politics and society. The Roman philosopher Seneca, for instance, asserted that the bee monarch leads by <i>clementia</i> (mercy or mildness) - a form of leadership he found woefully lacking in contemporary Roman society. <br><br>
<span>Meat and man</span><br><br>
So far we have seen animals mostly playing a symbolic role in Graeco-Roman storytelling. There is also a very real way in which human and animal bodies come to merge: through the human consumption of meat.<br><br>
The ancient Greeks and Romans were ardent meat-eaters. Indeed meat-eating became a status symbol closely linked to the articulation of masculine identities. <br><br>
In classical Greece the male citizen received his equal share of meat after communal religious sacrifices carried out by the <i>polis</i> (“city-state”). Meat eating also features prominently in several anecdotes about successful ancient Greek athletes who toned their extraordinary bodies through the consumption of ridiculous amounts of meat.<br><br>
One of them – a boxer named Theagenes – even claimed to have gobbled up an entire oxen in one sitting. Another one – Milo of Croton – apparently gained his extraordinary strength by carrying a heifer on his back as a young man until both he and the heifer had grown up. <br><br>
Meanwhile at Rome, the elites sought to outdo each other by hosting ever more lavish dinner parties typically featuring one or several meat dishes. More often than not this involved attempts to serve a bigger or larger quantity of boar than their peers. <a href="https://penelope.uchicago.edu/Thayer/E/Roman/Texts/secondary/SMIGRA*/Sumtuariae_Leges.html">Roman sumptuary laws</a> eventually sought to control the worst excesses – albeit with limited success. <br><br>
<span>The shearwaters of Diomedea</span><br><br>
The real also blends into the imaginary in the story of a special kind of bird. The Scopoli Shearwater (<i>Calonectris Diomedea</i>) is a species common to the Adriatic and other parts of the Mediterranean Sea. One of its outstanding features is that its cries resemble that of a wailing baby. These birds feed on small fish, crustaceans, squid, and zooplankton and are both migratory and pelagic. <br><br>
The stories told about these birds by several ancient authors bring us to what is perhaps the most momentous way of exploring the human-animal boundary: the idea that in the realm of myth, at least, some humans, under certain conditions, could turn into animals and back again (metamorphosis). <br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://images.theconversation.com/files/581199/original/file-20240312-28-mfz55.jpg"><img alt="A shearwater in the sea." src="https://images.theconversation.com/files/581199/original/file-20240312-28-mfz55.jpg"></a>
<div class="captionc">A scopoli shearwater.
<br><div class="credit">D.serra1/shutterstock</div>
</div>
</div>
According to <a href="https://www.loebclassics.com/view/aelian-characteristics_animals/1958/pb_LCL446.15.xml">Aelian</a>, some shearwaters residing on a rocky, otherwise uninhabited island in the Mediterranean Sea showed puzzling behaviour. They duly ignored all non-Greeks arriving on their island. Yet if Greek people reached their shores they welcomed them with stretched wings, even settling down on their laps as if for a joint meal. <br><br>
What motivated this curious behaviour? <br><br>
The backstory explains that the birds were once human. They were the comrades of Diomedes, king of Argos, one of the Greeks fighting at Troy, who is said to have died on the same island now inhabited by the birds. Apparently, upon his death, his friends grieved so heavily the goddess Aphrodite turned them into birds – their cries forever bemoaning the passing of their comrade. <br><br>
On the face of it this story is merely another example of a myth explaining an outstanding feature in nature (the birds’ endearing <a href="https://www.birdlife.org/news/2021/05/31/seabird-month-corys-shearwater-calonectris-borealis/">human-like cry</a>). Yet there is more to the birds’ curious behaviour than meets the eye. In discriminating between Greeks and non-Greeks the birds seem to recall not only their former humanity but specifically their Greekness; they even seem to engage in the central Greek practice of extending friendship to guests (<i>xenia</i>) and the sharing of food. <br><br>
In doing so they illustrate a central point of ancient (and many modern) tales of metamorphosis: even though the body may turn animal, the mind remains human. As the seat of logos it contains our humanity while the body adds little, if anything, of substance.<br><br>
As such, rather than imagining what the world looks like from the point of view of a non-human creature, tales of metamorphosis ultimately come to reaffirm the view that the human stands apart from all other animals. <br><br>
<span>And so?</span><br><br>
<div class="lpanel450plain" style="width: 250px; margin-bottom: 0.5em">
<a href="https://images.theconversation.com/files/581186/original/file-20240312-26-wyc3p2.png"><img alt="The Trojan Horse and other stories: book cover" src="https://images.theconversation.com/files/581186/original/file-20240312-26-wyc3p2.png"></a>
<div class="captionc" style="margin-top:0; padding-top:0">
<br><div class="credit">Cambridge University Press</div>
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In the myth of the Minotaur, the Greek hero Theseus eventually enters the labyrinth in which the Minotaur is confined, tracking him down, and slaying him. With the help of a thread given to him by Ariadne, he finds his way back out to tell the tale.<br><br>
But trying to make sense of the Minotaur and other iconic creatures from the ancient world leads us down a rabbit hole into a place of blurred boundaries: where the human emerges as a contested figure somewhere in the space between mind and body, human and animal parts.<br><br>
In the end, then, there is no hard and fast boundary separating us from all other creatures – notwithstanding all efforts to dress ourselves up as different.
Rather, it is the <a href="https://www.cambridge.org/core/books/trojan-horse-and-other-stories/6DD8408FDBA4C5C6604536F6EC7406D5">negotiations between different facets of our identity</a> which make us human
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<a href="https://theconversation.com/profiles/julia-kindt-223239">Julia Kindt</a>, Professor, Department of Classics and Ancient History, <i><a href="https://theconversation.com/institutions/university-of-sydney-841">University of Sydney</a></i><br><br>
This article is republished from <a href="https://theconversation.com">The Conversation</a> under a Creative Commons license. Read the <a href="https://theconversation.com/friday-essay-from-political-bees-to-talking-pigs-how-ancient-thinkers-saw-the-human-animal-divide-218800">original article</a>.<br><br>
<div class="creditl"><a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Published by <i>The Conversation</i>.<br>Open access. <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">(CC BY 4.0)</a></div>
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What is obvious, is that the daft notion of human exceptionalism didn't come from the Bible, but the authors of it probably got it from the Ancient Greeks and simply incorporated it in the tales they invented to fill the gaps in their knowledge and understanding. What didn't seem to occur to them is the question, if we are made of different stuff, or constructed differently in some material way, to the rest of nature, why do we eat it to stay alive?
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com1tag:blogger.com,1999:blog-7583674511519808833.post-43740752521755710702024-03-15T12:45:00.003+00:002024-03-15T12:51:18.324+00:00Creationism in Crisis - Bird Watching In The Age Of Dinosaurs - About 70 Million Years Before 'Creation Week'<div class="title-box" style="height: 600px; display: none">
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<div class="left-column" style="text-align: left"><i>Hesperornis</i></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsxJlEx-8K26Rx7p4o4VMIs7HcHjEwRr_XK-fVyWQngUEpFTlReBUIYzJPu9v71JvE4_HSJ4Oqr4L_ivUUvu5wYBITdRoMxWgpu5YIwhH09WVJrCvlGhcPO4S0L-i41Xj_2zH3NAwuAZHPGPYW4iJgUIwQG-nb_saPI8G4t3ely4yVDvdRQyNqf-3c0M7r/s1600/Hesperornis-jaime-chirinos.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsxJlEx-8K26Rx7p4o4VMIs7HcHjEwRr_XK-fVyWQngUEpFTlReBUIYzJPu9v71JvE4_HSJ4Oqr4L_ivUUvu5wYBITdRoMxWgpu5YIwhH09WVJrCvlGhcPO4S0L-i41Xj_2zH3NAwuAZHPGPYW4iJgUIwQG-nb_saPI8G4t3ely4yVDvdRQyNqf-3c0M7r/s1600/Hesperornis-jaime-chirinos.webp"/></a></div>
<div class="rpanel450" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6cDp6ffzbIMABebyhVRml8nTwRAAKDV4Bf7ykKd96mK_L27MMLIohsydFOxYWlCEKDMFI3kRbY4yJ7pmO5Ad8K8Xr2tNC97jJDHgv6-uhhWpYYvxwN0ILskVP0U6NRloyu3M4518ohpjdSj04o54jlqk_Tiydekprn9_l6YVbjmcn06hqIemeExML65Or/s1600/Archaeopteryx.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6cDp6ffzbIMABebyhVRml8nTwRAAKDV4Bf7ykKd96mK_L27MMLIohsydFOxYWlCEKDMFI3kRbY4yJ7pmO5Ad8K8Xr2tNC97jJDHgv6-uhhWpYYvxwN0ILskVP0U6NRloyu3M4518ohpjdSj04o54jlqk_Tiydekprn9_l6YVbjmcn06hqIemeExML65Or/s1600/Archaeopteryx.jpg"/></a>
<div class="captionc"><i>Archaeopteryx</i><br><div class="credit">Credit: Dotted Yeti/Shutterstock</div></div>
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<a href="https://theconversation.com/a-brief-guide-to-birdwatching-in-the-age-of-dinosaurs-225286">A brief guide to birdwatching in the age of dinosaurs</a><br>
<br>
What would it have been like to go bird-watching in that very long period of pre-'Creation Week' history just before a cataclysmic meteor strike cause the extinction of almost all the dinosaurs, 66 million years before creationists believe their god created a small, flat planet with a dome over it in the Middle-east?<br>
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At that time, Earth had a large population of dinosaurs, some of which were later to become modern birds which evolved to fill the vacated niches formerly occupied by the dinosaurs, while another survivor, a small rat-like early mammal, the descendant of mammal-like reptiles radiated into modern mammals. <br>
<br>
For a period, these early birds, the avian dinosaurs which had evolved from the bipedal theropod dinosaurs, formed two major groups - the ornithuromorphs and the enantiornithine.
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<blockquote class="ai" >What information do you have on the evolution of the enantiornithines and ornithuromorphs dinosaurs?
Enantiornithines and ornithuromorphs are two important groups of birds that evolved during the Mesozoic Era, specifically during the Cretaceous period. Here's an overview of their evolution:
<ol class="dbl1 bold" style="margin-right: 10%">
<li><b>Enantiornithines:</b>
<ul type="disc">
<li>Enantiornithines were a diverse group of birds that lived during the Cretaceous period. They are often referred to as "opposite birds" because their shoulder joints were structured differently from modern birds, giving them a somewhat opposite appearance.</li>
<li>These birds were globally distributed and occupied various ecological niches, ranging from aquatic to terrestrial habitats.</li>
<li>Enantiornithines had teeth and clawed wings, features not present in modern birds. They also lacked a specialized breastbone (sternum) like that of modern birds.</li>
<li>Fossil evidence suggests that enantiornithines were quite successful and abundant during the Cretaceous, but they went extinct along with non-avian dinosaurs at the end of the Cretaceous period, about 66 million years ago.</li>
</ul></li>
<li><b>Ornithuromorphs:</b>
<ul type="disc">
<li>Ornithuromorphs are another group of birds that lived during the Cretaceous period. They are considered more closely related to modern birds than enantiornithines.</li>
<li>Unlike enantiornithines, ornithuromorphs had a keeled sternum, similar to modern birds, which likely provided a more efficient attachment for flight muscles.</li>
<li>Ornithuromorphs also had a toothless beak, indicating a more specialized diet compared to enantiornithines.</li>
<li>Fossil evidence suggests that ornithuromorphs evolved diverse body forms and lifestyles, including some species that were capable of powered flight over long distances.</li>
<li>Ornithuromorphs survived the mass extinction event at the end of the Cretaceous period and are believed to be the ancestors of modern birds.</li>
</ul></li>
</ol>
The evolution of both enantiornithines and ornithuromorphs represents important stages in the development of avian diversity and flight adaptation. While enantiornithines represent an early radiation of avian forms that ultimately went extinct, ornithuromorphs are thought to have given rise to the lineage that led to modern birds. Further discoveries and research continue to refine our understanding of the evolutionary relationships between these ancient birds and their modern descendants.
</blockquote>
<br>
What then would a cretaceous bird-watcher have seen? In the following article, reprinted from <i>The Conversation</i>, Abi Crane, a Postgraduate Researcher in Palaeontology, University of Southampton, explains what a time-travelling ornithologist might have seen. Her article is reprinted under a Creative Commons licence, reformatted for stylistic consistency:<br>
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<time datetime="2024-03-11T13:10:38Z">Published: March 11, 2024 1.10pm GMT</time><br>
<br>
<div class="title-box" style="background-image: url(https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBdYb5rRk_oTnH_wXUd9q30P7hGyMHuQ9nx8PHoWdwiaHEQRsYGmT5QuNqp0ob7Dz8-EdDCYYbVgiujsdKHv5LOkPrqQ91JUwXTGtlRotOoYl9SBbsJ7dQILPaKXQXTYXEGukzGiARinpSqg1GZ6rmSdKFMX5GGLDcqM9yg5goagWLYPbFaVGDtVJppDzK/s1600/Archaeopteryx_NT.jpg)"><span class="outlined-text" style="font-size: 75px; color: white">A brief guide to birdwatching in the age of dinosaurs</span></div><br>
<a href="https://theconversation.com/profiles/abi-crane-1474516">Abi Crane</a>, <i><a href="https://theconversation.com/institutions/university-of-southampton-1093">University of Southampton</a></i><br><br>
Have you ever wondered what it would be like to travel back in time to the age of dinosaurs? If you stumble upon a time machine, remember to bring your binoculars. Birdwatching is a popular hobby today, with an around <a href="https://www.wwt.org.uk/news-and-stories/blog/get-into-birdwatching/#:%7E:text=Bird%20watching%20in%20the%20UK,that%20we%20look%20after%20them.">3 million participants</a> in the UK alone, and in our modern world there are a staggering <a href="https://www.publish.csiro.au/pc/pdf/PCv27_BR4">11,000 species</a> of birds to spot. <br><br>
Despite the popularity of their modern-day descendants, we often forget about ancient birds because of their more famous dinosaur cousins.<br><br>
Birds are actually <a href="https://www.nhm.ac.uk/discover/how-dinosaurs-evolved-into-birds.html">a type of dinosaur</a>. They are closely related to smaller, agile meat-eating dinosaurs such as the <i>Velociraptor</i>. Ancient birds came in a variety of forms, from ones with teeth and claws to species barely distinguishable from farmyard <a href="https://www.nature.com/articles/d41586-020-00766-2">chickens</a>. <br><br>
So, if you were to point your binoculars over the heads of <i>Triceratops</i> and <i><a href="https://theconversation.com/five-things-you-probably-have-wrong-about-the-t-rex-220011">Tyrannosaurus rex</a></i>, what could you spot? Here is a quick introduction to six of the most interesting ancient bird species. <br><br>
<span><i>Archaeopteryx</i></span><br>
<br>
<i>Archaeopteryx</i> is <a href="https://www.nhm.ac.uk/discover/dino-directory/archaeopteryx.html">the iconic “dino-bird”</a> from the Jurassic period. The discovery of <i>Archaeopteryx</i> fossils in Germany over 150 years ago provided scientists with the first clues about the link between dinosaurs and modern birds. <br><br>
At first glance, the skeleton of <i>Archaeopteryx</i> is just like any other meat-eating dinosaur – sharp teeth, clawed hands and a long bony tail. Surrounding the skeleton of specimens such as the <a href="https://www.museumfuernaturkunde.berlin/en/about/news/archaeopteryx-named-fossil-year">Berlin <i>Archaeopteryx</i></a> (discovered between <a href="https://artsandculture.google.com/story/archaeopteryx-lithographica-%E2%80%93-the-berlin-specimen-museum-fuer-naturkunde-berlin/1AVxj85ySOZ4JQ?hl=en">1874 and 1876</a>) however, are imprints of feathers which form a pair of distinctly bird-like wings.<br><br>
<div class="panelplain" style="margin; 1em auto"><img alt="3D rendering of black bird-like dinosaur flying through the sky" src="https://images.theconversation.com/files/580391/original/file-20240307-21-8fm1ve.jpg">
<div class="captionc"><i>Archaeopteryx</i> looked half way between a dinosaur and a modern bird.
<br><div class="credit"><a href="https://www.shutterstock.com/image-illustration/archaeopteryx-birdlike-dinosaur-flying-through-sky-1722734977">Dotted Yeti/Shutterstock</a></div>
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But for many years, palaeontologists debated whether <i>Archaeopteryx</i> could have used these wings to fly. Scientists now think it is likely that <i>Archaeopteryx</i> could have flown, but only <a href="https://www.nature.com/articles/s41467-018-03296-8">in short bursts </a>, like a pheasant. Recent technological advances have given us our first insights into dinosaur colour and studies of fossilised, pigmented cells have shown that <i>Archaeopteryx</i> had <a href="https://www.nature.com/articles/s41598-020-65336-y">matt black</a> wing feathers.<br><br>
<span><i>Confuciusornis</i></span><br><br>
This crow-sized bird had a beak like that of modern-day birds, but still had large, <a href="https://digitallibrary.amnh.org/items/fc74de43-ec0e-497f-a199-7f89b6b658b9">dinosaur-like claws</a> on its hands. It is thought that they lived in flocks, large numbers of which were killed by ash or gas in <a href="https://www.nature.com/articles/ncomms4151">volcanic eruptions</a> and preserved as fossils. Known from over <a href="https://www.researchgate.net/publication/326059155_A_taxonomical_revision_of_the_Confuciusornithiformes_Aves_Pygostylia">1,000 fossil specimens</a> from China, <i>Confuciusornis</i> is one of the most common fossil bird species.<br><br>
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<a href="https://images.theconversation.com/files/580395/original/file-20240307-30-nefob5.jpg"><img alt="Outline of dinosaur clearly preserved in rock" src="https://images.theconversation.com/files/580395/original/file-20240307-30-nefob5.jpg"></a>
<div class="captionc"><i>Confuciusornis sanctus</i> fossil, encased in rock.
<br><div class="credit"><a href="https://www.shutterstock.com/image-photo/dinosaur-fossil-confuciusornis-sanctus-rock-1232355214">Chawalit Chankhantha/Shutterstock</a></div>
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Some of these birds had a <a href="https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2008.0409?casa_token=dLetzDz5OIUAAAAA%3AKUyu-cMBlflBhPXtC6xu-PxSc6wFebScqXzE3LBa33EmqsrzLISDWi08ToliVPfTfyuuDI_psxm7fBY">pair of tail feathers</a> longer than their body, while others lacked these long feathers and would have looked comparatively stumpy. Scientists think these long-tailed birds were the males of the species and those with <a href="https://www.nature.com/articles/ncomms2377">short tails were females</a>. Like modern peacocks and peahens, the males probably used their extravagant tail feathers to woo the females.<br><br>
<span><i>Falcatakely</i></span><br><br>
Discovered in 2020, <i><a href="https://www.nature.com/articles/s41586-020-2945-x">Falcatakely</a></i>, from Madagascar, would have resembled a small, buck-toothed toucan. Its oversized, banana-shaped bill only had teeth <a href="https://www.nature.com/articles/d41586-020-03260-x">at the very tip</a>. Although we don’t know what this buck-toothed bird would have eaten, its close relatives ate a <a href="https://www.biorxiv.org/content/10.1101/2023.07.18.549506v2.abstract">variety of food</a>, including fruit, fish and even larger prey. <br><br>
Scientists think that birds such as <i>Falcatakely</i> could fly the same day they <a href="https://www.science.org/doi/full/10.1126/science.1100000">hatched from their egg</a>, unlike birds today which spend their first weeks or months helpless in the nest.<br><br>
<span><i>Hesperornis</i></span><br><br>
One of the weirdest birds from the age of dinosaurs, <i>Hesperornis</i> would have looked something like a six-foot-tall penguin with a beak full of <a href="https://link.springer.com/article/10.1186/s12862-016-0753-6#Sec27">sharp teeth</a>. Its <a href="https://www.mdpi.com/1424-2818/14/4/267">tiny arms</a> would have made T rex look like a weightlifter, so it definitely couldn’t have used them to fly. <br><br>
<div class="panelplain" style="margin; 1em auto"><img alt="Illustration of bird with tiny wings perched on a rock" src="https://images.theconversation.com/files/580394/original/file-20240307-18-16mtuh.jpg">
<div class="captionc"><i>Hesperornis</i> was an aquatic bird that lived at the time of the dinosaurs.
<br><div class="credit"><a href="https://www.shutterstock.com/image-illustration/hesperornis-aquatic-bird-that-lived-time-1118302547">Daniel Eskridge/Shutterstock</a></div>
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Instead, <i>Hesperornis</i> used its oversized <a href="https://www.sciencedirect.com/science/article/pii/S0031018217307149">feet to propel</a> itself through the water like a modern cormorant. Out of the water, <i>Hesperornis</i> walked <a href="https://www.sciencedirect.com/science/article/pii/S0031018217307149">awkwardly upright</a> and probably couldn’t travel far overland.<br><br>
<span><i>Vegavis and Asteriornis</i></span><br><br>
Towards the end of the dinosaurs’ reign, the earliest groups of modern birds began to appear. The first of these birds to be discovered was <i><a href="https://www.nature.com/articles/nature03150">Vegavis</a></i> from Antarctica, which in the time of dinosaurs would have been <a href="https://www.sciencedirect.com/science/article/pii/S0031018201004527">covered in trees</a> rather than ice. <br><br>
It was probably an ancestor of ducks and geese and one exceptional fossil of <i>Vegavis</i> even has a rare <a href="https://www.nature.com/articles/nature19852">preserved vocal organ</a>. Analysis of this fossil suggested that <i>Vegavis</i> couldn’t make a songbird melody but could have made simple noises such as goose-like honks.<br><br>
Sixty-six million years ago, not long before the <a href="https://www.pnas.org/doi/abs/10.1073/pnas.2006087117">asteroid impact</a>, which caused the extinction of the non-bird dinosaurs, lived <i><a href="https://www.nature.com/articles/s41586-020-2096-0">Asteriornis</a></i>. This quail-sized bird from Belgium was an ancestor of modern ducks and chickens. Although it would have looked unremarkable compared to the <a href="https://www.cambridge.org/core/journals/netherlands-journal-of-geosciences/article/stratigraphic-ranges-of-mosasaurs-in-belgium-and-the-netherlands-late-cretaceous-and-cephalopodbased-correlations-with-north-america/2601C3D2DD398B92DFEDA122E82F9991">giant swimming lizards</a> and <a href="https://www.nature.com/articles/s41586-022-05445-y">huge, toothed seagulls</a> it lived alongside, this may have been to its advantage.<br><br>
Scientists think that the small size of birds such as <i>Asteriornis</i> helped them to survive the <a href="https://academic.oup.com/sysbio/article/67/1/1/3960267">mass extinction</a>. Because smaller animals need less food and take less time to reproduce, these humble birds were able to survive and evolve into the birds you can see through your binoculars today.
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<a href="https://theconversation.com/profiles/abi-crane-1474516">Abi Crane</a>, Postgraduate Researcher in Palaeontology, <i><a href="https://theconversation.com/institutions/university-of-southampton-1093">University of Southampton</a></i><br><br>
This article is republished from <a href="https://theconversation.com">The Conversation</a> under a Creative Commons license. Read the <a href="https://theconversation.com/a-brief-guide-to-birdwatching-in-the-age-of-dinosaurs-225286">original article</a>.<br><br>
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No sign there then that biologists are about to abandon the Theory of Evolution and replace it with childish creationism complete with magic and supernatural magicians. I wonder where the creationist cult leaders who tell their dupes that this is about to happen, any day now, real soon! got that daft idea from. It can't have been anything a professional biologist ever said.
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-78314021981935703382024-03-14T20:55:00.003+00:002024-03-14T20:59:17.455+00:00Creationism in Crisis - Rice Paddy Snakes In Thailand Diversified About 2.5 Million Years Before 'Creation Week'<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left"><i>Hypsiscopus plumbeus</i></div>
<div class="right-column" style="text-align: right">Photo: Bryan L. Stuart</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU2whXOfaMZveT0csvt4eexjFgk6dLT4A9Q7FawglXwfBMMfGv3dK-3LaFoVHusMGPwuo-NRz3vQ46NMozs7_4xMNiPqtl3oKLrVdJaq3M9QBEb5uPOHtXh02TzitC4z9CwSKxSJHHIc59YQohAIJe9VEtK1SWSiczIzKdBrU7it6stY9t-wgsAL7QVNt7/s1600/01hqv708pwsjf9r0pkqwqee59h.jpeg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU2whXOfaMZveT0csvt4eexjFgk6dLT4A9Q7FawglXwfBMMfGv3dK-3LaFoVHusMGPwuo-NRz3vQ46NMozs7_4xMNiPqtl3oKLrVdJaq3M9QBEb5uPOHtXh02TzitC4z9CwSKxSJHHIc59YQohAIJe9VEtK1SWSiczIzKdBrU7it6stY9t-wgsAL7QVNt7/s1600/01hqv708pwsjf9r0pkqwqee59h.jpeg"/></a></div>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggjQ7aalSKuBooX85mYJGwcglCQFUVTR74PFfBlgCtoe_2YuaBYmFdxJVM0B51oUC834GVAhNnwJQNhyphenhyphenW-zvArlcP6ptMbAg3YCD1Zykbg37v_bdSPZmwa-QtZpnPO-tm3V60m0_RgJAqjnTo2qpA5pd90Y7SpttG_2iHcpATpZQg7rGkBEzFDbGa5rsv5/s1600/01hqxyszkzx2p9k7g6reh70sha.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggjQ7aalSKuBooX85mYJGwcglCQFUVTR74PFfBlgCtoe_2YuaBYmFdxJVM0B51oUC834GVAhNnwJQNhyphenhyphenW-zvArlcP6ptMbAg3YCD1Zykbg37v_bdSPZmwa-QtZpnPO-tm3V60m0_RgJAqjnTo2qpA5pd90Y7SpttG_2iHcpATpZQg7rGkBEzFDbGa5rsv5/s1600/01hqxyszkzx2p9k7g6reh70sha.jpg"/></a>
<div class="captionc"><i>Hypsiscopus murphyi sensu</i><br><div class="credit">Photo: Bryan Stuart</div></div>
</div>
<a href="https://news.ku.edu/news/article/rice-paddy-snake-diversification-was-driven-by-geological-and-environmental-factors-in-thailand-molecular-data-suggests">Rice paddy snake diversification was driven by geological and environmental factors in Thailand, molecular data suggests | KU News</a><br>
<br>
In one of those far-away places that the simple-minded authors of the story in Genesis about a small flat Earth with a dome over it being magicked up out of nothing in the Middle East, 10,000 years ago, could never have guessed existed, and some 2.5 million years before they though Earth existed, major environmental changes were driving the diversification of a species of snake into several descendant species, just as the Theory of Evolution predicts.<br>
<br>
If those simple-minded Bronze Age pastoralists had known about it and understood its significance in terms of the history of life on Earth and the dynamic geology of the planet, just imagine how different their imaginative tale would have been! As it was, they had to do their best with what little knowledge and understanding they had.<br>
<br>
The snake in question was the Rice Paddy snake, otherwise known as a mud snake, and the far-away place was Thailand where the rise of the Khorat Plateau caused environmental changes that resulted in the evolutionary diversification of the <i>Hypsiscopus</i> genus.<br>
<br>
The team of researchers from various American and Southeast Asian Universities, who have shown this link between environmental change and evolutionary radiation in a genus was led by Dr. Justin Bernstein, of the University of Kansas Center for Genomics. Their findings are published open access in <a href="https://www.nature.com/articles/s41598-024-54744-z"><i>Scientific Reports</i></a> and are explained in a Kansas University news release:
<a name='more'></a>
<blockquote class="blockit">A University of Kansas study of rice paddy snakes in Southeast Asia gives key details to their diversification and natural history, adding molecular evidence that the rise of the Khorat Plateau and subsequent environmental shifts in Thailand may have altered the course of the snakes’ evolution some 2.5 million years ago. The findings were published today in the journal Scientific Reports.<br>
<br>
Researchers say the implications could help tell the story of diversification more broadly in the region.<br>
<div class="block"><p>This paper concerns mud snakes typically found in aquatic systems across Southeast Asia, South Asia, East Asia, Australia and New Guinea. Deeper-level relationships regarding their evolution have recently begun to be studied, particularly through genome-scale data. However, finer-scaled evolutionary patterns remain to be fully revealed.</p>
<div class="creditl">Dr. Justin M. Bernstein, Lead author<br>
Center for Genomics<br>
University of Kansas, Lawrence, KS, USA.</div></div>Bernstein, who currently serves at the University of Texas-Arlington, said the mud snakes, a family known as the Homalopsidae, are commonly found today in aquatic systems. Bernstein’s newest work on the homalopsids focuses on a subgroup called rice paddy snakes that are commonly found in agricultural fields and freshwaters streams in Southeast Asia. <br>
<br>
Although recent research has touched on the diversity of rice paddy snakes, their geographic distribution has touched off scientific speculation: One hypothesis suggests that around 2.5 million years ago, a plateau in Central Thailand, known as the Khorat Plateau, emerged from the ground, leading to the separation and subsequent diversification of snake populations over time. Indeed, molecular data provided insights into the timing of species diversification that aligned with the formation of the plateau.<br>
<br>
However, a later genome-scale study challenged this hypothesis by pushing the divergence date backward, predating the plateau's formation.<br>
<div class="block"><p>This discrepancy raises questions about the accuracy of different datasets in determining evolutionary timelines. To address this, our paper employs more limited molecular datasets but with more robust analyses and denser sampling to test the hypothesis. Our results suggest that the group indeed diversified after the Khorat Plateau rose, and environmental changes over time further contributed to their divergence.</p>
<div class="creditl">Dr. Justin M. Bernstein</div></div>Past that, the research team found varied differences in preferred habitats among different snake species using past and present niche models, hinting that other environmental factors might have influenced their routes toward diversification and geographic distribution. <br>
<br>
Bernstein’s collaborator included co-author Rafe Brown, KU professor of ecology & evolutionary biology and curator-in-charge of the Herpetology Division at KU’s Natural History Museum & Biodiversity Institute. Other co-authors included Harold Voris and Sara Ruane of the Field Museum in Chicago; Bryan Stuart of the North Carolina Museum of Natural Sciences; the late Daryl Karns of Hanover College; Jimmy McGuire of the University of California-Berkeley, Djoko Iskandar of the Institut Teknologi Bandung in Indonesia; Awal Riyanto of the National Research and Innovation Agency of Indonesia; Camilo Calderón‐Acevedo of the State University of New York: College of Environmental Science and Forestry; Marcelo Gehara of Rutgers University-Newark; and J. Angel Soto‐Centeno of Rutgers University-Newark and the American Museum of Natural History. <br>
<br>
Bernstein and his collaborators relied on molecular data along with ecological niche modeling to shed new light on the rice paddy snakes, which depended on data about where specimens were located in the field. This approach could help conservation efforts going forward, or predictions of how species might fare in climate change scenarios.<br>
<div class="block"><p>The whole point of ecological niche modeling, put simply, is if I take, say, 100 occurrence points for those snakes, and then I use 19 environmental data layers that correspond with each point, and compare it to a background — which would be the landscape with its environmental data regardless of snake occurrence points — do we see correlations and patterns? You're trying to determine the habitat suitability of your species of interest across a broad landscape, including areas where they have not been recorded from.</p>
<p>These 19 layers containing the environmental factors are ‘stacked’ in a way that each GPS coordinate — where a snake occurrence record is — has a set of 19 environmental variables associated with it.</p>
<div class="creditl">Dr. Justin M. Bernstein</div></div>He said the environmental data includes variables like temperature differences, seasonality and precipitation at different points in time, such as quarterly, monthly or annually.<br>
<br>
For instance, via this approach Bernstein said while these rice-paddy snakes don't exist in the Philippines, there are suitable habitats based off of where they live in Indochina. <br>
<div class="block"><p>Hypothetically they could live there. That doesn't mean they do. There is no evidence suggesting they are able to get across ocean waters and enter the Philippines, and it would be highly unlikely for that scenario to occur. But the analysis is just indicating there is suitable habitat elsewhere, in addition to where we find them now, and that can be really useful. If it's a continuous landscape and you haven't found any individuals of a species in a particular area, but you see high habitat suitability, maybe you can go find a population that is presently unknown to exist.</p>
<div class="creditl">Dr. Justin M. Bernstein</div></div>The research builds on two of Bernstein’s earlier works. One study combines genetic analyses of older museum specimens' mitochondrial DNA with fresher genetic samples from recent field collections of mud snakes to learn more about diversity of homalopsids, including rice paddy snakes. The other study is a more focused study that described a new rice paddy snake species and posited the hypothesis of the Khorat Plateau based on current data but lacked the power to test it.<br>
<br>
While many species of the mud snakes are drab, Bernstein said others are highly charismatic.<br>
<br>
<div class="block"><p>Some have tentacles as appendages on their face. You could find two of the same species in one hole, like a mud lobster hole, where one is white and black, and the other is bright red and black — very striking. Some have speckled yellow bellies, while others are black with bright orange flecks and stripes down their back. And other species have unique behaviors that are not seen in the 4,000-plus species of snakes. They are truly stunning snakes.</p>
<p>I saw a lot of opportunity in them as a model system for investigating biogeography. Honestly, using them more as a model system for understanding how species change or remain stable over time has been really valuable. We have several studies we want to pursue further, and many more in the works, and it all begins with understanding their evolutionary relationships.</p>
<div class="creditl">Dr. Justin M. Bernstein</div></div>Ultimately, the mud snake’s value may be in serving to show how species, and their morphological diversity, evolves over time, as well as how other organisms may react to changes in the ecosystems they live in.
</blockquote>
The team give more technical detail in their open access paper in <i>Scientific Reports</i>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: <i>Hypsiscopus</i>), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that <i>Hypsiscopus</i> diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest <i>Hypsiscopus</i> diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of <i>Hypsiscopus</i>, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.<br>
<br>
<span>Introduction</span><br>
<br>
Widely distributed taxa can serve as excellent model systems to test biogeographic hypotheses, especially in regions with complex geologic histories and a mosaic of geological features. One group that includes several wide-ranging taxa, in one of the most complex regions are the mud snakes; Old World mud snakes of the family Homalopsidae consist of 57 species in 26 genera distributed throughout South and Southeast Asia, Australia, and New Guinea<sup class="x-small"><a class="newtooltip">1</a></sup>. Homalopsids are found across aquatic environments with muddy substrates and varying salinities (e.g., rice paddies, tidal flats, mangroves, swamp forests, freshwater lakes and streams)<sup class="x-small"><a class="newtooltip">2</a></sup>. These mud snakes exhibit a variety of feeding behaviors<sup class="x-small"><a class="newtooltip">3</a></sup>, diets<sup class="x-small"><a class="newtooltip">4</a></sup> and morphological adaptations such as rostral mechanoreceptors<sup class="x-small"><a class="newtooltip">5</a></sup> and salt glands<sup class="x-small"><a class="newtooltip">6</a></sup>. Recently, phylogenetic studies with multilocus datasets have expanded on the evolutionary relationships and divergence times of Homalopsidae<sup class="x-small"><a class="newtooltip">7</a></sup>. A few genera of mud snakes are extremely abundant in aquatic systems of Southeast Asia and have some of the most widespread distributions of any terrestrial vertebrate<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a></sup>. This makes them ideal for investigating how Southeast Asia’s complex geologic history<sup class="x-small"><a class="newtooltip">8</a>,<a class="newtooltip">9</a></sup> has generated patterns of diversity observed today.<br>
<br>
Rice paddy snakes of the genus <i>Hypsiscopus</i> consist of four species. The newly described <i>Hypsiscopus murphyi</i> is distributed around and north of Thailand’s Khorat Plateau, and <i>H. plumbeus</i> is found around and south of the Khorat Plateau, and on the Indonesian islands as far east as Sulawesi<sup class="x-small"><a class="newtooltip">7</a></sup>. <i>Hypsiscopus matannensis</i> and <i>H. indonesiensis</i> are endemic to Sulawesi, the eastern limit of the distribution of the genus (Fig. 1). Phylogenetic investigations of homalopsids using mitochondrially-driven multilocus data have placed the <i>Hypsiscopus</i> origin at ~ 2.5 million years ago (mya)<sup class="x-small"><a class="newtooltip">7</a></sup>. Thus, it is hypothesized that the tectonic uplift event that led to the Khorat Plateau at ~ 2.5 mya<sup class="x-small"><a class="newtooltip">9</a>,<a class="newtooltip">10</a></sup> may have been responsible for the diversification of rice paddy snakes<sup class="x-small"><a class="newtooltip">7</a></sup>. However, date estimates of recent systematic works of Homalopsidae using genomic data pre-date the formation of the plateau with an estimated divergence of ~ 4 mya. These two studies<sup class="x-small"><a class="newtooltip">7</a>,<a class="newtooltip">11</a></sup>, each yielding conflicting divergence dates around the Khorat Plateau hypothesis, use different depths of DNA sequencing and different divergence date estimation techniques.
<div class="panelplain" style="margin: 1em auto"><div style="margin: 0 1em"><span>Figure 1.</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7AfnUo-chWC7HCbQDItBB2a4z4_Co2rWUp7UVxSzPPM9pFS6qnMJERn3B45Kj4HoWQOHKr7YH1slnRq9OCXxouCUZzkxynB3cFJevlkhu07QzHDjNeZ7-MDx5GESja5jDl8tc4nqBgha2BB-XedUcoFDnbLCUSByNg_YEJQCBGIzBa66mQTae-CsTN02w/s1600/41598_2024_54744_Fig1_HTML.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7AfnUo-chWC7HCbQDItBB2a4z4_Co2rWUp7UVxSzPPM9pFS6qnMJERn3B45Kj4HoWQOHKr7YH1slnRq9OCXxouCUZzkxynB3cFJevlkhu07QzHDjNeZ7-MDx5GESja5jDl8tc4nqBgha2BB-XedUcoFDnbLCUSByNg_YEJQCBGIzBa66mQTae-CsTN02w/s1600/41598_2024_54744_Fig1_HTML.webp"/></a>
<div class="caption">Sampling map of <i>Hypsiscopus</i> in this study. Map is colored by elevation (0–4509 m). The Red River and Khorat Plateau boundary are shown by the solid red line and dashed orange line, respectively.<br><br><div class="credit">Photograph of <i>H. murphyi</i> by BLS.</div></div>
</div>
Estimates of clade divergence timing on molecular phylogenies are standard in systematic studies<sup class="x-small"><a class="newtooltip">12</a></sup>, especially parameter-heavy approaches that use model-based likelihood methods<sup class="x-small"><a class="newtooltip">13</a>,<a class="newtooltip">14</a></sup> which have helped in formulating and testing biogeographic hypotheses. Modern phylogenetics now frequently use genomic datasets that include thousands of loci, but this comes at the cost of major increases in computational burden and analysis run times. Potentially alleviating some of these costs, summary coalescent methods aim to reconstruct phylogenies rapidly and estimate divergence dates (e.g., ASTRAL15; treePL<sup class="x-small"><a class="newtooltip">16</a></sup>). Because of a higher number of informative sites and the potential to characterize evolutionary heterogeneity across independent genes, a greater number of loci is presumed to increase accuracy in divergence time estimates. Compared to single-gene or small multilocus datasets dated using computationally rigorous Bayesian methods like BEAST<sup class="x-small"><a class="newtooltip">17</a></sup>, phylogenomic datasets are assumed to provide a better representation of species divergence and, as such, may allow for finer scale temporal discrimination of alternate hypotheses in biogeography<sup class="x-small"><a class="newtooltip">18</a></sup>. However, the methods used to rapidly obtain divergence dates from genomic datasets may not be useful in a hypothesis-testing framework for particular geological events. This is due to genomic studies typically having lower sample sizes due to costs, thus possibly missing important population-level data, or because of the computation times associated with analysis of large datasets.<br>
<br>
Methods based on coalescent simulations of demographic models can be more intuitively customized to the study taxon to test specific evolutionary scenarios<sup class="x-small"><a class="newtooltip">19</a></sup>. Coalescent models can incorporate multilocus or genomic datasets and can be fine-tuned to test phylogeographic hypotheses with large sample sizes. Obtaining accurate divergence dates is critical for downstream studies that aim to identify the causal factors of population splits and speciation, especially at potential biogeographic barriers<sup class="x-small"><a class="newtooltip">20</a></sup>. Herein, we examine whether rice paddy snake diversification coincides with the rise of the Khorat Plateau and test for differences in each species’ environmental niche. The expansive range of the non-sister species <i>H. murphyi</i> and <i>H. plumbeus</i> (1.7 million km2 for <i>H. murphyi</i> and ~ 4 million km2 for <i>H. plumbeus</i>) means that they span a heterogeneous landscape of environmental, habitat, and topographic features. Phylogeographic structure and the maintenance of species limits driven by environmental heterogeneity has been documented in widely distributed taxa<sup class="x-small"><a class="newtooltip">21</a>,<a class="newtooltip">22</a>,<a class="newtooltip">23</a></sup>, including areas that contain well-known biogeographic barriers<sup class="x-small"><a class="newtooltip">24</a>,<a class="newtooltip">25</a></sup>. Given the wide distribution of rice paddy snakes, we examine if quantifiable differences in the environmental niches reflect phylogeographic structure in these snakes<sup class="x-small"><a class="newtooltip">26</a></sup>.<br>
<br>
In this study, we used newly obtained sequence data for <i>Hypsiscopus</i> to investigate the diversification of rice paddy snakes through Southeast Asia. We obtained 303 new DNA sequences of 6 nuclear and 2 mitochondrial genes, and combined these with previously published data to generate a dataset consisting of 653 sequences across 8 genes for 151 individuals. Using coalescent demographic models with priors that encompass known <i>Hypsiscopus</i> evolutionary history, we tested the hypothesis that the crown group of <i>Hypsiscopus</i> diversified ~ 2.5 mya when the tectonic uplift of the Khorat Plateau took place<sup class="x-small"><a class="newtooltip">9</a>,<a class="newtooltip">10</a></sup>. <i>Hypsiscopus</i> is one of few taxa that have parapatric distributions around the plateau and are abundant enough to obtain a dense sampling scheme for evolutionary studies, making them an ideal system to test our diversification hypothesis. We aim to identify modes of speciation in Southeast Asia, which are often referred to in regards to the prevailing paradigm in this region: Pleistocene sea-level fluctuations. We performed quantitative morphological, molecular phylogenetic, and ecological analyses to investigate homalopsid phenotypic and genetic diversity, and predict that environmental data will yield quantifiable niche differences between the two widespread species: <i>H. murphyi</i> and <i>H. plumbeus</i>.<br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOjZ6fzaAroVq8kYSLbrzWsdapCoDJsCZPz0z7PcSIenJjzibKN74M0y0QaQ1muUDRwB_H3eDgmQYD-otEKn08sgv_U_Ww4qHYzmkR6CG_5PcE23A5_ySTUXqPC9nD7MdE1XaKshZpQ5C6EAgtUYHvIqfHkHCinpr5wlO5nYMErIuBE0vMTiTkxpXRpk6R/s1600/41598_2024_54744_Fig2_HTML.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOjZ6fzaAroVq8kYSLbrzWsdapCoDJsCZPz0z7PcSIenJjzibKN74M0y0QaQ1muUDRwB_H3eDgmQYD-otEKn08sgv_U_Ww4qHYzmkR6CG_5PcE23A5_ySTUXqPC9nD7MdE1XaKshZpQ5C6EAgtUYHvIqfHkHCinpr5wlO5nYMErIuBE0vMTiTkxpXRpk6R/s1600/41598_2024_54744_Fig2_HTML.webp"/></a>
<div class="caption">Molecular and morphological diversity in Hypsiscopus. Left) Phased concatenated phylogeny of <i>Hypsiscopus</i> (only one allele shown).<i> Hypsiscopus murphyi</i> is split into two subclades: East of the Red River (red) and west of the Red River (blue). Black circles at nodes represent strongly supported relationships (UFB ≥ 95 and SH-aLRT values ≥ 80). Scale bar in substitutions per site. Upper right) The six demographic scenarios tested in PipeMaster. Topology is based on the concatenated phylogeny (left), with both populations of <i>H. murphyi</i> collapsed into a single tip. The asterisk (*) shows the model with the highest support (Is). Bottom right) Linear discriminant analysis (LDA; 27 variables), showing three species of rice paddy snakes in morphospace. Points are shown with 68% Gaussian data ellipses. Density rugs (colored lines on axes) correspond to each point in morphospace. Density plots reflect the density of points in the plot for each species (colors correspond to the phylogeny).</div>
<hr>
<div style="margin: 0 1em"><span>Figure 3</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi89Jm0YGg9Rhz3t-CvrBH-ft0OUn2D0G4cOkMls6Zf09P22YZUcc7O_Wr3wshI-o2bojUzXjwhmYyXAGMuPFfUuRwB2gfmsKTGP9X5GYv5rFaYI0h2GTK0sJadnCLxrN9rvXskuxkdaOL8CNB4vbKbaTSocPuc4R5wm5gg7YxT5E4lPGeSTcRdF-mCLb6C/s1600/41598_2024_54744_Fig3_HTML.webp" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" data-original-height="1170" data-original-width="968" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi89Jm0YGg9Rhz3t-CvrBH-ft0OUn2D0G4cOkMls6Zf09P22YZUcc7O_Wr3wshI-o2bojUzXjwhmYyXAGMuPFfUuRwB2gfmsKTGP9X5GYv5rFaYI0h2GTK0sJadnCLxrN9rvXskuxkdaOL8CNB4vbKbaTSocPuc4R5wm5gg7YxT5E4lPGeSTcRdF-mCLb6C/s1600/41598_2024_54744_Fig3_HTML.webp"/></a><div class="caption">Ecological niche models of <i>H. murphyi</i>, <i>H. plumbea</i>, and <i>H. matannensis</i>. Colors represent habitat suitability, with warmer colors indicating higher habitat suitability based on environmental variables. Full-size images of each niche model can be found in Supplementary Figs. S5–S10.</div>
</div><br>
<div class="creditl">Bernstein, J.M., Voris, H.K., Stuart, B.L. et al. <br>
Integrative methods reveal multiple drivers of diversification in rice paddy snakes. <br>
<i>Sci Rep</i> <b>14</b>, 4727 (2024). https://doi.org/10.1038/s41598-024-54744-z<br>
<br>
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Published by Springer Nature Ltd. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote><br>
Creationists will need to ignore how well the geological changes map onto the genetic changes as the genus diversified. Although correlation doesn't establish causality, it <b>does</b> add additional weight to the Theory of Evolution by Natural Selection that predicts environmental change will result in evolutionary change.<br>
<br>
and of course, dedicated creationist delusionists will need to ignore the fact that these geological/environmental changes and the genetic changes as this genus of snake diversified all happened in that long period of Earth's history that happened before creationism’s god hit upon the idea of magicking a small, flat planet with a dome over it, out of nothing.
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{n: "2", text: "Murphy, J. C. Homalopsid Snakes: Evolution in the Mud (Krieger Publishing Company, 2007)"},
{n: "3", text: "Jayne, B. C., Voris, H. K. & Ng, P. K. L. How big is too big? Using crustacean-eating snakes (Homalopsidae) to test how anatomy and behaviour affect prey size and feeding performance. Biol. J. Linn. 123, 636–650 (2018).",
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{n: "8", text: "Hall, R. Southeast Asia’s changing palaeogeography. Blumea 54, 148–161 (2009).",
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-57903640290148789412024-03-14T00:45:00.002+00:002024-03-14T20:45:50.297+00:00Creationism in Crisis - Dinosaur Footprints In Alaska from 100 Million Years Before 'Creation Week'!<div class="title-box" style="display: none">
<div class="postTitle" style="font-size: 40px"></div>
<div class="horizontalBox" style="gap: 0">
<div class="left-column" style="text-align: left; flex: 3">Part of the Nanushuk Formation, visible as a darker slanted rock layer, rises in a bluff above a bend of the Kukpowruk River. A large number of dinosaur tracks were found in this area.</div>
<div class="right-column" style="text-align: right; flex: 1">Photo: Anthony Fiorillo</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_tgJ9S1dWf6GkK6J2SWkquGyrSNXLs1rpZJ0DjE3IZgEZIxHCwTwI56dg5Q13dxPEDGIApivl7FO4CD5oWmGOLTFycUAgwAOnB-gCnpiu0j1xydQORH-ERYWp_kcVMwIZNZXKo8_4qh_8Q2virHtDJ-W_zglU5AoVs8eLaDLpED2G2ggVnOw_Paj2qyB1/s1600/NanushukFormation.jpeg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_tgJ9S1dWf6GkK6J2SWkquGyrSNXLs1rpZJ0DjE3IZgEZIxHCwTwI56dg5Q13dxPEDGIApivl7FO4CD5oWmGOLTFycUAgwAOnB-gCnpiu0j1xydQORH-ERYWp_kcVMwIZNZXKo8_4qh_8Q2virHtDJ-W_zglU5AoVs8eLaDLpED2G2ggVnOw_Paj2qyB1/s1600/NanushukFormation.jpeg"/></a>
</div>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1z6J4U5Z3D105VLQuke40F-lXmtrssoO08j70bewbYee_DALeWhnjpspIUeP9FXFhLQSCtUvsc3u1i2jeDVvhfpyi2FKEYcurvxT8BGawKj9PrUDbhPVXV71BM_lEM4bt7nq0HuTCa1dKB6zvBU09O8qoYc6_IWnGzxg294hXSNqrvQteeDM7GtMYIxd9/s770/TheropodTrack.jpeg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1z6J4U5Z3D105VLQuke40F-lXmtrssoO08j70bewbYee_DALeWhnjpspIUeP9FXFhLQSCtUvsc3u1i2jeDVvhfpyi2FKEYcurvxT8BGawKj9PrUDbhPVXV71BM_lEM4bt7nq0HuTCa1dKB6zvBU09O8qoYc6_IWnGzxg294hXSNqrvQteeDM7GtMYIxd9/s320/TheropodTrack.jpeg"/></a>
<div class="captionc">A theropod track lies in rock near the west bank of the Kukpowruk River.<br><br><div class="credit">Photo: Anthony Fiorillo </div></div>
</div>
<a href="https://www.gi.alaska.edu/news/alaska-dinosaur-tracks-reveal-lush-wet-environment">Alaska dinosaur tracks reveal a lush, wet environment | Geophysical Institute</a><br>
<br>
About 100 million yearsd before creationism's god decided to create a small flat planet with a dome over it to keep the water about its sky out, there were dinosaurs living in what is now northern Alaska. The problem for creationists is that the people who wrote their favourite creation myths were ignorant both of dinosaurs and Alaska so had no idea their tales needed to include something about them, which is why everything they wrote about either happened within a day or two's walk if the Canaanite Hills or were plagiarized from nearby cultures.<br>
<br>
Now a team of paleontologists and archaeologists have discovered fossilised dinosaur footprints and the remains of plants in the Nanushuk Formation that show the climate there was warmer and wetter than today, at a time when species were migrating over the landbridge between Siberia in Asia and North America.<br>
<br>
Unlike the Paluxy hoax, which had creationists fooled for the best part of a decade, there were no human footprints (hand-carved or otherwise) associated with these dinosaur tracks.<br>
<br>
Because creationists will try to falsify the aging of the Nanshuk Formation, claiming the method must have been flawed to such an extent that if made 10,000 years or less look like 100 million years, here is actually how the dating was done - it’s; those dreaded zircons in volcanic deposits again, plus stratigraphy based on index fossils found in rocks of known age:
<blockquote class="ai">Do you have any information on the Nanushuk Formation in northern Alaska and how its age was estimated?
The Nanushuk Formation is a geological formation located in northern Alaska, particularly in the North Slope region. It is primarily composed of sandstone, siltstone, and shale, and it contains significant oil and gas reserves. The formation is of great interest to geologists and petroleum geologists due to its hydrocarbon potential.<br>
<br>
The age of the Nanushuk Formation has been estimated through various methods, including biostratigraphy and radiometric dating of volcanic ash layers within the formation. Biostratigraphy involves the study of fossil assemblages found within the rocks to determine their relative ages. By comparing the fossils present in the Nanushuk Formation to those found in other formations with well-established ages, geologists can infer the approximate age of the Nanushuk Formation.<br>
<br>
Additionally, radiometric dating techniques, such as radiocarbon dating or uranium-lead dating, can be used to determine the absolute ages of specific minerals or volcanic ash layers within the formation. These methods rely on the decay of radioactive isotopes within the rocks to estimate the time since their formation.<br>
<br>
Through a combination of these techniques, geologists have estimated that the Nanushuk Formation was deposited during the Late Cretaceous period, approximately 70 to 80 million years ago. However, the precise age estimates may vary depending on the specific location within the formation and the methods used for dating.
</blockquote>
The team, led by Dr. Anthony R. Fiorillo of the New Mexico Museum of Natural History & Science, Albuquerque, USA and including Professor Paul McCarthy of University of Alaska Fairbanks (UAF) College of Natural Science and Mathematics, have published their findings open access in the journal <i>Geosciences</i>. It is explained in a UAF news item:
<a name='more'></a>
<blockquote class="blockit">
<div class="rpanel48plain" >
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihPjdld8kV0CsQAMVa7GEuk5I90eE1mrtgkiDZ55S0spajEIRaasvPwoaFa7n3j2O5B5gnM85q_CjdXF-6pQrD-IJBuGzyxDgV-5Xexl2YWtvMqJbBaZh2baCpsFsV96QcO5Lr7tNeICkIbslIwdCFV9W5Jfqo95yjLws4oO1zjzVCmZXk5ry3awNVjoC9/s1600/FindingsMap.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihPjdld8kV0CsQAMVa7GEuk5I90eE1mrtgkiDZ55S0spajEIRaasvPwoaFa7n3j2O5B5gnM85q_CjdXF-6pQrD-IJBuGzyxDgV-5Xexl2YWtvMqJbBaZh2baCpsFsV96QcO5Lr7tNeICkIbslIwdCFV9W5Jfqo95yjLws4oO1zjzVCmZXk5ry3awNVjoC9/s1600/FindingsMap.jpg"/></a>
<div class="caption">A map shows locations of dinosaur tracks and fossilized tree trunks and other plant life found along the Kukpowruk River.<br><div class="credit">Image: Anthony Fiorillo</div></div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg0ouLJhZcZVGOwKCKwvW8yAQR2RRi_qbzujrE8NiupS2xFqLx-1CzMFsmQBojM3kB1KnnMn_gv505qr1UzQ-sy-tBSTQ1NFMA8qYB8j0_7nEsLR4nmg3DAzKyVxgWKPFECp6PwTHF8IiQSz3WrdcAF3jdG-QcB38u0Y9aFxODjfd86-DlzrZnVOrOSxUC-/s1600/KukpowrukRiver.jpeg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg0ouLJhZcZVGOwKCKwvW8yAQR2RRi_qbzujrE8NiupS2xFqLx-1CzMFsmQBojM3kB1KnnMn_gv505qr1UzQ-sy-tBSTQ1NFMA8qYB8j0_7nEsLR4nmg3DAzKyVxgWKPFECp6PwTHF8IiQSz3WrdcAF3jdG-QcB38u0Y9aFxODjfd86-DlzrZnVOrOSxUC-/s1600/KukpowrukRiver.jpeg"/></a>
<div class="caption">The Kukpowruk River flows through tundra in northwest Alaska. Fieldwork for the dinosaur study centered on Coke Basin, a circular geologic feature along the river, about 60 miles south of Point Lay and 20 miles inland from the Chukchi Sea coast.<br><div class="credit">Photo: Anthony Fiorillo</div></div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEji-NSjZdccMaV73W-clsgJJHc07lJnnUvkE5QRh9mhjzMDkBWY_ejnIHYRP147Hzak9FxHpFoGSQCOH1R5NE8idf8pLzA5pcSF8alg13sMJMZwnyaq_4SSL4uKuUU3aeK_POJ8nPDxitcD1bBZDcSgUkSPQVg6MkjtkS2baDX9dUSPbRVFV_wc9eaWQlpz/s1600/FossilTrunk.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEji-NSjZdccMaV73W-clsgJJHc07lJnnUvkE5QRh9mhjzMDkBWY_ejnIHYRP147Hzak9FxHpFoGSQCOH1R5NE8idf8pLzA5pcSF8alg13sMJMZwnyaq_4SSL4uKuUU3aeK_POJ8nPDxitcD1bBZDcSgUkSPQVg6MkjtkS2baDX9dUSPbRVFV_wc9eaWQlpz/s1600/FossilTrunk.jpg"/></a>
<div class="caption">A fossilized standing tree trunk approximately 2 feet in diameter is rooted in floodplain mudstone and sandstone in the Nanushuk Formation in northwest Alaska.<br><div class="credit">Photo: Paul McCarthy</div></div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-0UCOMqv_n6pn1lRiCwUkXf8CuwLgeCT-yVOo-oRfFoJCBN1kWMWhdGwYQtg-EH7PbKOIPcZ8EEqOkO0-MqUx4GZ58-NBygB2yWdi0XUwBaoAvbkvbOxkNKKZg6R8g24-SjQJtNJ78WqOuzjq85jvrjuO_v5f_p6eA1TP46tpl1hIg4YLjUW7_fOUEtI7/s1600/FossilRoots.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-0UCOMqv_n6pn1lRiCwUkXf8CuwLgeCT-yVOo-oRfFoJCBN1kWMWhdGwYQtg-EH7PbKOIPcZ8EEqOkO0-MqUx4GZ58-NBygB2yWdi0XUwBaoAvbkvbOxkNKKZg6R8g24-SjQJtNJ78WqOuzjq85jvrjuO_v5f_p6eA1TP46tpl1hIg4YLjUW7_fOUEtI7/s1600/FossilRoots.jpg"/></a>
<div class="caption">Large carbonaceous root traces lace splay sandstone in the Nanushuk Formation in northwest Alaska.<br><div class="credit">Photo: Paul McCarthy</div></div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKIp2e8Q3UoXVFuAEcdSJFb_e9en8wR4xzIe-3sum-E7KKcKuG2e2_CqaQuJmIGjj9kVU-BLXPHDRsw6EkZT0hKh3gHbhcSoKR_mbF68j5nD9Z-zWPda81wAlK735CkzsoM44tvOyhFcQfETfODRgeHjI1I2tyqoYtzFuvSxKtT8V-Bk8jaiGwcNg6Yacd/s1600/FiorilloMcCarthy.jpeg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKIp2e8Q3UoXVFuAEcdSJFb_e9en8wR4xzIe-3sum-E7KKcKuG2e2_CqaQuJmIGjj9kVU-BLXPHDRsw6EkZT0hKh3gHbhcSoKR_mbF68j5nD9Z-zWPda81wAlK735CkzsoM44tvOyhFcQfETfODRgeHjI1I2tyqoYtzFuvSxKtT8V-Bk8jaiGwcNg6Yacd/s1600/FiorilloMcCarthy.jpeg"/></a>
<div class="caption">Anthony Fiorillo, left, and Paul McCarthy hold an Explorers Club banner during their Alaska research.<br><div class="credit">Photo: Antony Fiorillo </div></div>
</div>A large find of dinosaur tracks and fossilized plants and tree stumps in far northwestern Alaska provides new information about the climate and movement of animals near the time when they began traveling between the Asian and North American continents roughly 100 million years ago.<br>
<br>
The findings by an international team of scientists led by paleontologist Anthony Fiorillo were published Jan. 30 in the journal Geosciences. Fiorillo researched in Alaska while at Southern Methodist University. He is now executive director of the New Mexico Museum of Natural History and Science.<br>
<br>
University of Alaska Fairbanks geology professor Paul McCarthy, with the UAF Geophysical Institute and UAF College of Natural Science and Mathematics, was a leading contributor to the research. He and UAF graduate student Eric Orphys are among the eight co-authors.<br>
<br>
Fiorillo and McCarthy are longtime collaborators. <br>
<br>
<div class="blockl"><p>We've had projects for the last 20 years in Alaska trying to integrate sedimentology, dinosaur paleontology and the paleoclimate indicators. We’ve done work in three other formations — in Denali, on the North Slope and in Southwest Alaska — and they're about 70 million years old. This new one is in a formation that's about 90 to 100 million years old.</p>
<div class="credit">Professor Paul McCarthy, co-corresponding author<br>
College of Natural Science and Mathematics<br>
University of Alaska Fairbanks, Fairbanks, Alaska, USA.</div></div>Fiorillo said the additional age is notable.<br>
<br>
<div class="blockl"><p>What interested us about looking at rocks of this age is this is roughly the time that people think of as the beginning of the Bering Land Bridge — the connection between Asia and North America. We want to know who was using it, how they were using it and what the conditions were like.</p>
<div class="creditl">Dr. Anthony R. Fiorillo, lead author<br>
New Mexico Museum of Natural History & Science, <br>
Albuquerque, NM, USA</div></div>Research into the paleoclimate can help scientists understand the warming world of today, the authors write. <br>
<br>
<div class="blockl"><p>The mid-Cretaceous was the hottest point in the Cretaceous. The Nanushuk Formation gives us a snapshot of what a high-latitude ecosystem looks like on a warmer Earth.</p>
<div class="creditl">Professor Paul McCarthy.</div></div>
<span>A rich find of evidence</span><br>
<br>
The Nanushuk Formation is an outcropped layer of sedimentary rock 800 to 5,000 feet thick across the central and western North Slope. It dates to roughly 94 million to 113 million years ago in the mid-Cretaceous Period and about when the Bering Land Bridge began.<br>
<br>
The fieldwork occurred in 2015-2017 and centered on Coke Basin, a circular geologic feature of the Nanushuk Formation. The basin is in the DeLong Mountains foothills along the Kukpowruk River, about 60 miles south of Point Lay and 20 miles inland from the Chukchi Sea.<br>
<br>
In the area, Fiorillo and McCarthy found approximately 75 fossil tracks and other indicators attributed to dinosaurs living in a riverine or delta setting.<br>
<br>
<div class="blockl"><p>This place was just crazy rich with dinosaur footprints. [One site stands out] We were at a spot where we eventually realized that for at least 400 yards we were walking on an ancient landscape. On that landscape we found large upright trees with little trees in between and leaves on the ground. We had tracks on the ground and fossilized feces. It was just like we were walking through the woods of millions of years ago.</p>
<div class="creditl">Dr. Anthony R. Fiorillo.</div></div>
They found numerous fossilized tree stumps, some 2 feet in diameter.<br>
<br>
The Nanushuk Formation encompasses rock of marine and non-marine characteristics and composition, but the authors’ research focuses primarily on the non-marine sediments exposed along the upper Kukpowruk River.<br>
<div class="block"><p>One of the things we did in our paper was look at the relative frequencies of the different kinds of dinosaurs. What was interesting to us was that the bipedal plant eaters were clearly the most abundant. One of the things that was interesting is the relative frequency of bird tracks.</p>
<div class="creditl">Dr. Anthony R. Fiorillo</div></div>
<br>
Two-legged plant eaters accounted for 59% of the total tracks discovered. Four-legged plant eaters accounted for 17%, with birds accounting for 15% and non-avian, mostly carnivorous, bipedal dinosaurs at 9%.<br>
<br>
The authors point out that nearly half of North America’s shorebirds breed in the warm months of today’s Arctic. They suggest that the high number of fossil bird tracks along the Kukpowruk River indicates the warm paleoclimate was a similar driver for Cretaceous Period birds.<br>
<br>
<span>A wet and warm place</span><br>
<br>
Carbon isotope analysis of wood samples led to a determination that the region received about 70 inches of precipitation annually. This record of increased precipitation during the mid-Cretaceous provides new data that supports global precipitation patterns associated with the Cretaceous Thermal Maximum, the authors write.<br>
<br>
The Cretaceous Thermal Maximum was a long-term trend approximately 90 million years ago in which average global temperatures were significantly higher than those of today.<br>
<div class="block"><p>The temperature was much warmer than it is today, and what’s possibly more interesting is that it rained a lot. The samples we analyzed indicate it was roughly equivalent to modern-day Miami. That’s pretty substantial.</p>
<div class="creditl">Dr. Anthony R. Fiorillo</div></div>
<br>
Of note is that the Alaska site investigated by Fiorillo and McCarthy was about 10 to 15 degrees latitude farther north in the mid-Cretaceous than it is today.<br>
<br>
McCarthy’s role as a fossil soils expert was to analyze old rocks and sediments to interpret the type of environment that existed at the time.<br>
<div class="block"><p>We can say here's a river channel, here's a flood deposit, here's a levee, here's the floodplain, here's a swamp. And so, if we're able to find tracks in that section, then you can sometimes say that a group of dinosaurs seems to have really liked being here as opposed to there.</p>
<p>This puts a new dot on the map and tells us there's a lot here, and it fits into the bigger picture. The big picture is we're trying to get better resolution on what life was like in the high latitudes back at the time the dinosaurs were roaming around.</p>
<div class="creditl">Dr. Anthony R. Fiorillo</div></div>
Fiorillo said the site indicates there’s much more work to be done.<br>
</blockquote><br>
More technical data is in the team's open access paper in <i>Geosciences</i><br>. In addition, there is a section devoted to radiometric dating, which, to the annoyance of creationists no doubt, included <a href="https://rosarubicondior.blogspot.com/2024/01/creationism-in-crisis-something-for.html#UPb" target="_blank">Uranium-Lead (U-Pb) dating of zircons</a>. The team used two techniques termed LA-ICP-MS and CA-ID-TIMS:
<blockquote class="ai">In the context of U-Pb zircon dating, what do the terms, LA-ICP-MS and CA-ID-TIMS stand for and what are they?
In the context of U-Pb zircon dating, LA-ICP-MS and CA-ID-TIMS are two different techniques used to analyze zircon crystals for age determination.
<ol class="dbl1 bold">
<li><b>LA-ICP-MS:</b>
<ul type="disc">
<li>LA stands for Laser Ablation.</li>
<li>ICP-MS stands for Inductively Coupled Plasma Mass Spectrometry.</li>
</ul>
In LA-ICP-MS, a laser beam is used to ablate small amounts of material from the surface of a zircon crystal. The ablated material is then transported into an inductively coupled plasma (ICP), where it is ionized. The resulting ions are then analyzed using a mass spectrometer (MS). By measuring the isotopic ratios of uranium and lead in the zircon crystal, geologists can determine its age.</li>
<li><b>CA-ID-TIMS:</b>
<ul type="disc">
<li>CA stands for Chemical Abrasion.
<li>ID-TIMS stands for Isotope Dilution Thermal Ionization Mass Spectrometry.
</ul>
In CA-ID-TIMS, the zircon crystals undergo a chemical abrasion process to remove the outer layers that may have experienced lead loss or contamination. This step ensures that the zircon sample being analyzed is as pristine as possible. After chemical abrasion, the zircon crystals are dissolved, and the uranium and lead isotopes are separated and purified. The isotopic ratios are then measured using a thermal ionization mass spectrometer (TIMS). This technique provides precise and accurate age determinations, particularly for older zircon crystals.</li>
</ol>
Both LA-ICP-MS and CA-ID-TIMS are widely used in geochronology to determine the ages of zircon crystals and other minerals. They offer complementary advantages and are often used in conjunction to obtain robust age constraints for geological events.</blockquote>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
The Nanushuk Formation (Albian–Cenomanian) crops out over much of the central and western North Slope of Alaska, varying from ≈1500 to ≈250 m thick from west to northeast. The Nanushuk Formation records an inter-tonguing succession of marine and nonmarine conglomerate, sandstone, mudstone, and coal. These rock units comprise the Kukpowruk and Corwin formations of the former Nanushuk Group, respectively. Work presented here is centered in the foothills of the DeLong Mountains along the Kukpowruk River, from an area west of Igloo Mountain in the Coke Basin to the Barabara Syncline, approximately 80 km to the north. A radiometric date recovered from a tuff in our study area suggests a Cenomanian age for at least some of these rocks. Outcrops along the Kukpowruk River contain a well-preserved fossil flora previously recovered from marine, marginal marine, and terrestrial sediments. Our own work focuses on detailed measured sections of terrestrial rocks, interpretation of sedimentary facies and facies associations, and documentation of fossil vertebrates. Eight facies associations are identified in the study area that together are interpreted to represent meandering fluvial and upper delta plain environments. Plant fossils are common and include standing tree trunks up to 58 cm in diameter at some locations. Approximately 75 newly discovered tracksites, and a heretofore unknown, rich fossil vertebrate ichnofauna, are present. The ichnofaunal assemblage includes evidence of small and large theropod dinosaurs (including birds) and bipedal and quadrupedal ornithischian dinosaurs. Approximately 15% of the dinosaur ichnofauna record is represented by fossil bird tracks. Wood fragments from the Nanushuk Formation were analyzed for their carbon isotopic composition to relate δ13C to mean annual precipitation. Samples averaged −26.4‰ VPDB, suggesting an average MAP of 1412 mm/year. This record of increased precipitation in the Nanushuk Fm. during the mid-Cretaceous provides new data that supports global precipitation patterns associated with the Cretaceous Thermal Maximum. This work provides an important framework for much-needed further paleoecological and paleoclimatic analyses into greenhouse conditions in the terrestrial Cretaceous Arctic during this important window in time.<br>
<br>
<span>1. Introduction</span><br>
<br>
It is a truism that the pace of human-caused changes to global climate is increasingly overwhelming ecosystems that have, in general, been relatively stable over several thousands of years. As the world’s human population continues to explode in size at the same time as rapid climate change, it is forcing a reshaping of conservation paradigms that now include looking to the past for guidance on crucial aspects of ecosystems and their health [<a class="newtooltip">1</a>]. The prevailing conservation paradigm has been to hold ecosystems to a now appreciated unrealistic idealized model of stasis. But now it is becoming clear that new approaches using historical as well as novel landscapes provide insights into key issues such as drivers of biodiversity, fundamental processes within ecosystems, and the interplay between biota and climate [<a class="newtooltip">2</a>,<a class="newtooltip">3</a>,<a class="newtooltip">4</a>]. Sedimentary rocks from the Late Cretaceous Arctic and sub-Arctic present an opportunity to assess ecosystems that existed during an extreme planetary greenhouse condition.<br>
<br>
The mid to Late Cretaceous of Alaska represents one of these time periods with terrestrial Cretaceous deposits ranging from the Albian to the Maastrichtian. While much work has been advanced for the Late Cretaceous Polar Arctic (Prince Creek Formation), detailed reconstruction of the mid-Cretaceous Nanushuk Formation still requires a comprehensive and quantitative approach. The Albian–Cenomanian of Alaska was arguably warmer than the Late Cretaceous Polar Arctic [<a class="newtooltip">5</a>,<a class="newtooltip">6</a>]. More broadly, the mid-Cretaceous was also a period of global environmental and evolutionary change that included rising sea levels, diversification of flowering plants, and vertebrate faunal diversification and turnover [<a class="newtooltip">7</a>,<a class="newtooltip">8</a>,<a class="newtooltip">9</a>,<a class="newtooltip">10</a>].<br>
<br>
The Albian–Cenomanian time was the earliest episode of faunal exchange between Beringia and Asia, e.g., [<a class="newtooltip">11</a>]. This route between the North American and Asian continents has repeatedly been key to the dispersal of organisms starting during the time represented by the Nanushuk Formation up to the more recent Pleistocene faunal exchanges. While the Nanushuk Formation is prominent across all of northern Alaska, this study focuses on exposures of the unit along the Kukpowruk River in far northwestern Alaska (Figure 1). Here, we build on the detailed earlier paleobotanical survey work by Spicer and Herman [<a class="newtooltip">12</a>] and provide new sedimentological, paleontological, and paleoclimatological data for this region. While their seminal work [<a class="newtooltip">12</a>] provided needed insights into floral communities ranging from marsh/heath communities to forested river margin communities found along the Kukpowruk River, their study did not provide information on fossil vertebrates and paleoclimate, with only limited sedimentological detail. As such, this study takes the first major steps to improve our understanding of this critical window in deep time.<br>
<br>
<div class="panelplain" style="margin: 1em 5%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1K10vjEi5WROcJMutC5anmT0p9PVxbALfmik1hOC0XNj5YRTHG4KgbSKKSdEMPr_PPbC88J1xCPiwe8OOJj-JVLppWR6pbWJ0pvBHMOh13MLshDEd0sQROUw1sFPlXlpJZZaEnHeANV-ntqTAYw-4WMTMuPuzBGSbIJV6gOggNCK5iemtzsF8AXVnXMog/s1600/geosciences-14-00036-g001.png" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1K10vjEi5WROcJMutC5anmT0p9PVxbALfmik1hOC0XNj5YRTHG4KgbSKKSdEMPr_PPbC88J1xCPiwe8OOJj-JVLppWR6pbWJ0pvBHMOh13MLshDEd0sQROUw1sFPlXlpJZZaEnHeANV-ntqTAYw-4WMTMuPuzBGSbIJV6gOggNCK5iemtzsF8AXVnXMog/s1600/geosciences-14-00036-g001.png"/></a>
<div class="caption"><b>Figure 1.</b> (<b>A</b>) Map of Alaska with a star showing location of study area. (<b>B</b>) Map of Kukpowruk River showing locations of fossil vertebrate tracksites (designated by combination of numbers and letters) in this study, and fossil plant sites (designated by only numbers) from study by Spicer and Herman [<a class="newtooltip">12</a>]. (C–E) More detailed maps of areas of high concentration of fossil footprint sites.</div></div>
<span>2. Geologic Framework</span><br>
<br>
The Nanushuk Fm. and coeval upper Torok Fm. fill the western part of a large, east–west trending, peripheral foreland basin across the west-central North Slope of Alaska. The basin is bounded to the south by the Brooks Range fold and thrust belt [<a class="newtooltip">13</a>]. The fold and thrust belt comprises a succession of sedimentary rocks thrust northward that are partly contemporaneous with rifting on the northern flank [<a class="newtooltip">13</a>,<a class="newtooltip">14</a>]. The Colville foreland basin formed due to the load imposed by thrust faulted allochthons within the growing Cretaceous Brooks Range, followed by sediment deposition eroded from them. Orogen-wide uplift and erosion between 135–95 Ma resulted in the deposition of clastic sediments to the north and northeast, including early Albian to Cenomanian fluvial–deltaic strata of the Nanushuk Fm. [<a class="newtooltip">15</a>,<a class="newtooltip">16</a>].<br>
<br>
The Nanushuk Fm. and upper Torok Fm. are present in the northern foothills belt and in the subsurface of the North Slope coastal plain (Figure 2). The Nanushuk Fm. is a succession of inter-tonguing marine and nonmarine rocks interpreted as marine shelf, delta plain, strandplain, fluvial, and alluvial overbank deposits [<a class="newtooltip">14</a>,<a class="newtooltip">15</a>,<a class="newtooltip">16</a>,<a class="newtooltip">17</a>,<a class="newtooltip">18</a>,<a class="newtooltip">19</a>,<a class="newtooltip">20</a>,<a class="newtooltip">21</a>,<a class="newtooltip">22</a>,<a class="newtooltip">23</a>]. Mull et al. [<a class="newtooltip">24</a>] revised the stratigraphy of the Albian–Cenomanian Nanushuk Group, which included the marine Tuktu, Grandstand, and Ninuluk formations, the predominantly nonmarine Chandler and Corwin formations, and the marine–nonmarine Kukpowruk Formation. Mull et al. [<a class="newtooltip">24</a>] downgraded the Nanushuk Group to formation status, incorporating all six formations of the former Nanushuk Group. Thickness estimates for the Nanushuk Fm. range from 2750 m along the Chukchi Sea coast in the west [<a class="newtooltip">21</a>] to a zero edge ≈75 km east of Umiat, and in the vicinity of the modern Colville delta. The Nanushuk Fm. crops out in the northern Brooks Range foothills belt and coastal plain, comprising a lower dominantly marine unit of inter-tonguing shallow-marine shale, siltstone, and sandstone (Tuktu and Grandstand formations of former usage), that grades to the north to east-northeast into outer-shelf, slope, basinal shale, and minor sandstone of the upper Torok Fm. [<a class="newtooltip">15</a>,<a class="newtooltip">16</a>]. This grades up-section into primarily nonmarine mudstone, coal, sandstone, and conglomerate (Chandler Formation of former usage). These nonmarine rocks intertongue with rocks representing coastal facies within the Nanushuk Fm. [<a class="newtooltip">15</a>,<a class="newtooltip">16</a>]. Overall, the Nanushuk Fm. comprises a thick regressive package, interrupted many times by marine flooding that resulted from delta lobe shifting and abandonment.<br>
<div class="panelplain" style="margin: 1em 5%">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUU5B1Wx267dT8kSxKHIG2nut0gRnGXcA_h8Abl4TwOSH9YJ_9QqK_nmxwDQvxBgv302DYBA0MN8t760iAzV3CanhP_zWAuH61_e-xd6ttsUKst_iCtmBaQx6cyIZUdittMPNoDiqIK6xuWkmvHyBcfOaa9h9ohFgeYaqzu1zVG85wuZjNq5vVYqNVhvu/s1600/geosciences-14-00036-g002-550.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUU5B1Wx267dT8kSxKHIG2nut0gRnGXcA_h8Abl4TwOSH9YJ_9QqK_nmxwDQvxBgv302DYBA0MN8t760iAzV3CanhP_zWAuH61_e-xd6ttsUKst_iCtmBaQx6cyIZUdittMPNoDiqIK6xuWkmvHyBcfOaa9h9ohFgeYaqzu1zVG85wuZjNq5vVYqNVhvu/s1600/geosciences-14-00036-g002-550.webp"/></a>
<div class="caption"><b>Figure 2.</b> Stratigraphic nomenclature for Cretaceous and Paleocene rock units of the North Slope of Alaska.</div></div>
Throughout the western North Slope of Alaska, an angular unconformity bounds the Nanushuk Fm., separating nonmarine Cretaceous rocks from overlying Pleistocene sediments. In the central North Slope and the subsurface of the eastern National Petroleum Reserve-Alaska (NPRA), Cenomanian intertonguing fluvial sandstone, paludal mudstone and coal, and shallow-marine sandstone and silty shale overlies dominantly nonmarine Nanushuk rocks [<a class="newtooltip">15</a>,<a class="newtooltip">25</a>]. These 350 m thick intertonguing nonmarine and marine rocks were included in the Niakogon Tongue (Chandler Formation) and Ninuluk Formation of former usage, and now part of the Nanushuk Formation, and record a change from regression to regional transgression [<a class="newtooltip">25</a>]. At outcrop and in the subsurface where the lower contact of the Nanushuk with the Seabee Fm. is present, the Seabee typically consists of a thin, basal transgressive lag of fine- to medium-grained sandstone a few cm to dm thick that grades into thin-bedded fine- to very fine-grained sandstone a few meters thick that is overlain by bentonite-rich mudstone. Alternatively, the basal lag may be abruptly overlain solely by bentonite-rich mudstone.<br>
<br>
Alhbrandt et al. [<a class="newtooltip">21</a>] recognized two major delta systems in the Nanushuk Fm.; the Corwin Delta, on the western side of the basin, and the Umiat Delta on the eastern side. Both the Corwin and Umiat Deltas are not individual deltas, instead representing thick deltaic depocenters, or complexes, comprising the deposition of many individual delta lobes. Fisher et al. [<a class="newtooltip">18</a>] suggested that the eastern delta was river dominated. Ahlbrandt et al. [<a class="newtooltip">21</a>] and Huffman et al. [<a class="newtooltip">20</a>] indicated that both delta complexes were river dominated, but they also suggested that the Umiat delta complex was affected by greater wave reworking. Recent work suggests that river- and wave-reworking of delta complexes varies temporally as well as spatially in the eastern Nanushuk Fm., with initial wave dominance followed by subsequent river influence in shallower, more wave-limited conditions created by earlier parasequence progradation and shelf construction [<a class="newtooltip">26</a>].<br>
<br>
Previous work indicates high mud and low sand contents in the Corwin delta complex [<a class="newtooltip">16</a>,<a class="newtooltip">20</a>,<a class="newtooltip">27</a>], suggesting that the western delta complex was characterized by river-dominated delta lobes that prograded east-northeastward obliquely along the Colville basin axis [<a class="newtooltip">20</a>,<a class="newtooltip">21</a>,<a class="newtooltip">28</a>]. In the Wainwright # 1 core to the northeast of our study area, LePain and Decker [<a class="newtooltip">28</a>] documented lower and upper delta plain facies in the subsurface. Our outcrop facies analysis documents nonmarine sediments similar to their upper delta plain or alluvial plain facies. Biostratigraphic data indicates an early Albian to late Albian age for the Corwin Delta complex along the Chukchi Sea coast, which becomes younger in the east and north [<a class="newtooltip">19</a>,<a class="newtooltip">21</a>]. The Corwin delta complex dominated depositional patterns in the western two-thirds of the foreland basin [<a class="newtooltip">15</a>] at a paleolatitude of ≈75° N [<a class="newtooltip">29</a>].<br>
<br>
<span>3. Radiometric Data from Study Area</span><br>
<br>
LA-ICP-MS U-Pb zircon geochronology allows in situ grain spatial resolution [<a class="newtooltip">29</a>] and high single grain resolution throughput (usually >100 grains per sample analysis), which is required for (a) dating complex zircons, (b) detrital studies, and (c) accurately dating bentonites with a potential detrital or xenolith component. Determining crystallization/eruption or maximum deposition age “calls” from LA-ICP-MS U-Pb zircon data are complicated by potential undetermined Pb loss for young zircons (<~400 Ma), matrix mismatch, and large N analysis resulting in apparently robust populations of younger grains that are just an artifact of instrumental statistical spread [<a class="newtooltip">30</a>,<a class="newtooltip">31</a>,<a class="newtooltip">32</a>].<br>
<br>
CA-ID-TIMS has higher accuracy and precision and can usually mitigate the effects of potential Pb loss [<a class="newtooltip">33</a>], but this whole grain technique is time intensive, resulting in fewer grains analyzed per sample (usually ~3 to 7 grains) and no in situ grain spatial resolution. Hence, there is a tradeoff between LA-ICP-MS and CA-ID-TIMS U-Pb zircon dating applications. Many labs are now screening zircon grains via large N LA-ICP-MS U-Pb analysis and then performing CA-ID-TIMS U-Pb zircon analysis on select grains [<a class="newtooltip">34</a>]. This dual-technique combination, though powerful, adds significant expense and time.<br>
<br>
Furthermore, these dual-technique studies have demonstrated that selecting the LA-ICP-MS U-Pb zircon youngest statistical population (YSP), which is the weighted mean of the youngest statistical population (2 or more grains) that produces a mean square weighted deviation (MSWD) close to 1, approximates CA-ID-TIMS U-Pb zircon results from the same sample [<a class="newtooltip">35</a>,<a class="newtooltip">36</a>]. A variation of this approach is the youngest mode weighted mean (YMWM), which uses the LA-ICP-MS zircon dates that define the youngest age mode from a kernel density estimate peak that consists of at least three grains that overlap at 2 sigma uncertainty with an MSWD that approximates 1 [<a class="newtooltip">32</a>,<a class="newtooltip">34</a>]. We use a modified version of the YSP and YMWM age determinations by utilizing an iterative approach that captures the largest population of young grains that overlap at 2 sigma uncertainty with an MSWD that approximates 1. We call this approach the largest youngest statistical population (L-YSP) and favor it, because it allows the parsing of potential young tails that may have experienced Pb loss and older detrital and/or xenolith grains [<a class="newtooltip">37</a>]. The results are often like those from Tuffzirc [<a class="newtooltip">38</a>], which follows a similar approach, but uses a not-explained modified 2 sigma uncertainty overlap and can capture older grains that do not approximate depositional–eruption ages.<br>
<br>
We applied a 10% uncertainty filter to remove less precise grains with possible isotopic/analytical concerns. We use the macro-spread sheet from Herriot et al. [<a class="newtooltip">36</a>] to both iteratively select grains and to calculate a weighted average age and systematic uncertainty. Based on the weighted average age of 34 out of 103 zircon grains dated, we determined an eruption age of 97.20 ± 0.53 with an MSWD of 0.98 for the bentonite sample 15-EO-8-17-2 (<b>Figure 3</b>).
<div class="panelplain" style="margin: 1em 5%">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2qzEWYe-Sb_H3n1asmNQ33WcMKbg5q4KmSXI-W3nJP742auqrVq9Lhz7e8xuEVE0hOha9J8DsWTCHlkwYTlEi6YVO-nM7Vt6dKs_eurTu7y15tDYgQfflhsqUA-XiAWUaA8XPW0BYmr_Ir1OOFW3NEXLIfKp72BtxKIswrpIkAsxt45qLzZAHJNJvbKpx/s1600/geosciences-14-00036-g003-550.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2qzEWYe-Sb_H3n1asmNQ33WcMKbg5q4KmSXI-W3nJP742auqrVq9Lhz7e8xuEVE0hOha9J8DsWTCHlkwYTlEi6YVO-nM7Vt6dKs_eurTu7y15tDYgQfflhsqUA-XiAWUaA8XPW0BYmr_Ir1OOFW3NEXLIfKp72BtxKIswrpIkAsxt45qLzZAHJNJvbKpx/s1600/geosciences-14-00036-g003-550.webp"/></a>
<div class="caption"><b>Figure 3.</b> Plot of 206 Pb/238 Pb data that yielded an age of 97.1 Ma.</div></div>
<span>4. Sedimentology</span><br>
<br>
While the Nanushuk Formation encompasses marine and nonmarine facies, this paper focuses primarily on nonmarine fluvial sediments of the rock unit that are exposed along the upper Kukpowruk River (Figure 4). Plant fossils, reflecting successional, riparian, and interfluve environments (Figure 5A) [<a class="newtooltip">12</a>], and upright tree trunks in situ (up to 58 cm diameter) are relatively common in nonmarine facies along the Kukpowruk River.<br>
<div class="panelplain" style="margin: 1em 5%">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMp42bh3UWHhBlDFmIzNl4eo0KZBnp1L8PRcsI89SK3u1jDmu9uD1rrmXbpE6oUAVq-eqPzATMM0GDdX6dUstfN5jvroyXBzKM0sWE5cVKAuyGLOa9E9IZSsIfyliMTaw4RCq_VOvHIed0-lRcK0qTd_fs7dBSTB7W4bylXXBvtHwwdK9O5ual94vlRkwT/s1600/geosciences-14-00036-g004a-550.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMp42bh3UWHhBlDFmIzNl4eo0KZBnp1L8PRcsI89SK3u1jDmu9uD1rrmXbpE6oUAVq-eqPzATMM0GDdX6dUstfN5jvroyXBzKM0sWE5cVKAuyGLOa9E9IZSsIfyliMTaw4RCq_VOvHIed0-lRcK0qTd_fs7dBSTB7W4bylXXBvtHwwdK9O5ual94vlRkwT/s1600/geosciences-14-00036-g004a-550.webp"/></a>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4jRtKjWCS1T4bLaqBOq2BMtt4shJhq1yOgN-S409dFgn66SVKvUrNFlzDPDrMubIcELmJLbn22tAHs-1xVxQ40V-BdqzrGgCDcEXI9tCcyE_Q_PTOYSY_37Wmwfh7_v-fRgYqN-dv5OGmCdDLVWad2Od_YqSy-plf3L2cDiULIWRUHGU2a_lLuTmu-6HN/s1600/geosciences-14-00036-g004a.png"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4jRtKjWCS1T4bLaqBOq2BMtt4shJhq1yOgN-S409dFgn66SVKvUrNFlzDPDrMubIcELmJLbn22tAHs-1xVxQ40V-BdqzrGgCDcEXI9tCcyE_Q_PTOYSY_37Wmwfh7_v-fRgYqN-dv5OGmCdDLVWad2Od_YqSy-plf3L2cDiULIWRUHGU2a_lLuTmu-6HN/s1600/geosciences-14-00036-g004a.png"/></a>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHX6SCh8tg-HuXVRoZNxZNvD40Srd6ndTmklU4HrpFWVthm4ey4P7OXlfXc39avF-U1kL5TwlvF92lognOPswRpNwilOxtvyJ9-I39WuEIbXH1xrO1iNf4rMw1n1dLnHjR8x-Ncd9-Co7tB1Rdi6tVgV10jzUKvIlYMUOiFIlmKQeuvAFGFBrPUTR_wMbB/s1600/geosciences-14-00036-g004c.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHX6SCh8tg-HuXVRoZNxZNvD40Srd6ndTmklU4HrpFWVthm4ey4P7OXlfXc39avF-U1kL5TwlvF92lognOPswRpNwilOxtvyJ9-I39WuEIbXH1xrO1iNf4rMw1n1dLnHjR8x-Ncd9-Co7tB1Rdi6tVgV10jzUKvIlYMUOiFIlmKQeuvAFGFBrPUTR_wMbB/s1600/geosciences-14-00036-g004c.webp"/></a>
<div class="caption"><b>Figure 4.</b> Representative measured sections of fluvial sedimentary successions along the Kukpowruk River, NW Alaska. Legend is shown in lower right. Representative measured sections of fluvial successions along the Kukpowruk River, NW Alaska. See <b>Figure 3</b> for legend. Representative measured sections of fluvial successions along the Kukpowruk River, NW Alaska. See <b>Figure 3</b> for legend.<br></div></div>
<div class="panelplain" style="margin: 1em 5%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnsP2_gVoCJrvQbIaGwrbgtV5sRYNL3ADZjCSI7xzMQJdrIF6NdP3QpTmbgFer9O3iYY9PkzE2wUclTVnYQmupXTNbmULQrDdxr7SwMc534WbSVPq7-XIUDOL7LK5nTw6C1wlYBBR_4MLn7qPp5dZmPyvo85zzgOP2gHLPDM0xfTmWgwfuL0Ex6O84bGDW/s1600/geosciences-14-00036-g005-550.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnsP2_gVoCJrvQbIaGwrbgtV5sRYNL3ADZjCSI7xzMQJdrIF6NdP3QpTmbgFer9O3iYY9PkzE2wUclTVnYQmupXTNbmULQrDdxr7SwMc534WbSVPq7-XIUDOL7LK5nTw6C1wlYBBR_4MLn7qPp5dZmPyvo85zzgOP2gHLPDM0xfTmWgwfuL0Ex6O84bGDW/s1600/geosciences-14-00036-g005-550.jpg" width="100%"/></a>
<div class="caption"><b>Figure 5.</b> (<b>A</b>) Interbedded sandstone, siltstone, shale, and coal typical of floodplain facies. (<b>B</b>) Multi-story channel-fill sandstone. (<b>C</b>) Floodplain mudstone and sandstone with standing trees at base (not shown). (<b>D</b>) Trough cross-bedded channel sandstone. (<b>E</b>) Standing tree trunk rooted in floodplain mudstone and sandstone (max. 58 cm diameter). (<b>F</b>) Floodplain mudstone with standing tree (adjacent to hammer length = 33 cm). (<b>G</b>) Interbedded, ripple-laminated sandstone, siltstone, shale, and coal typical of a poorly drained floodplain. (<b>H</b>) Large carbonaceous root traces in splay sandstone. (<b>I</b>) Ripple cross-laminated sandstone with abundant organic fragments (coffee grounds) on forests. (<b>J</b>) Floodplain mudstone coarsening upward into splay and levee sandstone sheets.</div></div> <br>
<br>
<div class="creditl">Fiorillo, A.R.; McCarthy, P.J.; Shimer, G.; Suarez, M.B.; Takasaki, R.; Chinzorig, T.; Kobayashi, Y.; O’Sullivan, P.; Orphys, E. <br>
New Dinosaur Ichnological, Sedimentological, and Geochemical Data from a Cretaceous High-Latitude Terrestrial Greenhouse Ecosystem, Nanushuk Formation, North Slope, Alaska. <br>
<i>Geosciences</i> 2024, <b>14</b>, 36. https://doi.org/10.3390/geosciences14020036<br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by MDPI, Basel, Switzerland. Open access. <br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
So, conclusive evidence there then that there were dinosaurs living in a warm wet environment in what is now northern Alaska about 100 million years before, according to their favourite book of origin myths, the Bible, there was an Earth for them to live on.<br>
<br>
Any normal people, confronted with compelling and unarguable evidence that their favourite myths are wrong, would stop believing otherwise and start to live in the real world not the fantasy the mythic cult requires them to live in.<br>
<br>
Not creationists, however. Through a combination of self-idolatrous arrogance, hypocrisy and theophobic psychosis, they will perform any mental gymnastics needed to stick with their falsified beliefs and ignore the evidence that refutes them. The correct term for this is intellectual and scientific bankruptcy.
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<div class="panelplain" style="padding: 1em; margin: 0; height: 675px"><br><center><span class="t2">Ten Reasons To Lose Faith: And Why You Are Better Off Without It</span></center><br>
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<div class="left-column" style="flex: 1"><a target="_blank" href="https://www.amazon.com/dp/1530431956?&_encoding=UTF8&tag=rosarub-20&linkCode=ur2&linkId=ee7df9227d554e95c07dabb677ac7650&camp=1789&creative=9325"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjV7ys1fJWghEiilpJ-ltMJKBAJGIccmbAZHatW48ji6wV00OOyX2aTagxdjUJMDIeIoLfe-xl4tCh7QX1FXsLJdQDrrVmY5yZWZ-ihUuy1-ZXPsWpESwI1kJdO2NDA5B63OgxUFXG4HsODIi-kCkNHIpeCFxeFpv7BUfOjbMxE-9BLLH51VwZtx1OsU1VN/s1600/Ten_Reasons_To_Lose__Cover_for_Kindle%20%283%29.jpg"/></a>
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<div class="right-column" style="flex: 1.5">This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.<br>
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{n: "2", text: "Nogués-Bravo, D.; Rodríguez-Sánchez, F.; Orsini, L.; de Boer, E.; Jansson, R.; Morlon, H.; Fordham, D.A.; Jackson, S.T. Cracking the code of biodiversity responses to past climate change. Trends Ecol. Evol. 2018, 33, 765–776."},
{n: "3", text: "Williams, J.W.; Ordonez, A.; Svenning, J.C. A unifying framework for studying and managing climate-driven rates of ecological change. Nat. Ecol. Evol. 2021, 5, 17–26."},
{n: "4", text: "Kiessling, W.; Smith, J.A.; Raja, N.B. Improving the relevance of paleontology to climate change policy. Proc. Natl. Acad. Sci. USA 2023, 120, e2201926119."},
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{n: "6", text: "Fiorillo, A.R.; McCarthy, P.J.; Kobayashi, Y.; Suarez, M.B. Cretaceous dinosaurs across Alaska show the role of paleoclimate in structuring ancient large-herbivore populations. Geosciences 2022, 12, 161."},
{n: "7", text: "Hedges, S.B.; Parker, P.H.; Sibley, C.G.; Kumar, S. Continental breakup and the ordinal diversification of birds and mammals. Nature 1996, 381, 226–229."},
{n: "8", text: "Dilcher, D. Toward a new synthesis: Major evolutionary trends in the angiosperm fossil record. Proc. Natl. Acad. Sci. USA 2000, 97, 7030–7036."},
{n: "9", text: "Lloyd, G.T.; Davis, K.E.; Pisani, D.; Tarver, J.E.; Ruta, M.; Sakamoto, M.; Hone, D.W.; Jennings, R.; Benton, M.J. Dinosaurs and the Cretaceous terrestrial revolution. Proc. R. Soc. B: Biol. Sci. 2008, 275, 2483–2490."},
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{n: "16", text: "Molenaar, C.M. Depositional history and seismic stratigraphy of Lower Cretaceous rocks in the National Petroleum Reserve in Alaska and adjacent areas. In U.S. Geological Survey Professional Paper; U.S. Geological Survey Bulletin: North Slope, AK, USA, 1988; Volume 1399, pp. 593–621."},
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{n: "20", text: "Huffman, A.C., Jr.; Ahlbrandt, T.S.; Bartsch-Winkler, S. Geology and exploration of the National Petroleum Reserve in Alaska, 1974 to 1982. In U.S. Geological Survey Professional Paper; U.S. Geological Survey Bulletin: North Slope, AK, USA, 1988; Volume 1399, pp. 281–298."},
{n: "21", text: "Ahlbrandt, T.S.; Huffman, A.C.; Fox, J.E.; Pasternack, I. Depositional Framework and Reservoir-Quality Studies of Selected Nanushuk Group outcrops, North Slope, Alaska; U.S. Geological Survey Circular: North Slope, AK, USA, 1979; Volume 794, pp. 14–31."},
{n: "22", text: "LePain, D.L.; McCarthy, P.J.; Kirkham, R. Sedimentology and sequence stratigraphy of the middle Albian–Cenomanian Nanushuk Formation in outcrop, central North Slope, Alaska. Alaska Division of Geological & Geophysical Surveys. Rep. Investig. 2009, 2009, 1–86."},
{n: "23", text: "McCarthy, P.J. Alluvial Facies and Paleosols in the Cretaceous Nanushuk Formation, Kanayut River, North Slope, Alaska: Preliminary Results from the 2001 Field Season; Alaska Division of Geological & Geophysical Surveys: North Slope, AK, USA, 2003; Volume 1–19."},
{n: "24", text: "Mull, C.G.; Houseknecht, D.W.; Bird, K.J. Revised Cretaceous and Tertiary stratigraphic nomenclature in the Colville Basin, northern Alaska. In U.S. Geological Survey Professional Paper; U.S. Geological Survey Bulletin: North Slope, AK, USA, 2003; Volume 1673, pp. 1–51. Available online: https://pubs.usgs.gov/pp/p1673/text.html (accessed on 5 May 2023).",
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{n: "25", text: "Detterman, R.L.; Bickel, R.S.; Gryc, G. Geology of the Chandler River region, Alaska. In U.S. Geological Survey Professional Paper; U.S. Geological Survey Bulletin: North Slope, AK, USA, 1963; Volume 303-E, pp. 233–324."},
{n: "26", text: "Shimer, G.T.; McCarthy, P.J.; Hanks, C.L. Sedimentology, stratigraphy, and reservoir properties of an unconventional, shallow, frozen petroleum reservoir in the Cretaceous Nanushuk Formation at Umiat field, North Slope, Alaska. Am. Assoc. Pet. Geol. Bull. 2014, 98, 631–661."},
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{n: "28", text: "LePain, D.L.; Decker, P.L. Lithofacies analysis of the Wainwright #1 continuous core, western Arctic Slope, Alaska: Transition from lower to upper delta plain environments in the Albian-Cenomanian Nanushuk Formation. In Alaska Division of Geological & Geophysical Surveys Report of Investigation; Alaska Division of Geological & Geophysical Surveys: North Slope, AK, USA, 2016; Volume 3, pp. 1–56."},
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-66754978914148606162024-03-13T13:08:00.004+00:002024-03-13T13:16:18.418+00:00How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?<div class="title-box" style="height: 533px; display: none">
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<div class="left-column" style="text-align: left">Giraffe trio crossing plain, Etosha, Namibia</div>
<div class="right-column" style="text-align: right">Photo: Mogens Trolle</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKfL5nnLIRVh6nb3y6dRmRr1OF79zZVVO0r6c4P6ORjAP_hI2n-fwrXQpheNZ9_wtz6qBPx_l8N2WqaFDRVWksGgi0udEMo3loReofxxvnL4mRj71-woIxbuhm3R52jebU7J9IKgfEWM0zw6931iz5ydIExw6XkRyBm9j_YhM66WN0RcV3nEkm7axtELth/s1600/Giraffe-trio-crossing-plain_Etosha-Namibia_Mogens-Trolle_1_.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKfL5nnLIRVh6nb3y6dRmRr1OF79zZVVO0r6c4P6ORjAP_hI2n-fwrXQpheNZ9_wtz6qBPx_l8N2WqaFDRVWksGgi0udEMo3loReofxxvnL4mRj71-woIxbuhm3R52jebU7J9IKgfEWM0zw6931iz5ydIExw6XkRyBm9j_YhM66WN0RcV3nEkm7axtELth/s1600/Giraffe-trio-crossing-plain_Etosha-Namibia_Mogens-Trolle_1_.jpg"/></a></div>
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<div class="captionc">Reticulated giraffe, Buffalo Springs, Kenya. Photo: Mogens Trolle<br><br><div class="credit">Photo: Mogens Trolle</div></div>
</div>
<a href="https://www1.bio.ku.dk/english/news/2024/gene-flow-in-giraffes-and-what-it-means-for-their-conservation/">Gene flow in giraffes and what it means for their conservation – Department of Biology - University of Copenhagen</a><br>
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In an evolutionary picture that resembles that of humans, giraffes appear to have speciated, or partially speciates at different times and in different parts of their range, then hybridized, before splitting again with regular gene-flow between the groups.<br>
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Similarly, though over a greater range, humans seems to have partially speciated into isolated populations in Africa before coming together again and spreading to Eurasia as <i>Homo erectus</i> which then split into Neanderthals, Denisovans and possibly others before meeting up with <i>H. sapiens</i> coming out of Africa in a second wave, to interbreed with the Eurasian species. The result is genetically distinct populations with evidence of ancient hybridization and gene flow.<br>
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Because conservation efforts tend to be directed at the species level, it is important for giraffe conservation to determine whether there is a single pan-African species with local sub-species or whether there are four or more species, each with a smaller population and therefore more vulnerable to habitat destruction and extinction.<br>
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To try to resolve this issue, as part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen, scientist carried out an extensive genome analysis to establish whether the different populations have been genetically isolated for long enough to be regarded as distinct species, even though, in captivity, they freely interbreed.<br>
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The results were a little surprising but highlight the difficulty in determining whether speciation has occurred within a population where differentiation is still in progress and few barriers to hybridisation have arisen. The problem is compounded by the fact that there is not a fixed definition of species, although biologists understand what the term means in a given context.<br>
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I've previously written blog posts about this problem, <a href="https://rosarubicondior.blogspot.com/2014/03/evolution-has-more-to-crow-about.html" target="_blank">using the Eurasian crows</a> as an example - an article incidentally which was recommended reading for Scottish biology students doing their 'Highers'.<br>
<br>
The researchers have published their findings open access in the online Cell Press journal, <i>Current Biology</i> and explain it in a news item from the University of Copenhagen Biology Department:
<a name='more'></a>
<blockquote class="blockit"><b style="font-size: larger">EVOLUTION Giraffes, with their bizarre body plan, have always held a special place in the minds of evolutionary biologists and non-experts alike. In a new study, led by a team of researchers from the University of Copenhagen, whole-genome sequencing data was used to investigate the evolutionary processes occurring within giraffes. In particular, the authors were interested in establishing whether different populations of giraffes really have been isolated from each other for extended periods of time, which is normally a requirement before new species can arise.</b><br>
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Giraffes are a beautiful and powerful example of what adaptive evolution can achieve. However, in recent years they have attained notoriety for a completely different reason: it has been suggested that instead of one giraffe species, there might be no fewer than four different species. Such dramatic taxonomic reappraisals in highly conspicuous and well-known “flagship” taxa are very unusual. The suggestion caused some uproar in the scientific community and received a lot of media attention. Much is at stake, because the way that most nature conservation works is focused on species, meaning that each species must receive its own dedicated conservation action plan and must be monitored individually. If we recognize four rather than one species of giraffe, it follows that each of them will have a lower population size and be more vulnerable to extinction, not only raising the conservation stakes considerably, but also the conservation costs.<br>
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<span>Giraffes form four distinct, but not isolated lineages - and some are even hybrids</span><br>
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The results of the new study, published today in Current Biology, confirm that giraffes are highly genetically structured, which means that populations tend to become differentiated from each other rather easily. It also means that giraffes do appear to be separated into evolutionary lineages that are quite genetically distinct from each other. But there were also some big surprises:<br>
<div class="block"><p>When we started getting results from our analyses of gene flow between different giraffe lineages, we had to check twice. The results showed not just a little gene flow here and there, but major hybridization events. For example, the reticulated giraffe, which occurs in Kenya, Ethiopia, and Somalia, appears to be the result of a 40%-60% mixture of an ancient northern lineage and an ancient southern lineage of giraffes, and therefore a hybrid. Today, the other descendants of these ancient northern and southern giraffes sit at either end of the giraffe tree and are highly genetically differentiated, but at some time in the past they evidently met and interbred, giving rise to the reticulated giraffe.</p>
<div class="creditl">Dr. Laura D. Bertola, co-first authors
Department of Biology<br>
University of Copenhagen, Copenhagen, Denmark.</div></div>The team also found historical gene flow among several other branches of the giraffe tree, and in fact there are so many gene flow events among giraffe lineages that the evolutionary history within giraffes resembles a “reticulated” network rather than a tree.<br>
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<span>What this means for giraffes and their conservation</span><br>
<br>
Biologists do not agree on what the best definition of species is, nor how to resolve at what stage two populations are sufficiently different that they belong to two different species. However, it is often assumed that extensive gene flow can only take place between populations that belong to the same, and not different, species. Therefore, the finding of widespread historical gene flow between giraffe lineages that are today highly genetically differentiated raises important doubts about whether or not high genetic differentiation is necessarily a sure sign of speciation, at least in giraffes.<br>
<div class="block"><p>Our findings touch on a very delicate matter in biology, namely that we do not have a universally agreed species concept. Therefore, it can be very difficult to settle how many species there are within a group. However, we show something more tangible which has so far been overlooked in evolutionary studies on giraffes: namely that giraffe lineages have had extensive gene flow among them. Giraffes seem to have retained their ability to interbreed freely, which they also still do in captivity. So, instead of solving how many species of giraffes there are, we prefer to highlight that gene flow has occurred pretty freely among even the most genetically differentiated lineages of giraffes, whenever conditions were right for this to happen.</p>
<div class="creditl">Associate Professor Rasmus Heller, co-senior author<br>
Department of Biology<br>
University of Copenhagen, Copenhagen, Denmark.</div></div>
The study also concludes that regardless of the number of giraffe species, the different lineages are so genetically differentiated that they definitely deserve extensive protection in all parts of their range. If we want to protect biodiversity effectively, we cannot stop at the species level, but also need to look at the diversity within and between species.<br>
<div class="block"><p>Giraffes are such endlessly fascinating animals, and this study confirms just how much genetic variation there is even on small geographical scales. This provides a further incentive for conserving all the different lineages of giraffes, whether they be called species, subspecies, populations or whatever. Studies that focus on the whole complexity of the evolutionary process are needed, instead of studies focusing on answering simplified binary questions such as whether or not there is one, four or dozens of species, whatever that may be.</p>
<div class="creditl">Yoshan Moodley, co-author<br>
Department of Biological Sciences<br>
University of Venda, Thohoyandou, Republic of South Africa.</div></div>
The study is part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen. This research framework is an associated partner project of the African BioGenome Project - an African-led initiative to use genomics in the service of conservation and capacity building in Africa.<br>
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Find the article <a href="https://www.cell.com/current-biology/fulltext/S0960-9822%2824%2900234-3" target="_blank"><i>Current Biology</i></a>
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<blockquote class="blockit"><div class="rpanel450plain" style="margin-bottom: 0.5em"><div style="margin: 0 1em"><span>Graphical Abstract</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfVeXM4_6ULZFeT0LvonKrrltaVLIj6eVokAEHApgrkMQKNqC0x0re1SM__SNDfKNkuoyQGg7qyL7B9dofeElepk2lvcgjIIr-jWjyU7VUiGTYHrC-bS9CfhhjPttl2e1oC4UXPva9F4Q87J7s90G4K-UtljMH0x3V1aSktfNlwvkkoGny-8c9cTeAdCoT/s1600/fx1%20%284%29.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfVeXM4_6ULZFeT0LvonKrrltaVLIj6eVokAEHApgrkMQKNqC0x0re1SM__SNDfKNkuoyQGg7qyL7B9dofeElepk2lvcgjIIr-jWjyU7VUiGTYHrC-bS9CfhhjPttl2e1oC4UXPva9F4Q87J7s90G4K-UtljMH0x3V1aSktfNlwvkkoGny-8c9cTeAdCoT/s1600/fx1%20%284%29.jpg"/></a></div>
<span>Highlights</span>
<ul type="disc">
<li>Giraffes show exceptional genetic structure despite lack of physical barriers.
<li>Giraffes have a complex evolutionary history, with high levels of gene flow.
<li>Reticulated giraffes are a hybrid lineage.
<li>For effective conservation, diversity within giraffes needs to be taken into account.
</ul>
<span>Summary</span><br>
<br>
Strong genetic structure has prompted discussion regarding giraffe taxonomy,<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a>,<a class="newtooltip">3</a></sup> including a suggestion to split the giraffe into four species: Northern (<i>Giraffa c. camelopardalis</i>), Reticulated (<i>G. c. reticulata</i>), Masai (<i>G. c. tippelskirchi</i>), and Southern giraffes (<i>G. c. giraffa</i>).<sup class="x-small"><a class="newtooltip">4</a>,<a class="newtooltip">5</a>,<a class="newtooltip">6</a></sup> However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.<br>
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<span>Motivation and aims</span><br>
<br>
In many species and species groups there is no obvious bifurcating tree that describes taxonomic relationships satisfactorily,<sup class="x-small"><a class="newtooltip">7</a></sup> and previous studies have shown that interspecific introgression is common and may even play a role in speciation in multiple mammalian lineages,<sup class="x-small"><a class="newtooltip">8</a></sup> including canids,<sup class="x-small"><a class="newtooltip">9</a></sup> felids,<sup class="x-small"><a class="newtooltip">10</a>,<a class="newtooltip">11</a></sup> and bears.<sup class="x-small"><a class="newtooltip">12</a></sup> Giraffes (<i>Giraffa</i> sp.) provide an interesting case study, as these widely dispersed megaherbivores have been described as strongly diverged yet with a contested taxonomy.<sup class="x-small"><a class="newtooltip">1</a></sup> Although the IUCN (International Union for Conservation of Nature) only recognizes a single species with nine subspecies,<sup class="x-small"><a class="newtooltip">13</a></sup> in recent years there have been proposals to classify giraffes into four separate species.<sup class="x-small"><a class="newtooltip">4</a>,<a class="newtooltip">5</a>,<a class="newtooltip">6</a></sup> High levels of genetic differentiation, even between directly neighboring populations, have been central in this newly suggested classification. However, others have pointed out that different genetic markers do not show congruent results and that, depending on the methodology used, one, three, or six species could be distinguished.<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a>,<a class="newtooltip">3</a></sup><br>
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Historically, giraffes had a continent-wide range throughout savannah habitats in sub-Saharan Africa; however, their range has recently become severely fragmented as a result of anthropogenic habitat conversion and degradation.<sup class="x-small"><a class="newtooltip">14</a>,<a class="newtooltip">15</a></sup> Giraffe populations are estimated to have declined 40% in the past 30 years, restricting them mostly to conservation areas.<sup class="x-small"><a class="newtooltip">15</a>,<a class="newtooltip">16</a></sup> Assessing both historical and contemporary gene flow will help understand unresolved phylogeographic patterns but can also be used to inform conservation actions. This is particularly relevant since giraffes are frequently translocated,<sup class="x-small"><a class="newtooltip">17</a></sup> and insights into genetic relationships should be taken into account when selecting source and target populations for conservation translocations.<sup class="x-small"><a class="newtooltip">18</a>,<a class="newtooltip">19</a></sup> Motivated by this, we aimed to explore the evolutionary and demographic history of giraffes using whole-genome data from across the range, covering all previously described major lineages.<br>
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<span>Sequencing and quality control</span><br>
<br>
We generated medium depth (≈20X) whole-genome sequencing data for 47 giraffes from 12 localities in six countries (Table S1). In addition, we obtained published whole-genome sequencing data for 43 other giraffes from 17 localities in 11 countries,<sup class="x-small"><a class="newtooltip">4</a>,<a class="newtooltip">20</a></sup> as well as a giraffe<sup class="x-small"><a class="newtooltip">21</a></sup> and an okapi (<i>Okapia johnstoni</i>)<sup class="x-small"><a class="newtooltip">20</a>,<a class="newtooltip">22</a></sup> reference genome and sequencing data from another okapi<sup class="x-small"><a class="newtooltip">20</a>,<a class="newtooltip">22</a></sup> and a pronghorn (<i>Antilocapra americana</i>)<sup class="x-small"><a class="newtooltip">22</a></sup> as outgroups. After mapping, 11 samples were excluded due to low average depth (<6X) or highly skewed, i.e., non-symmetric, depth distributions. One individual from a pair of close (first degree) relatives was also removed, leaving 78 samples spanning 27 localities in 13 countries and all four major lineages (Figure 1A). Excluded samples are listed in Table S1 (light gray shading).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPSENqkVqDp0qNOBQ-gpFfBQPP07PoNk7YnVOQbzUUppyqw14lNBiqzr0Lt0hfi505xVNJJjLGo84Mi5m_FchXZWuV_e_oVAYVrblQfUQMsoJXzUIXdMrhSDzRo0n-EsvBe0KuNV8idS0ZoyqrHgg5usyx9cF3EbLEWELXuxFhUdnTCS3OIailJYuBXd3i/s1600/gr1_lrg.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPSENqkVqDp0qNOBQ-gpFfBQPP07PoNk7YnVOQbzUUppyqw14lNBiqzr0Lt0hfi505xVNJJjLGo84Mi5m_FchXZWuV_e_oVAYVrblQfUQMsoJXzUIXdMrhSDzRo0n-EsvBe0KuNV8idS0ZoyqrHgg5usyx9cF3EbLEWELXuxFhUdnTCS3OIailJYuBXd3i/s1600/gr1_lrg.jpg"/></a>
<div class="caption"><b>Figure 1 Sampling and population structure of giraffes</b><br>
<br>
(A) Distribution of giraffe samples used in this study, colored according to inferred sublineages. Contemporary giraffe distribution, fragmented from a formerly more continuous distribution is shown in green.<sup class="x-small"><a class="newtooltip">13</a></sup><br>
<br>
(B) ADMIXTURE results assuming K = 4 (upper barplot) and K = 10 (bottom barplot). EvalAdmix results, displaying the correlation of residuals for assessing model fit from ADMIXTURE, are shown as correlation plots above the K = 4 and below the K = 10 barplot. Gray asterisks (∗) highlight the related individuals within the Reticulated giraffe, and black asterisks indicate samples that have been excluded due to admixture signal (>10% ancestry proportion). Also see <a href="https://www.cell.com/cms/10.1016/j.cub.2024.02.051/attachment/1e2166a0-edc9-45b4-bf94-3d0ec082c9d5/mmc1" target="_blank">Figure S1</a>.<br>
<br>
(C) Neighbor-joining tree based on pairwise Identity-by-State (IBS), illustrating the substructure within the major lineages.</div>
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<div class="caption"><b>Figure 2 Genetic differentiation and migration rates of giraffes</b><br>
<br>
(A) Table showing genetic differentiation between sublineages, expressed by pairwise Hudson FST derived from the site frequency spectrum (SFS).<br>
<br>
(B) EEMS plot showing migration rates (log(<i>m</i>)) between sampling localities across the giraffe range, with high log(<i>m</i>) rates indicating increased gene flow and low log(<i>m</i>) rates indicating reduced gene flow under the null model of isolation by distance.<br>
<br>
(C) EEMS plot showing migration rates inferred at a local scale in eastern Africa (black box), where three major giraffe lineages occur but appear geographically isolated.</div>
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<div class="caption"><b>Figure 4. Complex evolutionary history of giraffes, including admixture between major evolutionary lineages based on data mapped to an okapi reference genome</b><br>
<br>
(A) f-branch (f<sub>b</sub>) heatmap for seven giraffe sublineages, excluding Nubian and Angolan, to reduce complexity as a result of intraspecific gene flow. The shading of the heatmap refers to excess allele sharing between branches located on the tree on the y axis (relative to its sister branch) and the sublineages identified on the x axis. Gray cells are combinations of branches and populations for which the f-branch cannot be calculated given the topology of the tree.<br>
<br>
(B) Highest scoring admixture graph with two admixture events, including seven giraffe sublineages, exploring 0 to 5 admixture events. The gray triangles indicate that it is uncertain where along the branch these admixture events took place, as well as that introgression may not have occurred as a single pulse.<br>
<br>
(C) f-branch (f<sub>b</sub>) heatmap for all nine giraffe sublineages. The shading of the heatmap refers to excess allele sharing between branches located on the tree on the y axis (relative to its sister branch) and the sublineage identified on the x axis. Gray cells are combinations of branches and populations for which the f-branch cannot be calculated given the topology of the tree.<br>
<br>
(D) Highest scoring admixture graph with three admixture events, including nine giraffe sublineages. Another version of this figure based on giraffe data mapped to a giraffe reference genome is included as <a href="https://www.cell.com/cms/10.1016/j.cub.2024.02.051/attachment/3dfe7335-ff3a-465c-9f6a-c3c621947ea1/mmc2" target="_blank">Data S1</a>H. Original admixture graphs, including drift parameters, for two, three, and five admixture events are available as <a href="https://www.cell.com/cms/10.1016/j.cub.2024.02.051/attachment/3dfe7335-ff3a-465c-9f6a-c3c621947ea1/mmc2" target="_blank">Data S1</a>G for data mapped to okapi and <a href="https://www.cell.com/cms/10.1016/j.cub.2024.02.051/attachment/3dfe7335-ff3a-465c-9f6a-c3c621947ea1/mmc2" target="_blank">Data S1</a>I for data mapped to giraffe.</div>
</div>
</div>
</div><br>
<br>
<div class="creditl">Bertola, Laura D.; Quinn, Liam; Hanghøj, Kristian; Garcia-Erill, Genís; et al. <br>
Giraffe lineages are shaped by major ancient admixture events<br>
<i>Current Biology</i> (2024); 10.1016/j.cub.2024.02.051<br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by Elsevier Inc. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
As the authors point out, this problem is the result not of the Theory of Evolution (TOE) being wrong or inadequate, but because it is right; the giraffes are in the process of a prolonged evolution from a single pan-African species into possibly four or more genetically isolated populations that could then be classified as different species.<br>
<br>
This problem is no comfort for creationists, firstly because it confirms the TOE and secondly because it confirms that the fuzzy definition of 'species' reflects the reality of how species form and how speciation is an ongoing process over sometimes very many years, particularly with a slow generation time, unlike the daft notion of 'kind' which seems to be a flexible as creationists need it to be.<br>
<br>
Secondly, because the genetic evidence is that giraffes have been present and slowly differentiating in Africa for very much longer than creationists believe Earth has existed. This genetically diverse populations could not have formed within the last few thousand years from two survivors of a global flood.<br>
<br>
Thirdly, because creating a species then giving different populations different genomes that just happen to look like the different populations evolved from a common ancestor millions of years ago and from an ancestor they share more remotely with the okapi, is not an act of intelligence but an act of deception, if the evidence of the genome is false.
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<div class="panelplain" style="padding: 1em; margin: 0; height: 675px"><br><center><span class="t2">The Unintelligent Designer: Refuting The Intelligent Design Hoax</span></center><br>
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<div class="right-column" style="flex: 1.5">ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.<br>
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<div class="panelplain" style="padding: 1em; margin: 0; height: 675px"><br><center><span class="t2">Ten Reasons To Lose Faith: And Why You Are Better Off Without It</span></center><br>
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<div class="right-column" style="flex: 1.5">This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.<br>
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{n: "12", text: "Kumar V.; Lammers F.; Bidon T.; Pfenninger M.; Kolter L.; Nilsson M.A.; Janke A. The evolutionary history of bears is characterized by gene flow across species. Sci. Rep. 2017; 746487"},
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{n: "16", text: "Muller Z.; Bercovitch F.; Brand R.; Brown D.; Brown M.; Bolger D. Giraffa camelopardalis (amended version of 2016 assessment). The IUCN Red List of Threatened Species, 2018"},
{n: "17", text: "Muller Z.; Lee D.E.; Scheijen C.P.J.; Strauss M.K.L.; Carter K.D.; Deacon F. Giraffe translocations: A review and discussion of considerations. Afr. J. Ecol. 2020; 58: 159-171",
url: "https://onlinelibrary.wiley.com/doi/10.1111/mam.12165"},
{n: "18", text: "Bertola L.D.; Miller S.M.; Williams V.L.; Naude V.N.; Coals P.; Dures S.G.; Henschel P.; Chege M.; Sogbohossou E.A.; Ndiaye A.; et al. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo). Evol. Appl. 2022; 15: 22-39 https://doi.org/10.1111/eva.13318",
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{n: "22", text: "Chen L.; Qiu Q.; Jiang Y.; Wang K.; Lin Z.; Li Z.; Bibi F.; Yang Y.; Wang J.; Nie W.; et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science. 2019; 364eaav6202 https://doi.org/10.1126/science.aav6202",
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
<br />
Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-6349651297235553292024-03-12T21:12:00.001+00:002024-03-12T21:13:45.137+00:00Malevolent Design - How The Malaria Parasite is 'Designed' To Evolve And Outwit Medical Science
<div class="title-box" style="height: 470px; display: none">
<div class="postTitle" style="font-size: 48px"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left">The Malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic.</div>
<div class="right-column" style="text-align: right"> Credit: Karen Arnott/EMBL-EBI,<br>Isabel Romero Calvo/EMBL</div>
</div>
</div><br>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhg3TImo33bp20iVjDe0AYcykx46c8ufjgpfZlpq_xOTssBfX-Yzh-TinRDa7rCwcgWhA3ia37M6ERAWZWkGdqu0Zp9GFj02k16geQSw6XKCNVMd4XOyLzVJFkLtoDY-OGy3rlAdxzeJrd1muuzqz5Eyx3Z8i3y3ZyqzdmD_SECak_8TTWIT_l4-LQ5m2_B/s1600/2024-Malaria-PLOS-Biology-1000x600-1.jpeg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhg3TImo33bp20iVjDe0AYcykx46c8ufjgpfZlpq_xOTssBfX-Yzh-TinRDa7rCwcgWhA3ia37M6ERAWZWkGdqu0Zp9GFj02k16geQSw6XKCNVMd4XOyLzVJFkLtoDY-OGy3rlAdxzeJrd1muuzqz5Eyx3Z8i3y3ZyqzdmD_SECak_8TTWIT_l4-LQ5m2_B/s1600/2024-Malaria-PLOS-Biology-1000x600-1.jpeg"/></a></div>
<a href="https://www.embl.org/news/science/the-malaria-parasite-generates-genetic-diversity-using-an-evolutionary-copy-paste-tactic/">The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic | EMBL</a><br>
<br>
Devotees of creationism’s divine malevolence would be conflicted by this news if they understood it, because it shows the creative genius of any intelligent designer who could come up with this system, but, it looks like it did so (if you believe it couldn't happen naturally) by setting up an evolutionary process that creationists are obliged by dogma to believe doesn't work.<br>
<br>
The news is that the organisms that causes malaria, <i>Plasmodium falciparum,</i> is 'designed' to quickly find a way to overcome the anti-malarial drugs medical science has developed to cure people suffering from it and to prevent others from getting malaria, by evolving very quickly.<br>
<br>
The discovery was by researchers at European Molecular Biology Laboratory's (EMBL’s) European Bioinformatics Institute who have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. Copy-paste' is a way of doing something creationists insist is impossible without the aid of god-magic of increasing the genetic information in a genome and making it available for evolution by mutation and selection without any loss of function in the original copied genes.<br>
<br>
The team have recently published their finding in the open access journal PLOS Biology and describe it in an EMBL news item:<br>
<a name='more'></a>
<blockquote class="blockit"><span style="font-size: xx-large">The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic</span><br>
<br>
<span style="font-weight: normal"><i>Plasmodium falciparum</i>, a malaria parasite, uses gene conversion to produce genetic diversity in two surface protein genes targeted by the human immune system</span><br>
<div class="block" style="font-size: normal"><span>Summary</span><br>
<ul class="dbl1 blob">
<li>All modern <i>Plasmodium falciparum</i>, the deadliest malaria parasite in humans, are descendants of one initial infection and so are very closely related, with relatively limited genetic differences.</li>
<li>A long-standing mystery in the field has revolved around a very few locations in the <i>P. falciparum</i> genome where there are ‘spikes’ of mutations – far more than anywhere else. </li>
<li>Researchers at EMBL-EBI have identified two genes in which these unusual mutation spikes result from DNA being copied and pasted from one gene to another.</li>
</ul><br>
</div>
By dissecting the genetic diversity of the most deadly human malaria parasite – <i>Plasmodium falciparum</i> – researchers at EMBL’s European Bioinformatics Institute (EMBL-EBI) have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. <br>
<br>
Malaria is most commonly transmitted through the bites of female Anopheles mosquitoes infected with <i>P. falciparum</i>. The latest world malaria report states that in 2022, there were an estimated 249 million malaria cases and over 600,000 malaria deaths across the globe. 94% of malaria cases and 95% of malaria deaths are found in Africa, with infants, pregnant women, travellers, and people with HIV/AIDS being at higher risk.<br>
<br>
The new study, published in the journal PLOS Biology, provides key insights into the evolutionary history of <i>P. falciparum</i> through the analysis of two genes that encode surface proteins critical to immune evasion. The genes in question are DBLMSP and DBLMSP2.<br>
<br>
These findings deepen our understanding of how the malaria parasite has evolved and could help to inform new approaches to vaccine development, offering hope for more effective prevention methods against a disease that continues to impact millions globally.<br>
<br>
<span>Copy-paste genetics </span><br>
<br>
Usually, the sequence of an individual’s gene is inherited from their parents, but in some circumstances, part of a gene sequence can be copied between different genes on the same DNA molecule – this is known as non-allelic gene conversion. This process has been linked to the evolution of important gene families, including those involved in the functioning of the human immune system. <br>
<br>
One of this study’s key discoveries is that gene conversion takes place between the <i>P. falciparum</i> DBLMSP and DBLMSP2 genes and results in increased genetic diversity within the surface proteins of the parasite. Since these proteins are exposed to, and interact with our immune system, they are potential vaccine targets, and a fuller understanding of their genetic diversity could be very valuable for vaccine design. <br>
<br>
“The discovery of ‘copy-paste’ genetics within malaria’s DNA reveals the impact of an underestimated evolutionary mechanism,” said Brice Letcher, Postdoctoral Researcher at the Laboratory for Biology and Modelling of the Cell (LBMC, France) and former PhD student at EMBL-EBI. “Here we show that gene conversion was a potentially important strategy behind malaria’s ability to adapt and thrive in humans, including possibly to evade the human immune system. Understanding this genetic flexibility offers new perspectives on malaria’s persistence in and adaptation to the human host.”<br>
<br>
<span>Mapping hidden genetic diversity in malaria parasites</span><br>
<br>
Any immune-interacting protein is potentially a vaccine target, but knowledge of global genetic diversity is an important requirement for vaccine development. For example, influenza and SARS-CoV-2 vaccines are developed based on the knowledge of how their genomes have evolved. However, the very unusual hotspots of genetic diversity in the <i>P. falciparum</i> DBLMSP and DBLMSP2 genes are so extreme that current algorithms for mapping genetic variants failed to capture them, leaving researchers unaware of a large proportion of the variation in these genes. <br>
<br>
To address this, the researchers developed new bioinformatics software that uses genome graphs and analysed a broad sample of parasites from 29 countries. This new approach revealed a wide range of previously hidden variants, and with these, they were able to demonstrate that multiple gene conversion events had occurred. These new variants, available for download from the website linked to the study, provide a valuable resource for the malaria research community. <br>
<div class="block"><p>Genome graphs are a great bioinformatics method to help us decode the complex genetic landscapes arising from the interplay between pathogens and human hosts. They allow us to take into account a broader spectrum of genetic diversity and obtain new insights into how pathogens like <i>P. falciparum</i> evolve and evade our immune defences.</p>
<div class="creditl">Dr. Sorina Maciuca, co-author<br>
Genomics Data Scientist at Genomics England, London, UK.</div></div>
<div class="block" style="font-size: normal; margin: 0 5%"><span>What are genome graphs?</span><br>
<br>
The traditional approach in genomics is to define one reference genome and describe any other genome as a set of small differences from this reference. This does not work well when genomes differ too much. Genome graphs take a population of genomes and build an ensemble reference which is aware of all of the genetic variation in the species.</div>
<div class="block"><p>This research provides a comprehensive map of genetic diversity of these two fascinating genes in <i>P. falciparum</i>. We have been trying to understand the unusual patterns in these genes for almost a decade now, and our best hypothesis had been that the really different "versions" of the gene were being preserved by natural selection, for unknown reasons. We have shown here that, in fact, this copying mechanism – gene conversion – has been repeatedly creating these anomalous different "versions" of the genes. This data not only enhances our grasp of malaria’s biology, but also will be valuable to researchers across the world studying these genes and their interaction with our immune system.</p>
<div class="creditl">Professor Zamin Iqbal, co-corresponding author<br>
Group Leader at EMBL-EBI<br>
and Professor of Algorithmic and Microbial Genomics<br>
University of Bath, Somerset, UK</div></div>
</blockquote>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
While the malaria parasite <i>Plasmodium falciparum</i> has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell–infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical <i>P. falciparum</i> transmission bottleneck.<br>
<br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5uW7w6QrHERKqJYC-16GD0TTLw92AoLLMK3AZGxLimmGyrAUNhyphenhyphenWalhgvKgcodV0y9aQ_ioCMQwqzz7Kx8g7UzqVCeyEqdXprqelqpS9Y4J3haeLW_ayOL6dSkWusnUQ3W0lmXapJswg6wwBtjUALYsCw-OxSU9MwhRJSgkmDYSuwB9SmTN0z8m_kWJ14/s1600/journal.pbio.3002507.g002.PNG" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5uW7w6QrHERKqJYC-16GD0TTLw92AoLLMK3AZGxLimmGyrAUNhyphenhyphenWalhgvKgcodV0y9aQ_ioCMQwqzz7Kx8g7UzqVCeyEqdXprqelqpS9Y4J3haeLW_ayOL6dSkWusnUQ3W0lmXapJswg6wwBtjUALYsCw-OxSU9MwhRJSgkmDYSuwB9SmTN0z8m_kWJ14/s1600/journal.pbio.3002507.g002.PNG"/></a>
<div class="caption"><b>Fig 2. Deeply diverged private and shared lineages in DBLMSP1/2.</b><br>
<br>
We built a hierarchical clustering tree of all unique DBL-spanning protein sequences (see Methods). The inner ring colours sequences by gene of origin (DBLMSP, DBLMSP2), and the outer ring shows species of origin, for <i>P. falciparum</i> and its 3 most closely related species. Three main lineages exist in the tree, labelled A, B, and C: Lineages A and C contain only representatives of DBLMSP2 and DBLMSP, respectively (“private lineages”), and lineage B contains representatives of both (“shared lineage”). The data and code to generate this Figure can be found at <a href="https://zenodo.org/doi/10.5281/zenodo.7677547" target="_blank">https://zenodo.org/doi/10.5281/zenodo.7677547</a>.</div>
</div>
<span>Introduction</span><br>
<br>
<i>Plasmodium falciparum</i> is a single-celled eukaryotic parasite causing malaria disease in humans. Malaria burden remains high worldwide, with 241 million cases and 627,000 deaths in 2020 according to WHO [<a class="newtooltip">1</a>]. The high burden is in part due to <i>P. falciparum’s</i> ability to evade the human immune system, mediated by 2 main mechanisms [<a class="newtooltip">2</a>]. Firstly, cell-surface–exposed antigens targeted by the immune system are produced by functionally redundant gene families. For example, merozoites, the parasite life stage infecting human red blood cells (RBCs), use different members of the Rh and EBA families for invasion [<a class="newtooltip">2</a>], and different members of the var, rifin, and stevor families enable infected RBCs to bind to the host microvasculature [<a class="newtooltip">3</a>]. Secondly, surface antigens are highly diverse at the sequence and immunological levels. In the var family, diversity is mainly generated by frequent recombination and gene conversion (sequence copy-pasting) events, occurring both between orthologs during sexual reproduction, and paralogs on the same genome during asexual replication [<a class="newtooltip">4</a>–<a class="newtooltip">7</a>].<br>
<br>
Historically, several cell-surface antigens called merozoite surface proteins (MSPs) were found to display unusual genealogies, with exactly 2 deeply diverged lineages: This includes MSP1, MSP2, MSP3, and MSP6 [<a class="newtooltip">8</a>–<a class="newtooltip">11</a>]. Such deep divergence suggests ancient origins and possible maintenance by balancing selection for immune escape [<a class="newtooltip">12</a>,<a class="newtooltip">13</a>], but Roy and colleagues showed that neither this nor neutral evolution should produce exactly 2 lineages, and with such a deep most recent common ancestor [<a class="newtooltip">14</a>]. In addition, loci with such extreme diversity levels are at odds with <i>P. falciparum</i>’s overall low diversity levels, likely due to its very recent origin (10,000 to 50,000 years ago) in humans from a common ancestor with gorilla-infecting <i>P. praefalciparum</i> [<a class="newtooltip">15</a>–<a class="newtooltip">17</a>].<br>
<br>
In this study, we focussed on 2 MSPs called DBLMSP and DBLMSP2, both among the most diverse genes in <i>P. falciparum</i> [<a class="newtooltip">18</a>], and both encoding cell-surface–exposed antigens recognised by the human immune system [<a class="newtooltip">19</a>,<a class="newtooltip">20</a>]. They are part of an 8-gene tandemly arrayed family of paralogs, as identified from sequence sharing: All 8 genes possess an N-terminal signal sequence, 6 (including DBLMSP and DBLMSP2) possess a C-terminal SPAM domain, and DBLMSP and DBLMSP2 further uniquely possess a DBL domain [<a class="newtooltip">20</a>] (illustrated in S1 Fig). DBL domains mediate a number of important malarial host–pathogen interactions, including between erythrocyte binding antigen (EBA) gene products and RBCs during invasion [<a class="newtooltip">21</a>,<a class="newtooltip">20</a>], and between var gene products on infected RBCs and various human receptors, enabling sequestration [<a class="newtooltip">22</a>]. However, their function in DBLMSP and DBLMSP2 remains largely unknown [<a class="newtooltip">23</a>].<br>
<br>
The evolutionary history of <i>P. falciparum</i> surface antigens, including DBLMSP and DBLMSP2, has been difficult to study until now because of reference bias: Reads spanning highly diverged nonreference alleles fail to align to a reference genome, making them hard to reconstruct. To address this, we previously developed gramtools, a software for mapping reads and genotyping using a genome graph incorporating multiple references simultaneously [<a class="newtooltip">24</a>,<a class="newtooltip">25</a>]. In this study, we developed a new pipeline combining local assembly to reconstruct DBLMSP and DBLMSP2 alleles together with gramtools for comprehensive genotyping. Applying it to Illumina population sequencing data, we assembled the first comprehensive set of alleles for these genes, across >3,500 global <i>P. falciparum</i> samples. Studying these in detail, we found that although DBLMSP and DBLMSP2 have diverged substantially, 1 specific region (the DBL domain) contains sequences shared across both genes. We found clear evidence this was driven by gene conversion of DBL sequence between the 2 genes, thus creating highly diverse gene lineages despite the recent gorilla-to-human transmission bottleneck. Interestingly, we also found evidence that DBLMSP2 may have evolved a constrained function specifically in humans.<br>
<br>
For the remainder of this paper, we refer to DBLMSP and DBLMSP2 collectively as DBLMSP1/2.
</blockquote><br>
So, what are creationists to make of this evidence that <b>if</b> there was any intelligence involved in this redesign of the parasite that causes malaria so it could evade medical science's anti-malarial drugs, it used an evolutionary process to make it happen? And where does this leave Michael J Behe's embarrassing claim (for creationists) and false dichotomy fallacy, that anti-malarial resistance in <i>P. falciparum</i> could not have evolved so was 'intelligently'[sic] designed, as his 'proof' that a designer god really exists and is making chemistry and/or physics do things they couldn't do on their own?
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{n: "23", text: "Crosnier C, Iqbal Z, Knuepfer E, Maciuca S, Perrin AJ, Kamuyu G, et al. Binding of Plasmodium falciparum Merozoite Surface Proteins DBLMSP and DBLMSP2 to Human Immunoglobulin M Is Conserved among Broadly Diverged Sequence Variants *. J Biol Chem. 2016 Jul 1;291(27):14285–14299. pmid:27226583",
url: "https://doi.org/10.1074/jbc.M116.722074"},
{n: "24", text: "Maciuca S, del Ojo Elias C, McVean G, Iqbal Z. A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference. In: Frith M, Storm Pedersen CN, editors. Algorithms in Bioinformatics. Cham: Springer International Publishing; 2016. p. 222–233. (Lecture Notes in Computer Science)."},
{n: "25", text: "Letcher B, Hunt M, Iqbal Z. Gramtools enables multiscale variation analysis with genome graphs. Genome Biol. 2021 Dec;22(1):259. pmid:34488837",
url: "https://doi.org/10.1186/s13059-021-02474-0"}
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com1tag:blogger.com,1999:blog-7583674511519808833.post-5113219324835160212024-03-12T15:46:00.055+00:002024-03-12T16:25:32.179+00:00Unintelligent Malevolence - Pathogens 'Designed' to Beat Medical Science In Two Different Ways<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left"><i>Acinetobacter baumannii</i></div>
<div class="right-column" style="text-align: right"><i>Escherichia coli</i></div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTyomhR9AtavcZ_rSxxGOLor1weGTk3AyowiR04sFcopYJFI2iWcpif0LEk313pKjCwrQNhejMPd-XU-Tp0hhi1PCVGCKIp0BHa8O5hS1IlLW31gn7_YONg6Hz5WeperditPbyedfXEW6BtqRETcGQHcFBeqoxIEGOqCOqmioEP6iiTz7JERJUsqhai0qW/s1600/e-coli-a-baumannii-cdc_n.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTyomhR9AtavcZ_rSxxGOLor1weGTk3AyowiR04sFcopYJFI2iWcpif0LEk313pKjCwrQNhejMPd-XU-Tp0hhi1PCVGCKIp0BHa8O5hS1IlLW31gn7_YONg6Hz5WeperditPbyedfXEW6BtqRETcGQHcFBeqoxIEGOqCOqmioEP6iiTz7JERJUsqhai0qW/s1600/e-coli-a-baumannii-cdc_n.jpg"/></a></div>
<div class="rpanel450plain" >
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlbOALzk48CRKGDWGDiJcqqNrjiFIFH-IEVA4VanH1BMhplQPIGVWys4nOsk4jJSw4ycMqyqOWqruaG9WVkOC1-UWDsKZE-4VDCeR2aU29yLiPTlD951T7qXet_jjYgZ5OYEyhWUQdQjoO6vrkhyphenhyphenEszk-SyC1wA_Nt2PJk3Vj9qvERbbPzviwhqJzV-qdx/s1600/A.baumannii_visualized_using_Scanning_electron_microscopy.png"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlbOALzk48CRKGDWGDiJcqqNrjiFIFH-IEVA4VanH1BMhplQPIGVWys4nOsk4jJSw4ycMqyqOWqruaG9WVkOC1-UWDsKZE-4VDCeR2aU29yLiPTlD951T7qXet_jjYgZ5OYEyhWUQdQjoO6vrkhyphenhyphenEszk-SyC1wA_Nt2PJk3Vj9qvERbbPzviwhqJzV-qdx/s1600/A.baumannii_visualized_using_Scanning_electron_microscopy.png"/></a>
<div class="captionc" style="padding-bottom: 0"><i>Acinetobacter baumannii</i> seen under a scanning electron-microscope</div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1tZTGIOiDIhwTrDVBEukLW1UBfdLnOe6kw-WKGuk2Nll7N-w_k7AxwhYPCkOZ-40yrnnI2L2QocsL4f03dwCCjoxQEtzc64byjOdUYwm3C0sA5M1wgZ5T45NCjHvaie7k9GuL_I_ueQ75N1pIWm-Yd6kQ5224R42eh2BNxky-o662dHajhWdT3iMzWWq-/s1600/e-coli.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1tZTGIOiDIhwTrDVBEukLW1UBfdLnOe6kw-WKGuk2Nll7N-w_k7AxwhYPCkOZ-40yrnnI2L2QocsL4f03dwCCjoxQEtzc64byjOdUYwm3C0sA5M1wgZ5T45NCjHvaie7k9GuL_I_ueQ75N1pIWm-Yd6kQ5224R42eh2BNxky-o662dHajhWdT3iMzWWq-/s1600/e-coli.jpg"/></a>
<div class="captionc"><i>Escherichia coli</i></div>
</div>
<a href="https://sbpdiscovery.org/news/what-makes-a-pathogen-antibiotic-resistant">What makes a pathogen antibiotic-resistant? | Sanford Burnham Prebys</a><br>
<br>
One of todays examples of the stupidity of creationism is something of a novelty. Usually, by applying the central tenets of creationism, any putative designer of living things like parasites either appears malevolent (and sometime it has to be said, malevolent at a near genius level in the ways it finds to make us and other animals sick) or it looks incompetent in that its 'solutions' are often to problems of its own making and more often than not to solutions it designed for one side of an arms race which it now trets as problems for the other side.<br>
<br>
But today's example can only be described as an example of incompetent malevolennce, as creationism's putative designer, faced with the same 'problem' of medical science developing antibiotics effective against two different species of pathogen, set about designign two completely different 'solutions' to this problem. - Talk about re-inventing the wheel!<br>
<br>
The pathogens are: <i>Escherichia coli</i> and <i>Acinetobacter baumannii</i>. <br>
<br>
Creationists will probably be familiar with <i>Escherichia coli</i> (<i>E. coli</i>) because they believe their guru, Michael J Behe, 'proved' their god exists by claiming (falsely) that <i>E. coli's</i> flagellum must have been intelligently designed because he didn't know it evolved out of a pre-exiting structure and couldn't think how else it could have evolved. But then such is the standard of creationist apologetics!<br>
<br>
What Behe had unwitting done was destroy the traditional excuse creationists use to explain pathogens like <i>E. coli</i> by blaming them on another 'designer' called 'Sin' which somehow creates living organisms although the creationit designer god is the only entitiy capable of designing livign things, so any example of 'intelligent design, real or imaginary, if 'proof' of this designer god's existance.<br>
<br>
So, what creationists are now left with is an <i>E.coli</i> with a flegellum designed by their god to make it better at making us sick, and now resitant to antibiotics to help it win against medical science trying to prevent it makign us sick!<br>
<br>
But what creationists are less likely to be familiar with is the pathogen, <i>Acinetobacter baumannii</i>, so here is a little background:
<a name='more'></a>
<blockquote class="ai">What information do you have on the pathogen, <i>Acinetobacter baumannii</i>?
<i>Acinetobacter baumannii</i> is a Gram-negative bacterium that has gained significant attention due to its ability to cause infections, particularly in healthcare settings. Here's some information about this pathogen:
<ol class="dbl1 bold">
<li><b>Classification:</b> <i>Acinetobacter baumannii</i> is a member of the genus <i>Acinetobacter</i>, which includes several other species. It is a non-motile, <a class="newtooltip">aerobic bacterium</a>.
<li><b>Healthcare-Associated Infections (HAIs):</b> <i>Acinetobacter baumannii</i> is known for causing various healthcare-associated infections, including pneumonia, bloodstream infections, urinary tract infections, and wound infections. These infections often occur in patients who are already ill or have compromised immune systems, such as those in intensive care units (ICUs).
<li><b>Antibiotic Resistance:</b> One of the most concerning aspects of <i>Acinetobacter baumannii</i> is its ability to develop resistance to multiple antibiotics. It has become notorious for its resistance to many commonly used antibiotics, including carbapenems, which are often considered the last line of defense against multidrug-resistant bacteria. This resistance can make infections difficult to treat and can lead to increased morbidity and mortality rates.
<li> <b>Environmental Resilience:</b> <i>Acinetobacter baumannii</i> is known for its ability to survive in various environments, including hospital surfaces and medical equipment. This resilience contributes to its persistence in healthcare settings and its potential to cause outbreaks.
<li><b>Virulence Factors:</b> <i>Acinetobacter baumannii</i> possesses various virulence factors that contribute to its ability to cause infections. These include outer membrane proteins, lipopolysaccharides, and enzymes that aid in evasion of the host immune response and colonization of host tissues.
<li><b>Prevention and Control:</b> Due to its resistance and ability to cause healthcare-associated infections, preventing the spread of <i>Acinetobacter baumannii</i> is crucial. This involves strict infection control measures in healthcare settings, including hand hygiene, environmental cleaning, and appropriate use of antibiotics to minimize the development of resistance.
</ol>
Overall, <i>Acinetobacter baumannii</i> poses a significant challenge in healthcare settings due to its ability to cause infections, its resistance to multiple antibiotics, and its persistence in the environment. Efforts to prevent and control its spread are essential for minimizing the impact of infections caused by this pathogen.
</blockquote>
How the discovery was made that these two pathogens have developed antibiotic resistance in two entirely different ways is the subjec of an open access paper in <i>npj Antimicrobials and Resistance</i> and a news release from the research insitute Sanford Burnham Prebys where the lead rearcher, Dr. Andrei L. Osterman, is based:
<div class="rpanel450plain fb-post" style="margin: 1em 0.5em" data-href="https://www.facebook.com/sbpdiscovery/posts/pfbid0yWVrX7CtSRUrx4pamteF9V5CxAaQ2JA6peGhGUYHJz5bU5CL43jTHmZnn9DrHxGUl" data-width="450" data-show-text="true" lazy-load="true"><blockquote cite="https://www.facebook.com/sbpdiscovery/posts/907878881341410" class="fb-xfbml-parse-ignore"><p>In a new study, Sanford Burnham Prebys researchers, led by Andrei L. Osterman, Ph.D., combined experimental evolution in...</p>Posted by <a href="https://www.facebook.com/sbpdiscovery">Sanford Burnham Prebys</a> on <a href="https://www.facebook.com/sbpdiscovery/posts/907878881341410">Thursday, 7 March 2024</a></blockquote></div>
<blockquote class="blockit"><span style="font-weight: normal">Researchers compared two common bacterial foes and two specific drugs, looking for deeper explanations and clinical implications.</span><br>
<br>
Antimicrobial resistance is a story of constantly moving parts and players. With every new or tweaked antibiotic or antimicrobial drug, the targeted pathogens begin the evolutionary dance of acquiring resistance, prompting researchers to constantly develop workarounds or entirely new classes of medicine.<br>
<br>
Understanding the underlying mechanisms of acquired antimicrobial resistance is critical to the fight, a case of knowing one’s enemy. In a new paper published March 2, 2024 in <i>npj Antimicrobials and Resistance</i>, part of the Nature Portfolio, researchers at Sanford Burnham Prebys, working with Roche Pharma Research and Early Development, describe how two notable pathogens—<i>Escherichia coli</i> and <i>Acinetobacter baumannii</i>—employ distinctly different tools to fend off antibiotic attack.<br>
<div class="blockl" style="width: 39%; margin: 1em 0.5em 1em 0; "><p>This work was conceived as a comparative study of the mechanisms and dynamics of resistance acquisition for two drugs and two bugs. Comparing mutational landscapes triggered by the same drug in two distinct bugs allows us to deduce both shared and unique evolutionary trajectories toward resistance. A comparison of two drugs in the same bug reveals shared and unique mechanistic features of fundamental and translational importance, from drug discovery to rational optimization of treatment regimens.</p>
<div class="creditl">Dr. Andrei L. Osterman, Ph.D., senior author<br>
Sanford Burnham Prebys.</div></div>
Both pathogens studied are gram-negative bacteria with shared characteristics, but also notable differences.<br>
<br>
For the most part, <i>E. coli</i> is a bacterium routinely found in the guts of humans and animals, where it resides with no ill effect. Some strains, however, do cause harm, everything from mild gastroenterological distress to urinary tract infections, respiratory illness and pneumonia.<br>
<br>
<i>Acinetobacter baumannii</i> is more problematic, particularly in clinical settings where it can cause severe infections, some life-threatening.<br>
<br>
Andei Osterman, Ph.D.Both bacteria have developed resistance to most current antibiotic treatments.<br>
<br>
In their paper, Osterman and colleagues combined experimental evolution in a continuous culturing device (morbidostat) with whole genome sequencing of evolving cultures to track how <i>E. coli</i> and <i>A. baumannii</i> acquired drug resistance against a pair of antibiotics that inhibit DNA gyrase, an essential enzyme in bacteria.<br>
<br>
Inhibiting the enzyme disrupts DNA synthesis and, subsequently, causes the bacteria to die. One antibiotic—ciprofloxacin—has been in active clinical use since 1987; the other—GP6—is experimental.<br>
<br>
The researchers found that pathogenic bacteria with acquired resistance to ciprofloxacin remained susceptible to effective antimicrobial treatment by GP6 drug. However, the opposite was not true: evolution of resistance to GP6 also triggered resistance to ciprofloxacin.<br>
<br>
These findings underscored that <i>E. coli</i> and <i>A. baumannii</i> employ shared and unique mechanisms to acquire resistance to these two types of drugs.<br>
<div class="block"><p>Bacteria acquire resistance as a result of random mutational events that happen in the DNA replication as uncorrected ‘typos. These spontaneously emerge in a handful of drug-resistant variants/strains out of godzillions of neutral mutations) under selective pressure.</p>
<div class="creditl">Dr. Andrei L. Osterman, Ph.D</div></div>
<br>
(A godzillion is a descriptive term, not a precise unit of measurement. It refers to a number of enormous size. In this case a number ranging between 108 to 109 neutral mutations.)<br>
<br>
These harmful mutations may underlie several types of resistance mechanisms, including modifying the protein targets of a given drug, the ability of bacterial cells to expel compounds (drugs) before they cause harm (efflux) and special bacterial enzymes that inactivate active drug compounds.<br>
<br>
Osterman said the work advances progress toward developing “resistibility profiles” of established and novel antimicrobial drugs, which would help set forth “boundaries for possible combinational treatment, including clinically relevant multidrug resistant strains. Our acquired knowledge provides crucial guidelines for all these translational activities.”<br>
<br>
The findings are not limited to <i>E. coli</i> and <i>A. baumannii</i>. They have potential to at least partially predict resistance drivers across other closely related species posing significant health risks, including <i>Pseudomonas</i>, <i>Salmonella</i> and <i>Klebsiella</i> spp. all difficult-to-treat bacterial pathogens linked to serious and sometimes deadly infections.<br>
<br>
Additional authors on the study include Semen A. Leyn, James E. Kent, Jaime E. Zlamal and Marinela L. Elane, all at Sanford Burnham Prebys; and Maarten Vercruysse, Rocha Pharma.
</blockquote>
Technical details are given in the team's open access paper in <i>npj Antimicrobials and Resistance</i>:
<blockquote class="blockit"><span>Abstract</span><br>
<br>
Comprehensive knowledge of mechanisms driving the acquisition of antimicrobial resistance is essential for the development of new drugs with minimized resistibility. To gain this knowledge, we combine experimental evolution in a continuous culturing device, the morbidostat, with whole genome sequencing of evolving cultures followed by characterization of drug-resistant isolates. Here, this approach was used to assess evolutionary dynamics of resistance acquisition against DNA gyrase/topoisomerase TriBE inhibitor GP6 in <i>Escherichia coli</i> and <i>Acinetobacter baumannii</i>. The evolution of GP6 resistance in both species was driven by a combination of two classes of mutational events: (i) amino acid substitutions near the ATP-binding site of the GyrB subunit of the DNA gyrase target; and (ii) various mutations and genomic rearrangements leading to upregulation of efflux pumps, species-specific (AcrAB/TolC in <i>E. coli</i> and AdeIJK in A. baumannii) and shared by both species (MdtK). A comparison with the experimental evolution of resistance to ciprofloxacin (CIP), previously performed using the same workflow and strains, revealed fundamental differences between these two distinct classes of compounds. Most notable were non-overlapping spectra of target mutations and distinct evolutionary trajectories that, in the case of GP6, were dominated by upregulation of efflux machinery prior to (or even in lieu) of target modification. Most of the efflux-driven GP6-resistant isolates of both species displayed a robust cross-resistance to CIP, while CIP-resistant clones showed no appreciable increase in GP6-resistance.<br>
<br>
<span>Introduction</span><br>
<br>
DNA gyrase GyrA/B and topoisomerase IV ParC/E are bacterial type II topoisomerases. Both enzyme complexes are vital for DNA replication, transcription and decatenation of daughter chromosomes in bacteria and have significant structural and sequence differences from the human type II topoisomerases<sup class="x-small"><a class="newtooltip">1</a></sup>. These proteins are established targets for common clinical antibiotics of the fluoroquinolone class<sup class="x-small"><a class="newtooltip">2</a></sup> and for new drug discovery campaigns<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">4</a></sup>.<br>
<br>
The mechanism of action of fluoroquinolones involves binding at the topoisomerase-DNA interface, which allows DNA cleavage while suppressing the ligation reaction, thus introducing multiple deleterious nicks in the chromosome<sup class="x-small"><a class="newtooltip">5</a></sup>. Despite excellent efficacy against a broad spectrum of bacterial pathogens, the clinical utility of fluoroquinolones is hampered by rapidly spreading resistance driven largely by amino acid substitutions in a drug-binding site of its cognate targets that do not impair their enzymatic functions<sup class="x-small"><a class="newtooltip">6</a></sup>. These limitations of fluoroquinolones prompted numerous efforts to develop new type II topoisomerase inhibitors with a different binding mode and mechanism of action to avoid cross-resistance<sup class="x-small"><a class="newtooltip">7</a></sup>. Thus, Novobiocin, an aminocoumarin class antibiotic targeting the ATP-binding site of GyrB, was introduced into clinical practice in the 1960s, but discontinued in 1999 due to insufficient efficacy and safety<sup class="x-small"><a class="newtooltip">8</a></sup>. Two non-quinolone antibiotics have reached Phase III of clinical trials: (i) Zoliflodacin, a first-in-class spiropyrimidinetrione antibiotic<sup class="x-small"><a class="newtooltip">9</a></sup>; and (ii) Gepotidacin, which belongs to a novel class of triazaacenaphthylenes<sup class="x-small"><a class="newtooltip">10</a></sup>. These drugs bind in different sites at the topoisomerase-DNA interface showing no cross-resistance with fluoroquinolones. A novel tricyclic class of pyrimidoindole GyrB/ParE inhibitors (TriBE inhibitors) active against a broad range of Gram-negative bacterial pathogens was introduced by Trius Therapeutics in 2013<sup class="x-small"><a class="newtooltip">11</a></sup>.<br>
<br>
The goal of this study was to assess the mutational landscape and evolutionary dynamics of resistance acquisition against the TriBE inhibitor GP6<sup class="x-small"><a class="newtooltip">12</a></sup> in the model system of <i>Escherichia coli</i> and in the important nosocomial pathogen <i>Acinetobacter baumannii</i>. This knowledge is essential for fundamental mechanistic understanding and for a comparative assessment of bacterial resistibility to this novel drug candidate. To this end, we applied a workflow combining experimental evolution in a continuous culturing device, the morbidostat, with high-coverage whole genome sequencing (WGS) of evolving bacterial populations followed by genotype-to-phenotype characterization of selected drug-resistant clones. This workflow (introduced in a model study of triclosan<sup class="x-small"><a class="newtooltip">13</a></sup> and schematically illustrated in Supplementary Fig. S1) was recently applied to the experimental evolution of resistance of three Gram-negative bacterial species to the most common fluoroquinolone drug ciprofloxacin (CIP)<sup class="x-small"><a class="newtooltip">14</a></sup>. This study revealed shared evolutionary trajectories toward CIP resistance driven by a limited set of missense mutations in the GyrA/B target (Stage I) followed by additional mutations leading to upregulation of species-specific efflux pumps (Stage II). In <i>A. baumannii</i>, (but not in <i>E. coli</i>), additional Stage II mutational events included amino acid substitutions in the secondary target ParC/E that also led to a substantial increase of the MIC of CIP (MIC<sup style="x-small">CIP</sup>). This work provided a technological and conceptual foundation for a comparative resistomics assessment of a non-quinolone GyrB/ParE inhibitor GP6 reported here.<br>
<br>
The performed analysis revealed fundamental mechanistic differences between these two distinct classes of type II topoisomerase inhibitors. Observed differences encompass non-overlapping spectra of target mutations and distinct evolutionary trajectories, dominated by deregulation of the efflux machinery in Stage I of evolution of resistance to GP6, prior to or even in lieu of target mutations. These differences also manifest in asymmetric cross-resistance profiles. While selected GP6 resistant (GP6<sup style="x-small">R</sup>) clones displayed a comparably increased resistance to CIP, none of the previously characterized CIP resistant (CIP<sup style="x-small">R</sup>) clones showed any increase in the MIC of GP6 (MIC<sup style="x-small">GP6</sup>). Overall, this study illustrates the utility of the morbidostat-based comparative resistomics approach for the assessment of resistibility of new drug candidates.
<div class="panelplain" style="margin: 1em auto"><div style="margin: 0 1em"><span>Fig. 1: Cumulative area plots reflecting the evolutionary dynamics of the two major types of driver mutations.</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLaBlszOysFiDY-GKwCGJacOTvUb4MHxtimjTGR_Psd8nyJBPJ_thRSnC4W36oj902a4zyyLr-ik0tR1hnYn3v2Cn-RacfXbpZR-L3xJQXo2PGeFmG6sjH27LmLO2-CUOzYyt_UgRWtcQ7N_REqJq1hSD98SWKoYU1Vl04Ko46btLPOR9qap3uSVRdiLaG/s1600/44259_2024_21_Fig1_HTML.webp"><img alt="" border="0" data-original-height="1364" data-original-width="2051" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLaBlszOysFiDY-GKwCGJacOTvUb4MHxtimjTGR_Psd8nyJBPJ_thRSnC4W36oj902a4zyyLr-ik0tR1hnYn3v2Cn-RacfXbpZR-L3xJQXo2PGeFmG6sjH27LmLO2-CUOzYyt_UgRWtcQ7N_REqJq1hSD98SWKoYU1Vl04Ko46btLPOR9qap3uSVRdiLaG/s1600/44259_2024_21_Fig1_HTML.webp"/></a>
<div class="caption">(i) target modifications (red area) and (ii) mutations leading to efflux upregulation (blue area); and other potentially relevant mutations (grey area). In a simplified form, the plots represent WGS data obtained for population samples in time series of collected during experimental evolution of resistance to GP6 in <i>E. coli</i> and <i>A. baumannii</i> in this study vs CIP from the previous study<sup class="x-small"><a class="newtooltip">14</a></sup>. The variant abundance data corresponding to each of the 6 reactors (5 in case of <i>A. baumannnii</i>_CIP) were summed up by the three categories and plotted as the average number of mutations per cell (Y-axis) vs time (X-axis). The plots reflect combined relative abundances of SNV and IS insertions, but not CNVs (loci amplifications or deletions) that cannot be accurately quantified in population WGS data (reflected in separate plots in Supplementary Fig. <a href="https://www.nature.com/articles/s44259-024-00021-y#MOESM1" target="_blank">S3</a>).</div>
<div style="margin: 0 1em"><span>Fig. 2: Three-dimensional projection of detected mutations in DNA gyrase complex conferring resistance to CIP or GP6 drugs.</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdG1gD5dPTiL79CBSopk70HHFx1-iocx4fo6ng4WiKQc4q5cs9ATo3NaVmMegk5COiZ6MlE0jnIWJcXP9dQ6DkDHXc9yf4Smv6OlnTQN-ynzz1V8fZ1dFAQ3wbQ-gOPxwcvoabrYrvAcaOLx-90QijVAokmJfCKNnY_dpwQwtmJVivvwvtGmgz_YZbIHZA/s1600/44259_2024_21_Fig2_HTML.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdG1gD5dPTiL79CBSopk70HHFx1-iocx4fo6ng4WiKQc4q5cs9ATo3NaVmMegk5COiZ6MlE0jnIWJcXP9dQ6DkDHXc9yf4Smv6OlnTQN-ynzz1V8fZ1dFAQ3wbQ-gOPxwcvoabrYrvAcaOLx-90QijVAokmJfCKNnY_dpwQwtmJVivvwvtGmgz_YZbIHZA/s1600/44259_2024_21_Fig2_HTML.webp"/></a>
<div class="caption"><b>a</b> The structure of E. coli DNA Gyrase complex with DNA (PDB ID: 6RKW). GyrA subunits are colored shades of green; GyrB subunits are colored shades of blue; DNA is colored yellow. The location of GP6 (orange, modeled from 4KSG) and CIP (pink, modeled from PDB ID: 5BTC) binding sites are depicted by spheres. The amino acid residues (colored magenta) detected as mutational variants during the morbidostat-based evolution of resistance to GP6 or CIP are also shown. The areas outlined by two dashed boxes are expanded to focus on (<b>b</b>) GP6 and (<b>c</b>) CIP (variants present in the second molecule of the homodimer are not labeled).</div>
<hr />
<div style="margin: 0 1em"><span>Fig. 3: Mutational events in efflux systems observed in experimental evolution of GP6 resistance in E. coli and A. baumannii; comparison with CIP resistance studies<sup class="x-small"><a class="newtooltip">14</a></sup></span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhP6Z_DihW8mXjw_b4zWqAp7hGR91IwI11tiOclCCixcUibHCt_ScYV8lnOaqAVRY6RlFNm3uUuH0VECJaq5Zgb8U2PSYl1e8mqSCOS5ESUOR3j1SLcnPDUHRFsfxI2ViLHQJBdv8UiDgbe3V1XF8kQdUJ3sYjKqq1fKp4CHn9blyjZKNq6odq4t7EmbBOk/s1600/44259_2024_21_Fig3_HTML.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhP6Z_DihW8mXjw_b4zWqAp7hGR91IwI11tiOclCCixcUibHCt_ScYV8lnOaqAVRY6RlFNm3uUuH0VECJaq5Zgb8U2PSYl1e8mqSCOS5ESUOR3j1SLcnPDUHRFsfxI2ViLHQJBdv8UiDgbe3V1XF8kQdUJ3sYjKqq1fKp4CHn9blyjZKNq6odq4t7EmbBOk/s1600/44259_2024_21_Fig3_HTML.webp"/></a>
<div class="caption">Gene coloring scheme: light blue – components of efflux transporters; dark blue – transcriptional repressors; red – transcriptional activators (including two-component systems); Grey – other genes. GP6-selected mutational events are shown above the affected genes, CIP-selected – below the genes. The positions of mutational events are shown by triangles (colored depending on type of events as shown below the diagram) and numbers reflecting the number of their independent occurrences.</div>
<hr />
<div style="margin: 0 1em"><span>Fig. 4: The order of occurrence and impact of mutations and their combinations driving the evolution of resistance to GP6 in E. coli and A. baumannii, a comparison with the experimental evolution of CIP resistance (modified from ref. <sup class="x-small"><a class="newtooltip">14</a></sup>).</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2vc6_fynUO_K-wnlf5skaQE1HJ_gxiaQDS1Bd2UW9JM0JkMpe6P_tS8EVPV6A96sEbbj4DEQXe2WXBb4GXasjo6GmMF6x9JU9kmRIoB3NWTZHJo4zuz1HlALP5SqlE8RCGcTnUDtNXCgUj16qdYPg9wbATTcMDM46_3lfE5ibsjayTc9w8ubxRjHdlsv6/s1600/44259_2024_21_Fig4_HTML.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2vc6_fynUO_K-wnlf5skaQE1HJ_gxiaQDS1Bd2UW9JM0JkMpe6P_tS8EVPV6A96sEbbj4DEQXe2WXBb4GXasjo6GmMF6x9JU9kmRIoB3NWTZHJo4zuz1HlALP5SqlE8RCGcTnUDtNXCgUj16qdYPg9wbATTcMDM46_3lfE5ibsjayTc9w8ubxRjHdlsv6/s1600/44259_2024_21_Fig4_HTML.webp"/></a>
<div class="caption">Only main driver mutations represented in characterized clones (from Supplementary Table <a href="https://www.nature.com/articles/s44259-024-00021-y#MOESM2" target="_blank">S3A–D</a>) are shown leading to: (i) target modification (orange background palette); and (ii) efflux upregulation (blue background palette). The impact of these mutations on MIC (fold change) of respective drugs (MIC<sup class="x-small">GP6</sup> or MIC<sup class="x-small">CIP</sup>) is shown above the corresponding variants. Intermediate variants (mostly, single mutants not represented in isolated clones) hypothesized based on dynamic plots (Supplementary Fig. <a href="https://www.nature.com/articles/s44259-024-00021-y#MOESM1" target="_blank">S3</a>) are indicated by dashed borders and arrows.</div>
<hr />
<div style="margin: 0 1em"><span>Fig. 5: Correlation plot of changes in MIC values of GP6 and CIP compounds in <i>E. coli</i> and <i>A. baumannii</i>.</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKbfVsmIEn4O0T5Z9X5e6pV-OXAah1zk538rm_fUPSdI7qqBLdjpwN9NwO38Fc-RPNGk9rTxC7Oe1YvO_Zan7WA67ZmI1O_XoX2CqV6pvzsSujF55RLy3BnuROv76g7sXqfbrobIdvK3jQmNaDYZGKqPqEnJA1gFDJ7_btba2ta1czkAjL4tpG0MOG72J4/s1600/44259_2024_21_Fig5_HTML.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKbfVsmIEn4O0T5Z9X5e6pV-OXAah1zk538rm_fUPSdI7qqBLdjpwN9NwO38Fc-RPNGk9rTxC7Oe1YvO_Zan7WA67ZmI1O_XoX2CqV6pvzsSujF55RLy3BnuROv76g7sXqfbrobIdvK3jQmNaDYZGKqPqEnJA1gFDJ7_btba2ta1czkAjL4tpG0MOG72J4/s1600/44259_2024_21_Fig5_HTML.webp"/></a>
<div class="caption">MIC values were observed over a panel of ~40 nonredundant clones selected from morbidostat-based studies on experimental evolution of resistance to GP6 (yellow and green symbols) or CIP (orange and light-brown symbols) in <i>E. coli</i> (triangles) and <i>A. baumannii</i> (circles). Corresponding mutational variants (only driver mutations) are shown as data labels using a matching font color. Complete mutational and MIC data are provided in Supplementary Table <a href="https://www.nature.com/articles/s44259-024-00021-y#MOESM2" target="_blank">S3A–D</a>. Plotted values reflect fold-change of MIC (FC) measured for both drugs in each clone as compared to a respective MIC of the unevolved parental strain. Two outlined areas illustrate a clear separation between CIP<sup class="x-small">R</sup>-evolved isolates (that do not show any increase in MIC to GP6) and GP6 <sup class="x-small">R</sup>-evolved isolates (many of which show an appreciable cross-resistance to CIP).</div>
</div><br>
<br>
<div class="creditl"><a href="https://rdcu.be/dAZwz" target="_blank">Leyn, S.A., Kent, J.E., Zlamal, J.E. et al. <br>
Two classes of DNA gyrase inhibitors elicit distinct evolutionary trajectories toward resistance in gram-negative pathogens.
<i>npj Antimicrob Resist</i> <b>2</b>, 5 (2024). https://doi.org/10.1038/s44259-024-00021-y</a><br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by Springer Nature. Open access<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
Regular readers of these blog posts and of my illustrated book, <a href="https://amzn.to/48SU7LF" target="_blank"><i>The Malevolent Designer: Why Nature's God is not Good</i></a>, will be more that a little acquainted with the idea that, if there were such a ting as an intelligent designer, it can only be regarded as malevolent in that is puts so much effort into designing ways to make its creation suffer with parasites such as viruses, bacteria, worms of all descriptions and protozoa such as Plasmodium falciparum and <i>Trypanosoma brucei</i> that cause malaria and sleepign sickness respectively.<br>
<br>
But I think this is the first case I've come across where, any putative intelligent designer would have to be so fanatically devoted to making us sick that it has deigned two different ways for pathogenic bacteria to win in the latest twist in the arms race between them and human medical science in the form of antibiotic resistance.<br>
<br>
The fact that creationists would prefer us to think of their putative designer in such a light, or to take from it the 'unique' ability to create livign organiams and give that to 'Sin' as well, shows us that the agenda of the creation cult is not to promulgate worship and wonder of what they claim is an all-lovign god, but to win recruits for as sect with a hidden, political agenda. Creationism was perhaps the first of the extreme right, post-truth cults who argue that you can't trust the experts so should believe what those ignorant of the facts tell you - an alternative view of reality that says ignore the evidence and believe what I tell you to believe.<br>
<br>
And the creationist dupes willingly queue up to be fooled by them because they've bought into the notion that their childish, fairy-tale fantasy world is a better description of it than anything science can provide, because their ignorant intuition trumps facts.
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{n: "2", text: "Fabrega, A., Madurga, S., Giralt, E. & Vila, J. Mechanism of action of and resistance to quinolones. Microb. Biotechnol. 2, 40–61 (2009).",
url: "https://doi.org/10.1111%2Fj.1751-7915.2008.00063.x"},
{n: "3", text: "Collin, F., Karkare, S. & Maxwell, A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl. Microbiol. Biotechnol. 92, 479–497 (2011).",
url: "https://link.springer.com/doi/10.1007/s00253-011-3557-z"},
{n: "4", text: "Khan, T. et al. DNA gyrase inhibitors: Progress and synthesis of potent compounds as antibacterial agents. Biomed. Pharmacother. 103, 923–938 (2018).",
url: "https://doi.org/10.1016%2Fj.biopha.2018.04.021"},
{n: "5", text: "Chen, C. R., Malik, M., Snyder, M. & Drlica, K. DNA gyrase and topoisomerase IV on the bacterial chromosome: quinolone-induced DNA cleavage. J. Mol. Biol. 258, 627–637 (1996).",
url: "https://doi.org/10.1006%2Fjmbi.1996.0274"},
{n: "6", text: "Hooper, D. C. & Jacoby, G. A. Mechanisms of drug resistance: quinolone resistance. Ann. NY Acad. Sci. 1354, 12–31 (2015).",
url: "https://doi.org/10.1111%2Fnyas.12830"},
{n: "7", text: "Dighe, S. N. & Collet, T. A. Recent advances in DNA gyrase-targeted antimicrobial agents. Eur. J. Med. Chem. 199, 112326 (2020).",
url: "https://doi.org/10.1016%2Fj.ejmech.2020.112326"},
{n: "8", text: "Food and Drug Administration, H. Determination That ALBAMYCIN (Novobiocin Sodium) Capsule, 250 Milligrams, Was Withdrawn From Sale for Reasons of Safety or Effectiveness. Federal Reg. 76, 3143–3144 (2011)."},
{n: "9", text: "Basarab, G. S. et al. Responding to the challenge of untreatable gonorrhea: ETX0914, a first-in-class agent with a distinct mechanism-of-action against bacterial Type II topoisomerases. Sci. Rep. 5, 11827 (2015).",
url: "https://doi.org/10.1038%2Fsrep11827"},
{n: "10", text: "Bax, B. D. et al. Type IIA topoisomerase inhibition by a new class of antibacterial agents. Nature 466, 935–940 (2010).",
url: "https://doi.org/10.1038%2Fnature09197"},
{n: "11", text: "Tari, L. W. et al. Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum dual-targeting antibacterial agents. PLoS One 8, e84409 (2013).",
url: "https://doi.org/10.1371%2Fjournal.pone.0084409"},
{n: "12", text: "Tessier, P. R. & Nicolau, D. P. In vitro activity of novel gyrase inhibitors against a highly resistant population of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 57, 2887–2889 (2013).",
url: "https://doi.org/10.1128%2FAAC.01740-12"},
{n: "13", text: "Leyn, S. A. et al. Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. Microb. Genom. 7. https://doi.org/10.1099/mgen.0.000553 (2021).",
url: "https://doi.org/10.1099/mgen.0.000553"},
{n: "14", text: "Zlamal, J. E. et al. Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens. mBio. 12, e0098721 (2021).",
url: "https://doi.org/10.1128%2FmBio.00987-21"},
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<center>If you've enjoyed my blog please show your appreciation
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<br />
Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-21782750911389381172024-03-11T23:47:00.007+00:002024-03-11T23:52:28.659+00:00Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
</div><br>
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<div class="caption"><div class="credit">Photo by <a href="https://unsplash.com/@shimikumi32?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Kumiko SHIMIZU</a> on <a href="https://unsplash.com/photos/selective-focus-of-green-plants-Pxa0yJ2Elxc?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Unsplash</a></div></div>
</div>
<a href="https://www.ox.ac.uk/news/2024-03-07-world-s-most-prolific-co2-fixing-enzyme-slowly-getting-better">The world’s most prolific CO<sub style="small">2</sub>-fixing enzyme is slowly getting better | University of Oxford</a><br>
<br>
The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, <a href="https://amzn.to/3Va14EI" target="_blank"><i>The Unintelligent Designer: Refuting the Intelligent Design Hoax</i></a> as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.<br>
<br>
Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO<sub style="small">2</sub>) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.<br>
<br>
But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.<br>
<blockquote class="ai">Tell me all about RuBisCo and why it's so inefficient.
RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:
<a name='more'></a>
<ol class="dbl1 bold">
<li><b>Substrate specificity:</b> RuBisCo can react with both carbon dioxide (CO<sub style="small">2</sub>) and oxygen (O<sub style="small">2</sub>). This property is known as oxygenase activity, and it results in the wasteful process of photorespiration. When RuBisCo combines with oxygen instead of carbon dioxide, it produces a molecule that cannot be used in further carbon fixation. This results in a loss of fixed carbon and energy for the plant.</li>
<li><b>Low catalytic efficiency:</b> Compared to other enzymes, RuBisCo has a relatively slow catalytic rate. This means it can process only a limited number of substrate molecules per unit of time, which can limit the overall rate of carbon fixation in plants.</li>
<li><b>RuBisCo activation:</b> RuBisCo requires the presence of a specific activator molecule, ribulose-1,5-bisphosphate (RuBP), to function effectively. However, the activation process is slow and inefficient, leading to a significant portion of RuBisCo molecules being inactive at any given time.</li>
<li><b>Photorespiration:</b> As mentioned earlier, RuBisCo's oxygenase activity leads to the production of a compound that undergoes a series of reactions known as photorespiration. This process consumes energy and reduces the efficiency of carbon fixation by competing with the Calvin cycle.</li>
<li><b>Evolutionary history:</b> RuBisCo is thought to be one of the oldest enzymes, dating back billions of years. Its structure and catalytic properties may have evolved at a time when atmospheric conditions were different, with higher carbon dioxide concentrations and lower oxygen levels. As a result, RuBisCo's efficiency in current atmospheric conditions (with relatively low CO<sub style="small">2</sub> and high O<sub style="small">2</sub> levels) may be compromised.</li>
</ol>
Despite its inefficiencies, RuBisCo remains essential for photosynthesis and the overall productivity of plant ecosystems. Efforts to improve its efficiency through genetic engineering and synthetic biology are ongoing, with the goal of enhancing crop yields and mitigating the effects of climate change.<br>
<br>
<span>How does the efficiency of RuBisCo compare to that of other enzymes in terms of reactions catalysed per second?</span><br>
<br>
In terms of reactions catalyzed per second, RuBisCo typically has a lower turnover number compared to many other enzymes. Turnover number, also known as kcat, represents the number of substrate molecules converted to product per unit time by a single enzyme molecule.<br>
<br>
For RuBisCo, its turnover number is relatively low, typically in the order of 1-10 reactions per second. This is due to its relatively slow catalytic rate compared to many other enzymes. In contrast, some enzymes can have turnover numbers in the range of hundreds to thousands of reactions per second.<br>
<br>
The low turnover number of RuBisCo contributes to its inefficiency in carbon fixation, as it limits the rate at which carbon dioxide can be converted into organic molecules during photosynthesis. This inefficiency is one of the reasons why RuBisCo is often targeted for improvement in efforts to enhance plant productivity and address challenges such as climate change.
</blockquote>
But, according to a new study by three biologists in the Department of Biology, Oxford University, RuBisCo is not stuck in an evolutionary rut, unable to change without becoming even worse at all. It has been evolving, albeit almost imperceptibly slowly over time at least in the angiosperms, as a rate of about 1 nucleotide substitution every 900,000 years on average, compared to say, the SARS-CoV-2 virus that causes COVID-19, which has evolved at about 1 nucleotide substitution every two weeks! This amounts to one amino acid substitution every 2.7 million years<br>
<br>
Incredibly slow though this rate of evolution of RuBisCo is (and that slow rate can be added to the list of reasons it is so inefficient) this is not good news for creationists. It means that not only have they to explain why their putative intelligent designer created such an inefficient enzyme in the first place but why it is now correcting its mistake so slowly. A super-intelligent, omniscient designer would not have made a mistake in the first place and would not now be correcting that mistake at a snail's pace.<br>
<br>
The Oxford scientists who made this discovery have published their work, open access, in the journal PNAS and describe it in a news item from the University of Oxford:
<blockquote class="blockit">New research led by the University of Oxford has found that rubisco – the enzyme that fuels all life on Earth – is not stuck in an evolutionary rut after all. The largest analysis of rubisco ever has found that it is improving all the time – just very, very slowly. These insights could potentially open up new routes to strengthen food security. The results have been published today in <a href="https://www.pnas.org/doi/10.1073/pnas.2321050121" target="_blank">Proceedings of the National Academy of Sciences [PNAS]</a>.<br>
<br>
The most abundant enzyme on Earth, rubisco, has been providing the energy which fuels life on our planet for the last three billion years. While rubisco fixes billions of tons of CO<sub style="small">2</sub> each year, the enzyme is notoriously inefficient. This has created a biological paradox that has puzzled researchers for decades. Why is the enzyme that has been fuelling life for over 3 billion years not much better at doing its job? Many plant scientists have debated whether the enzyme is stuck in an 'evolutionary rut', making it impossible for it to get any better.<br>
<br>
But new research from the University of Oxford has revealed that rubisco is continually improving, but that this improvement is occurring at a glacial pace.<br>
<div class="block"><p>Our research demonstrates for the first time that evolution is consistently improving rubisco and that further improvement of the enzyme is possible. Importantly, this insight provides renewed optimism for efforts to engineer the enzyme to help feed the world.</p>
<div class="creditl">Jacques Bouvier, lead author <br>
Department of Biology, <br>
University of Oxford, Oxford, UK.</div></div>
<br>
The researchers analysed rubisco gene sequences from across a wide range of photosynthetic organisms and quantified the rate of rubisco evolution for the first time. They found that its sequence has altered in minute increments of just one DNA base change every 900,000 years – a stark contrast from the COVID-19 genome, for example, which is evolving one base change every two weeks. This puts rubisco in the 1% of slowest evolving genes on Earth.<br>
<br>
Despite this slow rate of change, the researchers found that the enzyme is harnessing this evolution to get better at fixing CO<sub style="small">2</sub>. The authors also found that this slowly improving CO<sub style="small">2</sub> fixation is resulting in improvements to photosynthesis; plants are evolving to get better at turning CO<sub style="small">2</sub> into sugar, but the rate of improvement is so slow that it appears frozen.<br>
<br>
For decades scientists have aspired to engineer an improved rubisco to boost growth and yields of crop plants. But despite much effort, success has been limited, and many have wondered whether rubisco is already optimised, making these attempts futile. However, the insights from this study offer renewed hope. In particular, unravelling the mystery of what is holding back rubisco’s rate of evolution may uncover new ways of enhancing crop yields.<br>
<div class="block" style="margin-bottom: 0"><p>Because rubisco assimilates the sugars which fuel life on Earth, improving this enzyme is one of the most promising avenues to help combat food insecurity. There has been heated debate as to whether there is scope to improve the enzyme; our new research provides a clear answer to this question. If evolution can improve rubisco, so can we!</p>
<div class="creditl">Jacques Bouvier. </div></div>
<div class="block"><p>We have shown that rubisco is not frozen in time but is instead continually evolving to get better. We now need to understand the factors that are holding rubisco back to enable us to realise its true potential.</p>
<div class="creditl">Professor Steven Kelly, senior author<br>
Department of Biology<br>
University of Oxford, Oxford, UK</div></div>
<br>
This new insight offers encouragement to efforts which aim to increase yields in food, fibre, and fuel crops by targeting rubisco engineering. Improving rubisco could be key to supporting the food needs of a growing global population.
</blockquote>
<blockquote class="blockit"><span>Significance</span><br>
<br>
Rubisco is the most abundant enzyme on Earth and is the source of almost all biological carbon. Here we uncover the trajectory of rubisco adaptive evolution in plants. We reveal that rubisco has experienced continuous directional selection toward higher carbon dioxide/oxygen specificity, carboxylase turnover, and carboxylation efficiency. Moreover, we find that this directional selection toward improved catalytic efficiency has resulted in a corresponding improvement in leaf-level CO<sub style="small">2</sub> assimilation. Together, these findings have significant implications for our understanding of the past, present, and future of rubisco evolution.<br>
<br>
<span>Abstract</span><br>
<br>
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that <i>rbcL</i> is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO<sub style="small">2</sub>/O<sub style="small">2</sub> specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO<sub style="small">2</sub> assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO<sub style="small">2</sub> assimilation in plants.<br>
<br>
Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) converts atmospheric CO<sub style="small">2</sub> into the sugars that fuel the majority of life on Earth. The enzyme evolved ~3 billion years ago when the atmosphere contained high levels of CO<sub style="small">2</sub> (≥10,000% present atmospheric levels) and comparatively little O<sub style="small">2</sub> (≤0.1% present atmospheric levels) (Fig. 1) (<a class="newtooltip">1</a>–<a class="newtooltip">7</a>). Since emergence, the enzyme has helped guide the atmosphere on a trajectory of increasing O<sub style="small">2</sub> and declining CO<sub style="small">2</sub> (<a class="newtooltip">1</a>, <a class="newtooltip">8</a>) such that current concentrations of CO<sub style="small">2</sub> (0.04%) and O<sub style="small">2</sub> (20.95%) are inverted compared to when the enzyme first evolved (Fig. 1).<br>
<br>
<div class="panelplain" style="margin: 1em auto"><div style="margin: 0 1em"><span>Fig. 1.</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4j2pz4leYGXARX0Z9XGYfRo9Uiyrk7g55Eeod3znWJppTc_YTNW8BJ_RL27ZyzJzPoRmurm3v8H_dKxclAKPz92tp264YwkopB3uzCVpBEfHJyOwP7E53GqXp2vyeRbacZyPkqb9YP38kl4Zpa4bn0JbP_mGa9qy6sameD6LbPYhAoubPy621tj5ayS5n/s1600/pnas.2321050121fig01.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4j2pz4leYGXARX0Z9XGYfRo9Uiyrk7g55Eeod3znWJppTc_YTNW8BJ_RL27ZyzJzPoRmurm3v8H_dKxclAKPz92tp264YwkopB3uzCVpBEfHJyOwP7E53GqXp2vyeRbacZyPkqb9YP38kl4Zpa4bn0JbP_mGa9qy6sameD6LbPYhAoubPy621tj5ayS5n/s1600/pnas.2321050121fig01.jpg"/></a>
<div class="caption">The evolutionary history of rubisco in the context of atmospheric CO<sub style="small">2</sub> (%) and O<sub style="small">2</sub> (%) following divergence from the ancestral rubisco-like protein (RLP). Important branch points in the phylogeny at which rubisco diverged into different evolutionary lineages are indicated by gray vertical bars. To provide additional context, the time-period at which the First and Second Great Oxidation events occurred along this evolutionary trajectory are also labeled and referenced as gray vertical bars. Graphics of atmospheric CO<sub style="small">2</sub> and O<sub style="small">2</sub> levels were adapted from the TimeTree resource [<a href="http://www.timetree.org" target="_blank">http://www.timetree.org</a>; (<a class="newtooltip">9</a>)].</div>
</div>
Although all extant rubisco are descended from a single ancestral rubisco-like protein (<a class="newtooltip">10</a>–<a class="newtooltip">12</a>), the enzyme is found in a variety of compositional forms across the tree of life (Fig. 1) (<a class="newtooltip">13</a>, <a class="newtooltip">14</a>). The simplest manifestations are the Form II and Form III variants found in protists, archaea, and some bacteria which are composed of a dimer, or dimers, of the ~50 kDa rubisco large subunit (RbcL) (<a class="newtooltip">14</a>–<a class="newtooltip">17</a>). In contrast, Form I rubisco is a hexadecamer comprised of four RbcL dimers organized in an antiparallel core capped at either end by the ~15 kDa rubisco small subunit (RbcS) (<a class="newtooltip">14</a>, <a class="newtooltip">18</a>). Of these three Forms, only Form I and II have been recruited for oxygenic photosynthesis (<a class="newtooltip">17</a>), with Form I being responsible for the vast majority of global CO<sub style="small">2</sub> assimilation (<a class="newtooltip">17</a>, <a class="newtooltip">19</a>).<br>
<br>
Within Form I rubisco the active site is located in RbcL (<a class="newtooltip">16</a>, <a class="newtooltip">20</a>, <a class="newtooltip">21</a>). As a result, interspecific differences in Form I kinetics are primarily attributable to sequence variation in RbcL (<a class="newtooltip">22</a>–<a class="newtooltip">33</a>). Despite not playing a direct role in catalysis, RbcS influences the function of rubisco (<a class="newtooltip">34</a>, <a class="newtooltip">35</a>) and its incorporation in the holoenzyme enables its higher kinetic efficiency (<a class="newtooltip">36</a>). Specifically, RbcS enhances the stability and assembly of the holoenzyme complex (<a class="newtooltip">21</a>, <a class="newtooltip">37</a>–<a class="newtooltip">42</a>), improves the efficiency of CO<sub style="small">2</sub> binding (<a class="newtooltip">43</a>), and is thought to act as a reservoir for CO<sub style="small">2</sub> accumulation (<a class="newtooltip">44</a>). Accordingly, rubisco function is altered when RbcS is mutated (<a class="newtooltip">45</a>–<a class="newtooltip">47</a>), or when chimeric holoenzymes are created in vivo (<a class="newtooltip">48</a>–<a class="newtooltip">52</a>) and in vitro (<a class="newtooltip">53</a>–<a class="newtooltip">58</a>). Moreover, there is increasing recognition of the importance of both environment (<a class="newtooltip">59</a>) and organ-specific (<a class="newtooltip">60</a>, <a class="newtooltip">61</a>) differences in plant RbcS isoform expression on holoenzyme catalysis. However, even though RbcS influences holoenzyme function, sequence variation in RbcL remains the primary determinant of variation in kinetics (<a class="newtooltip">22</a>–<a class="newtooltip">33</a>).<br>
<br>
Although there is kinetic variability between rubisco orthologs, the enzyme is considered to be an inefficient catalyst. For example, the maximum substrate-saturated turnover rate of Form I rubisco (<12 s<sup class="small">−1</sup>) (<a class="newtooltip">62</a>) is slower than average (<a class="newtooltip">63</a>). In addition, rubisco catalyzes a reaction with O<sub style="small">2</sub> (<a class="newtooltip">64</a>–<a class="newtooltip">66</a>) that is competitive with CO<sub style="small">2</sub> and results in the loss of fixed carbon via photorespiration (<a class="newtooltip">67</a>–<a class="newtooltip">69</a>). As a consequence, rubisco appears poorly suited to the current O<sub style="small">2</sub>-rich/CO<sub style="small">2</sub>-poor atmosphere (Fig. 1). Moreover, it appears that instead of improving enzyme function, multiple lineages have evolved alternative strategies to overcome rubisco’s shortcomings. For example, higher rates of CO<sub style="small">2</sub> assimilation are often achieved either by synthesizing large quantities of rubisco [~50% of soluble protein in plants (<a class="newtooltip">70</a>) and some microbes (<a class="newtooltip">71</a>, <a class="newtooltip">72</a>)], or by operating CO<sub style="small">2</sub>-concentrating mechanisms (<a class="newtooltip">73</a>–<a class="newtooltip">75</a>). As a result, many have questioned whether the enzyme is already perfectly adapted and whether further kinetic improvements are possible (<a class="newtooltip">16</a>, <a class="newtooltip">65</a>, <a class="newtooltip">69</a>, <a class="newtooltip">76</a>–<a class="newtooltip">80</a>). Obtaining answers to these questions would shed light on the “rubisco paradox”—helping to explain why this enzyme of such paramount importance appears poorly adapted for its role.<br>
<br>
The initial hypothesis that attempted to explain the above rubisco paradox proposed that rubisco is constrained by catalytic trade-offs that limit the enzyme’s adaptation. This theory was pioneered by two studies (<a class="newtooltip">81</a>, <a class="newtooltip">82</a>) which found antagonistic correlations between rubisco kinetic traits and proposed that these trade-offs were caused by constraints on its catalytic mechanism. However, recent evidence has questioned this hypothesis as the sole mechanism to explain the rubisco paradox. Specifically, analysis of larger species sets have revealed that kinetic trait correlations are not strong (<a class="newtooltip">83</a>–<a class="newtooltip">85</a>). In addition, phylogenetic signal in rubisco kinetics causes kinetic trait correlations to be overestimated unless phylogenetic comparative methods are employed (<a class="newtooltip">22</a>, <a class="newtooltip">23</a>). Thus, when larger datasets are analyzed with phylogenetic methods, the strength of catalytic trade-offs are substantially reduced (<a class="newtooltip">22</a>, <a class="newtooltip">23</a>). Instead, phylogenetic constraints have had a larger impact on limiting enzyme adaptation compared to catalytic trade-offs (<a class="newtooltip">22</a>, <a class="newtooltip">23</a>). These recent findings motivate a revaluation of the rubisco paradox, and an investigation of whether rubisco is evolving for improved catalysis and CO<sub style="small">2</sub> assimilation in plants.<br>
<br>
Here, we address these issues through a phylogenetic interrogation of the molecular and kinetic evolution of the Form I holoenzyme. We reveal that RbcL has evolved at a slower rate than >98% of all other gene/protein sequences across the tree of life. Through simultaneous evaluation of molecular and kinetic evolution of rubisco during the radiation of C<sub class="small">3</sub> angiosperms, we reveal that the enzyme has been continually evolving toward improved CO<sub style="small">2</sub>/O<sub style="small">2</sub> specificity, carboxylase turnover rate, and carboxylation efficiency. Furthermore, we demonstrate that enhanced rubisco evolution is associated with increased rates of CO<sub style="small">2</sub> assimilation and higher photosynthetic nitrogen-use efficiencies. Thus, rubisco is not perfectly adapted, but is slowly evolving toward improved catalytic efficiency and CO<sub style="small">2</sub> assimilation.
</blockquote>
There is a great deal for creationists to devise strategies for ignoring here:<br>
<br>
Firstly, there is the embarrassment of RuBisCo itself which provides such compelling evidence for a mindless utilitarian evolutionary process which is predicted to produce suboptimal, near-enough-is-good-enough processes that then become fixed in the phylogenic tree, and against any involvement of intelligence, let alone omniscient, omnipotent intelligence, in the design, because such designs would be perfect examples of maximal efficiency combined with minimal complexity.<br>
<br>
Secondly, there is the evidence that, slow though it is, RuBisCo has changed over time to gradually improved efficiency, albeit more slowly than 98% of other examples of evolving biological systems and many orders of magnitude more slowly than, for example, viruses. At first sight this might not appear to be a problem for creationism, except that changing to become more efficient means the original was sub-optimal as are the current versions, which are still evolving. An intelligent designer, even <b>if</b> it had realised its original design was less than perfect, would have produced a new, improved version is a single step, not at the painfully slow rate of 1 nucleotide substitution per 900,000 years.<br>
<br>
Lastly, there is the evidence from this paper that the scientists have no doubt that the changes are an evolutionary change, and that the reason for RuBisCo's legendary inefficiency was due to a mindless evolutionary process, and that RuBisCo is an evolved and evolving enzyme, with no hint that supernatural intervention was involved at any point.<br>
<br>
From being a major embarrassment for those creationists who understand it, RuBisCo has just become an even bigger embarrassment for creationism.
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<div class="right-column" style="flex: 1.5">This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.<br>
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{n: "70", text: "E. Carmo-Silva, J. C. Scales, P. J. Madgwick, M. A. J. Parry, Optimizing Rubisco and its regulation for greater resource use efficiency. Plant Cell Environ. 38, 1817–1832 (2015), https://doi.org/10.1111/pce.12425."},
{n: "71", text: "L. S. Sarles, F. R. Tabita, Derepression of the synthesis of D-ribulose 1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum. J. Bacteriol. 153, 458–464 (1983).",
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{n: "72", text: "F. R. Tabita, Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective. Photosynth. Res. 60, 1–28 (1999).",
url: "https://doi.org/10.1023/A:1006211417981"},
{n: "73", text: "A. Flamholz, P. M. Shih, Cell biology of photosynthesis over geologic time. Curr. Biol. 30, R490–R494 (2020).",
url: "https://doi.org/10.1016/j.cub.2020.01.076"},
{n: "75", text: "U. Schlüter et al., Brassicaceae display variation in efficiency of photorespiratory carbon recapturing mechanisms. J. Exp. Bot. 74, 6631–6649 (2023), https://doi.org/10.1093/jxb/erad250.",
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{n: "76", text: "W. L. Ogren, Photorespiration: Pathways, regulation, and modification. Annu. Rev. Plant Physiol. 35, 415–442 (1984).",
url: "https://doi.org/10.1146/annurev.pp.35.060184.002215"},
{n: "80", text: "R. E. Sharwood, O. Ghannoum, S. M. Whitney, Prospects for improving CO2 fixation in C3-crops through understanding C4-Rubisco biogenesis and catalytic diversity. Curr. Opin. Plant Biol. 31, 135–142 (2016), https://doi.org/10.1016/j.pbi.2016.04.002.",
url: "https://doi.org/10.1016/j.pbi.2016.04.002"},
{n: "81", text: "Y. Savir, E. Noor, R. Milo, T. Tlusty, Cross-species analysis traces adaptation of Rubisco toward optimality in a low-dimensional landscape. Proc. Natl. Acad. Sci. U.S.A. 107, 3475–3480 (2010).",
url: "https://doi.org/10.1073/pnas.0911663107"},
{n: "82", text: "G. G. B. Tcherkez, G. D. Farquhar, T. J. Andrews, Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc. Natl. Acad. Sci. U.S.A. 103, 7246–7251 (2006).",
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{n: "83", text: "A. I. Flamholz et al., Revisiting trade-offs between rubisco kinetic parameters. Biochemistry 58, 3365–3376 (2019), https://doi.org/10.1021/acs.biochem.9b00237.",
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{n: "85", text: "P. L. Cummins, The coevolution of RuBisCO, Photorespiration, and carbon concentrating mechanisms in higher plants. Front. Plant Sci. 12, 662425 (2021).",
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-19693241021967733352024-03-11T00:55:00.004+00:002024-03-11T00:57:13.507+00:00Malevolent Design - How a Bacterium Carries a Virus That Selectively Kills Male Insects And Only Allows Infected Females To Breed<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
</div><br>
<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3SbgPqirqvvJOxn9O_C1cHBGk_5CJ40LEOLii5aa5BTOmurm-Pi5738p4eg1z6ARJLuYNYrnAg3CQlU3mlT-F-Q02SytRUYkJ4u4-CZZ7ErkSUVNvmm1ANoYPkqWV7cNgxEfJlSakE-fYWl97MzJNY-P4RIjjKEgv4Ka4KUebZYBtWk7IT7SdNxng83Xv/s1600/testeswolbachia_creditrupinderkaur_43.jpg" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" data-original-height="1125" data-original-width="1500" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3SbgPqirqvvJOxn9O_C1cHBGk_5CJ40LEOLii5aa5BTOmurm-Pi5738p4eg1z6ARJLuYNYrnAg3CQlU3mlT-F-Q02SytRUYkJ4u4-CZZ7ErkSUVNvmm1ANoYPkqWV7cNgxEfJlSakE-fYWl97MzJNY-P4RIjjKEgv4Ka4KUebZYBtWk7IT7SdNxng83Xv/s1600/testeswolbachia_creditrupinderkaur_43.jpg"/></a></div>
<a href="https://www.psu.edu/news/eberly-college-science/story/how-does-virus-hijack-insect-sperm-control-disease-vectors-and-pests/">How does a virus hijack insect sperm to control disease vectors and pests? | Penn State University</a><br>
<br>
Wolbachia are a genus of bacteria that form a symbiotic relationship with about 50% of arthropod species, including insects and spiders but they can also manipulate the species for their own ends (in terms of breeding success). They are aided in this by a virus which is incorporated in their genome which has been shown to join forces with Wolbachia to ensure their own reproductive success in the form of females infected with the virus-bearing Wolbachia.<br>
<br>
So completely have Wolbachia integrated with insects that one species of fruit fly has the entire Wolbachia genome incorporated into its own genome, making it, biologically, both bacterium and fruit fly.<br>
<br>
One way Wolbachia ensure their own survival at the expense of the species of insect they infect is by making the sperm and egg incompatible if the female is not also a carrier of the right species of Wolbachia. And, to be on the safe side, two proteins produced by the virus break the sperm's DNA so any resulting embryo will be defective and will fail to develop. This ensures that only the females carrying the infection can breed, so increasing the Wolbachia and its virus in the gene pool.<br>
<br>
The team who discovered this nasty little virus and how it acts selfishly, was co-led by Professor Seth R. Bordenstein, of the One Health Microbiome Center at Pennsylvania State University. They have published their findings in <i>Science</i> and described it in a Penn State News item.<br>
<br>
But first, a little background on Wolbachia:
<a name='more'></a>
<blockquote class="ai">Tell me all about Wolbachia bacteria and what they do to male insects.
Wolbachia is a genus of bacteria that infects a wide range of arthropods, including insects, spiders, and crustaceans. They are one of the most common and widespread symbionts in the world, estimated to infect up to 40% of all insect species. Wolbachia are intracellular bacteria, meaning they live inside the cells of their host organisms.
Here are some key characteristics and effects of Wolbachia bacteria:
<ol class="dbl1 bold">
<li><b>Reproductive Manipulation:</b> One of the most notable features of Wolbachia is their ability to manipulate the reproductive biology of their hosts. They can induce several reproductive alterations, including:
<ul type="disc">
<li><b>Cytoplasmic Incompatibility (CI):</b> This is the most well-known effect of Wolbachia. When an infected male mates with an uninfected female or a female carrying a different strain of Wolbachia, the embryos fail to develop properly, leading to reduced viability or death. However, when both partners are infected with the same strain of Wolbachia, the embryos develop normally. This phenomenon gives infected females a reproductive advantage, as they can successfully reproduce with infected males while uninfected females cannot.</li>
<li><b>Feminization:</b> In some cases, Wolbachia can cause genetic males to develop as females or intersex individuals. This occurs because Wolbachia can alter the sex determination mechanisms of their hosts, leading to the development of female characteristics in genetic males.</li>
<li><b>Male Killing:</b> In certain species, Wolbachia selectively kills male embryos during development, skewing the sex ratio of the population towards females. This can enhance the reproductive success of infected females, as they have fewer competitors for resources.</li>
<li><b>Parthenogenesis Induction:</b> Wolbachia can induce parthenogenesis, a form of asexual reproduction where females produce offspring without mating with males. This allows infected females to reproduce even in the absence of males, further enhancing their reproductive success.</li>
</ul></li>
<li><b>Protection Against Pathogens:</b> Wolbachia can also provide protection to their host organisms against certain pathogens. They do this by interfering with the replication and transmission of viruses such as dengue, Zika, and chikungunya viruses in mosquitoes. This has led to research into using Wolbachia-infected mosquitoes as a method of controlling the spread of mosquito-borne diseases.</li>
<li><b>Vertical Transmission:</b> Wolbachia are primarily transmitted vertically from mother to offspring. They are often found within the reproductive tissues of their hosts, ensuring their transmission to the next generation via the eggs.</li>
<li><b>Diversity and Evolution:</b> Wolbachia exhibit a high level of diversity, with multiple strains and variants infecting different host species. They can also undergo horizontal transfer between host species, contributing to their evolutionary dynamics.</li>
</ol>
Overall, Wolbachia bacteria have profound effects on the reproductive biology and ecology of their host organisms. Their ability to manipulate host reproduction has important implications for the evolution of host populations, as well as potential applications in the control of insect pests and the spread of vector-borne diseases.<br><br>
<span>Is anything known about the evolutionary origins of Wolbachia?</span><br>
<br>
The evolutionary origins of Wolbachia bacteria are still a subject of debate among researchers, but several lines of evidence suggest that they have co-evolved with their arthropod hosts over millions of years. Some key points regarding the evolutionary origins of Wolbachia include:
<ol class="dbl1 bold">
<li><b>Ancient Association:</b> Wolbachia are believed to have ancient origins, with estimates suggesting they may have been present in arthropods for hundreds of millions of years. Fossil evidence of Wolbachia has been found in ancient insects preserved in amber, indicating that they have been associated with their hosts for a long time.</li>
<li><b>Vertical Transmission:</b> The primary mode of transmission of Wolbachia is vertical, from mother to offspring via the eggs. This mode of transmission suggests a long co-evolutionary history with their hosts, as it allows the bacteria to persist within host populations over generations.</li>
<li><b>Diverse Host Range:</b> Wolbachia infect a wide range of arthropod species, including insects, spiders, and crustaceans. The diversity of host species suggests that Wolbachia have had ample opportunity to co-evolve with different host lineages over evolutionary time.</li>
<li><b>Phylogenetic Studies:</b> Phylogenetic analyses of Wolbachia and their host organisms have provided insights into their evolutionary relationships. Studies have suggested that Wolbachia strains often cluster with their host species, indicating co-speciation and long-term association between the bacteria and their hosts.</li>
<li><b>Horizontal Transfer:</b> While vertical transmission is the primary mode of Wolbachia transmission, there is also evidence of horizontal transfer between host species. Horizontal transfer events may contribute to the spread of Wolbachia across different host lineages and influence their evolutionary dynamics.</li>
</ol>
Overall, while the exact evolutionary origins of Wolbachia remain uncertain, evidence suggests that they have co-evolved with their arthropod hosts over long periods, shaping their biology and ecology in intricate ways. Further research into the evolutionary history of Wolbachia and their interactions with their hosts will continue to provide insights into their origins and evolutionary dynamics.
</blockquote>
<blockquote class="blockit">A widespread bacteria called Wolbachia and a virus that it carries can cause sterility in male insects by hijacking their sperm, preventing them from fertilizing eggs of females that do not have the same combination of bacteria and virus. A new study led by microbiome researchers at Penn State has uncovered how this microbial combination manipulates sperm, which could lead to refined techniques to control populations of agricultural pests and insects that carry diseases like Zika and dengue to humans.<br>
<br>
The study published today (March 8) in <a href="https://www.science.org/doi/10.1126/science.adk9469" target="_blank"><i>Science</i></a>.<br>
<div class="block"><p>Wolbachia is the most widespread bacteria in animals and lives symbiotically within the reproductive tissues of about 50% of insect species, including some mosquitos and flies. Wolbachia has genes from a virus called prophage WO integrated into its genome. These genes — cifA and cifB — allow the bacteria to remarkably manipulate sperm and quickly spread through an insect population for their own good.<br>
<div class="creditl"><a href="http://bordensteinlab.com/" target="_blank">Seth R. Bordenstein</a>, co-corresponding author<br>
Professor of biology and entomology<br>
Director of the <a href="http://microbiome.psu.edu/" target="_blank">One Health Microbiome Center</a><br>
Departments of Biology and Entomology<br>
Pennsylvania State University, PA, USA.</div></div>
When a male and female insect that both have Wolbachia mate, they successfully reproduce and pass on the bacteria. But when a male with Wolbachia mates with a female with no Wolbachia, the sperm are rendered lethal to the fertilized eggs, succumbing them to death. This system cunningly increases the proportion of offspring with Wolbachia and the virus in the next generation, because females with the bacteria successfully reproduce more frequently than females without.<br>
<br>
This system is being used in several ongoing pilot studies across the world to control insect pests and the harmful viral diseases they carry. For example, to control a population of agricultural or human pests that do not have the bacteria, scientists release males with Wolbachia in order to crash the population.<br>
<div class="block"><p>One of Wolbachia’s superpowers is that it blocks pathogenic RNA viruses such as Zika, dengue and chikungunya virus, so mosquitos with Wolbachia do not pass these viruses on to people when they bite. So, releases of both male and female mosquitos with Wolbachia in an area where it isn’t already present leads to replacement of the population with mosquitos that can no longer pass on a viral disease. The World Mosquito Program is now using Wolbachia to control viruses in 11 countries. With this study, we reveal the underlying mechanics of how this process works so we can fine-tune the technique to expand its scope in vector control measures.</p>
<div class="creditl">Professor Seth R. Bordenstein.</div></div>
Wolbachia’s prophage WO genes code for proteins that interfere with normal development of sperm cells. These proteins impact a critical transformation during sperm development, when the sperm’s genome is repackaged and the sperm changes from a canoe-shape into a more refined needle-like shape. <br>
<div class="block"><p>This shape change is incredibly important to the success of sperm, and any interference can impact the sperm’s ability to travel in the female reproductive tract and successfully fertilize the egg. The transition is highly conserved in almost everything from insects to humans. Defects in this process can also cause male sterility in humans.</p>
<div class="creditl">Assistant professor <a href="https://ento.psu.edu/directory/rjk6018" target="_blank">Rupinder Kaur</a>, co-corresponding author<br>
Departments of Biology and Entomology<br>
Pennsylvania State University, PA, USA.</div></div>
<br>
According to the researchers, sperm is particularly prone to DNA damage and repair during this transition. In this study, they found that sperm exposed to Wolbachia, or the Cif proteins alone, had an elevated level of DNA damage at this stage. The DNA damage, if not repaired in a timely fashion, can result in abnormal sperm genome packaging, male infertility and embryonic inviability.<br>
<div class="block"><p>These results confirmed the impact of Wolbachia and Cif proteins at this stage of sperm development, but we still wanted to know what was happening at earlier stages to trigger these changes. We conducted a series of tests to explore the structure and biochemical function of the Cif proteins and found that they can cleave messenger molecules called long non-coding RNA, which sets the stage to interfere with downstream development and function of the sperm.</p>
<div class="creditl">Assistant professor Rupinder Kaur</div></div>
<br>
The researchers used fruit flies with Wolbachia to test the potential link between the bacteria and long non-coding RNA. They found that Wolbachia — or the Cif proteins alone — reduced the amount of these RNAs. Additionally, mutant flies with reduced expression of these RNAs in conjunction with Wolbachia had elevated levels of embryonic inviability because it augmented the defective transition process of sperm development. So, Kaur explained, the virus proteins control sperm by depleting the long non-coding RNAs required for a normal sperm function.<br>
<div class="block"><p>Long non-coding RNAs do not make any proteins themselves, but they can have profound impacts on regulating the function of other genes required for sperm development. By altering this non-coding part of the genome, we found that Cif proteins start impacting sperm right from the earliest stages of development. Wolbachia’s prophage WO genes act like master puppeteers, manipulating sperm development in a way that allows their genes and the symbiotic bacteria to quickly spread through arthropod populations.</p>
<div class="creditl">Professor Seth R. Bordenstein.</div></div>
<br>
Because the process of sperm development looks similar across the animal kingdom, the researchers said that knowledge of this process could lend insight into sterility challenges in humans as well as inform new control methods of harmful insect populations. <br>
<div class="block"><p>Now that we have reverse engineered this process, we can fine tune methods of population control with Wolbachia that are already in use. We plan to take advantage of this knowledge to augment currently existing disease vector and pest control methods, and perhaps emulate the technique without Wolbachia or virus proteins in the long-term.</p>
<div class="creditl">Assistant professor Rupinder Kaur</div></div>
In addition to Bordenstein and Kaur, the research team includes Angelina McGarry, research technologist II at Penn State; J. Dylan Shropshire, assistant professor at Lehigh University; and Brittany Leigh, a postdoctoral researcher at Vanderbilt University at the time of the research.
</blockquote>
Sadly, the team's research paper is behind a paywall:
<blockquote class="blockit"><span>Abstract</span><br>
<br>
The extent to which prophage proteins interact with eukaryotic macromolecules is largely unknown. In this work, we show that cytoplasmic incompatibility factor A (CifA) and B (CifB) proteins, encoded by prophage WO of the endosymbiont Wolbachia, alter long noncoding RNA (lncRNA) and DNA during Drosophila sperm development to establish a paternal-effect embryonic lethality known as cytoplasmic incompatibility (CI). CifA is a ribonuclease (RNase) that depletes a spermatocyte lncRNA important for the histone-to-protamine transition of spermiogenesis. Both CifA and CifB are deoxyribonucleases (DNases) that elevate DNA damage in late spermiogenesis. lncRNA knockdown enhances CI, and mutagenesis links lncRNA depletion and subsequent sperm chromatin integrity changes to embryonic DNA damage and CI. Hence, prophage proteins interact with eukaryotic macromolecules during gametogenesis to create a symbiosis that is fundamental to insect evolution and vector control.<br>
<br>
<div class="creditl"><a href="https://www.science.org/doi/10.1126/science.adk9469" target="_blank">Rupinder Kaur et al. ,<br>
Prophage proteins alter long noncoding RNA and DNA of developing sperm to induce a paternal-effect lethality.<br>
<i>Science</i> <b>383</b>, 1111-1117 (2024). DOI:10.1126/science.adk9469</a><br>
<br>
© 2024 The authors. Published by the American Association for the Advancement of Science.<br>
Reprinted with kind permission under licence #5745590955131</div>
</blockquote>
It's hard to think of a more malevolent design than a bacterium that infects a species, bringing along a virus to help it manipulate its hosts reproduction for its own and its viruses benefit, even to the extent of killing developing embryos unless both parents are infected with the same strain of bacterium, so giving infected insects an advantage.<br>
<br>
But for the most bizarre of reasons, creationists would rather we had that view of their putative designer than understand how this is the work of a mindless natural process not involving supernatural magic.<br>
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<div class="right-column" style="flex: 1.5">This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.<br>
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<div class="right-column" style="flex: 1.5">ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.<br>
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<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-64184593699458145182024-03-10T18:31:00.001+00:002024-03-10T18:31:17.381+00:00Unintelligent Design - How Epigenetic Settings Are Passed To Daughter Cells - Even William Heath Robinson Would Be Impressed<div class="title-box" style="height: 800px; display: none">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhT3BDHM1ayg0Makv6HB2jLrbP3gqa0S1jyH0VMpgSieD0awaitjACRcIWqfgp5eCJL2wBX_KCQ85FEZlgR4v6I_R6MuyTgZPl9jUsAxN4UAypMBcr6AQlJDii7Cz8gima_669I-3VLyJ21_TnatWj30xBVu0tVoUu7f_K4C5APkiUyuF559PIlFrEGglYj/s1600/Pic3C.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhT3BDHM1ayg0Makv6HB2jLrbP3gqa0S1jyH0VMpgSieD0awaitjACRcIWqfgp5eCJL2wBX_KCQ85FEZlgR4v6I_R6MuyTgZPl9jUsAxN4UAypMBcr6AQlJDii7Cz8gima_669I-3VLyJ21_TnatWj30xBVu0tVoUu7f_K4C5APkiUyuF559PIlFrEGglYj/s1600/Pic3C.jpg"/></a></div>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaTjN7ac9opfayfRkt8W9AQrOQz584OQXObvhyphenhyphen1EzjJsslLZ6Wc0gZdpYtoxR67YH3vqgkxWIXkp8zgkC8nZG3rYBSXyhgw_FTJ44iC-tt85cgSHepjhFJDVPuc10j1Y8Rd8Hk-xh8OoNytJfzSgaqgmFVn8mPIqiIGSXdAuXpw_DKFN5X00P8Y5HFRqoc/s1600/Pic3D.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaTjN7ac9opfayfRkt8W9AQrOQz584OQXObvhyphenhyphen1EzjJsslLZ6Wc0gZdpYtoxR67YH3vqgkxWIXkp8zgkC8nZG3rYBSXyhgw_FTJ44iC-tt85cgSHepjhFJDVPuc10j1Y8Rd8Hk-xh8OoNytJfzSgaqgmFVn8mPIqiIGSXdAuXpw_DKFN5X00P8Y5HFRqoc/s1600/Pic3D.jpg"/></a></div>
<a href="https://www.hku.hk/press/press-releases/detail/27124.html">Cracking Epigenetic Inheritance: HKU Biologists Discovered the Secrets of How Gene Traits are Passed on - Press Releases - Media - HKU</a><br>
<br>
It all started when single-celled organisms started to form colonies of like-minded individuals. The easiest way to do it was for the two daughter cells of a dividing cell to stick together instead of going their own way. They in turn would have had more daughter cells until they formed large clump of cells, but, unless the cells began to perform distinct functions, there was no advantage to forming clumps like that instead of each cell going its own way and fending for itself. Fortunately, there were no large predators around, otherwise a clump of cells would have made a tasty snack and the whole idea would have been abandoned as too risky by half, and we would be stuck now with a world of single-celled organisms and nothing else.<br>
<br>
However, with the trial and error which characterises biological development, some of the cells in the clump began to perform specialist functions. For example, as the clump got larger, specialist cells would have been needed to exchange gasses with the environment or the cells at the centre would have been deprived of oxygen and their waste in the form of carbon dioxide would have accumulated because diffusing across a large mass of cells would be too slow to keep up with production and the supply of oxygen would be too slow to keep up with the demand. The same thing applied to getting nutrients into the center of the clump.<br>
<br>
So, the clumps which had specialist cells fared better in the competition for resources than those which were just undifferentiated clumps. In fact, the clumps with specialised cells would probably have eaten the undifferentiated clumps and become predators. And with predators there was pressure for increased specialisation for movement, ingestion and excretion, for more efficient respiration and for reproduction. And predation also produced pressure for more motility, for senses like sight and smell and maybe hearing and as the organisms became more complex so they needed nervous systems to coordinate their activities and process and respond to the stimuli their senses were receiving from their environment and some would have evolved defensive armour such as scales and spikes and hard shells and internal structures like cartilage and bone to give their bodies shape and form and to make their swimming apparatus stiffer and more powerful.<br>
<br>
But what they never managed to do was find a different way to produce all the different specialist cells by a different method to that used by their single-celled ancestors, so every cell in their body had the full genome whether they needed it or not, and more often than not, they didn't need most of it. A bone cell doesn't need to do what a nerve cell does, and a nerve cell doesn't need to do what a muscle cell does, and neither muscle nor nerve cells need to make bone, and what else needs to make elbow skin other than an elbow skin cell, except perhaps a scrotum skin cell? Yet they all have the genes for doing everything any one cell needs to do.<br>
<br>
So, cue creationism's intelligent [sic] designer who has been designing and modifying all these different clumps of specialised cells but who, for some reason, seems incapable of recognising that its designs are heading for disaster unless it can think up a way to make sure each specialised cell has only the genes it needs. For reasons which no creationist apologist has ever managed to explain, their putative designer always behaves as though it can't undo a bad design and start again but is compelled to try to make the best of what it has muddled through with so far. In every way, creationism’s 'intelligent [sic] designer' behaves just like a mindless process operating without a plan, handicapped by acute amnesia, and constantly surprising itself with a new problem it designed just yesterday.<br>
<br>
Just like the eccentric British designer and cartoonist, William Heath Robinson, no solution to a problem can be too complex even if it creates a new problem for which another overly complex solution has to be found. Unlikely objects, designed for a completely different purpose, will be pressed into service; a stepladder will be balanced precariously on top of a piano and an umbrella will be used to push a button when prodded by a sink plunger swinging on a length of knotted string. A labour-saving device for peeling potatoes will take half a dozen, intense and serious-looking men to operate it and peeling the potatoes will take considerably longer than had each man been given a potato peeler and left to get on with it. Eggs will be fried in a frying pan held over a candle lit by a match rubbed against a matchbox which swings into action when released by a lever when the scuttle-full of coal, or the boulder suspended on knotted string, lands on it. <br>
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Every hot-air ballon will have had several leaks mended with patches in a different fabric as will every set of bellows used to blow out the candle at the right time or make the fire burn up when needed to make the hot air balloon rise, which will be held down by a coal-scuttle full of coal until a man with nothing else to do, cuts the string with a pair of scissors when prodded in the back by an umbrella operated by a wheel with broken spokes joined together with sticks tied on with more string or held together with bent nails.<br>
<br>
And the whole 'irreducibly complex', 'intelligently designed' machine would fail if just one component was taken away or a piece of knotted string broke.<br>
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So, what did creationism's intelligent designer produce to solve the problem of too many genes for the specialised cells? It produced the overly complex solution of epigenetics of course! There was no going back and starting again for our intrepid, muddle through, mend and make do, near-enough-is-good-enough utilitarian designer. Going back and starting again would have been far too simple.<br>
<br>
So complex is this system, that a team of researchers has only just worked out how cells pass on their epigenetic settings to their daughter cells.<br>
<br>
Their findings are the subject of a paper in <i>Nature</i> and a news release from the University of Hong Kong:<br>
<br>
<blockquote class="blockit"><div class="panelplain">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBOPxb7g6wljhK8AHvRcPpIKYi8fXDVIQlwrChrTix-MJ8ZqlU9UAas3OKOgsUyhqHRT8xA4nx-krkCosBYEG01nuyLBe-THRU6oXF0AqRFrpaLyygJHit3GiG1UwBpgAX_vG9iXjcoHwW14BwE7ynwZEqnn50C9wd271OVz5J0cO8miI44ZsE8H9QnD-9/s1600/Picture2.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBOPxb7g6wljhK8AHvRcPpIKYi8fXDVIQlwrChrTix-MJ8ZqlU9UAas3OKOgsUyhqHRT8xA4nx-krkCosBYEG01nuyLBe-THRU6oXF0AqRFrpaLyygJHit3GiG1UwBpgAX_vG9iXjcoHwW14BwE7ynwZEqnn50C9wd271OVz5J0cO8miI44ZsE8H9QnD-9/s1600/Picture2.jpg"/></a>
<div class="caption"><b>Figure 2.</b>The cryo-EM structure of the yeast replisome in complex with FACT and parental histones (A) and its atomic model (B). <br><div class="credit">Modified from Li et al, Nature (2004)</div></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiDqd4dgO2I4p_EcgIX87ZiX6hTOf9-fPfSJjZqMrVGjMe0GXk6es1kQR4yUEN59nhSIh9Cq-CBLL-poUuBdhGAE813y46dlNG-I_Pb_OxvzfCsW3Ufrj6IbpB7d9R8O5lrbftieQjeF4CYU_dWSammEaxnaKCGtHV9D4eg6bY4eifWQ4mF_oZ2zKHd3ho/s1600/Picture3.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiDqd4dgO2I4p_EcgIX87ZiX6hTOf9-fPfSJjZqMrVGjMe0GXk6es1kQR4yUEN59nhSIh9Cq-CBLL-poUuBdhGAE813y46dlNG-I_Pb_OxvzfCsW3Ufrj6IbpB7d9R8O5lrbftieQjeF4CYU_dWSammEaxnaKCGtHV9D4eg6bY4eifWQ4mF_oZ2zKHd3ho/s1600/Picture3.jpg"/></a>
<div class="caption">Figure 2. The cryo-EM structure of the yeast replisome in complex with FACT and parental histones (A) and its atomic model (B). <br><div class="credit">Modified from Li et al, Nature (2004)</div></div>
</div>
A research team led by Professor Yuanliang ZHAI at the School of Biological Sciences, The University of Hong Kong (HKU) collaborating with Professor Ning GAO and Professor Qing LI from Peking University (PKU), as well as Professor Bik-Kwoon TYE from Cornell University, has recently made a significant breakthrough in understanding how the DNA copying machine helps pass on epigenetic information to maintain gene traits at each cell division. Understanding how this coupled mechanism could lead to new treatments for cancer and other epigenetic diseases by targeting specific changes in gene activity. Their findings have recently been published in Nature.<br>
<br>
<span>Background of the Research</span><br>
<br>
Our bodies are composed of many differentiated cell types. Genetic information is stored within our DNA which serves as a blueprint guiding the functions and development of our cells. However, not all parts of our DNA are active at all times. In fact, every cell type in our body contains the same DNA, but only specific portions are active, leading to distinct cellular functions. For example, identical twins share nearly identical genetic material but exhibit variations in physical characteristics, behaviours and disease susceptibility due to the influence of epigenetics. Epigenetics functions as a set of molecular switches that can turn genes on or off without altering the DNA sequence. These switches are influenced by various environmental factors, such as nutrition, stress, lifestyle, and environmental exposures.<br>
<br>
In our cells, DNA is organised into chromatin. The nucleosome forms a fundamental repeating unit of chromatin. Each nucleosome consists of approximately 147 base pairs of DNA wrapped around a histone octamer which is composed of two H2A-H2B dimers and one H3-H4 tetramer. During DNA replication, parental nucleosomes carrying the epigenetic tags, also known as histone modifications, are dismantled and recycled, ensuring the accurate transfer of epigenetic information to new cells during cell division. Errors in this process can alter the epigenetic landscape, gene expression and cell identity, with potential implications for cancer and ageing. Despite extensive research, the molecular mechanism by which epigenetic information is passed down through the DNA copying machine, called the replisome, remains unclear. This knowledge gap is primarily due to the absence of detailed structures that capture the replisome in action when transferring parental histones with epigenetic tags. Studying the process is challenging because of the fast-paced nature of chromatin replication, as it involves rapid disruption and restoration of nucleosomes to keep up with the swift DNA synthesis.<br>
<br>
In previous studies, the research team made significant progress in understanding the DNA copying mechanism, including determining the structures of various replication complexes. These findings laid a solid foundation for the current research on the dynamic process of chromatin duplication.<br>
<br>
<span>Summary of Research Findings</span><br>
<br>
This time, the team achieved another breakthrough by successfully capturing a key snapshot of parental histone transfer at the replication fork. They purified endogenous replisome complexes from early-S-phase yeast cells on a large scale and utilised cryo-electron microscopy (cryo-EM) for visualisation.<br>
<br>
They found that a chaperone complex FACT (consisting of Spt16 and Pob3) interacts with parental histones at the front of the replisome during the replication process. Notably, they observed that Spt16, a component of FACT, captures the histones that have been completely stripped off the duplex DNA from the parental nucleosome. The evicted histones are preserved as a hexamer, with one H2A-H2B dimer missing. Another protein that involved in DNA replication, Mcm2, takes the place of the missing H2A-H2B dimer on the vacant site of the parental histones, placing the FACT-histone complex onto the front bumper of the replisome engine, called Tof1. This strategic positioning of histone hexamer on Tof1 by Mcm2 facilitates the subsequent transfer of parental histones to the newly synthesised DNA strands. These findings provide crucial insights into the mechanism that regulates parental histone recycling by the replisome to ensure the faithful propagation of epigenetic information at each cell division.<br>
<br>
This study, led by Professor Zhai, involved a collaborative effort that spanned nearly eight years, starting at HKUST and concluding at HKU. He expressed his excitement about the findings, ‘It only took us less than four months from submission to Nature magazine to the acceptance of our manuscript. The results are incredibly beautiful. Our cryo-EM structures offer the first visual glimpse into how the DNA copying machine and FACT collaborate to transfer parental histone at the replication fork during DNA replication. This knowledge is crucial for elucidating how epigenetic information is faithfully maintained and passed on to subsequent generations. But, there is still much to learn. As we venture into uncharted territory, each new development in this field will represent a big step forward for the study of epigenetic inheritance.’<br>
<br>
The implications of this research extend beyond understanding epigenetic inheritance. Scientists can now explore gene expression regulation, development, and disease with greater depth. Moreover, this breakthrough opens up possibilities for targeted therapeutic interventions and innovative strategies to modulate epigenetic modifications for cancer treatment. As the scientific community delves deeper into the world of epigenetics, this study represents a major step towards unravelling the complexities of replication-coupled histone recycling.<br>
<br>
<span>About the Research Team</span><br>
<br>
Apart from Professor Yuanliang Zhai’s lab, the research team also includes Professor Xiang David Li from Department of Chemistry of HKU, Professor Yang Liu and Professor Keda Zhou from School of Biomedical Sciences of HKU, Professor Shangyu Dang from Division of Life Science of HKUST, and others. Learn more about Professor Yuanliang Zhai’s work and his research team: <a href="https://www.scifac.hku.hk/people/zhai-yuanliang" target="_blank">https://www.scifac.hku.hk/people/zhai-yuanliang</a> or <a href="https://zhai95.wixsite.com/mysite-1" target="_blank">https://zhai95.wixsite.com/mysite-1</a><br>
<br>
Co-authors include Mr Yuan Gao, Mr Jian Li, Dr Zhichun Xu from School of Biological Sciences (SBS) of HKU; Dr Ningning Li, Ms Yujie Zhang, Dr Jianxun Feng from School of Life Sciences of PKU, Dr Daqi Yu and Dr Jianwei Lin from Department of Chemistry of HKU, and Dr Yingyi ZHANG from Biological Cryo- EM Center of HKUST.<br>
<br>
The journal paper can be accessed here: <a href="https://zhai95.wixsite.com/mysite-1" target="_blank">https://www.nature.com/articles/s41586-024-07152-2</a>
</blockquote><br>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
In eukaryotes, DNA compacts into chromatin through nucleosomes<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a></sup>. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">4</a></sup>. Here we report cryo-electron microscopy structures of yeast (<i>Saccharomyces cerevisiae</i>) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A–H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3–H4 tetramer, while the vacant H2A–H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3–H4 dimer and extends across the tetramerization interface of the H3–H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3–H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.<br>
<br>
<div class="creditl"><a href="https://www.nature.com/articles/s41586-024-07152-2" target="_blank">Li, N., Gao, Y., Zhang, Y. et al. <br>
Parental histone transfer caught at the replication fork. <br>
Nature (2024). https://doi.org/10.1038/s41586-024-07152-2</a><br>
<br>
© 2024 Springer Nature Ltd.<br>
Reprinted under the terms of <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">s60</a> of the <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">Copyright, Designs and Patents Act 1988</a>.</div>
</blockquote>
This Heath-Robinson solution to a problem which no intelligent designer would design in the first place, is repeated in every one of your 17 trillion cells and in every cell of every multicellular organism on the planet. A hugely wasteful and error-prone, needlessly complex system of which any intelligent designer would be ashamed, but which creationist frauds fool their ignorant dupes into believing is evidence of intelligence. In reality of course, it's evidence of exactly the opposite.<br>
<br>
It's not even humorous and entertaining like William Heath-Robinson's ridiculously complicated, irreducibly complex, machines.
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-31911520208069978452024-03-10T00:20:00.003+00:002024-03-10T00:26:40.867+00:00Covidiot News - Just Because You Haven't Had COVID-19 Yet, Doesn't Mean You Won't!<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox" style="color: black">
<div class="left-column" style="text-align: left; flex: 2">The SARS-CoV-2 virus needs to attach to receptors to gain access to our cells.</div>
<div class="right-column" style="text-align: right; flex: 1">Kateryna Kon/Shutterstock</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none"><a href="https://images.theconversation.com/files/463953/original/file-20220518-19-cupowl.jpg"><img src="https://images.theconversation.com/files/463953/original/file-20220518-19-cupowl.jpg"></a></div>
<div class="rpanel450plain"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3v7-fM3AG8yOyM_NPkvg216Etm9s91knBdM4BF1wOM8j9UHKQJNf3SXJkYrkq2NhkQcVZZNxG2cl84swSHQE6zlVj8xkvREkTUNOojRNem5IiQfAfv5RqGSFGc-M8ZekmfxSGzAoyqSaWJGCR8lQREicltFuAiGvB_hdwx-3n4DkYgrg/s1600/coronavirus-2.tmb-479v.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3v7-fM3AG8yOyM_NPkvg216Etm9s91knBdM4BF1wOM8j9UHKQJNf3SXJkYrkq2NhkQcVZZNxG2cl84swSHQE6zlVj8xkvREkTUNOojRNem5IiQfAfv5RqGSFGc-M8ZekmfxSGzAoyqSaWJGCR8lQREicltFuAiGvB_hdwx-3n4DkYgrg/s1600/coronavirus-2.tmb-479v.jpg"></a></div>
<a href="https://theconversation.com/havent-had-covid-yet-it-could-be-more-than-just-luck-181708">Haven't had COVID yet? It could be more than just luck</a><br>
<br>
There are some scary questions for creationists at the end of this article. They follow on naturally from what's being discussed, so creationists should probably avoid reading too far, unless they have a responsible adult with them.<br>
<br>
This article from <i>The Conversation</i> is from May 2022, when we were into the second year of the COVID-19 pandemic and most vulnerable people had had the two-step vaccinations and many would have had the spring booster. At that point neither me nor my partner had had COVID-19, which we put down to rigorously following the recommendations regarding mask-wearing, social distancing, hand washing, etc. and had tried to reduce our vulnerability to the sever forms of it by losing about 3 stone in weight and, in my case, getting my blood pressure under control with medication. We also tried to ensure our immune systems were healthy by taking vitamin D3, vitamin C, zinc and iron supplements. <br>
<br>
In the early days of the pandemic, even before the official restrictions on social contact, we had observed the basic rules of hygiene and everyone who came into the house used hand-cleanser at the front door. I had even managed to obtain a supply of face-masks and plastic gloves online, which we wore at all times outside the house. Every package that was delivered to the house was left for several hours before we touched it, and all our weekly shopping was delivered or bought with click and collect. Delivered bags were left for four hours before unpacking. And we took weekly tests just in case we had it asymptomatically. All that might seem a little over the top now, but we were vindicated as events were to prove.<br>
<br>
We put the fact that we hadn't caught it by mid-2022 down to our preventative measures, not to luck or genetics - a view that was vindicated last year when we both came back from a two-week vacation in France with a mild form of COVID-19, despite having had all the boosters on offer. We probably picked it up in a crowded airport or on the plane, where all the social distancing measures had been forgotten and even face masks were no longer worn. We both felt like we had a mild case of flu for a couple of days and after a week we were testing negative. Had we contracted it in Spring 2020, the outcome would probably have been very different as we had no immunity, and both had three of the risk-factors - overweight, high BP and over 70. In addition, my partner had had a mastectomy and was receiving treatment for breast cancer.<br>
<br>
One reason you can't ever be sure that you won't catch COVID-19 is because the virus keeps mutating to produce new variants so, even <b>if</b> you were fortunate enough to have natural or acquired immunity to the variants so far, it is quite possible that the next or subsequent variants will have evolved a way round it. The following chart from the UK NHS, shows the rise and fall of the main variants over the course of the pandemic:<br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjx9jQsFKASY7uUsuf_g0UeEALpZVvfYP_HnQvsikyEfpvbpENsPKiHDVH7Knz-YcYn7OTzaeTQZRBA87IhFCqQeUllw9XU666tVyZ85TrPz39dx1nBxpBQ2NzwRey7K-v5Wff7MFOVxiST47ERaYDPzxO_4qmaQd4rwCDlsHAKvRskRqK4m8wvmfjETNhy/s1600/Screenshot%202024-03-09%20233717.png"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjx9jQsFKASY7uUsuf_g0UeEALpZVvfYP_HnQvsikyEfpvbpENsPKiHDVH7Knz-YcYn7OTzaeTQZRBA87IhFCqQeUllw9XU666tVyZ85TrPz39dx1nBxpBQ2NzwRey7K-v5Wff7MFOVxiST47ERaYDPzxO_4qmaQd4rwCDlsHAKvRskRqK4m8wvmfjETNhy/s1600/Screenshot%202024-03-09%20233717.png"/></a>
<div class="caption"><div class="credit">Source: <a href="https://ukhsa-dashboard.data.gov.uk/topics/covid-19" target="_blank">NHS UKHSA Date Dashboard</a></div>
</div></div>
But still, a few people managed to stay free from the virus. In the following article, reprinted from <i>The Conversation</i> under a Creative Commons license, Lindsay Broadbent, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, explains why. Her article has been reformatted for stylistic consistency:
<a name='more'></a>
<div style="border: solid Black 2px; border-radius: 20px; background-color:cornsilk; padding: 1em; color: DarkBlue; margin: 1em 0 1em">
<a href="https://theconversation.com/uk"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtjgccyP-2wbUH2Pszt5rI3PWgttFGwpL9WZ_WWd6fpCQwbP8-oPCQljiwUUDw0VjsQame1hi9fdoaVNUUXb0A67wF5AIcrzI9bcME2uudgqtMVhobCp5liwk-xNkVT3cMfq-S1hjF6hfUfUc9hFjZwIAHaVGiHFJoonPnhldia8zGGFkCYcEfMOgDIg/s1600/logo-horizontal-en-df7faf4238d541b16db76bba081fdd73.png" width="33%"/></a><br>
<time datetime="2022-05-18T15:16:24Z">Published: May 18, 2022 4.16pm BST</time><br>
<br>
<div class="title-box" style="background-image: url(https://images.theconversation.com/files/463952/original/file-20220518-11-i1zy58.jpg)"><span class="outlined-text">Haven’t had COVID yet? It could be more than just luck</span><div class="caption"><div class="credit">I Wei Huang/Shutterstock</div></div>
</div><br>
<a href="https://theconversation.com/profiles/lindsay-broadbent-1009352">Lindsay Broadbent</a>, <i><a href="https://theconversation.com/institutions/queens-university-belfast-687">Queen's University Belfast</a></i><br>
<br>
We all know a few of those lucky people who, somehow, have managed to avoid ever catching COVID. Perhaps you’re one of them. Is this a Marvel-esque superpower? Is there any scientific reason why a person might be resistant to becoming infected, when the virus seems to be everywhere? Or is it simply luck?<br><br>
More than <a href="https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19latestinsights/infections#infections">60% of people</a> in the UK have tested positive for COVID at least once. However, the number of people who have actually been infected with SARS-CoV-2, the virus that causes COVID-19, is thought to be higher. The calculated rate of <a href="https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2787098">asymptomatic infections</a> varies depending on the study, though most agree it’s fairly common. <br><br>
But even taking into account people who have had COVID and not realised it, there is still likely a group of people who never have. The reason why some people appear immune to COVID is one question that has persisted throughout the pandemic. As with so much in science, there isn’t (yet) one simple answer. <br><br>
We can probably dismiss the Marvel-esque superpower theory. But science and luck likely both have a role to play. Let’s take a look.<br><br>
The simplest explanation is that these people have never come into contact with the virus.<br><br>
This could certainly be the case for people who have been shielding during the pandemic. People at <a href="https://www.bmj.com/content/369/bmj.m1985">significantly greater risk</a> of severe disease, such as those with chronic heart or lung conditions, have had a tough couple of years. <br><br>
Many of them continue to take precautions to avoid potential exposure to the virus. Even with additional safety measures, many of these people have ended up with COVID. <br><br>
Due to the high level of community transmission, particularly with the extremely transmissible omicron variants, it’s very unlikely that someone going to work or school, socialising and shopping hasn’t been near someone infected with the virus. Yet there are people who have experienced high levels of exposure, such as hospital workers or family members of people who have had COVID, who have somehow managed to avoid testing positive.<br><br>
We know from several studies vaccines not only reduce the risk of severe disease, but they can also cut the chance of household transmission of SARS-CoV-2 by <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262621/">about half</a>. So certainly vaccination could have helped some close contacts avoid becoming infected. However, it’s important to note that these studies were done pre-omicron. The data we have on the effect of vaccination on omicron transmission is still limited.<br>
<div class="readmore"><a href="https://theconversation.com/four-strange-covid-symptoms-you-might-not-have-heard-about-181217">Four strange COVID symptoms you might not have heard about</a></div>
<span class="t2">Some theories</span><br><br>
One theory around why certain people have avoided infection is that, although they are exposed to the virus, it fails to establish an infection even after gaining entry to the airways. This could be due to a lack of the <a href="https://www.nature.com/articles/s41588-021-01006-7">receptors needed</a> for SARS-CoV-2 to gain access to cells.<br><br>
Once a person does become infected, researchers have identified that differences in the <a href="https://www.sciencedirect.com/science/article/pii/S1931312820302365?via%3Dihub">immune response</a> to SARS-CoV-2 play a role in determining the <a href="https://www.nature.com/articles/s41586-020-2588-y">severity of symptoms</a>. It is possible that a quick and robust immune response could prevent the virus from replicating to any great degree in the first instance.<br><br>
The efficacy of our immune response to infection is largely defined by our age and our <a href="https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0568-8">genetics</a>. That said, a healthy lifestyle certainly helps. For example, we know that <a href="https://pubmed.ncbi.nlm.nih.gov/16497887/">vitamin D deficiency</a> can increase the risk of certain infections. Not getting <a href="https://www.nature.com/articles/s42003-021-02825-4">enough sleep</a> can also have a detrimental effect on our body’s ability to fight invading pathogens.<br><br>
<div class="panelplain" style="margin: 1em auto"><img alt="An illustration of SARS-CoV-2, the coronavirus that causes COVID-19." src="https://images.theconversation.com/files/463953/original/file-20220518-19-cupowl.jpg">
<div class="captionc">The SARS-CoV-2 virus needs to attach to receptors to gain access to our cells.
<div class="credit"><a href="https://www.shutterstock.com/image-illustration/sarscov2-viruses-binding-ace2-receptors-on-1687909009">Kateryna Kon/Shutterstock</a>
</div>
</div>
</div>
Scientists studying the <a href="https://www.covidhge.com/">underlying causes</a> of severe COVID have identified a genetic cause in nearly <a href="https://covid19.nih.gov/news-and-stories/decoding-genetics-behind-covid19-infection">20% of critical cases</a>. Just as genetics could be one determining factor of disease severity, our genetic makeup may also hold the key to resistance to SARS-CoV-2 infection.<br><br>
I research SARS-CoV-2 infection on nasal cells from human donors. We grow these cells on plastic dishes which we can then add virus to and investigate how the cells respond. During our research we found one donor whose cells <a href="https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0266412">could not be infected</a> with SARS-CoV-2.<br><br>
We discovered some really interesting genetic mutations, including several involved with the body’s immune response to infection, that could explain why. A mutation we identified in a gene involved with sensing the presence of a virus has previously been shown to confer <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001117/">resistance to HIV</a> infection. Our research is on a small number of donors and highlights that we’re still only scraping the surface of research into genetic susceptibility or resistance to infections. <br><br>
There’s also the possibility that previous infection with other types of coronaviruses results in <a href="https://www.nature.com/articles/s41467-021-27674-x">cross-reactive immunity</a>. This is where our immune system may recognise SARS-CoV-2 as being similar to a recent invading virus and launch an immune response. There are <a href="https://theconversation.com/coronaviruses-a-brief-history-135506">seven coronaviruses</a> that infect humans: four that cause the common cold, and one each that cause Sars (severe acute respiratory syndrome), Mers (Middle East respiratory syndrome) and COVID.<br><br>
How long-lasting this immunity may be is another question. Seasonal coronaviruses that circulated pre-2020 were able to <a href="https://www.nature.com/articles/s41591-020-1083-1">reinfect</a> the same people after 12 months. <br>
<div class="readmore"><a href="https://theconversation.com/the-common-cold-might-protect-you-from-coronavirus-heres-how-158461">The common cold might protect you from coronavirus – here's how</a></div>
If you’ve managed to avoid COVID to date, maybe you do have natural immunity to SARS-CoV-2 infection, or perhaps you’ve just been lucky. Either way, it’s sensible to continue to take precautions against this virus that we still know so little about.<br>
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<a href="https://theconversation.com/profiles/lindsay-broadbent-1009352">Lindsay Broadbent</a>, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, <i><a href="https://theconversation.com/institutions/queens-university-belfast-687">Queen's University Belfast</a></i><br><br>
This article is republished from <a href="https://theconversation.com">The Conversation</a> under a Creative Commons license. Read the <a href="https://theconversation.com/havent-had-covid-yet-it-could-be-more-than-just-luck-181708">original article</a>.<br><br>
<div class="creditl"><a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Published by <i>The Conversation</i>.<br>Open access. <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">(CC BY 4.0)</a></div>
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There are a few points for creationists to be made here:<br>
<ol class="dbl1 bold">
<li><b>If</b> the virus had been even more deadly and if medical science had not come up with a vaccine, would you expect the proportion of the population who have a natural immunity to increase, decrease or remain the same? That's how natural selection works!</li>
<li>If there were such a thing as a benevolent, intelligent designer at work, why did it only give a small number of people this ability to avoid becoming infected with coronaviruses, when, had it so chosen, it could have given that ability to all of us?</li>
<li>Why, in the arms race between the virus and medical science, if you believe in intelligent design rather than evolution, does it look like a designer is on the side of the virus in that it designs a new version of the SARS-CoV-2 virus every few weeks, while medical scientists work to keep up with it?</li>
</ol>
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<div class="panelplain" style="padding: 1em; margin: 0; height: 675px"><br><center><span class="t2">The Unintelligent Designer: Refuting The Intelligent Design Hoax</span></center><br>
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<div class="right-column" style="flex: 1.5">ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.<br>
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<div class="panelplain" style="padding: 1em; margin: 0; height: 675px"><br><center><span class="t2">Ten Reasons To Lose Faith: And Why You Are Better Off Without It</span></center><br>
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<div class="left-column" style="flex: 1"><a target="_blank" href="https://www.amazon.com/dp/1530431956?&_encoding=UTF8&tag=rosarub-20&linkCode=ur2&linkId=ee7df9227d554e95c07dabb677ac7650&camp=1789&creative=9325"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjV7ys1fJWghEiilpJ-ltMJKBAJGIccmbAZHatW48ji6wV00OOyX2aTagxdjUJMDIeIoLfe-xl4tCh7QX1FXsLJdQDrrVmY5yZWZ-ihUuy1-ZXPsWpESwI1kJdO2NDA5B63OgxUFXG4HsODIi-kCkNHIpeCFxeFpv7BUfOjbMxE-9BLLH51VwZtx1OsU1VN/s1600/Ten_Reasons_To_Lose__Cover_for_Kindle%20%283%29.jpg"/></a>
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<div class="right-column" style="flex: 1.5">This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.<br>
<br>
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
<br />
Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-81104038889702960262024-03-09T20:34:00.041+00:002024-03-09T20:53:19.082+00:00Creationism in Crisis - Geobiologists Discover The Cause of Earth's First Mass Extinctions Event - 550 Million Years Before 'Creation Week'<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox" style="gap: 0">
<div class="left-column" style="text-align: left; flex: 2">Impressions of the Ediacaran fossils Dickinsonia (at center) with the smaller anchor shaped Parvancorina (left) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia. </div>
<div class="right-column" style="text-align: right; flex: 1">Photo: Scott Evans.</div>
</div>
</div><br>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg78jq-XMaSB3gJpHF2Ddk_5s7PnQ1LjLfnfENL7QRRUMZBQOrjuOZkAOAm9yXSbXL0cUcsAeSzwb0GewFSug_MPhsXikYy-ILDreBOp1V_SvAEODKX4bUdqIqYv6dPvHe2bGp160vACuF_jW2JWs13lBLDUNAqxtp476nSuYrZCax1Vsixu1Uq9HQl_g/s1600/image.jpg" ><img alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg78jq-XMaSB3gJpHF2Ddk_5s7PnQ1LjLfnfENL7QRRUMZBQOrjuOZkAOAm9yXSbXL0cUcsAeSzwb0GewFSug_MPhsXikYy-ILDreBOp1V_SvAEODKX4bUdqIqYv6dPvHe2bGp160vACuF_jW2JWs13lBLDUNAqxtp476nSuYrZCax1Vsixu1Uq9HQl_g/s1600/image.jpg"/></a><div class="caption">Impressions of the Ediacaran fossils Dickinsonia (at center) with the smaller anchor shaped Parvancorina (left) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia. <br>
<div class="credit">Photo: Scott Evans.</div></div></div>
<a href="https://vtx.vt.edu/articles/2022/11/science-ediacaran_first_mass_extinction_event_scott_evans.html">Geobiologists shine new light on Earth’s first known mass extinction event 550 million years ago | VTx | Virginia Tech</a><br>
<br>
A big problem for Creationists, especially those who believe the Bible was written by an infallible creator god, so think Earth is just a few thousand years old, is that science keeps finding evidence that Earth is billions of years old, and finding fossils of the life-forms that were around then.<br>
<br>
As though that wasn't refutation enough, a team of scientists from Virginia Tech have now explained the mass extinction that wiped out most of these early life forms several billion years ago - giving the lie that they were intelligently designed by a god with the ability of foresight. Such a god would have known about the future mass extinctions and either prevented it, designed his creations to survive it or at least waited till it was safe to create things. Creating things to go extinct is not the act of an intelligent or sane creator.<br>
<br>
This mass extinction appears not to have been a sudden event, such as that that resulted in the extinction of the non-avian dinosaurs and large marine reptile predators, but to have occurred in two phases that resulted in a loss of about 80% of species and separated by about 10 million years.<br>
<br>
But before creationists get over-excited, this does not mean all the Ediacarans were extinct at the Cambrian 'explosion' so the Cambrian biota had no ancestors. It means that there were still about 20% of the Ediacaran biota to evolve over the 6 million years of the Cambrian 'explosion' into the Cambrian biota.<br>
<br>
The Ediacaran mass extinction was probably caused by falling Oxygen levels as Ediacarans that had evolved large mass to surface-area ratios suffered from a loss of oxygen more so than those which had retained a smaller mass to surface area ratio. <br>
<br>
How this mass extinction was identified and related to changes in global oxygen levels was the subject of an open access paper in PNAS and a Virginal Tech News item:<br>
<blockquote class="blockit">A new study by Virginia Tech geobiologists traces the cause of the first known mass extinction of animals to decreased global oxygen availability, leading to the loss of a majority of animals present near the end of the Ediacaran Period some 550 million years ago.<br>
<br>
The research spearheaded by Scott Evans, a postdoctoral researcher in the Department of Geosciences, part of the Virginia Tech College of Science, shows this earliest mass extinction of about 80 percent of animals across this interval.
<div class="block"><p>This included the loss of many different types of animals, however those whose body plans and behaviors indicate that they relied on significant amounts of oxygen seem to have been hit particularly hard. This suggests that the extinction event was environmentally controlled, as are all other mass extinctions in the geologic record.</p>
<div class="creditl">Dr Scott D. Evans, lead author<br>
Department of Geosciences<br>
Virginia Tech, Blacksburg, VA, USA</div></div>
Evans’ work was published today [7 November 2022] in the Proceedings of the National Academy of Sciences, a peer-reviewed journal of the National Academy of Sciences. The study was co-authored by Shuhai Xiao, also a professor in the Department of Geosciences, and several researchers led by Mary Droser from the University of California Riverside’s Department of Earth and Planetary Sciences, where Evans earned his master’s degree and Ph.D.<br>
<div class="block" class="bottom-margin: 0"><p>Environmental changes, such as global warming and deoxygenation events, can lead to massive extinction of animals and profound disruption and reorganization of the ecosystem. This has been demonstrated repeatedly in the study of Earth history, including this work on the first extinction documented in the fossil record. This study thus informs us about the long-term impact of current environmental changes on the biosphere.</p>
<div class="creditl">Shuhai Xiao, co-author<br>
Department of Geosciences<br>
Virginia Tech, Blacksburg, VA, USA.</div></div>
<div class="block"><p>[What exactly caused the drop in global oxygen?] The short answer to how this happened is we don't really know. It could be any number and combination of volcanic eruptions, tectonic plate motion, an asteroid impact, etc., but what we see is that the animals that go extinct seem to be responding to decreased global oxygen availability.</p>
<div class="creditl">Dr Scott D. Evans</div></div>The study by Evans and Xiao is timelier than one would think. In an unconnected study, Virginia Tech scientists recently found that anoxia, the loss of oxygen availability, is affecting the world’s fresh waters. The cause? The warming of waters brought on by climate change and excess pollutant runoff from land use. Warming waters diminish fresh water’s capacity to hold oxygen, while the breakdown of nutrients in runoff by freshwater microbes gobbles up oxygen.
<div class="block"><p>Our study shows that, as with all other mass extinctions in Earth's past, this new, first mass extinction of animals was caused by major climate change — another in a long list of cautionary tales demonstrating the dangers of our current climate crisis for animal life/</p>
<div class="creditl">Dr Scott D. Evans</div></div>
Some perspective: The Ediacaran Period spanned roughly 96 million years, bookended on either side by the end of Cryogenian Period — 635 million years ago — and the beginning of the Cambrian Period — 539 million years ago. The extinction event comes just before a significant break in the geologic record, from the Proterozoic Eon to the Phanerozoic Eon.<br>
<br>
There are five known mass extinctions that stand out in the history of animals, the “Big Five,” according to Xiao, including the Ordovician-Silurian Extinction (440 million years ago), the late Devonian Extinction (370 million years ago), the Permian-Triassic Extinction (250 million years ago), the Triassic-Jurassic Extinction (200 million years ago), and the Cretaceous-Paleogene Extinction (65 million years ago).<br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicEYeUuu_j8Zg1bIEwMURjVQ9uM8GDtbrH5oqS6UlNosw-Z5qz8NlPhQXEgd5tHs24LGPs-lIWQk47ic0LZsj45Ro2QXFYHJ6PjBCEgKiogrpGzFv5MfekSSi2F8KCsUjkcDz4nSE3XdyaQya_RM1quoW0wuUg9ukqQX2vUovd8mcGCb2sAoW3lqhXkc1L/s1600/image.jpeg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicEYeUuu_j8Zg1bIEwMURjVQ9uM8GDtbrH5oqS6UlNosw-Z5qz8NlPhQXEgd5tHs24LGPs-lIWQk47ic0LZsj45Ro2QXFYHJ6PjBCEgKiogrpGzFv5MfekSSi2F8KCsUjkcDz4nSE3XdyaQya_RM1quoW0wuUg9ukqQX2vUovd8mcGCb2sAoW3lqhXkc1L/s1600/image.jpeg"/></a><br>
<div class="caption">Impressions of the Ediacaran fossils Dickinsonia (at left) and related but rare form Andiva (at right) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.<br><div class="credit">Photo courtesy of Scott Evans.</div></div>
</div><br>
“Mass extinctions are well recognized as significant steps in the evolutionary trajectory of life on this planet,” Evans and team wrote in the study. Whatever the instigating cause of the mass extinction, the result was multiple major shifts in environmental conditions. “Particularly, we find support for decreased global oxygen availability as the mechanism responsible for this extinction. This suggests that abiotic controls have had significant impacts on diversity patterns throughout the more than 570 million-year history of animals on this planet,” the authors wrote.<br>
<br>
Fossil imprints in rock tell researchers how the creatures that perished in this extinction event would have looked. And they looked, in Evans’ words, “weird.”
<div class="block"><p>These organisms occur so early in the evolutionary history of animals that in many cases they appear to be experimenting with different ways to build large, sometimes mobile, multicellular bodies. There are lots of ways to recreate how they look, but the take-home is that before this extinction the fossils we find don't often fit nicely into the ways we classify animals today. Essentially, this extinction may have helped pave the way for the evolution of animals as we know them.</p>
<div class="creditl">Dr Scott D. Evans</div></div>
The study, like scores of other recent publications, came out of the COVID-19 pandemic. Because Evans, Xiao, and their team couldn't get access to the field, they decided to put together a global database based mostly on published records to test ideas about changing diversity. “Others had suggested that there might be an extinction at this time, but there was a lot of speculation. So we decided to put together everything we could to try and test those ideas.” Evans said. Much of the data used in the study was collected by Droser and several graduate students from the University of California Riverside.<br>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfqw2Pnx9m309V9WJYpClsqmdWRLUZ93RVInTApxYjwAjCdNteO6OuctZ563migFxvJJNb0JJae9ra0IUpxCuv95_JC424ABZ-ETst-1BRUZo3ZaLTPa9qlf0IPxnEdfOZK4cWJT2MZ3lAUiWKTZwAwNFyfNQqAz8Dqgij48IEaLSaUQAQdr1lKSdJWhRl/s1600/image%20%281%29.jpeg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfqw2Pnx9m309V9WJYpClsqmdWRLUZ93RVInTApxYjwAjCdNteO6OuctZ563migFxvJJNb0JJae9ra0IUpxCuv95_JC424ABZ-ETst-1BRUZo3ZaLTPa9qlf0IPxnEdfOZK4cWJT2MZ3lAUiWKTZwAwNFyfNQqAz8Dqgij48IEaLSaUQAQdr1lKSdJWhRl/s1600/image%20%281%29.jpeg"/></a>
<div class="caption">Impressions of the Ediacaran fossil Dickinsonia, one of the first mobile animals, in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia."><div class="credit">Photo courtesy of Scott Evans.</div></div>
</div>
</blockquote>
Technical details is in the team's open access paper on PNAS:
<blockquote class="blockit"><span>Significance</span><br>
Mass extinctions are well recognized as significant steps in the evolutionary trajectory of life on this planet. Here, we document the oldest known extinction of animals and test for potential causes. Our results indicate that, like younger diversity crises, this event was caused by major shifts in environmental conditions. Particularly, we find support for decreased global oxygen availability as the mechanism responsible for this extinction. This suggests that abiotic controls have had significant impacts on diversity patterns throughout the more than 570-My history of animals on this planet.<br>
<br>
<span>Abstract</span><br>
<br>
The Ediacara Biota—the oldest communities of complex, macroscopic fossils—consists of three temporally distinct assemblages: the Avalon (ca. 575–560 Ma), White Sea (ca. 560–550 Ma), and Nama (ca. 550–539 Ma). Generic diversity varies among assemblages, with a notable decline at the transition from White Sea to Nama. Preservation and sampling biases, biotic replacement, and environmental perturbation have been proposed as potential mechanisms for this drop in diversity. Here, we compile a global database of the Ediacara Biota, specifically targeting taphonomic and paleoecological characters, to test these hypotheses. Major ecological shifts in feeding mode, life habit, and tiering level accompany an increase in generic richness between the Avalon and White Sea assemblages. We find that ∼80% of White Sea taxa are absent from the Nama interval, comparable to loss during Phanerozoic mass extinctions. The paleolatitudes, depositional environments, and preservational modes that characterize the White Sea assemblage are well represented in the Nama, indicating that this decline is not the result of sampling bias. Counter to expectations of the biotic replacement model, there are minimal ecological differences between these two assemblages. However, taxa that disappear exhibit a variety of morphological and behavioral characters consistent with an environmentally driven extinction event. The preferential survival of taxa with high surface area relative to volume may suggest that this was related to reduced global oceanic oxygen availability. Thus, our data support a link between Ediacaran biotic turnover and environmental change, similar to other major mass extinctions in the geologic record.<br>
<br>
Soft-bodied fossils of the Ediacara Biota comprise the oldest communities of macroscopic organisms, including animals, and are critical for understanding the advent and diversification of complex life (<a class="newtooltip">1</a>, <a class="newtooltip">2</a>). However, equally important are the dynamics that lead to the disappearance of such animals (<a class="newtooltip">3</a>–<a class="newtooltip">6</a>). Two major drops in diversity of the Ediacara Biota have been recognized, an initial decrease between the White Sea and Nama assemblages and a second across the Ediacaran–Cambrian boundary (Fig. 1 and ref. (<a class="newtooltip">5</a>)). Although these events may be related, they are separated by more than 10 My and vary in magnitude and taxa impacted. The exceptional conditions required to preserve the Ediacara Biota also leave uncertainty around potential taphonomic biases that may contribute to such patterns. Diversity crises shaped the course of evolution in the Phanerozoic. Thus, a comprehensive understanding of each of these Ediacaran events is critical to determine the fate of Earth’s early animals.
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmyI5rdq7KxOSOevvuQrijvL4VYpyAXXnpovbpX9Om3JJng6AgXp-qOQxTidxOhUt3Fwmixu9IVop_KDfnqN4vYfXKjbaFU3BXHTScKHZMdVsjDj841s6PkWLh-P1Sdn_3EHHWBMunEg5bCjpThbc82jpYiIOvKwGIbpxyHyHFfsSKooW9pg8KH3Z1LJer/s1600/pnas.2207475119fig01.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmyI5rdq7KxOSOevvuQrijvL4VYpyAXXnpovbpX9Om3JJng6AgXp-qOQxTidxOhUt3Fwmixu9IVop_KDfnqN4vYfXKjbaFU3BXHTScKHZMdVsjDj841s6PkWLh-P1Sdn_3EHHWBMunEg5bCjpThbc82jpYiIOvKwGIbpxyHyHFfsSKooW9pg8KH3Z1LJer/s1600/pnas.2207475119fig01.jpg"/></a><div class="caption">Raw generic diversity (black squares), bootstrapped diversity (gray triangles), bootstrapped (<a class="newtooltip">42</a>) per taxon extinction rate (solid blue), and origination rate (dashed green). Error bars represent 1 SD. For bootstrapping analysis, database occurrences were randomly subsampled to 50 occurrences.</div>M</div>
Similar mechanisms have been proposed for losses of diversity during both the White Sea–Nama and Ediacaran–Cambrian transitions. One suggestion is that taxa did not go extinct but instead are not preserved in subsequent intervals (the “Cheshire cat” model of ref. (<a class="newtooltip">3</a>)). Biases may include differences in the paleolatitudes and paleoenvironments sampled as well as variable taphonomic windows preserving fossils from each assemblage (<a class="newtooltip">7</a>). Alternatively, these events may represent true extinctions triggered by either biotic or abiotic factors or some combination thereof (<a class="newtooltip">3</a>, <a class="newtooltip">5</a>). The biotic replacement model, generally attributing the demise of the Ediacara Biota to competition with more advanced “Cambrian-style” metazoans, focuses on the impact of bioturbators as indicated by increases in trace fossil diversity (e.g., ref. (<a class="newtooltip">8</a>)). Such ecosystem engineers are proposed to have fundamentally changed carbon packaging and fluid transport in the latest Ediacaran (<a class="newtooltip">3</a>, <a class="newtooltip">4</a>, <a class="newtooltip">8</a>–<a class="newtooltip">10</a>). Alternatively, the catastrophic extinction model posits that a major environmental perturbation led to the rapid loss of a variety of Ediacara taxa (<a class="newtooltip">3</a>, <a class="newtooltip">5</a>) supported by geochemical data for environmental conditions, such as changes in oxygen availability (e.g., ref. (<a class="newtooltip">11</a>)).<br><br>
<br>
Here, we use a holistic approach, combining the distribution, taphonomy, and ecology of constituent taxa, to investigate changes in the Ediacara Biota through compilation of global occurrence data. Specifically, we test for potential sampling biases in the form of major differences in the paleolatitudes, facies associations, or preservational modes that could account for apparent changes in taxonomic composition. Based on the lack of correlation between these factors, we then investigate paleoecological trends through the Ediacaran under the assumption that, as with other diversity crises in the fossil record (<a class="newtooltip">12</a>), patterns of selectivity across these intervals should reflect the factors responsible for such change. Analysis was conducted by comparing differences between the three assemblages—necessarily representing time-averaged groups of organisms on the order of millions to tens of millions of years—as in previous studies (e.g., refs. (<a class="newtooltip">3</a>, <a class="newtooltip">5</a>, <a class="newtooltip">13</a>)). However, we also examined patterns of change involving taxa that survived and went extinct at the end of the White Sea assemblage to investigate changes on relatively shorter geologic timescales.<br>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTm9KItVVqSKDd8_A0z80MnuB8vi1MkPvz-T04WqQOVGR6YTJgxhcYKpHddIQnIzMDO3fPZ7yXUvH7UhdM07p_A6D_k3gn4W7U1lYwI58COaA5tPuf6LIEBGyAmhJFbVajs61j8ee0bFJIp2mPgLCjmyD3B4g3Dcerogkkx25baMYgl5fQuTvsrjrwBC6t/s1600/pnas.2207475119fig02.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTm9KItVVqSKDd8_A0z80MnuB8vi1MkPvz-T04WqQOVGR6YTJgxhcYKpHddIQnIzMDO3fPZ7yXUvH7UhdM07p_A6D_k3gn4W7U1lYwI58COaA5tPuf6LIEBGyAmhJFbVajs61j8ee0bFJIp2mPgLCjmyD3B4g3Dcerogkkx25baMYgl5fQuTvsrjrwBC6t/s1600/pnas.2207475119fig02.jpg"/></a>
<div class="caption"><b>Fig. 2.</b> Paleogeographic distribution of fossil localities (A) within the three assemblages of the Ediacara Biota based on continental configurations by Merdith et al. (<a class="newtooltip">14</a>) and pie charts with the distribution of paleoenvironments (B) and modes of preservation (C) sampled for each assemblage, with “n” referring to the No. of formations/facies sampled in each time bin. See <a href="https://www.pnas.org/doi/10.1073/pnas.2207475119#supplementary-materials" target="_blank">SI Appendix, Fig. S1</a> for locality labels.</div>
</div>
<div class="creditl"><a href="https://www.pnas.org/eprint/NQ798P8DYI4SKEAQEWAQ/full" target="_blank">Evans, Scott D.; Tu, Chenyi; Rizzo, Adriana; Surprenant, Rachel L.; Boan, Phillip C.; McCandless, Heather; Marshall, Nathan; Xiao, Shuhai; Droser, Mary L.<br>
Environmental drivers of the first major animal extinction across the Ediacaran White Sea-Nama transition<br>
Proceedings of the National Academy of Sciences (PNAS) <b>119</b> 46, e2207475119, DOI: 10.1073/pnas.2207475119.</a></div>
</blockquote>
Mass extinctions alone are enough to refute the childish notion of creation by an omniscient designer, let alone an intelligent one, and of course one reason the Ediacaran biota doesn't get a mention in the Bible is because, like all the other extinct taxons, the primitive Bronze Age authors had not got the slightest idea that they ever existed or that Earth was old enough to have gone through several major geological era lasting hundreds of millions of years, and several mass extinctions which had wiped out most of the earlier species or they wouldn't have assumed everything was magically created as it was then, But then they only had what little knowledge their culture possessed out of which to concoct a believable story.
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-74576080340300046682024-03-09T14:21:00.001+00:002024-03-09T14:21:45.108+00:00Creationism in Crisis - Earth's Oldest Forest Was In Present-Day Dorset, UK - 390 Million Years Before Creationism's 'Creation Week'<div class="title-box" style="height: 810px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox" style="color: black">
<div class="left-column" style="text-align: left">Illustration of <i>Calamophyton</i> trees.</div>
<div class="right-column" style="text-align: right">Credit: Peter Giesen/Chris Berry</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf8WnVy-Of_Zx3aYchhQ8Dga6WZ_7kpopZPiUT6rk7h5HydDJafxtQKAJT02Vh5uhbXmMYriBhBElu56oFUxGY519_LPcoiHDcxkllqMIzuudACFu9Ve4a4yDmAlPJlq1c3lmQZvRRFeSUVjU09Dm5TNikxi8Lsv3qCKE6WbMUHfpIuJmIjkzQcDDgkbbl/s1600/CroppedTrees.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf8WnVy-Of_Zx3aYchhQ8Dga6WZ_7kpopZPiUT6rk7h5HydDJafxtQKAJT02Vh5uhbXmMYriBhBElu56oFUxGY519_LPcoiHDcxkllqMIzuudACFu9Ve4a4yDmAlPJlq1c3lmQZvRRFeSUVjU09Dm5TNikxi8Lsv3qCKE6WbMUHfpIuJmIjkzQcDDgkbbl/s1600/CroppedTrees.jpg"/></a></div>
<div class="rpanel450plain"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjj4ooJ_iNxGgqEtDIEugz4rVAywv2lTL61S-w2V6I10BBC95HHSGqaB-oYVNYY5zQYg43IB6TKCcsVqIXhAAeJ1KavdNGrKxQUHIvVBo7oeBeBkb4mF-PqAI4MzaGtaAX1XE7rOvFSmUwS9saRlIY7OdUpZM_A21zdf0slfheqn5eDEmyhDm8Bu3XvEhJj/s1600/plant-13-sh-750x585.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjj4ooJ_iNxGgqEtDIEugz4rVAywv2lTL61S-w2V6I10BBC95HHSGqaB-oYVNYY5zQYg43IB6TKCcsVqIXhAAeJ1KavdNGrKxQUHIvVBo7oeBeBkb4mF-PqAI4MzaGtaAX1XE7rOvFSmUwS9saRlIY7OdUpZM_A21zdf0slfheqn5eDEmyhDm8Bu3XvEhJj/s1600/plant-13-sh-750x585.webp"/></a>
<div class="captionc">Cliffs of the Hangman Sandstone Formation, where many of the fossils were found.<br><div class="credit">Credit: Neil Davies</div></div>
</div>
<a href="https://www.cam.ac.uk/stories/earths-earliest-forest-somerset">Earth’s earliest forest revealed in Somerset fossils</a><br>
<br>
Archaeologists have found what are believed to be the remains of the earliest forest so far discovered in Devonian sandstone rocks dated to 390 million years ago, which makes them 4 million years older than the previous record found in New York State, and means they were living almost 390 million years before creationism's 'Creation Week' when their god decided to create a small flat planet with a dome over it, centered on the Middle East. <br>
<br>
The fossils were discovered in coastal cliffs near Minehead, Dorset, England in what is known as the Eifelian Hangman Sandstone Formation and consist of primitive trees which were ancestral to today's trees but looked more like palm trees. The discovery is the subject of a paper in the <i>Journal of the Geological Society</i> and a news release from the University of Cambridge, UK.<br>
<br>
First a little about this rock formation:
<a name='more'></a>
<blockquote class="ai">What information do you have on the Eifelian Hangman Sandstone Formation of Somerset and Devon, particularly how the dates were arrived at?
The Eifelian Hangman Sandstone Formation is a geological formation located in Somerset and Devon, England. It is part of the Old Red Sandstone sequence, which is known for its rich fossil record and significance in understanding the Devonian period. Here's some information about the formation and how its dates were determined:
<ol class="dbl1 bold">
<li><b>Formation Characteristics:</b> The Hangman Sandstone Formation is primarily composed of sandstones, siltstones, and mudstones, with occasional conglomerates. These sedimentary rocks were deposited during the Eifelian Age of the Middle Devonian period, approximately 393 to 388 million years ago.
<li><b>Dating Methods:</b> The age of the Hangman Sandstone Formation was determined using various dating techniques, including biostratigraphy, radiometric dating, and stratigraphic correlation.
<ul type="disc">
<li><b>Biostratigraphy:</b> Fossils found within the formation, such as brachiopods, conodonts, and microfossils, provide valuable clues for dating. By comparing the assemblage of fossils to those found in formations of known ages, geologists can estimate the relative age of the Hangman Sandstone Formation.
<li><b>Radiometric Dating:</b> Radiometric dating techniques, such as uranium-lead dating or potassium-argon dating, may be applied to volcanic ash layers within or above the formation. These methods provide absolute ages for specific layers, helping to refine the overall age estimate.
<li><b>Stratigraphic Correlation:</b> Geologists correlate the Hangman Sandstone Formation with other formations of known ages in neighboring regions or globally. By identifying similar lithological characteristics and fossil assemblages, they can establish the relative age of the formation within the geological timescale.
</ul></li>
<li><b>Regional Context:</b> The Hangman Sandstone Formation is part of a larger geological sequence known as the Devonian Old Red Sandstone. This sequence is well-studied globally, allowing for precise dating and correlation of individual formations based on their characteristics and fossil content.
</ol>
Overall, the age of the Hangman Sandstone Formation of Somerset and Devon was determined through a combination of biostratigraphy, radiometric dating, and stratigraphic correlation, providing insights into the geological history of the region during the Devonian period.
</blockquote>
<blockquote class="blockit"><span style="font-size: x-large">The oldest fossilised forest known on Earth – dating from 390 million years ago – has been found in the high sandstone cliffs along the Devon and Somerset coast of South West England.</span> <br>
<br>
The fossils, discovered and identified by researchers from the Universities of Cambridge and Cardiff, are the oldest fossilised trees ever found in Britain, and the oldest known fossil forest on Earth. This fossil forest is roughly four million years older than the previous record holder, which was found in New York State.<br>
<br>
The fossils were found near Minehead, on the south bank of the Bristol Channel, near what is now a Butlin’s holiday camp. The fossilised trees, known as <i>Calamophyton</i>, at first glance resemble palm trees, but they were a ‘prototype’ of the kinds of trees we are familiar with today. Rather than solid wood, their trunks were thin and hollow in the centre. They also lacked leaves, and their branches were covered in hundreds of twig-like structures.<br>
<br>
These trees were also much shorter than their descendants: the largest were between two and four metres tall. As the trees grew, they shed their branches, dropping lots of vegetation litter, which supported invertebrates on the forest floor.<br>
<br>
Scientists had previously assumed this stretch of the English coast did not contain significant plant fossils, but this particular fossil find, in addition to its age, also shows how early trees helped shape landscapes and stabilise riverbanks and coastlines hundreds of millions of years ago. The results are reported in the Journal of the Geological Society.<br>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqGVoiA731SNwEu1fmiFSBYg4f5fo0ciD0Y4eFRTy4k3W6otuKFEiiMJSFo2HT5iyGfS5kd7EDqkFKPSvo4swk8OP7pTsbwiSsAqtsw5f6TLjBBkvWi1Poc5c1tyue_-JEHfFNdEkseFOjZ8j524wLqA2YOqpSMqw7Rwj1HLdQZYLa0SNlO-1xf-BdcJBh/s1600/plant-9-sh-2560x1440.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqGVoiA731SNwEu1fmiFSBYg4f5fo0ciD0Y4eFRTy4k3W6otuKFEiiMJSFo2HT5iyGfS5kd7EDqkFKPSvo4swk8OP7pTsbwiSsAqtsw5f6TLjBBkvWi1Poc5c1tyue_-JEHfFNdEkseFOjZ8j524wLqA2YOqpSMqw7Rwj1HLdQZYLa0SNlO-1xf-BdcJBh/s1600/plant-9-sh-2560x1440.jpg"/></a>
<div class="captionc">Scientists standing beside a large fossil of a tree stump.</div>
</div>
The forest dates to the Devonian Period, between 419 million and 358 million years ago, when life started its first big expansion onto land: by the end of the period, the first seed-bearing plants appeared and the earliest land animals, mostly arthropods, were well-established.<br>
<div class="block"><p>The Devonian period fundamentally changed life on Earth. It also changed how water and land interacted with each other, since trees and other plants helped stabilise sediment through their root systems, but little is known about the very earliest forests.</p>
<div class="creditl">Professor Neil S. Davies, first author<br>
Department of Earth Sciences<br>
University of Cambridge, Cambridge, UK.</div></div>
The fossil forest identified by the researchers was found in the Hangman Sandstone Formation, along the north Devon and west Somerset coasts. During the Devonian period, this region was not attached to the rest of England, but instead lay further south, connected to parts of Germany and Belgium, where similar Devonian fossils have been found.<br>
<div class="block"><p>When I first saw pictures of the tree trunks I immediately knew what they were, based on 30 years of studying this type of tree worldwide. It was amazing to see them so near to home. But the most revealing insight comes from seeing, for the first time, these trees in the positions where they grew. It is our first opportunity to look directly at the ecology of this earliest type of forest, to interpret the environment in which <i>Calamophyton</i> trees were growing, and to evaluate their impact on the sedimentary system.</p>
<div class="creditl">Dr Christopher Berry, co-author from
School of Earth and Environmental Sciences<br>
Cardiff University, Wales, UK.</div></div>
<div class="panelplain" style="margin:1em auto"><iframe title="Photomodeler 1 - 3D model by godevonian1" allow="fullscreen *; xr-spatial-tracking *;" allowfullscreen="" src="https://iframely.shorthand.com/EGsgZoB"></iframe></div>
<div class="panelplain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsQM-lEbsdbW0wyt2lW4zG4vTLkwZ5rIWQsjOuUF87nMUHZ5SKOX6z7uIFAxC4Hryt8nOnk57mTTa-rs0RXLJo4us02gthBuaw8sRUYIVyenddDYjqEeBsey8pZE2Ye_Ufhmcitfba16AO_HHWFXPRJ2NnhIJMF2prnSUPkQUOpHeR_4AZojJxY8qG1h2I/s1600/Small%20arthropod%20tracks.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsQM-lEbsdbW0wyt2lW4zG4vTLkwZ5rIWQsjOuUF87nMUHZ5SKOX6z7uIFAxC4Hryt8nOnk57mTTa-rs0RXLJo4us02gthBuaw8sRUYIVyenddDYjqEeBsey8pZE2Ye_Ufhmcitfba16AO_HHWFXPRJ2NnhIJMF2prnSUPkQUOpHeR_4AZojJxY8qG1h2I/s1600/Small%20arthropod%20tracks.jpg"/></a>
<div class="captionc">Small arthropod tracks</div></div>
The fieldwork was undertaken along the highest sea cliffs in England, some of which are only accessible by boat, and revealed that this sandstone formation is rich with plant fossil material from the Devonian period. The researchers identified fossilised plants and plant debris, fossilised tree logs, traces of roots and sedimentary structures, preserved within the sandstone. During the Devonian, the site was a semi-arid plain, crisscrossed by small river channels spilling out from mountains to the northwest.<br>
<div class="block"><p>This was a pretty weird forest – not like any forest you would see today. There wasn’t any undergrowth to speak of and grass hadn’t yet appeared, but there were lots of twigs dropped by these densely-packed trees, which had a big effect on the landscape.</p>
<p>The evidence contained in these fossils preserves a key stage in Earth’s development, when rivers started to operate in a fundamentally different way than they had before, becoming the great erosive force they are today. People sometimes think that British rocks have been looked at enough, but this shows that revisiting them can yield important new discoveries.</p>
<div class="creditl">Professor Neil S. Davies.</div></div>
This period marked the first time that tightly-packed plants were able to grow on land, and the sheer abundance of debris shed by the <i>Calamophyton</i> trees built up within layers of sediment. The sediment affected the way that the rivers flowed across the landscape, the first time that the course of rivers could be affected in this way.
<div class="panelplain" style="margin:1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6JVKMgs49Yi0jp3OpmBvuYj4DMOyq1VBJc7uYLrAppQHfMm8PchGd33CBFjaYH1g6gvRUd0BvQe5lfx3s1bJxnwx9qFBNBcw3yXocZa-fpx13SYFvKvnMTO-BW0UB9_K9TFWPwQvZZSGwgrXGayvY01n2-TLRp_ZpJycWO_HocqKDuLIkcyUri6wxUbz8/s1600/Fossilised%20logs.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6JVKMgs49Yi0jp3OpmBvuYj4DMOyq1VBJc7uYLrAppQHfMm8PchGd33CBFjaYH1g6gvRUd0BvQe5lfx3s1bJxnwx9qFBNBcw3yXocZa-fpx13SYFvKvnMTO-BW0UB9_K9TFWPwQvZZSGwgrXGayvY01n2-TLRp_ZpJycWO_HocqKDuLIkcyUri6wxUbz8/s1600/Fossilised%20logs.jpg"/></a>
<div class="captionc">Fossilised ripple marks on the forest floor with fossilised logs of <i>Calamophyton</i> trees<br><br><div class="credit">Credit: Neil Davies</div></div>
<hr />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZJG5wGpiyLm39J5NnB7BoovPKz5pm6LU9gpviUxDR3JgtGb5GfCcDYZCNV8nqYROB4WMwYHcXzxw3AAVCn9o7lHoQrgKJYXzhYDRRtB7jBbnoN10XPShwh8riO9o8jM4B6imip2dYT2_SzXv43Olr3Ckhg308BisXnt-zQtWGTgEpzsPUokNGhRf4a7Si/s1600/pw-1-sh-2560x1440.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZJG5wGpiyLm39J5NnB7BoovPKz5pm6LU9gpviUxDR3JgtGb5GfCcDYZCNV8nqYROB4WMwYHcXzxw3AAVCn9o7lHoQrgKJYXzhYDRRtB7jBbnoN10XPShwh8riO9o8jM4B6imip2dYT2_SzXv43Olr3Ckhg308BisXnt-zQtWGTgEpzsPUokNGhRf4a7Si/s1600/pw-1-sh-2560x1440.jpg"/></a>
<div class="captionc">Rocks at Porlock Weir, Somerset.<br><div class="credit">Credit: Neil Davies</div></div>
</div>
</blockquote>
More detail is given in the abstract to the team's paper in the <i>Journal of the Geological Society</i>, which, although the paper is stated to be open access, appears to be the only part available:<br>
<blockquote class="blockit"><span>Abstract</span><br>
<br>
The evolution of trees and forests through the Devonian Period fundamentally changed Earth's land biosphere, as well as impacting physical environments and geomorphology by stabilizing sediment and interacting with flowing air and water. From the mid Givetian Age onwards, lignophyte flora are known to have been key parts of the machinery in the ‘Devonian Landscape Factory’, but the impact of earlier forests, dominated by less woody cladoxylopsids, are not as well understood. In this paper we report evidence for a previously unrecognized cladoxylopsid forest landscape, archived within the Eifelian Hangman Sandstone Formation of Somerset and Devon, SW England. This unit has previously been considered palaeobotanically depauperate but is here shown to contain the earliest fossil evidence for such trees in the British record, as well as the oldest known evidence globally for the relative position of standing trees: in common parlance a ‘fossil forest’. In addition to abundant fossil material attributable to the cladoxylopsid tree <i>Calamophyton</i>, and other early Middle Devonian flora, the sedimentary context of the plant remains sheds light on the biogeomorphic impacts of these earliest forests. The trees colonized a sizeable distributive fluvial system (DFS) that was prone to seasonal disturbance events. The nature of the sedimentary system has created a bias to those facies where biogeomorphic signatures are most frequently recorded (from the distal parts of the system), but across the DFS there is evidence of plant-sediment interactions in the form of vegetation-induced sedimentary structures, rooting features, and accumulations of plant debris. Plant remains are also found in nearshore facies adjacent to the DFS, attesting to the development of a novel non-marine/marine teleconnection from the production and export of new biological sedimentary particles. The Hangman Sandstone Formation is illustrative of the revolutionary power of cladoxylopsid trees as biogeomorphic agents, forming densely spaced forests and shedding exceptionally abundant plant debris, whilst also impacting local landforms and sediment accumulations and profoundly changing landform resilience against flood disturbance events. These findings provide evidence that the Eifelian Stage (393.3-387.7 Ma) marks the onset of tree-driven changes to physical environments that would forever change Earth's non-marine landscapes and biosphere.<br>
<br>
<div class="creditl">Davies Neil S.; McMahon William J.; Berry Christopher M.<br>
Earth's earliest forest: fossilized trees and vegetation-induced sedimentary structures from the Middle Devonian (Eifelian) Hangman Sandstone Formation, Somerset and Devon, SW England.<br>
<i>Journal of the Geological Society</i> (2024) jgs2023-204; DOI: 10.1144/jgs2023-204<br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by The Geological Society. Open access. <br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
Apart from these fossils being dated to within that long period of Earth's history that occurred before 'Creation Week', of which the authors of the origin myths in the Bible were so obviously ignorant, there is another matter for creationists to try to find a way to ignore here:<br>
<br>
The growth of these early trees is entirely consistent with the Theory of Evolution in respect to trees and the colonisation of the land by plants, with the formation of sedimentary deposits consisting of plant matter processed by arthropods - the first animal life to colonise the land. And with these new sedimentary deposits, with the formation of rivers as agents of erosion and land formation.<br>
<br>
Of course, the authors of the Bible didn't see any need to explain how the rivers that ran through the land had formed because, to them, the notion of a magician making it all out of nothing with a few magic spells seems a perfectly sensible explanation.<br>
<br>
Fortunately, most people have grown up enough to know how childish that simplistic explanation is and understand how the invocation of magic to bridge a gap in understanding, doesn't explain anything in any way useful to humankind, or in a way that relates to the way the universe works in reality.
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-51077801042337485182024-03-09T00:53:00.003+00:002024-03-09T01:00:34.029+00:00Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left; flex: 2">Microscopic fluorescence image of a <i>C.tropicalis</i> mother worm. The worm carries eggs loaded with a toxin (red) which is expressed from a Toxin-Antidote selfish genetic element only when it was maternally inherited.</div>
<div class="right-column" style="text-align: right; flex: 1"> © Pinelopi Pliota/IMBA</div>
</div>
</div><br>
<a href="https://www.oeaw.ac.at/imba/research-highlights/news/revealing-the-evolutionary-origin-of-genomic-imprinting">Revealing the evolutionary origin of genomic imprinting </a><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjS3fz1Hs3YwKiJWM1umWYJNwVViR9Ui1X7lPu6qHFg4UzwL9jzBM3WXI_VArce9-0QrYU8thyphenhyphenNparJw6gjGcA1koGgC73naVDwbBvkEWBFXNWg23NWGj8KUGKtjeCRkPgDxfg3vU1VQtEkuPatx2QWiUW2qHftdN-w5v8Y_OZ87fcs738RdL_Q9YAv8LoS/s1600/csm_Fluorescence_Worm_Burga_Nature_Cover_Image_b04f2b7b7e.jpg" ><img alt="" border="0" data-original-height="400" data-original-width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjS3fz1Hs3YwKiJWM1umWYJNwVViR9Ui1X7lPu6qHFg4UzwL9jzBM3WXI_VArce9-0QrYU8thyphenhyphenNparJw6gjGcA1koGgC73naVDwbBvkEWBFXNWg23NWGj8KUGKtjeCRkPgDxfg3vU1VQtEkuPatx2QWiUW2qHftdN-w5v8Y_OZ87fcs738RdL_Q9YAv8LoS/s1600/csm_Fluorescence_Worm_Burga_Nature_Cover_Image_b04f2b7b7e.jpg"/></a></div>
<div class="rpanel450plain"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiciCxoD-AC1CfPzha_5oF6Kpkp43Ue0JW50JfURw-BR9ZHSEBEOE0SLnu5mS_QQTU5QCQS6XLfqsCOonOlEKI6MfkMO3S6pp8gfDTj_aLsOpMgQWFJElkYebdg8hRIaCIDhnLPsE7kX64jZFyuyUdL4FfQEXQGz3mxp_nuXstp26ZWWRJmDzlJD37rYz6u/s1600/20-05-0192.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiciCxoD-AC1CfPzha_5oF6Kpkp43Ue0JW50JfURw-BR9ZHSEBEOE0SLnu5mS_QQTU5QCQS6XLfqsCOonOlEKI6MfkMO3S6pp8gfDTj_aLsOpMgQWFJElkYebdg8hRIaCIDhnLPsE7kX64jZFyuyUdL4FfQEXQGz3mxp_nuXstp26ZWWRJmDzlJD37rYz6u/s1600/20-05-0192.jpg"/></a><div class="captionc"><i>Caenorhabditis elegans</i></div></div>
<br>
Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.<br>
<br>
This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.<br>
<br>
But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
<blockquote class="ai">What exactly are 'selfish genetic elements' and what do they do?
Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.<br>
<br>
One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.<br>
<br>
Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.<br>
<br>
Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
</blockquote>
In the case of the nematode, <i>Caenorhabditis elegans</i>, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:
<a name='more'></a>
<blockquote class="ai">Do you have any information on the selfish genetic elements known as TAs in the nematode <i>C elegans</i>?
Yes, TAs, short for "Toxic Ascaris," are a class of selfish genetic elements found in the nematode <i>Caenorhabditis elegans</i>. They were first discovered in studies investigating the genetics of the nematode's reproductive system.<br>
<br>
TAs are composed of two genetic components: the "toxin" gene and the "antidote" gene. The toxin gene encodes a protein that is toxic to sperm or embryos, while the antidote gene encodes a protein that neutralizes the toxin. These elements exploit the genetic machinery of <i>C. elegans</i> to bias their own transmission during reproduction.<br>
<br>
The mechanism of action of TAs involves the preferential destruction of competing sperm or embryos that lack the antidote gene. This biased transmission allows TAs to spread through the population, even if they are harmful to the overall fitness of the organism.<br>
<br>
TAs represent an intriguing example of the evolutionary arms race between selfish genetic elements and their hosts. While TAs can confer a reproductive advantage to themselves, they can also impose a fitness cost on the nematode population if left unchecked. Therefore, the evolutionary dynamics of TAs in <i>C. elegans</i> are of interest to researchers studying genetic conflict, reproductive biology, and evolutionary theory.<br>
<br>
<span class="t2">So any advantage for the "toxin" gene is only realised if the "antidote gene" is also inherited with it?</span><br>
<br>
Yes, that's correct. The advantage conferred by the "toxin" gene of TAs is only realized if the "antidote" gene is inherited along with it. This is because the toxin produced by the "toxin" gene would harm the organism's reproductive cells or embryos unless it is neutralized by the antidote produced by the "antidote" gene.<br>
<br>
The presence of both the toxin and antidote genes in the same individual allows the toxin to be produced and function without harming the organism itself. However, when the toxin gene is inherited without the antidote gene, the toxin can cause harm to the reproductive cells or embryos, potentially reducing the reproductive success of individuals lacking the antidote gene.<br>
<br>
This scenario creates a selective pressure for the co-inheritance of both the toxin and antidote genes. Individuals that possess both genes will be more likely to successfully transmit the TAs to the next generation, while those lacking either gene may experience reduced reproductive success. As a result, the evolutionary fate of TAs depends on the balance between the advantages they confer and the potential costs they impose on the host population.
</blockquote><br>
If any creationist can discern any intelligence behind the TAs in C. elegans, I'd like to know what it is.<br>
<br>
But what has that to do with the evolution of genomic imprinting?<br>
<br>
According to researchers at the Institute of Molecular Biotechnology at the Austrian Academy of Sciences (IMBA), genomic imprinting likely evolved from and arms race between the organism and TA's, as they describe in an open access paper in <i>Nature</i> and in an IMBA news release:
<blockquote class="blockit"><b>Some of our genes can be expressed or silenced depending on whether we inherited them from our mother or our father. The mechanism behind this phenomenon, known as genomic imprinting, is determined by DNA modifications during egg and sperm production. The Burga Lab at the Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences uncovered a novel gene regulation process, associated with the silencing of selfish genes, that could represent the first step in the evolution of imprinting. Their discovery, reported in Nature, could begin to solve the mystery of how and why imprinting first evolved.</b><br>
<br>
Alejandro Burga and his lab at IMBA, in collaboration with the lab of Eyal Ben-David at the Hebrew University, have reported the discovery of the first parent-of-origin effect in nematodes, in a study published in Nature on March 6, 2024. <br>
<br>
In diploid organisms, one set of chromosomes is inherited from each parent. However, not all of the genes contained within will be expressed equally; instead, some may be silenced depending on whether they were inherited from the mother or the father. This phenomenon, known as genomic imprinting, depends on DNA methylation, an epigenetic signal that is erased and rewritten in every generation. Genomic imprinting arose independently in mammals and plants over 100 million years ago. However, how this mechanism evolved has, so far, remained largely a mystery. Key to solving this enigma is understanding how parent-of-origin effects, the substrate for the evolution of imprinting, evolved in the first place. <br>
<br>
Thirty years ago, Denise Barlow, a pioneer in the study of imprinting working at the IMP, also located at the Vienna BioCenter, hypothesized that imprinting could be evolutionarily related to genome defense mechanisms that silence parasitic DNA elements called selfish genetic elements. Selfish elements and the defense mechanisms against them participate in an arms race: each evolves further to outcompete the other. Although much has been discovered about selfish element silencing in the thirty years since Denise Barlow postulated her theory, a direct connection between germline defense mechanisms and the origin of parent-of-origin effects was missing. <br>
<br>
The findings by the Burga lab provide the first clear example of how parent-of-origin effects can originate from the host small RNA genome defense pathway. Their findings point to the potential evolutionary origin of imprinting. <br>
<br>
<span>Curiosity paves the way for a new discovery</span> <br>
<br>
Sometimes in science, curiosity and attention to surprising details can lead to unexpected paths and new discoveries. This was the case when first author Pinelopi Pliota was studying selfish genetic elements in a new nematode model organism called <i>C. tropicalis</i>, a close cousin of the more widely studied C. elegans. Pliota was investigating toxin-antidote elements (TAs), a type of selfish element that has evolved a fascinating mechanism to ensure its own inheritance: “When a mother carries the TA, it will “poison” its eggs with a toxin that can only be countered by an antidote which is also present in the TA,” she explains, “this way, all descendants that don’t inherit the TA will either die or be developmentally delayed.” <br>
<br>
To generate the mothers they were studying, the group always crossed a mother <i>C. tropicalis</i> carrying the TA with a father not carrying it. “Pinelopi asked me if we had ever done these crossings the other way around,” explains Alejandro Burga, corresponding author of the publication. Her curiosity led to an interesting discovery: “To our surprise, this reciprocal crossing produced mothers incapable of poisoning their eggs. All of a sudden, there was no effect at all,” explains Pliota. Fascinated by this unexpected result, the team decided to study how inheriting the TA from the mother or the father could lead to different effects. “We wanted to understand how this happens, what the molecular basis of this parent-of-origin effect is,” says Burga. <br>
<br>
<span>Inhibiting the inhibitor: maternal mRNA licenses toxin expression </span><br>
<br>
To figure out the mechanism of the observed parent-of-origin effect, the Burga group decided to study the main germline defense mechanism against selfish genetic elements, known as the piRNA pathway. In the piRNA pathway, a coordinated effort of different small RNA molecules and proteins silences the expression of selfish elements during germline development to ensure genome stability in reproduction. <br>
<br>
The group, collaborating with the lab of Julius Brennecke, also at IMBA, were able to identify the piRNA molecules and proteins involved in silencing the toxin-antidote element. However, all these factors alone didn’t explain the parent-of-origin-specific results they were observing. The researchers were missing a piece in this puzzle.<br>
<br>
Fortunately, the Burga group had one last trick up their sleeve: “We knew from previous research that worms have evolved various ingenious ways to discriminate their own genes from foreign elements like a virus or a selfish element.” Burga says. “We realized that, in this case, the key missing element was maternal mRNA which is loaded into eggs.” <br>
<br>
They proved that, in maternal inheritance, the TA is accompanied by the toxin mRNA, which is expressed in the germline of the mother and loaded into the egg. The Burga group showed that this mRNA marks the TA as “own”, avoiding its silencing by the piRNA pathway. “This process is called epigenetic licensing, and its balance with the piRNA pathway determines whether a gene is expressed or not”. <br>
<br>
On the other hand, when the TA is inherited paternally, the lack of maternal mRNA means there is no licensing, leading to a strong repression of the toxin gene and very low levels of toxin being expressed. “By default, the piRNA pathway will silence the toxin gene,” explains Burga. “Unless there’s maternal mRNA that licenses it by repressing the piRNA pathway. This inhibition of the inhibitor is what causes the toxin gene to be active, and the eggs to be poisoned.”. <br>
<br>
Interestingly, this silencing pattern was observed to last for several generations, meaning that lack of licensing in one generation can even affect their great-grand-daughters. This is not the case in genomic imprinting, which gets reset in each generation. <br>
<br>
<span>Explaining the evolution of imprinting </span> <br>
<br>
The results from the Burga group cement the evolutionary link between parent-specific gene expression and host defence mechanisms, tracing the origins back to organisms that lack DNA methylation and canonical imprinting. Despite the differences between these processes in worms and mammals, the Burga group believes that the mechanism they described could represent an evolutionary first step for more advanced forms of inherited silencing. These more advanced forms of silencing ended up regulating the expression of the cell's endogenous genes, leading to the evolution of genomic imprinting
</blockquote>
And more technical detail and background is given in the open access paper in <i>Nature</i>:
<blockquote class="blockit"><span>Abstract</span><br>
<br>
Genomic imprinting—the non-equivalence of maternal and paternal genomes—is a critical process that has evolved independently in many plant and mammalian species<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a></sup>. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">4</a></sup>. Yet, how these epigenetic differences evolve in the first place is poorly understood<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">5</a>,<a class="newtooltip">6</a></sup>. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals<sup class="x-small"><a class="newtooltip">7</a>,<a class="newtooltip">8</a>,<a class="newtooltip">9</a></sup>. In reciprocal crosses between two <i>Caenorhabditis tropicalis</i> wild isolates, we found that the <i>slow-1/grow-1</i> TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the <i>slow-1</i> toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when <i>slow-1/grow-1</i> is maternally inherited, <i>slow-1</i> repression is halted by a translation-independent role of its maternal mRNA. That is, <i>slow-1</i> transcripts loaded into eggs—but not SLOW-1 protein—are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.<br>
<br>
<span>Main</span><br>
<br>
Diploid organisms carry two copies of each gene: one inherited from their mother and the other one from their father. Typically, these copies are functionally interchangeable. Imprinted genes are the exception to this rule. They keep an epigenetic memory of their gametic provenance, making maternal and paternal genomes non-equivalent, which has a large effect on embryonic development, species hybridization and human disease<sup class="x-small"><a class="newtooltip">10</a></sup>. Multiple theories have been put forward to explain the evolution of imprinting. The most accepted theory—kinship conflict—states that imprinting arises when there are conflicting interests between maternal and paternal genomes owing to differential investment in their offspring<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">4</a></sup>. Notably, this theory presupposes the existence of mechanisms that establish differences in the expression of maternal and paternal alleles—otherwise, there would be nothing to select on<sup class="x-small"><a class="newtooltip">3</a></sup>. This raises the critical question of how parent-of-origin effects on gene expression evolve in the first place.<br>
<br>
The discovery of the first imprinted loci in mammals led to the hypothesis that imprinting evolved from host defence mechanisms that use DNA methylation to keep viruses and parasitic genes at bay<sup class="x-small"><a class="newtooltip">11</a>,<a class="newtooltip">12</a></sup>. This is in line with the close proximity of many imprinted loci to transposable elements in plants<sup class="x-small"><a class="newtooltip">13</a>,<a class="newtooltip">14</a></sup> and piRNA-induced DNA methylation of a retrotransposon being critical for the paternal imprinting of mouse <i>Rasgrf1</i> (ref. <sup class="x-small"><a class="newtooltip">15</a></sup>). However, the evolutionary origins of imprinting remain poorly understood at the molecular level. More recently, histone modifications, such as H3K27me3, have been reported to act as imprinting marks independently of DNA methylation in mice<sup class="x-small"><a class="newtooltip">16</a></sup>. These observations have raised the possibility that a link between parent-of-origin-dependent gene expression and host defence mechanisms can also be found in organisms that lack DNA methylation but are rich in small regulatory RNAs, such as <i>Caenorhabditis elegans</i> and related nematodes<sup class="x-small"><a class="newtooltip">17</a></sup>. Here we dissect the mechanism behind a parent-of-origin effect on gene expression and provide a physiological context for the emergence of imprinting.<br>
<br>
<span>A TA with a parent-of-origin effect</span><br>
<br>
<i>C. tropicalis</i> is a hermaphroditic nematode that—unlike its more widely distributed relative <i>C. elegans</i>—inhabits exclusively equatorial regions<sup class="x-small"><a class="newtooltip">18</a></sup>. While studying genetic incompatibilities between the two <i>C. tropicalis</i> wild isolates NIC203 (Guadeloupe, France) and EG6180 (Puerto Rico, USA), we uncovered a maternal-effect TA, which we named <i>slow-1/grow-1</i> (ref. <sup class="x-small"><a class="newtooltip">9</a></sup>). This selfish element is located in NIC203 chromosome III and comprises three tightly linked genes: a maternally expressed toxin, <i>slow-1</i>, and two identical and redundant antidotes, <i>grow-1.1</i> and <i>grow-1.2</i>, which are expressed zygotically. For simplicity, we will refer to the two antidotes collectively as grow-1 unless specifically noted (Extended Data Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig6" target="_blank">1a</a> and <a href="https://www.nature.com/articles/s41586-024-07155-z#MOESM1" target="_blank">Supplementary Discussion</a>). <i>Slow-1</i> transcripts are maternally loaded into eggs prior to fertilization and remain stable in embryos, at least until the 20-cell stage. However, from the comma stage until hatching, <i>slow-1</i> transcripts are found only in the germline precursor cells<sup class="x-small"><a class="newtooltip">9</a></sup>. SLOW-1 is homologous to nuclear hormone receptors, whereas the antidote GROW-1 has no homology to known proteins. In crosses between TA carrier and non-carrier strains, heterozygous mothers poison all their eggs but only progeny that inherit the TA can counteract the toxin by zygotically expressing its antidote (Extended Data Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig6" target="_blank">1b</a>). Whereas wild-type worms typically take two days to develop from the L1 stage to the onset of egg laying, embryos poisoned by maternal SLOW-1 take on average four days. This developmental delay imposes a high fitness cost and favours the spread of the selfish element in the population<sup class="x-small"><a class="newtooltip">9</a></sup>.<br>
<br>
To study the inheritance of <i>slow-1/grow-1</i> TA, we previously generated a near-isogenic line strain (hereafter referred to as ‘NIL’) containing the <i>slow-1/grow-1</i> NIC203 chromosome III locus in an otherwise EG6180 background9. As expected, <i>slow-1</i> mRNA was detected in the NIL but not in EG6180 (Extended Data Fig. 1c). As previously reported, in crosses between NIL hermaphrodites and EG6180 males, the toxin induced developmental delay in all the F2 homozygous non-carrier (EG/EG) individuals9 (100% delay, <i>n</i> = 34; Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig1" target="_blank">1a</a>). However, we noticed an unexpected pattern of inheritance when performing the reciprocal cross. If EG6180 hermaphrodites were mated to <i>slow-1/grow-1</i> NIL males, most of their F2 EG/EG progeny were not developmentally delayed but phenotypically wild type (9.4% delay, <i>n</i> = 53; <i>P</i> ≤ 0.0001; Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig1" target="_blank">1a,b</a>). This was surprising, because known TAs—including <i>C. elegans</i> <i>peel-1/zeel-1</i> and <i>sup-35/pha-1</i>, the <i>Medea</i> locus in <i>Tribolium</i>, and the mouse homogeneously staining region (HSR) locus—affect non-carrier individuals regardless of whether the element is inherited from the maternal or paternal lineage<sup class="x-small"><a class="newtooltip">8</a>,<a class="newtooltip">19</a>,<a class="newtooltip">20</a>,<a class="newtooltip">21</a></sup> (Extended Data Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig6" target="_blank">1d</a>).<br>
<div class="panelplain" style="margin: 1em auto"><span class="t2"><div style="margin: 0 1em">Fig. 1: <i>slow-1/grow-1</i>, a selfish element with a parent-of-origin effect.</div></span>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP0933molqAwBomwvvOolGRZ48MidkTdgebOD7H3bZYHrVNVJtjd7hq2eX3E1PlJFdmRXH34t3ZrTBuSJO5XEd56o1I4DiPkSL2Hn6QccyvEwzRUgNkqevc7Jzv6RQ0DNvF4dulM50uZBmIqtqXgxsnolewzLYGVaw967kQH1stpXLdyMTS654rZ7fPW0o/s1600/41586_2024_7155_Fig1_HTML.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP0933molqAwBomwvvOolGRZ48MidkTdgebOD7H3bZYHrVNVJtjd7hq2eX3E1PlJFdmRXH34t3ZrTBuSJO5XEd56o1I4DiPkSL2Hn6QccyvEwzRUgNkqevc7Jzv6RQ0DNvF4dulM50uZBmIqtqXgxsnolewzLYGVaw967kQH1stpXLdyMTS654rZ7fPW0o/s1600/41586_2024_7155_Fig1_HTML.webp"/></a><div class="caption"><b>a</b>, Reciprocal crosses between the <i>slow-1/grow-1</i> TA NIL and the EG6180 parental strain. Maternal (M) or paternal (P) inheritance refers to the <i>slow-1/grow-1</i> locus. Worms with a significant developmental delay or larval arrest were categorized as delayed, otherwise they were classified as wild type (WT). Sample sizes (<i>n</i>) are shown for each phenotypic class. Error bars indicate 95% binomial confidence intervals calculated with the Agresti–Coull method. Each cross was performed independently at least twice with identical results (see Supplementary Table <a href="https://www.nature.com/articles/s41586-024-07155-z#MOESM1" target="_blank">1</a> for raw data). <b>b</b>, Activity of the NIC203 chromosome II TA in reciprocal crosses. Penetrance of the toxin, the percentage of F2 non-carrier individuals that are phenotypically affected, is used as a proxy for TA activity (<i>slow-1/grow-1</i> TA: M, <i>n</i> = 34; P, <i>n</i> = 53; <i>P</i> < 0.0001, NIC chromosome II TA: M, <i>n</i> = 44; P, <i>n</i> = 50; <i>P</i> = 0.27; two-sided Fisher’s exact test; data are mean ± 95% confidence interval). Chr., chromosome; NS, not significant. <b>c</b>, Reciprocal crosses between the NIL and EG6180 followed by RNA-seq of their F1 progeny indicate that <i>slow-1</i> transcripts are more abundant when maternally inherited (two-sided unpaired t-test; M, <i>n</i> = 7; P, <i>n</i> = 6; <i>P</i> = 0.0092; data are mean ± s.e.m.).</div></div>
We also investigated the inheritance pattern of two recently discovered maternal-effect TAs in <i>C. tropicalis</i> and <i>C. briggsae</i> that cause developmental delay<sup class="x-small"><a class="newtooltip">9</a>,<a class="newtooltip">22</a></sup>. However, we found no evidence of a parent-of-origin effect, indicating that this is not a general feature of non-lethal toxins (Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig1" target="_blank">1b</a> and Extended Data Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig6" target="_blank">1e</a>). Mito-nuclear incompatibilities could not explain the observed pattern because both parental lines carry the same mito-genotype (Extended Data Fig. <a href="https://www.nature.com/articles/s41586-024-07155-z#Fig6" target="_blank">1f</a>). Moreover, <i>C. tropicalis</i>, like all nematodes of the Rhabditida group, lacks de novo methyltransferases, making the involvement of mammalian-like epigenetic imprinting unlikely<sup class="x-small"><a class="newtooltip">23</a></sup>. Because parent-of-origin effects are extremely rare in nematodes and all reported cases involve transgenic reporters, we set out to investigate this phenomenon<sup class="x-small"><a class="newtooltip">24</a>,<a class="newtooltip">25</a></sup>.
</blockquote>
Can a creationists suggest a reason why any intelligent designer would design a selfish gene that ensures its own survival by killing carriers of the alleles that don't include the antidote to itself, and a species having what looks like an arms race with one of its own genes that have gone 'rogue' in this way?<br>
<br>
Or will they have to abandon the pretense that intelligent design is not Bible literalism in disguise and invoke the biblical myth of 'The Fall' to blame it on?
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-46096242404848240922024-03-08T13:36:00.001+00:002024-03-08T13:39:02.384+00:00Creationism in Crisis - Like Humans, Bumblebees Learn Through Social Interaction And May Have Cumulative Culture<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left; flex: 2">Bumblebees teaching each other to solve a complex puzzle</div>
<div class="right-column" style="text-align: right; flex: 1"></div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWSXr0vf6gAE7s9EM1Q6m-UOByWmm3KPOVRV7RDCK_4aMO_RappS3nJXvq0YMv1-hm4Rzf2nUX28Kj0C4CYXVPZEfhyphenhyphen3zYsKbPVn1QqQewZEeOkI6pUa0BUpEYOtwgocboZAvwMsyPWDktr_zuPGEQrl84bEw_usuMvTxVW-p71293PDh0dIgILWOf0Wip/s1600/Bees-640.jpg" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" data-original-height="410" data-original-width="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWSXr0vf6gAE7s9EM1Q6m-UOByWmm3KPOVRV7RDCK_4aMO_RappS3nJXvq0YMv1-hm4Rzf2nUX28Kj0C4CYXVPZEfhyphenhyphen3zYsKbPVn1QqQewZEeOkI6pUa0BUpEYOtwgocboZAvwMsyPWDktr_zuPGEQrl84bEw_usuMvTxVW-p71293PDh0dIgILWOf0Wip/s1600/Bees-640.jpg"/></a></div>
<div class="rpanel450plain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeSEbbqwvnz3qRSN1COy3Js2W7f-Qgxs0Mz5mSobvcUoLCPLKT1YueqwAXpaZ922b0_nsMkE7N1jiIe4PJHl7AXCtznO1thM5m4FxjN37ttetfauLmSScKmADJf45-3GkLzjZ74IQaOrl7C5tXQ2zjpwFBpMqwei7Tn5EOXwDbf1Edj5T89n9Y2eFzmpmA/s1600/Bombus_terrestris.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeSEbbqwvnz3qRSN1COy3Js2W7f-Qgxs0Mz5mSobvcUoLCPLKT1YueqwAXpaZ922b0_nsMkE7N1jiIe4PJHl7AXCtznO1thM5m4FxjN37ttetfauLmSScKmADJf45-3GkLzjZ74IQaOrl7C5tXQ2zjpwFBpMqwei7Tn5EOXwDbf1Edj5T89n9Y2eFzmpmA/s1600/Bombus_terrestris.jpg"/></a><div class="captionc">Buff-tailed Bumblebee, <i>Bombus terrestris</i><br>
<div class="credit">Source: <a href="https://en.wikipedia.org/wiki/Bombus_terrestris#/media/File:Bombus_terrestris.jpg" target="_blank">Wikipedia</a>.</div></div></div>
<a href="https://www.qmul.ac.uk/media/news/2024/se/bees-master-complex-tasks-through-social-interaction.html">Bees master complex tasks through social interaction - Queen Mary University of London</a><br>
<br>
A sacred Tenet of creationism is that we humans are a special creation by the creator of the universe who made everything just for us. They point to the many 'unique' traits and abilities of humans as evidence of this - the ability to teach and learn, to form cultures, even walking upright are frequently cited as examples. It's also a sacred Tenet of creationism that anything which might refute the sacred tenets of creationism must be ignore, hand-waved aside or misrepresented but never, ever acknowledged for what it is - a refutation of creationism.<br>
<br>
So, we can expect one or more of those tactics for handling the cognitive dissonance that news that bumble bees can teach and learn and so have at least the basis for forming cumulative cultures. The news itself comes in the form of an open access research paper in Nature by a team Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London. <br>
<br>
The team showed that a complex, two-step task, which needed to be performed to receive a reward in the form of a sweet liquid could be learned by bees who were allowed to watch a trained 'demonstrator' perform the task. The bees not only learned how to perform the steps involved but that there was a reward to be had for doing so.<br>
<br>
The 'demonstrators' had previously been trained by giving intermediate rewards as each stage was completed successfully, which were eventually withdrawn, leaving only the final reward. The experiment and its significance are explained in a Queen Mary University news release:
<a name='more'></a>
<blockquote class="blockit">In a groundbreaking discovery by Queen Mary scientists, bumblebees have been shown to possess a previously unseen level of cognitive sophistication. A new study, published in Nature, reveals that these fuzzy pollinators can learn complex, multi-step tasks through social interaction, even if they cannot figure them out on their own.<br>
<br>
This challenges the long-held belief that such advanced social learning is unique to humans, and even hints at the presence of key elements of cumulative culture in these insects. <br>
<br>
Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London, the research team designed a two-step puzzle box requiring bumblebees to perform two distinct actions in sequence to access a sweet reward at the end. Training bees to do this was no easy task, and bees had to be helped along by the addition of an extra reward along the way. This temporary reward was eventually taken away, and bees subsequently had to open the whole box before getting their treat.<br>
<br>
Surprisingly, while individual bees struggled to solve the puzzle when starting from scratch, those allowed to observe a trained "demonstrator" bee readily learned the entire sequence – even the first step – while only getting a reward at the end. <br>
<br>
This study demonstrates that bumblebees possess a level of social learning previously thought to be exclusive to humans. They can share and acquire behaviours that are beyond their individual cognitive capabilities: an ability thought to underpin the expansive, complex nature of human culture, and one previously thought to be exclusive to us. <br>
<div class="panelplain" style="margin: 1em auto"><iframe style="height: 440px" src="https://www.youtube.com/embed/jg3U8Sq13-A" title="Are bumblebees smarter than we think?" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe></div>
Dr Bridges emphasises the novelty of this finding:<br>
<div class="block"><p>This is an extremely difficult task for bees. They had to learn two steps to get the reward, with the first behaviour in the sequence being unrewarded. We initially needed to train demonstrator bees with a temporary reward included there, highlighting the complexity. Yet, other bees learned the whole sequence from social observation of these trained bees, even without ever experiencing the first step's reward. But when we let other bees attempt to open the box without a trained bee to demonstrate the solution, they didn’t manage to open any at all.</p>
<div class="creditl">Dr Alice D. Bridges, lead and co-corresponding author<br>
School of Biological and Behavioural Sciences<br>
Queen Mary University of London, London, UK.</div></div>
Beyond individual learning, this research opens exciting possibilities for understanding the emergence of cumulative culture in the animal kingdom. Cumulative culture refers to the gradual accumulation of knowledge and skills over generations, allowing for increasingly complex behaviours to develop. The bees' ability to learn such a complex task from a demonstrator suggests a potential pathway for cultural transmission and innovation beyond their individual learning capabilities. <br>
<br>
Professor Chittka further underscores the implications:<br>
<div class="block"><p>This challenges the traditional view that only humans can socially learn complex behaviour beyond individual learning. It raises the fascinating possibility that many of the most remarkable accomplishments of the social insects, like the nesting architectures of bees and wasps or the agricultural habits of aphid- and fungus-farming ants, may have initially spread by copying of clever innovators, before they eventually became part of the species-specific behaviour repertoires.</p>
<div class="creditl">Professor Lars Chttka, co-corresponding author.</div></div>
This groundbreaking research opens new avenues for understanding animal intelligence and the evolution of social learning. It challenges longstanding assumptions and paves the way for further exploration of the cognitive wonders hidden within the insect world, even hinting at the exciting possibility of cumulative culture amongst seemingly simple creatures.
</blockquote><br>
<br>
More technical detail is given in the teams open access research paper in <i>Nature</i>:
<blockquote class="blockit"><span>Abstract</span><br>
<br>
Culture refers to behaviours that are socially learned and persist within a population over time. Increasing evidence suggests that animal culture can, like human culture, be cumulative: characterized by sequential innovations that build on previous ones<sup class="x-small"><a class="newtooltip">1</a></sup>. However, human cumulative culture involves behaviours so complex that they lie beyond the capacity of any individual to independently discover during their lifetime<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a>,<a class="newtooltip">3</a></sup>. To our knowledge, no study has so far demonstrated this phenomenon in an invertebrate. Here we show that bumblebees can learn from trained demonstrator bees to open a novel two-step puzzle box to obtain food rewards, even though they fail to do so independently. Experimenters were unable to train demonstrator bees to perform the unrewarded first step without providing a temporary reward linked to this action, which was removed during later stages of training. However, a third of naive observer bees learned to open the two-step box from these demonstrators, without ever being rewarded after the first step. This suggests that social learning might permit the acquisition of behaviours too complex to ‘re-innovate’ through individual learning. Furthermore, naive bees failed to open the box despite extended exposure for up to 24 days. This finding challenges a common opinion in the field: that the capacity to socially learn behaviours that cannot be innovated through individual trial and error is unique to humans.<br>
<br>
<span>Main</span><br>
<br>
Culture in animals can be broadly conceptualized as the sum of a population’s behavioural traditions, which, in turn, are defined as behaviours that are transmitted through social learning and that persist in a population over time<sup class="x-small"><a class="newtooltip">4</a></sup>. Although culture was once thought to be exclusive to humans and a key explanation of our own evolutionary success, the existence of non-human cultures that change over time is no longer controversial. Changes in the songs of Savannah sparrows<sup class="x-small"><a class="newtooltip">5</a></sup> and humpback whales<sup class="x-small"><a class="newtooltip">6</a>,<a class="newtooltip">7</a>,<a class="newtooltip">8</a></sup> have been documented over decades. The sweet-potato-washing behaviour of Japanese macaques has also undergone several distinctive modifications since its inception at the hands of ‘Imo’, a juvenile female, in 19539. Imo’s initial behaviour involved dipping a potato in a freshwater stream and wiping sand off with her spare hand, but within a decade it had evolved to include repeated washing in seawater in between bites rather than in fresh water, potentially to enhance the flavour of the potato. By the 1980s, a range of variations had appeared among macaques, including stealing already-washed potatoes from conspecifics, and digging new pools in secluded areas to wash potatoes without being seen by scroungers<sup class="x-small"><a class="newtooltip">9</a>,<a class="newtooltip">10</a>,<a class="newtooltip">11</a></sup>. Likewise, the ‘wide’, ‘narrow’ and ‘stepped’ designs of pandanus tools, which are fashioned from torn leaves by New Caledonian crows and used to fish grubs from logs, seem to have diverged from a single point of origin<sup class="x-small"><a class="newtooltip">12</a></sup>. In this manner, cultural evolution can result in both the accumulation of novel traditions, and the accumulation of modifications to these traditions in turn. However, the limitations of non-human cultural evolution remain a subject of debate.<br>
<br>
It is clearly true that humans are a uniquely encultured species. Almost everything we do relies on knowledge or technology that has taken many generations to build. No one human being could possibly manage, within their own lifetime, to split the atom by themselves from scratch. They could not even conceive of doing so without centuries of accumulated scientific knowledge. The existence of this so-called cumulative culture was thought to rely on the ‘ratchet’ concept, whereby traditions are retained in a population with sufficient fidelity to allow improvements to accumulate<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a>,<a class="newtooltip">3</a></sup>. This was argued to require so-called higher-order forms of social learning, such as imitative copying<sup class="x-small"><a class="newtooltip">13</a></sup> or teaching<sup class="x-small"><a class="newtooltip">14</a></sup>, which have, in turn, been argued to be exclusive to humans (although, see a review of imitative copying in animals<sup class="x-small"><a class="newtooltip">15</a></sup> for potential examples). But if we strip the definition of cumulative culture back to its bare bones, for a behavioural tradition to be considered cumulative, it must fulfil a set of core requirements<sup class="x-small"><a class="newtooltip">1</a></sup>. In short, a beneficial innovation or modification to a behaviour must be socially transmitted among individuals of a population. This process may then occur repeatedly, leading to sequential improvements or elaborations. According to these criteria, there is evidence that some animals are capable of forming a cumulative culture in certain contexts and circumstances<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">16</a>,<a class="newtooltip">17</a></sup>. For example, when pairs of pigeons were tasked with making repeated flights home from a novel location, they found more efficient routes more quickly when members of these pairs were progressively swapped out, when compared with pairs of fixed composition or solo individuals<sup class="x-small"><a class="newtooltip">16</a></sup>. This was thought to be due to ‘innovations’ made by the new individuals, resulting in incremental improvements in route efficiency. However, the end state of the behaviour in this case could, in theory, have been arrived at by a single individual<sup class="x-small"><a class="newtooltip">1</a></sup>. It remains unclear whether modifications can accumulate to the point at which the final behaviour is too complex for any individual to innovate itself, but can still be acquired by that same individual through social learning from a knowledgeable conspecific. This threshold, often including the stipulation that re-innovation must be impossible within an individual’s own lifetime, is argued by some to represent a fundamental difference between human and non-human cognition<sup class="x-small"><a class="newtooltip">3</a>,<a class="newtooltip">13</a>,<a class="newtooltip">18</a></sup>.<br>
<br>
Bumblebees (<i>Bombus terrestris</i>) are social insects that have been shown to be capable of acquiring complex, non-natural behaviours through social learning in a laboratory setting, such as string-pulling<sup class="x-small"><a class="newtooltip">19</a></sup> and ball-rolling to gain rewards<sup class="x-small"><a class="newtooltip">20</a></sup>. In the latter case, they were even able to improve on the behaviour of their original demonstrator. More recently, when challenged with a two-option puzzle-box task and a paradigm allowing learning to diffuse across a population (a gold standard of cultural transmission experiments<sup class="x-small"><a class="newtooltip">21</a></sup>, as used previously in wild great tits<sup class="x-small"><a class="newtooltip">22</a></sup>), bumblebees were found to acquire and maintain arbitrary variants of this behaviour from trained demonstrators<sup class="x-small"><a class="newtooltip">23</a></sup>. However, these previous investigations involved the acquisition of a behaviour that each bee could also have innovated independently. Indeed, some naive individuals were able to open the puzzle box, pull strings and roll balls without demonstrators<sup class="x-small"><a class="newtooltip">19</a>,<a class="newtooltip">20</a>,<a class="newtooltip">23</a></sup>. Thus, to determine whether bumblebees could acquire a behaviour through social learning that they could not innovate independently, we developed a novel two-step puzzle box (Fig. 1a). This design was informed by a lockbox task that was developed to assess problem solving in Goffin’s cockatoos<sup class="x-small"><a class="newtooltip">24</a></sup>. Here, cockatoos were challenged to open a box that was sealed with five inter-connected ‘locks’ that had to be opened sequentially, with no reward for opening any but the final lock. Our hypothesis was that this degree of temporal and spatial separation between performing the first step of the behaviour and the reward would make it very difficult, if not impossible, for a naive bumblebee to form a lasting association between this necessary initial action and the final reward. Even if a bee opened the two-step box independently through repeated, non-directed probing, as observed with our previous box<sup class="x-small"><a class="newtooltip">23</a></sup>, if no association formed between the combination of the two pushing behaviours and the reward, this behaviour would be unlikely to be incorporated into an individual’s repertoire. If, however, a bee was able to learn this multi-step box-opening behaviour when exposed to a skilled demonstrator, this would suggest that bumblebees can acquire behaviours socially that lie beyond their capacity for individual innovation.<br>
<div class="panelplain" style="margin: 1em auto"><span class="t2"><div style="margin: 0 1em">Fig. 1: Two-step puzzle-box design and experimental set-up.</div></span>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwj4pTaSmWuLDAqzhDH0nrGrOMKAwi0oOwoAiTWo048_p_ysqLmXCOtg3QHRwVYu9PaQffIrIx5DVAKgCDZRgBn2ZQGfDqngHMUiGB9zwcwl945V0Jq5HPGt7mUikPBI2i008U3UrkSc6Hpy-AYDWz9gKBa3ros4PMkONvjVVbH-MVhYocaZnoFCO8fHCN/s1600/41586_2024_7126_Fig1_HTML%20%281%29.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwj4pTaSmWuLDAqzhDH0nrGrOMKAwi0oOwoAiTWo048_p_ysqLmXCOtg3QHRwVYu9PaQffIrIx5DVAKgCDZRgBn2ZQGfDqngHMUiGB9zwcwl945V0Jq5HPGt7mUikPBI2i008U3UrkSc6Hpy-AYDWz9gKBa3ros4PMkONvjVVbH-MVhYocaZnoFCO8fHCN/s1600/41586_2024_7126_Fig1_HTML%20%281%29.webp"/></a>
<div class="caption"><b>a</b>, Puzzle-box design. Box bases were 3D-printed to ensure consistency. The reward (50% w/w sucrose solution, placed on a yellow target) was inaccessible unless the red tab was pushed, rotating the lid anti-clockwise around a central axis, and the red tab could not move unless the blue tab was first pushed out of its path. See <a href="https://www.nature.com/articles/s41586-024-07126-4#MOESM1" target="_blank">Supplementary Information</a> for a full description of the box design elements. <b>b</b>, Experimental set-up. The flight arena was connected to the nest box with an acrylic tunnel, and flaps cut into the side allowed the removal and replacement of puzzle boxes during the experiment. The sides were lined with bristles to prevent bees escaping. <b>c</b>, Alternative action patterns for opening the box. The staggered-pushing technique is characterized by two distinct pushes (1, blue arrow and 2, red arrow), divided by either flying (green arrows) or walking in a loop around the inner side of the red tab (orange arrow). The squeezing technique is characterized by a single, unbroken movement, starting at the point at which the blue and red tabs meet and pushing through, squeezing between the outer side of the red tab and the outer shield, and making a tight turn to push against the red tab.</div></div>
The two-step puzzle box (Fig. 1a) relied on the same principles as our previous single-step, two-option puzzle box<sup class="x-small"><a class="newtooltip">23</a></sup>. To access a sucrose-solution reward, placed on a yellow target, a blue tab had to first be pushed out of the path of a red tab, which could then be pushed in turn to rotate a clear lid around a central axis. Once rotated far enough, the reward would be exposed beneath the red tab. A sample video of a trained demonstrator opening the two-step box is available (Supplementary Video 1). Our experiments were conducted in a specially constructed flight arena, attached to a colony’s nest box, in which all bees that were not currently undergoing training or testing were confined (Fig. 1b).<br>
<br>
In our previous study, several bees successfully learned to open the two-option, single-step box during control population experiments, which were conducted in the absence of a trained demonstrator across 6–12 days<sup class="x-small"><a class="newtooltip">23</a></sup>. Thus, to determine whether the two-step box could be opened by individual bees starting from scratch, we sought to conduct a similar experiment. Two colonies (C1 and C2) took part in these control population experiments for 12 days, and one colony (C3) for 24 days. In brief, on 12 or 24 consecutive days, bees were exposed to open two-step puzzle boxes for 30 min pre-training and then to closed boxes for 3 h (meaning that colonies C1 and 2 were exposed to closed boxes for 36 h total, and colony C3 for 72 h total). No trained demonstrator was added to any group. On each day, bees foraged willingly during the pre-training, but no boxes were opened in either colony during the experiment. Although some bees were observed to probe around the components of the closed boxes with their proboscises, particularly in the early population-experiment sessions, this behaviour generally decreased as the experiment progressed. A single blue tab was opened in full in colony C1, but this behaviour was neither expanded on nor repeated.<br>
<br>
Learning to open the two-step box was not trivial for our demonstrators, with the finalized training protocol taking around two days for them to complete (compared with several hours for our previous two-option, single-step box<sup class="x-small"><a class="newtooltip">23</a></sup>). Developing a training protocol was also challenging. Bees readily learned to push the rewarded red tab, but not the unrewarded blue tab, which they would not manipulate at all. Instead, they would repeatedly push against the blocked red tab before giving up. This necessitated the addition of a temporary yellow target and reward beneath the blue tab, which, in turn, required the addition of the extended tail section (as seen in Fig. 1a), because during later stages of training this temporary target had to be removed and its absence concealed. This had to be done gradually and in combination with an increased reward on the final target, because bees quickly lost their motivation to open any more boxes otherwise. Frequently, reluctant bees had to be coaxed back to participation by providing them with fully opened lids that they did not need to push at all. In short, bees seemed generally unwilling to perform actions that were not directly linked to a reward, or that were no longer being rewarded. Notably, when opening two-step boxes after learning, demonstrators frequently pushed against the red tab before attempting to push the blue, even though they were able to perform the complete behaviour (and subsequently did so). The combination of having to move away from a visible reward and take a non-direct route, and the lack of any reward in exchange for this behaviour, suggests that two-step box-opening would be very difficult, if not impossible, for a naive bumblebee to discover and learn for itself—in line with the results of the control population experiment.
</blockquote>
And yet another 'uniquely human' characteristic which creationists claim proves humans are a special creation unrelated to any other life on Earth turns out to be shared by another unrelated animal, in this case a common buff-tailed bumble bee, <i>Bombus terrestris</i>. Given how distantly related humans and bumble bees are, this is not likely to be something both have inherited from a common ancestor, so the most vicarious explanation is that it has evolved separately in both species.<br>
<br>
Since learning from others is the fundamental basis of cultural development, it would be interesting to see whether different populations of this bumblebee species have evolved different cultures, the way different populations of humans and chimpanzees have.
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-83458938044914549462024-03-08T01:29:00.002+00:002024-03-08T01:29:46.981+00:00Unintelligent Design - New Species Of Deep-Ocean Worm - But What Is It For, Exactly?<div class="title-box" style="height: 600px; display: none">
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<div class="left-column" style="text-align: left"><i>Pectinereis strickrotti</i></div>
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<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKKl2SJXJoCBcAprAOOHgGROWTJoPp4nYGPFHtwZxnbbfd87Juets02V6QWpp3Vcqoz7a-2neOEWFhOgVGrcdMOHX3eJqVFNmi0uNeolfiJ3TrnK6cPWeMKobYnoRI1PgiL2xah_1MbkXv_1jX74qJKJXxTLoqu5nq3lIyaGf7AUGQ82tP9QoRtzPNhoUm/s1600/img_2338snakeworm_800x500.jpg"><img alt="" border="0" data-original-height="500" data-original-width="800" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKKl2SJXJoCBcAprAOOHgGROWTJoPp4nYGPFHtwZxnbbfd87Juets02V6QWpp3Vcqoz7a-2neOEWFhOgVGrcdMOHX3eJqVFNmi0uNeolfiJ3TrnK6cPWeMKobYnoRI1PgiL2xah_1MbkXv_1jX74qJKJXxTLoqu5nq3lIyaGf7AUGQ82tP9QoRtzPNhoUm/s1600/img_2338snakeworm_800x500.jpg"/></a></div>
<a href="https://scripps.ucsd.edu/news/new-deep-sea-worm-discovered-methane-seep-costa-rica">New Deep-Sea Worm Discovered at Methane Seep off Costa Rica | Scripps Institution of Oceanography</a><br><br>
<div class="panelplain" style="1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKGI0m-un9gGu9r3Cl9_xuZXm76FM7Vp876oSHfEJ7SabCTRZ1YyA21EJq13hby2ess7cDQGu32MZX7IGXT4kBxvmV8NGvToZ4GCc2sc41Ltf7ho8e-qSq9aEthCruGuEOWan7w14c4F0Zwe4oE2a-Rh8c0HPpjCqBippbVvB2IM93D7UTcoQl4uUrr5wt/s1600/journal.pone.0297961.g001%20%281%29.PNG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKGI0m-un9gGu9r3Cl9_xuZXm76FM7Vp876oSHfEJ7SabCTRZ1YyA21EJq13hby2ess7cDQGu32MZX7IGXT4kBxvmV8NGvToZ4GCc2sc41Ltf7ho8e-qSq9aEthCruGuEOWan7w14c4F0Zwe4oE2a-Rh8c0HPpjCqBippbVvB2IM93D7UTcoQl4uUrr5wt/s1600/journal.pone.0297961.g001%20%281%29.PNG"/></a>
<div class="caption"><b>Fig 1. Pectinereis strickrotti gen. nov., sp. nov. in life.</b><br>
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A, B, D. Several epitokous males swimming near methane seeps of Mound 12 (~1,000 m depth) of the Costa Rica margin and videoed via the submersible DSV Alvin. A. A frame grab from a video taken on <i>Alvin</i> dive 4503 on Feb. 4, 2009. B and D. Frame grabs from video taken on <i>Alvin</i> dive 4987 on Nov. 2, 2018. C. A fragment of an atokous infaunal female was collected at the same depth and locality via sediment pushcore on <i>Alvin</i> dive 4984 on Oct. 30, 2018. A white egg ~350 μm in diameter is visible on the exterior. Scalebar 1 mm. E. An epitokous male swimming near methane seeps of Parrita Scar (~1,000 m depth) of the Costa Rica margin. The specimen was initially caught via slurp with the ROV SuBastian (dive S0218, Jan. 11, 2019) but escaped. <br><br>
<div class="credit">Images A, B, D, courtesy of Woods Hole Oceanographic Institute. E, courtesy of Schmidt Ocean Institute.</div></div>
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One of the hallmarks of good intelligent design is that the designed object must be designed for a purpose. No intelligent designer is going to waste time making something that doesn't have any use. Even a decorative use is a function. As the designer William Morris said, "Have nothing in your house that you do not know to be useful, or believe to be beautiful.", but creationism's designer seems to just design things for the sake of it - half a million different beetles, for example. And now we have the example of a deep-ocean worm that appears to have no other purpose than to make more deep-ocean worms.<br>
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It's almost exactly like these different organisms are being designed by a mindless, natural process without a plan and no sense of purpose!<br>
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According to creationist superstitions in Genesis, every living thing on Earth was created for the benefit of mankind, and, incidentally, named by Adam (as though Adam would have had enough time to name every living species!). So, a challenge to creationists is to tell us what these deep-ocean worms are for in terms of their utility value for humans, and how did Adam dive that deep to name them?<br>
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Its discovery if the subject of an open access paper in PLOS ONE and is described in a Scripps Institute for Oceanography news release:<br>
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<blockquote class="blockit">Greg Rouse, a marine biologist at UC San Diego’s Scripps Institution of Oceanography, and other researchers have discovered a new species of deep-sea worm living near a methane seep some 50 kilometers (30 miles) off the Pacific coast of Costa Rica. Rouse, curator of the Scripps Benthic Invertebrate Collection, co-authored a study describing the new species in the journal PLOS ONE that was published on March 6.<br>
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The worm, named <i>Pectinereis strickrotti</i>, has an elongated body that is flanked by a row of feathery, gill-tipped appendages called parapodia on either side, and Rouse said its sinuous swimming reminded him of a snake. The species was named after Woods Hole Oceanographic Institution’s Bruce Strickrott, lead pilot for the famed deep-sea submersible Alvin, who Rouse said was instrumental in the effort to locate and collect the creature. The research was supported by the National Science Foundation.<br>
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Rouse and his colleagues have encountered roughly 450 species at the Costa Rican methane seeps since 2009, with this latest discovery bringing the number of those species that were new to science to 48. These impressive stats underscore how much more there is left to learn about these ecosystems as well as their biological importance, said Rouse. <br>
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Methane seeps are parts of the seafloor where the powerful greenhouse gas methane escapes from rocks or sediment on the seafloor in the form of bubbles. Unlike deep-sea hydrothermal vents, methane seeps are typically not hotter than the surrounding water. But like hydrothermal vents, methane seep ecosystems are fueled by chemical energy rather than sunlight. This is because some microbes have evolved the ability to consume methane. The microbes that can make methane into food create the base of a food web that at the Costa Rican seeps is dominated by mussels, crabs, and soft-bodied polychaete worms like this new species, said Rouse.<br>
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Strickrott and Rouse first encountered the new species in 2009 at a depth of around 1,000 meters (3,280 feet) during a dive in the <i>Alvin</i> human-occupied submersible, which is operated by the Woods Hole Oceanographic Institution and owned by the U.S. Navy. <br>
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“We saw two worms near each other about a sub’s length away swimming just off the bottom,” said Strickrott. “We couldn’t see them well and tried to creep in for a closer look, but it’s hard to creep in a submarine and we spooked them.”<br>
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Finally, in 2018 the team was able to return to Costa Rica’s methane seeps with <i>Alvin</i>. On a dive to the same spot the worm was first sighted, known as Mound 12, Strickrott was astounded to encounter six or more individuals of the unidentified species they first saw there nearly a decade earlier. For some reason, the worms were much less skittish than they were in 2009 and, using a five-chambered vacuum canister device on Alvin that Strickrott calls the “slurp gun,” they carefully collected several specimens as well as images and video – enough to formally describe what proved to be a new species. <br>
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“The way this thing moved was so graceful, I thought it looked like a living magic carpet,” said Strickrott. “I’m honored that Greg [Rouse] saw fit to name this species after me, it means a lot.”<br>
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<i>Pectinereis strickrotti</i> is a 10-centimeter-long (4-inch) member of the ragworm family (Nereididae). Ragworms are a group of around 500 species of segmented, mostly-marine worms that look a bit like a cross between a centipede and an earthworm. They have elongated bodies with rows of bristled parapodia on their sides and a hidden set of pincer-shaped jaws that can be extruded for feeding. Many species of ragworm also have two distinct life stages: atoke and epitoke. In these species, the worm spends most of its life on the seafloor, often in a burrow, as a sexually immature atoke, but in their life’s final act they transform into sexually mature epitokes that swim up off the bottom into the water column to find mates and spawn.
<div class="panelplain" style="margin: 1em auto"><iframe src="https://www.youtube.com/embed/avZes9P0Zwo" title="New Species of Deep-Sea Worm Discovered off Costa Rica" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe><div class="caption">Males of the new species of deep-sea worm swimming near the seafloor off the coast of Costa Rica on Nov. 2, 2018. <br><div class="credit">Credit: Courtesy of Erik Cordes, Temple U./NSF/HOV Alvin/2018 ©Woods Hole Oceanographic Institution</div></div></div>
The team was able to collect three male <i>Pectinereis strickrotti</i> epitokes and part of one female. Following their successful collection, the team used the specimens to conduct anatomical analysis and to study the worm’s DNA to establish its evolutionary relationships within the ragworm family. The specimens now reside in Scripps’ Benthic Invertebrate Collection and the Museo de Zoología at the Universidad de Costa Rica.<br>
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Compared to most ragworms, <i>Pectinereis strickrotti</i> is unusual in several ways. First, it lives in the deep sea, while the majority of its evolutionary kin inhabit shallower waters. Second, its parapodia are covered in gills, while most ragworms absorb oxygen through their parapodia without the aid of true gills. The males had large spines at the end of their tails, which Rouse said might have something to do with reproduction but would require further study. Finally, owing to the total darkness at 1,000 meters (3,280 feet) under the sea, the new species is blind. Rouse said the worms probably have keen senses of smell and touch to help them navigate their inky world.<br>
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<i>Pectinereis strickrotti</i> has robust, even fearsome-looking jaws, but Rouse said their diet is still unknown and that the species could just as easily be feeding on bacteria as larger fare like other worms. Though its coloration would be a moot point in life, given its pitch black habitat, Rouse said the worm appeared rosy under Alvin’s lights, and that this was probably due to the color of its blood. <br>
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“We’ve spent years trying to name and describe the biodiversity of the deep sea,” said Rouse. “At this point we have found more new species than we have time to name and describe. It just shows how much undiscovered biodiversity is out there. We need to keep exploring the deep sea and to protect it.”<br>
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Rouse and other Scripps researchers will be heading back out to sea later this year in hopes of making even more deep-sea discoveries at methane seeps off the coasts of Alaska and Chile.<br>
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In addition to Rouse, Sonja Huč, Avery Hiley, and Ekin Tilic of Scripps contributed to the study. Tulio Villalobos-Guerrero of the Centro de Investigación Científica y de Educación Superior de Ensenada is the study’s first author and conducted the primary anatomical analysis.<br>
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The Scripps Oceanographic Collections are comprised of millions of biological and geological marine specimens, providing a record of the state of the ocean environment over the past century that serves as a resource to researchers and students all over the world. To support the collections, members of the public can join the membership group Friends of the Collections or consider naming a new species to support the research and preservation required to establish the species in the scientific record permanently.
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<blockquote class="blockit"><span>Abstract</span><br>
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Nereidid polychaetes are well known from shallow marine habitats, but their diversity in the deep sea is poorly known. Here we describe an unusual new nereidid species found at methane seeps off the Pacific coast of Costa Rica. Specimens of <i>Pectinereis strickrotti</i> gen. nov., sp. nov. had been observed dating back to 2009 swimming just above the seafloor at ~1,000 m depth but were not successfully captured until 2018. Male epitokes were collected as well as a fragment of an infaunal female found in a pushcore sample. The specimens were all confirmed as the same species based on mitochondrial COI. Phylogenetic analyses, including one based on available whole mitochondrial genomes for nereidids, revealed no close relative, allowing for the placement of the new species in its own genus within the subfamily Nereidinae. This was supported by the unusual non-reproductive and epitokous morphology, including parapodial cirrostyles as pectinate gills, hooked aciculae, elfin-shoe-shaped ventral cirrophores, and elongate, fusiform dorsal ligules emerging sub-medially to enlarged cirrophores. Additionally, the gill-bearing subfamily Dendronereidinae, generally regarded as a junior synonym of Gymnonereidinae, is reviewed and it is here reinstated and as a monogeneric taxon.<br>
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<span>Introduction</span><br>
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The diversity of Nereididae de Blainville, 1818 compared to other polychaete clades of family rank is well documented, with over 700 accepted species [<a class="newtooltip">1</a>–<a class="newtooltip">4</a>]. Nereidids are generally known from coastal regions, commonly confined to shallow marine habitats, although they also occur in brackish, freshwater, and even moist terrestrial environments [<a class="newtooltip">1</a>, <a class="newtooltip">5</a>–<a class="newtooltip">8</a>]. However, ~10% of the total diversity is known from deep-sea habitats. Currently, 69 nereidid species found in 13 genera are known from below 500 m depth [<a class="newtooltip">9</a>] from various habitats, including hydrothermal vents, cold seeps, polymetallic nodules, foraminifera ooze, whale carcasses, and sunken wood [<a class="newtooltip">10</a>–<a class="newtooltip">15</a>]. The best-represented genera are the polyphyletic Neanthes Kinberg, 1865 (16 species) and Nereis Linnaeus, 1758 (19 species), which includes the deepest known nereidid recorded, Nereis profundi Kirkegaard, 1956 from 7,290 m depth. One genus, the monotypic Typhlonereis Hansen, 1879 is exclusive to deep environments.<br>
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The deep sea encompasses a diverse, vast mosaic of understudied and poorly sampled habitats [<a class="newtooltip">16</a>]. Several surveys that have sampled deep waters from distinct regions suggest polychaete biodiversity is severely underestimated [<a class="newtooltip">17</a>–<a class="newtooltip">19</a>], rendering our knowledge of it limited [<a class="newtooltip">20</a>–<a class="newtooltip">22</a>]. We can assume, therefore, that oceanic depths still host a vast number of yet undescribed nereidid species, although it is noteworthy that there has been a relatively continual discovery of new deep-sea nereidids since about the 1960s (e.g., [<a class="newtooltip">6</a>, <a class="newtooltip">10</a>–<a class="newtooltip">12</a>, <a class="newtooltip">14</a>, <a class="newtooltip">15</a>, <a class="newtooltip">23</a>–<a class="newtooltip">36</a>].<br>
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While deep-water nereidids continue to be discovered, information about their behavior and inference about morphological adaptations has been scarce. According to Fauchald [<a class="newtooltip">11</a>, <a class="newtooltip">12</a>], deep-sea nereidids share a few unusual prostomial and parapodial features when compared to shallow-living relatives, such as the absence of eyes, prolonged appendages and chaetae, and posterior chaetigers with extended notopodia and elongated neuropodia. Notably, the reduction of eyes and the elongation of parapodial appendages and chaetae fall under the general specialization to aphotic environments of some subterranean and cave (troglobiotic) nereidids placed in Namanereidinae Hartman, 1959 [<a class="newtooltip">37</a>–<a class="newtooltip">39</a>]. These morphological adaptations, inherent to the ‘darkness syndrome’ [<a class="newtooltip">40</a>], have been shown for a few other polychaete clades containing cave and deep-sea members (e.g., Scalibregmatidae Malmgren, 1867 [<a class="newtooltip">41</a>] and Aphroditiformia Levinsen, 1883 [<a class="newtooltip">42</a>–<a class="newtooltip">45</a>]), suggesting that these are also convergent evolutionary traits for nereidids living at aphotic depths.<br>
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Genetic tools have been instrumental in developing a better understanding of the diversity among nereidids. Several new species or previously synonymized ones have been described, reinstated, or delimited through the integration of morphological data and molecular markers of apparently cryptic species (e.g., [<a class="newtooltip">46</a>–<a class="newtooltip">57</a>]). Molecular data has also been utilized to investigate phylogenetic relationships at a broader scale among nereidid taxa [<a class="newtooltip">15</a>, <a class="newtooltip">57</a>, <a class="newtooltip">58</a>]. Recently mitochondrial genomes (mitogenomes) have been sequenced for a variety of nereidid species (e.g., [<a class="newtooltip">59</a>–<a class="newtooltip">66</a>], providing a rich dataset to assess phylogenetic relationships with more confidence. Alves et al. [<a class="newtooltip">67</a>] assessed the monophyly and phylogenetic relationships of the presently accepted subfamilies and provided an ancestral state reconstruction of pharyngeal structures using mitogenomic data. They rejected the monophyly of the subfamilies Nereidinae de Blainville, 1818 and Gymnonereidinae Banse, 1977 as currently recognized and revealed that the occurrence of papillae and paragnaths may not be reliable features to diagnose major groups. We revisit the nereidid subfamily issue here with regards to Dendronereidinae Pillai, 1961.<br>
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This study describes a new, morphologically unusual, nereidid species belonging to a new genus using specimens found near methane seeps at ~1,000 m depth off Costa Rica in the eastern Pacific. This new species is remarkable for its dorsal and ventral anterior parapodial cirri, modified as gills, and hooked-shaped posterior aciculae, both unique features among Nereididae. Its mitochondrial genome was sequenced as well as those of two shallow-water nereidid species. This allowed for a new mitogenomic analysis to evaluate the position and relationships of the new genus within Nereididae. <br>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgauXB7fNaKEuLUa9G_3r-9gk31Nsar8VwBAGrmxmHt0a-lUK70J_NfasNI0m0yxz34e4k_ad-1S6K2qNORhRpwVm3B4DMPaxFhvMqWfJ6LBQH6Oym6E4pqkd4cuxQ3n37VzXi4F8SBKYNZB6ugM7lfM3mmgLJbtWn0HlCrJ1sMiT3PmIR8TdAY7h3uU6s/s1600/journal.pone.0297961.g002.PNG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgauXB7fNaKEuLUa9G_3r-9gk31Nsar8VwBAGrmxmHt0a-lUK70J_NfasNI0m0yxz34e4k_ad-1S6K2qNORhRpwVm3B4DMPaxFhvMqWfJ6LBQH6Oym6E4pqkd4cuxQ3n37VzXi4F8SBKYNZB6ugM7lfM3mmgLJbtWn0HlCrJ1sMiT3PmIR8TdAY7h3uU6s/s1600/journal.pone.0297961.g002.PNG"/></a>
<div class="caption"><b>Fig 2. Haplotype analysis and mitogenome phylogeny.</b><br>
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A. Haplotype network of COI data acquired for the three male and one female specimen of <i>Pectinereis strickrotti</i> gen. nov., sp. nov. The holotype sequence (male epitoke) is marked with * and has five base pairs different from the female (infaunal fragment). B. Maximum likelihood (ML) tree derived from analysis of the concatenated 15-gene mitochondrial genome dataset, with the 13 PCGs translated to amino acids. Support values at nodes are bootstrap support percentages after 1,000 pseudoreplicates.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL2xH1EstVErANNm9EHOuBtFo5sUSUmal6J4O9Cl2n6_I5IWBjpgGccGJe1uxAAe7lL7yerBXyrk1ngKllbHV1E5Ax1_VbCCfVsjg6nxtJF-nFlZS8g2W8VLREFj_HNRR1BBCW8tqQgZEfiqMpVrQ5cDBV1tgYnY43qp36ylgGRH9Tj1CYI7C-fWow9N-x/s1600/journal.pone.0297961.g004.PNG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL2xH1EstVErANNm9EHOuBtFo5sUSUmal6J4O9Cl2n6_I5IWBjpgGccGJe1uxAAe7lL7yerBXyrk1ngKllbHV1E5Ax1_VbCCfVsjg6nxtJF-nFlZS8g2W8VLREFj_HNRR1BBCW8tqQgZEfiqMpVrQ5cDBV1tgYnY43qp36ylgGRH9Tj1CYI7C-fWow9N-x/s1600/journal.pone.0297961.g004.PNG"/></a>
<div class="caption"><b>Fig 4. <i>Pectinereis strickrotti</i> gen. nov., sp. nov. male anatomy.</b><br>
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A, B, D-F. Paratype (SIO-BIC A9889), epitokous male: A, whole body of living specimen in dorsal view; B, anterior region of living specimen in dorsal view; D, prostomium of preserved specimen in frontal view; E, posterior end of preserved specimen in dorsal view; F, post-natatory chaetigers and pygidium of preserved specimen in dorsolateral view. C. Holotype (SIO-BIC A9836), epitokous male: anterior region of preserved specimen in dorsal view. Scale bars: A, ~20 mm; B, ~5 mm; C, 5 mm; D, 1 mm; E, 3 mm; F, 0.5 mm. <br><br><div class="credit">Credits: A, B, Ekin Tilic; C, Tulio Villalobos; D-F, Greg Rouse.</div></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG6zRe6kWA9_9lKNC4b0TUiM0ccSnNy4qY_cbPsPXV9gi0EXG8EhOKDS0Oed4TDfqbFvTq1TnJKDN-KeW9pnwHx7JJaxvpQ0eE_z92raOQl177vX46beG7I0QwM7BqdpuNhobvYgTo_AFLwbvYB0XMwLlyyMPu3OjO6IQDAnLTcLbQXcr4iB1f9L-vA89X/s1600/journal.pone.0297961.g005.PNG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG6zRe6kWA9_9lKNC4b0TUiM0ccSnNy4qY_cbPsPXV9gi0EXG8EhOKDS0Oed4TDfqbFvTq1TnJKDN-KeW9pnwHx7JJaxvpQ0eE_z92raOQl177vX46beG7I0QwM7BqdpuNhobvYgTo_AFLwbvYB0XMwLlyyMPu3OjO6IQDAnLTcLbQXcr4iB1f9L-vA89X/s1600/journal.pone.0297961.g005.PNG"/></a>
<div class="caption"><b>Fig 5. <i>Pectinereis strickrotti</i> gen. nov., sp. Nov. male anatomy details.</b><br>
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A, B, D, E. Holotype (SIO-BIC A9836), epitokous male: A, prostomium and everted proboscis in dorsal view (arrow pointing additional abnormal antennae); B, everted proboscis in ventral view; C, everted proboscis in lateral view; E, branchiferous chaetigers in ventrolateral view (numbers referring to chaetiger). D. Paratype (SIO-BIC A9889), epitokous male: dissected anterior end in ventral view. Abbreviations: brd, dorsal gills; brv, ventral gills; pb, pharyngeal bulb; oe, esophagus. Scale bars: A–C, 2 mm; D, 3 mm; E, 1 mm. <br><br><div class="credit">Credits: A-C, E: Tulio Villalobos; D, Greg Rouse.</div></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGOA35hDNnI4JEoN1iDF_cu6UVSASH5zMpko85qYasAUkWebq3yHSVT4CNvhBJjd5U7kW3NMNwFE7Y1MneMhLNZlRyqn_H8vieiEkV7fCeW-J3vtZnGE0x9wJGAJXbXs06RG-UMrSZFynyKaEhkAYaBhc2EMiBPH7w3FdFYAX-ElILCiPdXG0zsxH0HYNo/s1600/journal.pone.0297961.g006.PNG"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGOA35hDNnI4JEoN1iDF_cu6UVSASH5zMpko85qYasAUkWebq3yHSVT4CNvhBJjd5U7kW3NMNwFE7Y1MneMhLNZlRyqn_H8vieiEkV7fCeW-J3vtZnGE0x9wJGAJXbXs06RG-UMrSZFynyKaEhkAYaBhc2EMiBPH7w3FdFYAX-ElILCiPdXG0zsxH0HYNo/s1600/journal.pone.0297961.g006.PNG"/></a>
<div class="caption"><b>Fig 6. <i>Pectinereis strickrotti</i> gen. nov., sp. nov. male parapodia.</b><br>
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A-H. Holotype (SIO-BIC A9836), epitokous male: A, parapodium of chaetiger 2; B, parapodium of chaetiger 10; C, parapodial dorsal cirrus of chaetiger 5; D, parapodial ventral cirrus of chaetiger 5; E, parapodium of chaetiger 22; F, parapodium of chaetiger 33; G, parapodium of chaetiger 55; H, parapodium of chaetiger 146. I. Paratype (SIO-BIC A9889), epitokous male: parapodium of pre-pygidial (PM) chaetigers. White arrows indicate branchial filament. Abbreviations: dl, dorsal ligule; dp, dorsal cirrophore; ds, dorsal cirrostyle; in, inferior lobe; ml, median ligule; po, neuropodial postchaetal lobe; pr, notopodial prechaetal lobe; vl, ventral ligule; vp, ventral cirrophore; vs, ventral cirrostyle. Scale bars: A, B, E-H, 0.5 mm; C, D, I, 0.2 mm. <br><br><div class="credit">Credits: A-H, Tulio F. Villalobos; I, Greg Rouse.</div></div>
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<div class="creditl">Villalobos-Guerrero TF, Huč S, Tilic E, Hiley AS, Rouse GW (2024) <br>
A remarkable new deep-sea nereidid (Annelida: Nereididae) with gills. <br>
<i>PLoS ONE</i> <b>19</b>(3): e0297961. https://doi.org/10.1371/journal.pone.0297961<br>
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<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by PLoS. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote><br>
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As an example of the mindless process of evolution, this marine worm is a wonder; as an example of something intelligently designed for the benefit of humans, like creationists insist everything was, it makes no sense whatsoever. Why design a worm that lives so deep in the ocean that humans need special equipment even to be aware of it? And even if, unlike most creatinists you have the humility to take humans out of the equation, a worm that lives in a highly specialised environment and lives only to make more copies of itself, make no sense as the result of an intelligent design process because design without ultimate purpose is simply not intelligent design.
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<div class="panelplain" style="height: 1025px"><br><center><span class="t2">The Unintelligent Designer: Refuting The Intelligent Design Hoax</span></center><br>
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<div class="right-column" style="flex: 1.5">ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.<br>
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<div class="panelplain" style="height: 1025px"><br><center><span class="t2">The Malevolent Designer: Why Nature's God is Not Good</span></center><br>
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<div class="left-column" style="flex: 1"><a target="_blank" href="https://www.amazon.com/dp/B08L5K3376?&_encoding=UTF8&tag=rosarub-20&linkCode=ur2&linkId=28b7b75a32c9380874eaac84da42364d&camp=1789&creative=9325"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7gmq4ygYggF9B9CFCknVCPCDjXBYz6k14niMIa_GnLskwA8ruwsKEsEDcfaaIMYOAuTVAO7nAZb8QWn3yLkAnnrr6FxW8I-dMh6Z-LXAp9TF_eiWnGeHPI3-VeYMW97_J4C23UZQ2k41o3b-jgAA4O7W1RKYM6N3aTbjWIUyQBEkd_rMNK8bc1swo1h78/s1600/KindleMalevolentDesignerCover.jpg"/></a>
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<div class="right-column" style="flex: 1.5">This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.<br>
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com1tag:blogger.com,1999:blog-7583674511519808833.post-20021540203856971762024-03-07T16:29:00.002+00:002024-03-08T01:02:54.788+00:00Creationism in Crisis - Evolution of Porcini Fungus<div class="title-box" style="height: 600px; display: none">
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<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcDw-Ypejesj1qMWS6Qe_MLgXKn35Wa0yfbR1OWghK7RhRQ3H4usIud69BiOeXN-wJqkN_OYa1yU8vBU8BfzisSZ_OTyeXkpZbg5_fzt00TuA5TDSOIAvfCyR7OytXYExrnfx1vrknhMINEKBaWAecjCtV-5pM1lKKFIM8qDe3lqryUbGyfmtF_w5ajsJK/s1600/51GM8+IjOaL.jpg" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" data-original-height="361" data-original-width="500" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcDw-Ypejesj1qMWS6Qe_MLgXKn35Wa0yfbR1OWghK7RhRQ3H4usIud69BiOeXN-wJqkN_OYa1yU8vBU8BfzisSZ_OTyeXkpZbg5_fzt00TuA5TDSOIAvfCyR7OytXYExrnfx1vrknhMINEKBaWAecjCtV-5pM1lKKFIM8qDe3lqryUbGyfmtF_w5ajsJK/s1600/51GM8+IjOaL.jpg"/></a></div>
<a href="https://attheu.utah.edu/facultystaff/a-tale-of-terroir-porcinis-evolved-to-the-local-environment/">A tale of terroir: Porcinis evolved to the local environment – @theU</a>
<div class="panelplain" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxbb421jl_vAJzL9h9y0sLQmlUFvzQB8OpCXmRP4OwZMrI73bA6kSFk-4PK1mISJgM8V8eOio_q7NtyqpcY7NNLRlgnAsDSN5DVX4IvBS7TMuuJVSllslVfu5QXewuFEubgCkNmMXfi-WSmRHAt_R-2UtFS4l_2jNgOHgizTLxL2mrykPdSGYv4QaVJg/s1600/BasicStructureOfFungi_1200x628.png" ><img alt="Structure of Fungi" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxbb421jl_vAJzL9h9y0sLQmlUFvzQB8OpCXmRP4OwZMrI73bA6kSFk-4PK1mISJgM8V8eOio_q7NtyqpcY7NNLRlgnAsDSN5DVX4IvBS7TMuuJVSllslVfu5QXewuFEubgCkNmMXfi-WSmRHAt_R-2UtFS4l_2jNgOHgizTLxL2mrykPdSGYv4QaVJg/s1600/BasicStructureOfFungi_1200x628.png"/></a><div class="caption">This illustration is a little misleading because mycelia are often much larger than any of their mushrooms that appear on the surface of the soil or tree stumps. Fungi can grow up to a half a mile of the thread-like hyphae a day. In fact, the largest known organism on the planet is the Humongous Fungus (<i>Armillaria ostoyae</i>) in The Malheur National Forest, Oregon, measuring 2,385 acres (3.72 square miles) in area. It is estimated to be between 1900 and 8650 years old.<br>
<div class="credit">Photo credit: FoodPrint.org</div></div></div>
The edible porcine fungus (<i>Boletus edulis</i>) also known as the boletus or penny bun is highly prized culinary delicacy throughout much of Europe. However, there is something strange about it evolution, especially in North America, according to a new report in the journal <i>New Phytologist</i>.<br>
<br>
Creationists should note here that the scientists who produced the report see this 'problem' entirely within the Theory of Evolution by Natural Selection (TOE). The strangeness is not a problem for the theory but an example of how a fundamental principle of the theory - environmental selection - operates in North America.<br>
<br>
The 'problem' is that while <i>Boletus edulis</i> exists in North America as a number of different varieties and genetically distinct populations, probably caused not so much by geographical isolation as environmental adaptation, albeit with regular ingress from surrounding populations, In Eurasia, a single genetic lineage dominates from Spain to Georgia to Scandinavia, so the interesting question is why does is the species genetically continuous in Eurasia but fragmented in North America; what is the difference between the two landmasses that causes this difference. <br>
<br>
The Eurasian and North American populations are believed to have become separated during a period of climatic change and the onset of glaciation, 1.62–2.66 years ago.
Attempts to segregate populations of <i>Boletus edulis</i> into distinct species based on phenotype have foundered on the genetic evidence, illustrating how small genetic differences can give large phenotypic differences and how a species in the process of speciating passes through a stage at which the diverging populations have not diverged sufficiently to qualify as new taxons because the practice of taxonomy tries to fit a continuous process into a series of distinct events.<br>
<br>
The 'problem' is the subject of a free access paper in the journal <i>New Phytologist</i> by Keaton Tremble and Bryn T. M. Dentinger from Utah University, Utah, USA. together with J. I. Hoffman from Bielefeld University, Germany, and was described in a University of Utah press release:<br>
<br><a name='more'></a>
<blockquote class="blockit">The Dentinger Lab at the Natural History Museum of Utah has published a provocative new paper in the journal New Phytologist that describes their work with the much-beloved mushroom, <i>Boletus edulis</i>, better known by gastronomers worldwide as the porcini. In the paper, Keaton Tremble and Bryn Dentinger present a first-of-its-kind genetic survey of porcini mushrooms across the Northern Hemisphere. By evaluating the genetic code of these samples from across the globe, they learned that these delicious fungi evolved in surprising ways—contrary to the expectations of many who might think that geographic isolation would be the primary driver for species diversity. In fact, there are regions in the world where porcini maintain their genetic distinctiveness in local ecological niches, even if they are not isolated geographically from other genetic lineages.<br>
<br>
The French word <i>terroir</i>, made famous by viticulturists, immediately comes to mind. <i>Terroir</i> describes all of the local factors such as soil types, amount of sunshine, degree of slope, microclimate, soil microorganisms, etc., that make each plot of land yield distinctive wines. It is a celebration of the local ecology and its impact on the vines, grapes and finished product. Tremble and Dentinger’s new study offers mushroom hunters tantalizing data to claim that the porcinis in their secret forest patch express the qualities of their terroir in the same way as the best wines in the world.<br>
<br>
But this isn’t the point of the study. With the advent of genetic sequencing, most mycology genetic studies have focused on describing the unique characteristics of fungi in a small geographic area. Tremble and Dentinger wanted to do something different. Rather than just comparing a group of mushrooms from Colorado to a group in California in order to call them different species, they wanted to better understand the global trends in how the genetic code was preserved or changed in porcini. “Our study is important because it goes beyond overly simplistic sampling method used in the past,” states Dentinger.<br>
<br>
What they found is that porcini have evolved in different, but clearly recognizable ways across the globe. “In North America, there is a strong stratification of separate genetic populations in local areas, despite the fact that they aren’t reproductively isolated,” explains Tremble. “Yet in Europe, there is one lineage that dominates from Spain to Georgia to Scandinavia.”<br>
<br>
Evolutionary biologists typically believe that there is one evolutionary strategy that governs the speciation process for a particular organism, but Tremble and Dentinger have shown that porcini actually exhibit multiple, divergent strategies. In fact, this is the first genetic study of any organism to show such a result at a global scale.<br>
<br>
A related, significant result is a refutation of the traditional notion that isolation is the main way that species develop their uniqueness. As the Encyclopedia of Ecology (Second Edition, 2019) proudly states, “all evolutionary biologists agree that geographic isolation is a common, if not the most common, mechanism by which new species arise (Futuyma, 2013).”<br>
<br>
<span class="t2">More than identifying mushrooms</span><br>
<br>
It’s an exciting time to be a mycologist. Not only is the fungal kingdom barely explored and described, but DNA sequencing technology has introduced a seismic shift in how mycologists classify fungi. For millennia, humans have identified mushrooms that are good to eat from ones that are poisonous based on how they looked or their phenotype. But phenotypes can be deceiving – consider a brother and sister who have different hair colors, different nose shapes, etc. They are still more genetically similar to each other than to other people in the population. Thus, genetic similarities are considered the true marker of different species, bucking the trend of mushroom identification that stretches back to the beginning of humanity.<br>
<br>
On top of this, let’s remember that mushrooms are just the reproductive structure of the main organism, called a mycelium (see the illustration below, “The Basics of Fungi”). Like icebergs, mycelia only show us the tip of themselves, while the massive fungal body lives underground, bound up with the roots of trees. <i>Boletus edulis</i> spreads geographically thanks to the tiny spores released from the porcini mushrooms, borne on the wind, mammals and even flies. Thus, biologists are tempted to believe that in whatever geographic area where spores can fly, a species will be defined by the genetic mixing within this geographic space.<br>
<br>
Tremble and Dentinger’s study soundly refutes this assumption.<br>
<br>
In North America, different genetic lineages exist side-by-side, and despite genetic evidence of intermixing, local ecological factors played a bigger role in maintaining the distinction of these lineages. “Utah happens to be one of the areas where two distinct lineages live,” notes Dentinger. What these lineages show is that the local ecology is a stronger factor in maintaining their genetic distinctiveness than genetic flow from other lineages.<br>
<br>
“This paper shows that you don’t need isolation for genetic divergence,” Tremble asserts. “The force of ecological adaptation is so strong in <i>Boletus edulis</i> that even though you can disperse spores basically anywhere, there is strong selection to adapt to specific environments.”<br>
<br>
<span class="t2">The marvels of the dried porcini</span><br>
<br>
The secret to their study resides deep in the heart of natural history museums: collections of mushrooms. Tremble is a doctoral candidate in the School of Biological Sciences, defending his thesis in spring 2023 to receive his degree in evolutionary biology. He made a fortuitous choice when working with Dentinger as his advisor; as the curator of mycology at NHMU, Dentinger has established NHMU’s Genomics Lab to be able to analyze DNA quickly and efficiently. More importantly for this study, Dentinger’s professional contacts at natural history museums around the world helped Tremble access the 160 samples that would have been near impossible to collect otherwise.<br>
<br>
“You have to rely on opportunistic encounters in nature to collect a living sample,” Dentinger explains. “This is fundamentally different from working with plants, which are there in every season, and animals, which you can bait.” Thus, it would have taken an incredible amount of logistics, timing and luck to find, correctly identify and ship 160 different samples across the Northern Hemisphere back to the lab at NHMU.<br>
<br>
Instead, “our study was all possible thanks to fungaria,” Dentinger states, referring to the name for fungus collections in museums. They plumbed the depths of NHMU’s fungarium and reached out to collaborators around the globe.<br>
<br>
“Without the accumulated field work by 80 different people, this would not have been possible,” Tremble notes. All of the samples were dried porcini mushrooms, stable and ready for Tremble to extract their DNA. Since <i>Boletus edulis</i> mycelia have a surprisingly long lifespan (estimated to be up to 45 years), they used samples only dating back to 1950 to make sure that the study kept to just a few generations.<br>
<br>
Tremble used sophisticated software to run statistical analyses on these samples. He genotyped 792,923 SNPs (pronounced “snips,” short for single nucleotide polymorphisms), which are the individual ways in which the 160 porcini genomes differed from one another. In order to classify major lineages, he filtered out the SNPs that were only present in one sample (which would be considered just a “family unit” or individual variant) so that he could instead observe only major differences between genomes. In the end, Tremble identified six major lineages.<br>
<br>
Feeding his data into mathematical models, Tremble uncovered a complex web of genomic mixing, where lineages remained distinct despite evidence that other lineages had mixed with them. Their modeling and geographical sample data showed that this ability to remain distinct was due to environmental adaptation, not physical isolation.<br>
<br>
<span class="t2">Lineages or species?</span><br>
<br>
Tremble and Dentinger take a decidedly agnostic approach to the question of whether they should be identifying these 6 distinct lineages as “species.” They abstain from doing so in their paper because they want to focus on the genetic data and the larger questions related to strategies in evolutionary biology. Plus, that species discussion is one vexed conversation.<br>
<br>
“There is no formal process for defining a species,” Tremble notes, “it’s an ongoing debate. We didn’t want to call them species or subspecies because it automatically implies that they are separately evolving groups, which they definitely aren’t.” They decided to call them lineages because this term is genetically resolvable, that is, lineages can be quantifiably distinguished from one another using statistical genetic approaches.<br>
<br>
But that doesn’t mean they don’t want to tackle the taxonomy. “This is going to be a forthcoming article in a different journal,” Dentinger says. The world of fungi never experienced the Victorian-era explosion of identifying and naming species that happened with animals and plants. With only an estimated 5% of fungi diversity being identified, naming and taxonomy must happen, if only to help mycologists speak about their subject.<br>
<br>
However the species-subspecies taxonomy for <i>Boletus edulis</i> shakes out, Dentinger assures us of one thing: “<i>Terroir</i> is more important than people thought.”<br>
<br>
So, find a mushroom hunter and get on his or her good side in order to find the porcini best adapted to your palate.
</blockquote>
Technical detail and background to the research is given in the trio's free access paper in <i>New Phytologist</i>:
<blockquote class="blockit"><span class="t2">Summary</span><br>
<ul class="blob dbl1">
<li>In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, <i>Boletus edulis</i>, a globally distributed species complex with broad ecological amplitude.</li>
<li>By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure.</li>
<li>We show that <i>B. edulis</i> exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62–2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene–Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation.</li>
<li>Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.</li>
</ul><br>
<span class="t2">Introduction</span><br>
<br>
Understanding the complex evolutionary pathways by which populations diverge and new species form has long been a goal of evolutionary biology (Fisher, <a class="newtooltip">1930</a>; Theodosius, <a class="newtooltip">1982</a>). Beyond gaining fundamental knowledge about the mechanisms that generate and maintain diversity, understanding the evolutionary history of genotypes and phenotypes allows us to predict how these characteristics will be impacted by environmental change. However, this understanding is challenging to achieve because the evolutionary processes that drive genetic divergence, such as demography, introgression, and adaptation, rarely act in isolation (Coyne et al., <a class="newtooltip">2004</a>). Moreover, the dynamic interaction of these processes can produce differing signatures of divergence depending on the geographic and temporal scale of the study (Bierne et al., <a class="newtooltip">2013</a>; Martin et al., <a class="newtooltip">2013.1</a>; Peñalba et al., <a class="newtooltip">2019</a>). To overcome the limitations of scale, and disentangle the complex evolutionary web weaved by the speciation process, research must be conducted within a global context.<br>
<br>
Tractable systems that exhibit dynamic properties for which hypotheses can be generated and tested are essential to studying processes that give rise to genetic divergence in wild organisms. Species that are common, widely distributed geographically and ecologically, and highly variable are ideal targets for determining the genetic basis of divergence (Hoban et al., <a class="newtooltip">2016</a>). For example, systems such as the monkey flowers (<i>Mimulus</i> spp.) (Ferris et al., <a class="newtooltip">2017</a>; Puzey et al., <a class="newtooltip">2017.1</a>; Vallejo-Marín et al., <a class="newtooltip">2021</a>), black cottonwood (<i>Populus trichocarpa</i>) (Evans et al., <a class="newtooltip">2014</a>; Geraldes et al., <a class="newtooltip">2014.1</a>; McKown et al., <a class="newtooltip">2014.2</a>), and three-spine stickleback (<i>Gasterosteus aculeatus</i>) (Hohenlohe et al., <a class="newtooltip">2010</a>; Feulner et al., <a class="newtooltip">2015</a>; Marques et al., <a class="newtooltip">2018</a>) have been used to investigate how the complex interaction of demography, introgression, and local adaptation gives rise to genetic variation and population differentiation during speciation. However, none of these systems exhibit a truly global distribution or continuous ecological breadth, limiting our ability to investigate the interaction of evolutionary processes unconstrained by geography or ecology. Moreover, these examples give insight into processes in only a few plants and animals, limiting the generality of the observations. The third major eukaryotic lineage, Fungi, remains critically understudied (Coyne et al., <a class="newtooltip">2004</a>; Giraud et al., <a class="newtooltip">2008</a>; Gladieux et al., <a class="newtooltip">2014.3</a>) despite its ecological importance, enormous diversity, and more tractable genomes. The globally distributed prized edible ‘porcini’ mushroom, <i>Boletus edulis</i>, fulfills the need to study processes that both give rise to genome-wide divergence at a global scale and include organisms other than plants and animals.<br>
<br>
Boletus edulis Bull. (‘porcini’) is a well-known ectomycorrhizal species complex that is found in nearly all temperate ecosystems across the northern hemisphere (Smith, <a class="newtooltip">2005</a>). Due to extensive phenotypic variation (Fig. 1), the taxonomy of <i>B. edulis</i> is a matter of some controversy with many alternative classifications (Arora, <a class="newtooltip">2008.1</a>; Dentinger et al., <a class="newtooltip">2010.1</a>; Arora & Frank, <a class="newtooltip">2014.4</a>). Current molecular evidence is equally ambiguous, indicating that this complex group may be in the early stages of speciation (Coyne et al., <a class="newtooltip">2004</a>; Beugelsdijk et al., <a class="newtooltip">2008.2</a>; Dentinger et al., <a class="newtooltip">2010.1</a>; Tremble et al., <a class="newtooltip">2020</a>). Taken together, the combination of morphological variation, enormous ecological amplitude, holarctic distribution, and small genome (c. 50 Mbp) makes <i>B. edulis</i> an ideal natural system to investigate the roles of demography, introgression, adaptation, and isolation in the speciation process at a global scale. Here, we utilize population genomics, ecological niche, and demographic modeling to investigate the primary forces driving lineage divergence within <i>B. edulis</i> and to identify loci under putative selection within a global and historical context.<br>
<div class="panelplain" style="margin: 1em 5%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWaOOB2lHx90cuVFzluCY4NzctripRjs8Dgrb-KbRbSZgU9x4RoffaRe4qif0AYgZZhZLjM9Cg5aanzGDVm6Pcvfjq1gPZLMX5oMa1yRc6vR8eUTH0GD8HRQ_kYBIXfFg28ie1WhVoa5XzumdS7rcBfWbiNRv1DmoGyhe_UaZcavBOZa-upsvQJWg9AV29/s1600/nph18521-fig-0001-m.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWaOOB2lHx90cuVFzluCY4NzctripRjs8Dgrb-KbRbSZgU9x4RoffaRe4qif0AYgZZhZLjM9Cg5aanzGDVm6Pcvfjq1gPZLMX5oMa1yRc6vR8eUTH0GD8HRQ_kYBIXfFg28ie1WhVoa5XzumdS7rcBfWbiNRv1DmoGyhe_UaZcavBOZa-upsvQJWg9AV29/s1600/nph18521-fig-0001-m.jpg"/></a>
<div class="caption">Examples of phenotypic variation across the global distribution of <i>Boletus edulis</i>. Numerous attempts have been made to segregate groups of <i>B. edulis</i> into new species based on this phenotypic variation, yet these attempts have not been corroborated by genetic evidence.</div></div>
</blockquote>
Creationists wishing to maintain the childish delusion that the Theory of Evolution is about to be replaced in mainstream biology by their childish superstition involving magic and a supernatural magician creating things from nothing and making physics and chemistry do things they couldn't do on their own, might like to ignore how the scientists have no doubt at all that they are talking about an evolutionary process; the question is over the mechanism not the fact of evolution, with a side issue about whether evolution has progressed to the point that the different 'lineages' of <i>B. Edulis</i> between Eurasia and North America and within North America itself, have diverged enough to be regarded as distinct species.<br>
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
<br />
Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-22114088907772478962024-03-07T00:27:00.001+00:002024-03-07T00:27:37.538+00:00Creationism in Crisis - 500 Million Year-Old Fossils Reveal the Answer to an Evolutionary Riddle<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox" style="gap: 0">
<div class="left-column" style="text-align: left; flex: 2">Artist's reconstruction of <i>Gangtoucunia aspera</i> as it would have appeared in life on the Cambrian seafloor, circa 514 million years ago. The individual in the foreground has part of the skeleton removed to show the soft polyp inside the skeleton.</div>
<div class="right-column" style="text-align: right; flex: 1">Reconstruction by Xiaodong Wang</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5Dk5VmSOVtoGX1PCbt1z1UEgwUQ_QzllmSlHZpxbfbV5ef8ERfyAhhA7HXz1bqeJuhAo1lt91qf1ozGLx7O4ifo4EjyxFwiPzQd5gRjdtRoeOMQwe_Kh-roFsZ9uzvpLIsHg14TqL3Nr5skxuHAQTGokrA9Gf4vOMJqiO-Gzc7MsmMK5YEGJZ4g5H1A/s1600/Artistic%20reconstruction.jpeg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5Dk5VmSOVtoGX1PCbt1z1UEgwUQ_QzllmSlHZpxbfbV5ef8ERfyAhhA7HXz1bqeJuhAo1lt91qf1ozGLx7O4ifo4EjyxFwiPzQd5gRjdtRoeOMQwe_Kh-roFsZ9uzvpLIsHg14TqL3Nr5skxuHAQTGokrA9Gf4vOMJqiO-Gzc7MsmMK5YEGJZ4g5H1A/s1600/Artistic%20reconstruction.jpeg"></a><div class="caption">Artist's reconstruction of <i>Gangtoucunia aspera</i> as it would have appeared in life on the Cambrian seafloor, circa 514 million years ago. The individual in the foreground has part of the skeleton removed to show the soft polyp inside the skeleton. <br>
<br>
<div class="credit">Reconstruction by Xiaodong Wang.</div></div></div>
<a href="https://www.eurekalert.org/news-releases/969849">500 million year-old fossils reveal answer to evolutionary riddle | EurekAlert!</a><br>
<br>
It must be galling to the leaders of the Creationist cults when science closes yet another gap and casually refutes the misleading claims they have fooled their cult followers with. It's much easier for the frauds to play to the parochial ignorance and childish thinking of their followers who will always assume that if science can't explain something, the locally popular god must have done it, ignoring the false dichotomy fallacy underpinning that deception.<br>
<br>
Some of the gaps are artificial, obviously, being created by Creationists from misrepresentations of the actual science, such as claiming there are no transitional fossils showing, for example, a half chimpanzee - half human, but some of them are genuine gaps in the fossil record, although these tend to be ignored by creationist frauds because it would require a detailed knowledge of the evidence to appreciate where the real gaps are, and a detailed knowledge of the evidence is something no Creationist can afford to have.<br>
<br>
One such gap, until now, was the early evolution of skeletal animals. The first fossils of skeletal animals appeared in the fossil record 550-520 million years ago during the so-called the Cambrian Explosion, which must be one of the slowest explosions on record, occurring over several tens of millions of years, but nevertheless a period of rapid evolution and diversification into different body-plans in the early history of multicellular organisms. <br>
<br>
Many of these early fossils are simple hollow tubes ranging from a few millimetres to many centimetres in length. However, what sort of animals made these skeletons was almost completely unknown, because they lack preservation of the soft parts needed to identify them as belonging to major groups of animals that are still alive today.<br>
<br>
Now though, a team of palaeontologist led by Dr Luke A. Parry of the Department of Earth Sciences, University of Oxford, Oxford, UK, Dr Xiaoya Ma and PhD student Guangxu Zhang, of the Institute of Palaeontology, Yunnan University, Kunming, People's Republic of China, and Dr Jakob Vinther from the Schools of Earth Sciences and Biological Sciences, University of Bristol, UK have analysed a collection of exceptionally well preserved fossils from 514 million years ago that include four specimens of <i>Gangtoucunia aspera</i> with soft tissues still intact.<br>
<br>
Just to clarify that , soft-tissue term, before Creationist quote miners misrepresent it: fossilised soft tissue is not soft. It simply means the soft tissue was preserved long enough for it to become mineralised, just as bones, shells and teeth become mineralised in fossils of hard tissue. It is <b>not</b> evidence that these fossils are just a few thousand years old, like Creationist fraud claim dinosaur soft tissue fossils are (they are not soft either, by the way). <br>
<br>
Before long, we can expect Creationists to either be claiming these 'soft tissues' have been carbon-dated and found to be recent, or that they haven't been carbon-dated because the scientists were afraid they would be found to be recent!<br>
<br>
As the Oxford University News release explains:
<a name='more'></a>
<blockquote class="blockit">
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQylCnakttqWv-o1zGYDWtxLe8zuUiehLkxsyGoRzR78hhNSF77gCVq4u8nG0mnSdOdmjAGLjSu1r8sP5tBWB7CTXUlM_OYHP6pm_e-HiJb6n5eqlZeJ9OL46jV37rgYVypJE7ZUNqdkMfPNg1dXUcZgRCZ9PEOnjbCjP4ZtFZS5WhN-3D5OGL45r7ow/s1600/Gangtoucunia_diagram%20v2.png" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQylCnakttqWv-o1zGYDWtxLe8zuUiehLkxsyGoRzR78hhNSF77gCVq4u8nG0mnSdOdmjAGLjSu1r8sP5tBWB7CTXUlM_OYHP6pm_e-HiJb6n5eqlZeJ9OL46jV37rgYVypJE7ZUNqdkMfPNg1dXUcZgRCZ9PEOnjbCjP4ZtFZS5WhN-3D5OGL45r7ow/s1600/Gangtoucunia_diagram%20v2.png"/></a><div class="caption">Fossil specimen (left) and diagram (right) of <i>Gangtoucunia aspera</i> preserving soft tissues, including the gut and tentacle. <br>
<div class="credit">Image credit: Luke Parry and Guangxu Zhang.</div></div></div>
<div class="lpanel48plain"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvA4KsVJ-v58q0h30BDFDaCgzVmub2Hx_5ijaN6wm-Bm4mYSC2uqIlBsfHCtOh1b02JW7ev71IeTL9ZKeEOlHt785cTt1hd2lQ8TLw_hMuDi7lEvOCdkc7b8qecT3JeWgA-ZqiCqhPDcsDkrM3MsgdaoOm4JO1wm3x7M5A2xpgPoy63K_KbWxSEyW9eA/s1600/gangtoucunia_press1-01.png" ><img alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvA4KsVJ-v58q0h30BDFDaCgzVmub2Hx_5ijaN6wm-Bm4mYSC2uqIlBsfHCtOh1b02JW7ev71IeTL9ZKeEOlHt785cTt1hd2lQ8TLw_hMuDi7lEvOCdkc7b8qecT3JeWgA-ZqiCqhPDcsDkrM3MsgdaoOm4JO1wm3x7M5A2xpgPoy63K_KbWxSEyW9eA/s1600/gangtoucunia_press1-01.png"/></a><div class="caption">Fossil specimen of Gangtoucunia aspera preserving soft tissues, including the gut and tentacles (left and middle). The drawing at the right illustrates the visible anatomical features in the fossil specimens. <div class="credit">Image credit: Luke Parry and Guangxu Zhang.</div></div></div>The new collection of 514 million year old fossils includes four specimens of <i>Gangtoucunia aspera</i> with soft tissues still intact, including the gut and mouthparts. These reveal that this species had a mouth fringed with a ring of smooth, unbranched tentacles about 5 mm long. It’s likely that these were used to sting and capture prey, such as small arthropods. The fossils also show that <i>Gangtoucunia</i> had a blind-ended gut (open only at one end), partitioned into internal cavities, that filled the length of the tube.<br>
<br>
These are features found today only in modern jellyfish, anemones and their close relatives (known as cnidarians), organisms whose soft parts are extremely rare in the fossil record. The study shows that these simple animals was among the first to build the hard skeletons that make up much of the known fossil record. <br>
<br>
According to the researchers, <i>Gangtoucunia</i> would have looked similar to modern scyphozoan jellyfish polyps, with a hard tubular structure anchored to the underlying substrate. The tentacle mouth would have extended outside the tube, but could have been retracted inside the tube to avoid predators. Unlike living jellyfish polyps however, the tube of <i>Gangtoucunia</i> was made of calcium phosphate, a hard mineral that makes up our own teeth and bones. Use of this material to build skeletons has become more rare among animals over time.<br>
<br>
<div class="blockr"><p>This really is a one-in-million discovery. These mysterious tubes are often found in groups of hundreds of individuals, but until now they have been regarded as ‘problematic’ fossils, because we had no way of classifying them. Thanks to these extraordinary new specimens, a key piece of the evolutionary puzzle has been put firmly in place.</p>
<div class="creditl">Dr Luke Parry, Corresponding author<br>
Department of Earth Sciences<br>
University of Oxford, Oxford, UK</div></div>The new specimens clearly demonstrate that <i>Gangtoucunia</i> was not related to annelid worms (earthworms, polychaetes and their relatives) as had been previously suggested for similar fossils. It is now clear that <i>Gangtoucunia’s</i> body had a smooth exterior and a gut partitioned longitudinally, whereas annelids have segmented bodies with transverse partitioning of the body.<br>
<br>
The fossil was found at a site in the Gaoloufang section in Kunming, eastern Yunnan Province, China. Here, anaerobic (oxygen-poor) conditions limit the presence of bacteria that normally degrade soft tissues in fossils.<br>
<br>
<div class="blockl"><p>The first time I discovered the pink soft tissue on top of a <i>Gangtoucunia</i> tube, I was surprised and confused about what they were. In the following month, I found three more specimens with soft tissue preservation, which was very exciting and made me rethink the affinity of <i>Gangtoucunia</i>. The soft tissue of <i>Gangtoucunia</i>, particularly the tentacles, reveals that it is certainly not a priapulid-like worm as previous studies suggested, but more like a coral, and then I realised that it is a cnidarian.</p>
<div class="creditl">Guangxu Zhang, first author<br>
Yunnan Key Laboratory for Palaeobiology and MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment<br>
Institute of Palaeontology<br>
Yunnan University, Kunming, People's Republic of China.</div></div>
<div class="blockr"><p>A tubicolous mode of life seems to have become increasingly common in the Cambrian, which might be an adaptive response to increasing predation pressure in the early Cambrian. This study demonstrates that exceptional soft-tissue preservation is crucial for us to understand these ancient animals.</p>
<div class="creditl">Dr Xiaoya Ma, corresponding author<br>
Yunnan Key Laboratory for Palaeobiology and MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment<br>
Institute of Palaeontology<br>
Yunnan University, Kunming, People's Republic of China<br>
And Centre for Ecology and Conservation<br>
University of Exeter, Penryn, UK</div></div>Although the fossil clearly shows that <i>Gangtoucunia</i> was a primitive jellyfish, this doesn’t rule out the possibility that other early tube-fossil species looked very different. From Cambrian rocks in Yunnan province, the research team have previously found well-preserved tube fossils that could be identified as priapulids (marine worms), lobopodians (worms with paired legs, closely related to arthropods today) and annelids.<br>
<div class="panelplain" style="margin: 1em auto" ><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxcZ6qQdkU-q10hmbzbnUPHYezXsH4Y5BtALEIp0NOjtOgpB_adhHJm9LsK13xahL0NA_v8uqRe-Btp5krWhm_OeuQKfOSGv5lyol6TOp9KUH_pdyy3WHsyISu8a48YeDVc33dPLRUq9JWUEF5JIm7qusD5kfXndR_cMdklewlo7o98ySLVjrMlnT7FQ/s1600/gangtoucunia_press2-01-01.png" ><img alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxcZ6qQdkU-q10hmbzbnUPHYezXsH4Y5BtALEIp0NOjtOgpB_adhHJm9LsK13xahL0NA_v8uqRe-Btp5krWhm_OeuQKfOSGv5lyol6TOp9KUH_pdyy3WHsyISu8a48YeDVc33dPLRUq9JWUEF5JIm7qusD5kfXndR_cMdklewlo7o98ySLVjrMlnT7FQ/s1600/gangtoucunia_press2-01-01.png"/></a><div class="caption">Close up photograph of the mouth region of <i>Gangtoucunia aspera</i> showing the tentacles that would have been used to capture prey. <br>
<div class="credit">Image credit: Luke Parry and Guangxu Zhang.</div></div></div>
</blockquote>
<div class="rpanel450"><iframe class="pdf590" src="https://drive.google.com/file/d/1axUniAaE8zdsmsz5oeLs0BUvyfQT7SgT/preview#width=fitH"></iframe>
<div class="creditl"><a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghTFB5WM83VHZ9yx_Y0L2doTVMcmKeydsK9AQzHh9iKU4gtcdLo8ruByjrP8opeRMfZjh_R-yyriqLpzmdoAhvnjXlSqMjX7XaKKCYWzXo7_i4IpU_aEjXqXoPMRDFNOZ45LSO7pyAB7K1/s1600/CCBY.png" /></a>Copyright: © 2022 The authors.<br>Published by the Royal Society. open access. <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">(CC BY 4.0)</a></div></div>
More technical details are given in the scientists' <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2022.1623" target="_blank">open access paper</a> published in <i>Proceedings of the Royal Society B</i>:
<blockquote class="blockit"><span class="t2">Abstract</span><br><br>
Exoskeletal dwelling tubes are widespread among extant animals and early fossil assemblages. Exceptional fossils from the Cambrian reveal independent origins of tube dwelling by several clades including cnidarians, lophophorates, annelids, scalidophorans, panarthropods and ambulacrarians. However, most fossil tubes lack preservation of soft parts, making it difficult to understand their affinities and evolutionary significance. <i>Gangtoucunia aspera</i> (Wulongqing Formation, Cambrian Stage 4) was an annulated, gradually expanding phosphatic tube, with occasional attachments of multiple, smaller juveniles and has previously been interpreted as the dwelling tube of a ‘worm’ (e.g. a scalidophoran), lophophorate or problematicum. Here, we report the first soft tissues from <i>Gangtoucunia</i> that reveal a smooth body with circumoral tentacles and a blind, spacious gut that is partitioned by septa. This is consistent with cnidarian polyps and phylogenetic analysis resolves <i>Gangtoucunia</i> as a total group medusozoan. The tube of Gangtoucunia is phenotypically similar to problematic annulated tubular fossils (e.g. <i>Sphenothallus</i>, <i>Byronia</i>, <i>hyolithelminths</i>), which have been compared to both cnidarians and annelids, and are among the oldest assemblages of skeletal fossils. The cnidarian characters of <i>G. aspera</i> suggest that these early tubular taxa are best interpreted as cnidarians rather than sessile bilaterians in the absence of contrary soft tissue evidence.<br>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiF22xv4SjT0_BY-SCEDQks7l9MJ1Y3Vd5X451hDl6yxj2kKyhcBenr9Fsr7FM5OVPQxAs_FXj3rWJVbryedg3f3GVN1aDNbBfvI1kY0ecVATrmjGzFYXtrKg_Nt__Gd6c-vZ-mW93W4VCFy1YSnBSxz8cin9dhlzh2EYFDqb-7iZRpUL5X5gdIBUBZgA/s1600/rspb20221623f03.jpg" ><img alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiF22xv4SjT0_BY-SCEDQks7l9MJ1Y3Vd5X451hDl6yxj2kKyhcBenr9Fsr7FM5OVPQxAs_FXj3rWJVbryedg3f3GVN1aDNbBfvI1kY0ecVATrmjGzFYXtrKg_Nt__Gd6c-vZ-mW93W4VCFy1YSnBSxz8cin9dhlzh2EYFDqb-7iZRpUL5X5gdIBUBZgA/s1600/rspb20221623f03.jpg"/></a>
<div class="caption"><b>Figure 3.</b> Specimens preserving internal details of the digestive system. (a–d) YKLP 11437; (e–h) YKLP 11438. (a) Overview of specimen showing soft tissues partially extruded from the dwelling tube. (b) Detail of boxed region in (a) showing longitudinal gastric septa using low angle lighting. (c) Interpretative drawing of (b) highlighting the morphology of the digestive tract and gastric septa. (d) High angle light image of digestive tract showing extent of the gastric septa demarcated by dark linear structures. (e) Overview of specimen with high angle illumination. (f) Overview of specimen as in (e) with low angle illumination. (g) Interpretative drawing of region shown in (e,f) highlighting the trajectory and morphology of the digestive tract. (h) Close up of three dimensionally preserved septa.</div></div>
<br>
<div class="creditl"><a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2022.1623" target="_blank">Zhang, Guangxu; Parry, Luke A.; Vinther, Jakob; Ma, Xiaoya (2022)<br>
Exceptional soft tissue preservation reveals a cnidarian affinity for a Cambrian phosphatic tubicolous enigma<br>
<i>Proceedings of the Royal Society B: Biological Sciences</i>; 289(1986), 20221623. DOI: 10.1098/rspb.2022.1623</a><br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2022 The authors.<br>
Published by The Royal Society. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
So, we now know that the earliest skeletal animals were cnidarians, from the same group as corals, jellyfish and anemones, but with an exoskeleton composed of calcium phosphate - the predominant mineral in the bones of vertebrates, and another gap slams shut, albeit one of which most creationists would be totally unaware. <br>
<br>
On this occasion, the 'gap' proved to be the result of the right fossils not being found yet. The fact that they exist and neatly fill that gap is good evidence in itself that the Theory of Evolution is true, since the existence of these 'transitional' species is a prediction of the theory and finding them is a vindication of it.
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-84102244719045445652024-03-06T23:08:00.001+00:002024-03-07T00:19:28.816+00:00Creationism in Crisis - Sudden Climate Change Recorded In Marine Mollusc Shells - From 8,400 Years Before Creationism's Global Genocide<div class="title-box" style="height: 600px; display: none">
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<div class="left-column" style="text-align: left">Cantabrian Coast, Spain, where prehistoric people collected marine molluscs for food</div>
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<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoZzNyp1x-YP-kbHPyR8ulRpQyAQJcyFPz8_j4Pca1hYHEp2lNo_uHOvyXZ7rEUCqYjxsUEftv_Sy2J5roLlQkDXI0AIWqsGRgVaD4bfrORY4A82LfuKmG_RfFyIIFDkUkmtU29G20zHm4xO9FHFWYCoFj0bMpLY3pL25UncSZ-enKSC6KxPqOpAgfxeyj/s1600/COSTA%20CANT%C3%81BRICA_ASIER%20GARCIA%20ESCARZAGA.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoZzNyp1x-YP-kbHPyR8ulRpQyAQJcyFPz8_j4Pca1hYHEp2lNo_uHOvyXZ7rEUCqYjxsUEftv_Sy2J5roLlQkDXI0AIWqsGRgVaD4bfrORY4A82LfuKmG_RfFyIIFDkUkmtU29G20zHm4xO9FHFWYCoFj0bMpLY3pL25UncSZ-enKSC6KxPqOpAgfxeyj/s1600/COSTA%20CANT%C3%81BRICA_ASIER%20GARCIA%20ESCARZAGA.jpg"/></a></div>
<a href="https://www.uab.cat/web/newsroom/news-detail/marine-mollusc-shells-reveal-how-prehistoric-humans-adapted-to-intense-climate-change-1345830290613.html?detid=1345858458616">Marine mollusc shells reveal how prehistoric humans adapted to intense climate change - Universitat Autònoma de Barcelona - UAB Barcelona</a>
<br>
In an event known to geologists as the '8.2 Ka event', i.e. 8.2 Kilo anum (thousand years) event, a sudden flow of cold water melt-water from the North American lakes into the North Atlantic stopped the 'Atlantic Conveyer' from bringing warm water from the Gulf of Mexico up to the coast of Western Europe and with it warm, moist air. This even significantly and quite suddenly changed the climate to a colder, drier weather pattern which affected marine wildlife.<br>
<br>
That event was subsequently recorded in the shells of the marine molluscs the people living along the Cantabrian Coast of Northern Spain gathered for food, disposing of the shells in midden tips, such as in the El Mazo cave in Asturias, Spain. The 8.2 Ka event also had a profound effect on the human societies as their food disappeared or migrated to more equitable areas.<br>
<br>
If the creationists story of a global genocidal flood were true, then this record would have been swept away and destroyed, or at least buried under the predicted layer of silt and dead animal and plant remains that such a flood would have made inevitable. But there it is, looking for all the world like there never was a global flood and not so much as a centimeter of silt covering it.<br>
<br>
The midden in the El Mazo cave was in use for about 1500 years, producing a continuous stratigraphic record with a very high chronological resolution, which is now the subject of a paper in <i>Scientific Reports</i> by a team of archaeologists led by Asier García Escárzaga, current researcher from the Institute of Environmental Science and Technology (ICTA-UAB) and the Department of Prehistory of the Universitat Autònoma de Barcelona, together with Igor Gutiérrez Zugasti, from the Universidad de Cantabria (UC). The study was coordinated from the Universidad de La Rioja (UR) and the Max Planck Institute (Germany) alongside members of other academic centres (Max Planck Institute, University of Burgos, Universidad Complutense de Madrid and University of Faro).<br>
<br>
The study applies a multidisciplinary toolkit of archaeomalacological studies and stable oxygen isotope analyses to shell remains recovered from the shell midden site.<br><a name='more'></a>
<blockquote class="ai">How does measuring the δ<sup class="small">18</sup>O levels in marine mollusc shells tell archaeologists about the water temperature?
Measuring the δ<sup class="small">18</sup>O (delta-<sup class="small">18</sup>O) levels in marine mollusc shells can provide valuable insights into past water temperatures. Here's how it works:
<ol class="dbl1 bold">
<li><b>Isotopic Composition:</b> Oxygen comes in different isotopes, primarily <sup class="small">16</sup>O and <sup class="small">18</sup>O. The ratio of these isotopes (δ<sup class="small">18</sup>O) in water varies depending on factors like temperature and the source of the water.</li>
<li><b>Incorporation into Shells:</b> Marine molluscs incorporate the oxygen from seawater into their shells when they build them. The isotopic composition of the oxygen in the shell reflects the composition of the seawater at the time the shell was formed.</li>
<li><b>Temperature Dependency:</b> The ratio of <sup class="small">18</sup>O to <sup class="small">16</sup>O in seawater is influenced by temperature. Generally, colder water tends to have a higher proportion of <sup class="small">18</sup>O compared to <sup class="small">16</sup>O. This is because <sup class="small">18</sup>O is slightly heavier and less likely to evaporate or be incorporated into ice, so it's enriched in colder water.</li>
<li><b>Proxy for Past Temperatures:</b> By analyzing the δ<sup class="small">18</sup>O values in mollusc shells, scientists can infer the temperature of the seawater when the shell was formed. Higher δ<sup class="small">18</sup>O values suggest warmer water temperatures, while lower values indicate colder temperatures.</li>
<li><b>Calibration and Interpretation:</b> To use δ<sup class="small">18</sup>O values as a proxy for temperature, scientists often need to calibrate the relationship between δ<sup class="small">18</sup>O and temperature using modern samples. Once calibrated, they can apply this relationship to ancient shell samples to estimate past temperatures.</li>
<li><b>Additional Considerations:</b> It's essential to consider factors other than temperature that can influence δ<sup class="small">18</sup>O values, such as salinity and changes in the isotopic composition of seawater over time. However, with careful calibration and consideration of these factors, δ<sup class="small">18</sup>O analysis in mollusc shells can provide valuable information about past ocean temperatures, aiding archaeologists and paleoclimatologists in reconstructing past environments and climates.</li>
</ol>
</blockquote>
From the Universitat Autònoma de Barcelona (UAB) press release:<br>
<blockquote class="blockit">The results obtained by these scientists allowed them to determine that colder seawater temperatures, deduced from stable oxygen isotope values measured on marine shells, led to changes in the availability of different shellfish species. For instance, one of the most commonly consumed species, the warm-adapted species <i>P. lineatus</i>, decreased during the 8.2 ka event, while populations of cold-adapted <i>P. vulgata</i>, another commonly exploited species, increased. Intriguingly, the warm-adapted limpet <i>P. depressa</i> also increased during this cool period, owing to a higher resistance to cold temperatures than other warm-water species. <br>
<br>
Their results also revealed an increase in the intensification of mollusc exploitation by humans, as indicated by a decrease in average mollusc size and evidence for increased harvesting in more dangerous coastal areas. The authors argued that this occurred because of human demographic growth in these Atlantic coastal settings which acted as refugia during this cold event, encouraging populations to move there from further inland. Nevertheless, populations around El Mazo managed to avoid over exploiting their coastal resources, as average mollusc size very rarely decreased below 20mm, the minimum size specified by modern regulations to guarantee long-term species survival. <br>
<br>
“Our results suggest an ongoing application of local marine ecological knowledge by some of the last foragers in western Europe, despite major changes to climate and demography” says Asier García-Escárzaga lead author of the current study. <br>
<br>
The resolution provided by the combination of taxonomic, geochemical and chronological analysis of molluscs from archaeological sites has major implications for other studies seeking to determine the significance of climate change on marine environments, and can provide detailed clues to the magnitude and nature of future climate changes and their impacts on human societies.
</blockquote>
In their published paper the team say:
<blockquote class="blockit"><span class="t2">Abstract</span>
<br>
The cooling and drying associated with the so-called ‘8.2 ka event’ have long been hypothesized as having sweeping implications for human societies in the Early Holocene, including some of the last Mesolithic hunter-gatherers in Atlantic Europe. Nevertheless, detailed ‘on-site’ records with which the impacts of broader climate changes on human-relevant environments can be explored have been lacking. Here, we reconstruct sea surface temperatures (SST) from <sup class="small">18</sup>O values measured on subfossil topshells <i>Phorcus lineatus</i> exploited by the Mesolithic human groups that lived at El Mazo cave (N Spain) between 9 and 7.4 ka. Bayesian modelling of 65 radiocarbon dates, in combination with this <sup class="small">18</sup>O data, provide a high-resolution seasonal record of SST, revealing that colder SST during the 8.2 ka event led to changes in the availability of different shellfish species. Intensification in the exploitation of molluscs by humans indicates demographic growth in these Atlantic coastal settings which acted as refugia during this cold event.<br>
<br>
<span class="t2">Introduction</span><br>
<br>
Current global climate warming is having, and will continue to have, widespread consequences for humans. Looking to the past, multiple climatic and environmental changes have long been thought to have shaped human evolution and behaviour<sup class="x-small"><a class="newtooltip">1</a>,<a class="newtooltip">2</a>,<a class="newtooltip">3</a></sup>. The Holocene (11.7–0 ka cal BP) is a geological epoch characterized by comparative stable climatic conditions. However, that stability was punctuated by a series of sudden climate changes, particularly during the Early Holocene<sup class="x-small"><a class="newtooltip">4</a></sup>. Among these, the ‘8.2 ka event’ has been identified as the largest and most abrupt climatic event of the Holocene<sup class="x-small"><a class="newtooltip">5</a>,<a class="newtooltip">6</a></sup>. Climate scientists suggest that this ‘event’ was the result of an outburst of glacial meltwater from the Laurentide lakes in North America<sup class="x-small"><a class="newtooltip">7</a></sup>. The influx of cold water into the Atlantic Ocean led to a reduction of sea surface salinity and a decline of the Atlantic meridional overturning circulation (AMOC), provoking a reduction in sea surface temperatures (SST) across the North Atlantic<sup class="x-small"><a class="newtooltip">8</a></sup>. The cooling effects of this event have been documented in proxies from the Greenland ice cores<sup class="x-small"><a class="newtooltip">6</a></sup> and across Europe<sup class="x-small"><a class="newtooltip">5</a>,<a class="newtooltip">9</a>,<a class="newtooltip">10</a></sup>. Short and sharp periods of colder or drier conditions have also been recorded ~ 8.2 ka throughout the northern<sup class="x-small"><a class="newtooltip">11</a>,<a class="newtooltip">12</a>,<a class="newtooltip">13</a></sup> and southern hemispheres<sup class="x-small"><a class="newtooltip">11</a>,<a class="newtooltip">12</a>,<a class="newtooltip">14</a></sup>. Nevertheless, while now a well-established climatic phenomenon, the sweeping impacts of the ‘8.2 ka event’ on different environments often remain assumed rather than proven, and local records of marine or terrestrial conditions available at an appropriate resolution often remain lacking. Furthermore, while temperature or rainfall changes associated with the ‘8.2 ka event’ are often well-established, there are few palaeoclimatic proxies available that have enabled insights into the influence of the ‘8.2 ka event’ on the seasonality of climatic conditions in different parts of the world.<br>
<br>
These gaps relating to the impact of this cold event on local environments are problematic given that there have been a number of attempts to link the ‘8.2 ka event’ to changes in past human societies, with cooling and drying being argued to have stimulated behavioural or settlement responses<sup class="x-small"><a class="newtooltip">15</a>,<a class="newtooltip">16</a></sup>. In the Middle East, a 300-year period of drying and cooling has been associated with economic and cultural changes leading to an increase in social stratification and urbanism in the region<sup class="x-small"><a class="newtooltip">17</a></sup>. Aridity at ~ 8.2 ka has also been correlated with changes in settlement patterns and human subsistence in North and East Africa<sup class="x-small"><a class="newtooltip">18</a></sup>. On the Atlantic façade of Europe, the ‘8.2 ka event’ occurred at a time when some of the last Mesolithic hunter-gatherers in Europe were producing dense shell middens along the coast prior to the arrival of agriculture<sup class="x-small"><a class="newtooltip">19</a></sup>. Given the apparent reliance of human societies on marine resources, it has been hypothesised that this abrupt climate change must have affected the availability of exploited marine taxa and thus the foraging behaviours, settlement patterns, and spatial mobility of prehistoric human populations<sup class="x-small"><a class="newtooltip">20</a></sup>. However, as with previous examples, high-resolution local palaeoclimatic records that are directly associated with areas of human occupation have remained generally lacking<sup class="x-small"><a class="newtooltip">16</a></sup>. Moreover, given the known importance of seasonal patterns in subsistence strategies to hunter-gatherers<sup class="x-small"><a class="newtooltip">21</a>,<a class="newtooltip">22</a></sup>, seasonal records of changes in marine and terrestrial conditions are particularly important. Nonetheless, suitable proxies and precise sequence chronologies have remained scarce.<br>
<br>
Marine molluscs have very specific environmental requirements and are extremely sensitive to climate change, as revealed by previous studies across Atlantic Europe<sup class="x-small"><a class="newtooltip">23</a>,<a class="newtooltip">24</a></sup>. Recent research has demonstrated that the current rising of SST is forcing a rapid expansion of the northern limit of warm-adapted marine species<sup class="x-small"><a class="newtooltip">24</a>,<a class="newtooltip">25</a></sup>. Similarly, warmer conditions during the Early Holocene have been argued to have led to significant changes in species representation when compared to Pleistocene glacial conditions<sup class="x-small"><a class="newtooltip">26</a></sup>. Mollusc species recovered from archaeological deposits thus have high potential to provide temperature information of direct significance to humans occupying particular sites and exploiting marine resources<sup class="x-small"><a class="newtooltip">27</a></sup>. Recent developments in the radiocarbon dating of shell carbonate have improved our understanding of the dating of this material, allowing researchers to accurately determine the chronology of climate change decoded from shell remains<sup class="x-small"><a class="newtooltip">28</a></sup>. Beyond taxonomic indications, stable oxygen isotope ratios derived from archaeologically-recovered marine mollusc shells (<sup class="small">18</sup>O<sub class="small">shell</sub>) have been demonstrated to be powerful recorders of the seasonal SST variations experienced by that animal in the past<sup class="x-small"><a class="newtooltip">29</a>,<a class="newtooltip">30</a></sup>, offering unparalleled insights into the seasonality of marine environments relied upon by past human populations. Significantly, the effectiveness of these seasonal palaeothermometers has also been demonstrated on the European Atlantic façade for Phorcus lineatus (da Costa, 1778)<sup class="x-small"><a class="newtooltip">21</a>,<a class="newtooltip">31</a>,<a class="newtooltip">32</a></sup>, a topshell species that comprises a significant proportion of Mesolithic shell middens found in the region. The difficult task, until now, however, has been to find a shell midden with sufficient temporal resolution to enable inference of short and abrupt changes in climate conditions and human behaviour<sup class="x-small"><a class="newtooltip">19</a></sup>.<br>
<br>
Here, we report chronological, archaeomalacological and isotopic data from shellfish remains recovered from the site of El Mazo in northern Spain (Fig. <a href="https://www.nature.com/articles/s41598-022-10135-w#Fig1" target="_blank">1</a>; Supplementary Text <a href="https://www.nature.com/articles/s41598-022-10135-w#MOESM1" target="_blank">1</a>; Supplementary Fig. <a href="https://www.nature.com/articles/s41598-022-10135-w#MOESM1" target="_blank">1</a>). We performed a large number of radiocarbon measurements on different materials, including bone from terrestrial animals, microbotanical remains, and marine mollusc shells to generate a high-resolution chronological sequence of the human use of the cave. Meanwhile, measurements of <sup class="small">18</sup>O<sub class="small">shell</sub> on subfossil topshells <i>P. lineatus</i> were used to accurately reconstruct short-term changes in coastal SST throughout the Early Holocene. In addition, distributions of shell assemblages were quantified to determine marine mollusc species representation, diachronic changes in shell size, harvesting areas, and the occurrence of shell size selection by humans. Significantly, the site is unique in the context of the European Atlantic façade given its long stratigraphic sequence (9–7.4 ka cal BP), but especially, the high chronological resolution of each unit. As a result, it offers an important opportunity to decipher, for the first time, the duration and the seasonal impact of the 8.2 ka event on SST in Atlantic Europe, its impacts on littoral resources that were being heavily exploited by humans, and its broader ramifications for the settlement patterns and economies of some of the last dedicated hunter-gatherer groups in Europe prior to the expansion of domesticated plants and animals into the region. The study of ‘on-site’ palaeoenvironmental indicators, at a seasonal resolution, also demonstrates the significant potential of this methodology, which can be applied to multiple sites, to explore the overall, and intra-annual, effects of abrupt climate changes on specific environments where the resolution of archaeological sites allows.<br>
<div class="panelplain" style="margin: 1em auto"><div style="margin: 0 1em"><span class="t2">Figure 1</span></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_qkfMmM-YIZaJrYwB26ERjCDEOAD1URPRwDIZ7VIZcviu48UtdzkTw9LQhXrIsT5FCErP6Ca-cfF5AsDIanxWaxwN2OGQyu1X4G_BST22qj884pV0hlqQLTf9CtdK10EWwQNsspzWHjpiCltM3ng4nkJB-n0qlaBn03m0jXyGfshfxZoaICY32KcqI4ln/s1600/41598_2022_10135_Fig1_HTML.webp" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_qkfMmM-YIZaJrYwB26ERjCDEOAD1URPRwDIZ7VIZcviu48UtdzkTw9LQhXrIsT5FCErP6Ca-cfF5AsDIanxWaxwN2OGQyu1X4G_BST22qj884pV0hlqQLTf9CtdK10EWwQNsspzWHjpiCltM3ng4nkJB-n0qlaBn03m0jXyGfshfxZoaICY32KcqI4ln/s1600/41598_2022_10135_Fig1_HTML.webp"/></a>
<div class="caption">(<b>a</b>) Location of the study area (Cantabrian region, northern Spain) and the shell midden site of El Mazo. (<b>b</b>) External view of El Mazo; (<b>c</b>) topographic map of the site showing excavation areas and provenance of the studied samples (shaded squares), and (<b>d</b>) stratigraphy of the inner test pit (squares X15 and X16). Satellite map in the upper-left corner of (<b>a</b>) was created by authors using Adobe® Illustrator software. The original base map was extracted from the maps-for-free web site (https://maps-for-free.com/) (© Collaborators of OpenStreetMap, Open Database License [ODbL]). Map in the upper-right corner of (<b>a</b>) was generated by Alejandro Garcia-Moreno using ArcGIS software. Lower map of (<b>a</b>) was created by Luis C. Teira Mayolini using ArcGIS and Adobe Suite software.</div>
</div>
<div class="creditl">García-Escárzaga, A., Gutiérrez-Zugasti, I., Marín-Arroyo, A.B. et al. <br>
Human forager response to abrupt climate change at 8.2 ka on the Atlantic coast of Europe. <br>
Sci Rep 12, 6481 (2022). https://doi.org/10.1038/s41598-022-10135-w <br>
<br>
<a class="float-left" href="https://creativecommons.org/licenses/" target="_blank"><img style="width: 70px; border-radius: 0; border:0" src="https://1.bp.blogspot.com/-QDWEYPVEuD4/WQMHy_J82qI/AAAAAAAAWuQ/Dk3_T3riJCoqu_EpJPnLJRBXuZJY8937wCPcB/s1600/CCBY.png" /></a>Copyright: © 2024 The authors.<br>
Published by Springer Nature Ltd. Open access.<br>
Reprinted under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International license (CC BY 4.0)</a></div>
</blockquote>
So, in addition to the lack of any evidence of a global flood, we also have this 1,500 year record, in the form of a midden, of continuous habitation through the 8.2 Ka event, which takes it back to just 300 years after creationists claim the Universe was created, during which time we are expected to believe, humans migrated from the Middle East and established hunter-gatherer communities along the coast of Northn Spain, then, to cap it all, their midden tip miraculously survived a cataclysmic global flood and never had so much as a teaspoon full of the silt over it that such a flood would have produced, even if it hadn't washed the shells away.
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<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-48023935680801309452024-03-06T16:11:00.003+00:002024-03-06T16:45:36.789+00:00Creationism in Crisis - Earliest Toothless Bird From 120 Million Years Ago<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox" style="color: black">
<div class="left-column" style="text-align: left; flex: 2">Illustration showing the fossil skeleton of <i>Imparavis attenboroughi</i>, alongside a reconstruction of the bird in life. </div>
<div class="right-column" style="text-align: right; flex: 1">© Ville Sinkkonen.</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4q14uc_J1EAqiJcogpR8dao_gZLTHjbPK5h0dZPrzSat9AHTo5YIJ7ohCMl0XujjfqZsuCwPukCaT8jTT5XlELsNPD_IkrOORMj8FqkYM8cfQD1PdKLupTx0rII0gSiZP-B97DxzHycXQsYrx_oq-GBBYEJQfw1xcIwNYVLXpuQQGg69d4RiSlqVeLoiu/s1600/1709658044-image-19.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4q14uc_J1EAqiJcogpR8dao_gZLTHjbPK5h0dZPrzSat9AHTo5YIJ7ohCMl0XujjfqZsuCwPukCaT8jTT5XlELsNPD_IkrOORMj8FqkYM8cfQD1PdKLupTx0rII0gSiZP-B97DxzHycXQsYrx_oq-GBBYEJQfw1xcIwNYVLXpuQQGg69d4RiSlqVeLoiu/s1600/1709658044-image-19.webp"/></a></div>
<div class="rpanel450plain" style="margin-bottom: 0.5em">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBh56o-uGUECezDVtNMHpocjGGzOmN4LOM_P-AeWD324UAGwLO3y3NuNdSAf2Pe6y7kDYt7HaLmIlmrCsvpJ61O8q0TctZqU6dDmizFzuNWmGt0Ko0TBLXKmCXLtggyCBDwI_bzfmxjuTDjrSG_3X_aJ1PBhQG6lOmtAkTDtIV_BCnr73ISq8E5dpLB42_/s1600/_132848510_photo06-03-2024082156.jpg.webp"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBh56o-uGUECezDVtNMHpocjGGzOmN4LOM_P-AeWD324UAGwLO3y3NuNdSAf2Pe6y7kDYt7HaLmIlmrCsvpJ61O8q0TctZqU6dDmizFzuNWmGt0Ko0TBLXKmCXLtggyCBDwI_bzfmxjuTDjrSG_3X_aJ1PBhQG6lOmtAkTDtIV_BCnr73ISq8E5dpLB42_/s1600/_132848510_photo06-03-2024082156.jpg.webp"/></a>
<div class="captionc"><i>Imparavis attenboroughi</i>, a 'strange bird' named after Sir David Attenborough, British broadcaster and naturalist</div>
</div>
<a href="https://www.fieldmuseum.org/about/press/fossil-named-attenboroughs-strange-bird-was-the-first-of-its-kind-without-teeth">Fossil named “Attenborough’s strange bird” was the first of its kind without teeth - Field Museum</a><br>
<br>
It seems every week is a bad week for creationists, yet the wackadoodle cult staggers on, albeit with dwindling numbers, managing as always to ignore anything that shows their childish superstition to be wrong.<br>
<br>
On top of the <a href="https://rosarubicondior.blogspot.com/2024/03/creationism-in-crisis-giant-sea-lizards.html" target="_blank">recently-reported predatory marine lizard</a>, from 66 million years ago, we now have the earliest bird without the teeth of its enantiornithine ancestors. The enantiornithines were a diverse class of avian dinosaurs that went extinct 66 million years ago following the meteor impact that killed most of the dinosaurs. Only the ornithuromorphs survived, for reasons not completely understood, and they gave rise to all modern birds.<br>
<br><a name='more'></a>
<blockquote class="ai" style="width: 44%; float: right; margin-left: 0.5em;">What information do you have on the evolution of the enantiornithines and ornithuromorphs dinosaurs?
Enantiornithines and ornithuromorphs are two important groups of birds that evolved during the Mesozoic Era, specifically during the Cretaceous period. Here's an overview of their evolution:
<ol class="dbl1 bold" style="margin-right: 10%">
<li><b>Enantiornithines:</b>
<ul type="disc">
<li>Enantiornithines were a diverse group of birds that lived during the Cretaceous period. They are often referred to as "opposite birds" because their shoulder joints were structured differently from modern birds, giving them a somewhat opposite appearance.</li>
<li>These birds were globally distributed and occupied various ecological niches, ranging from aquatic to terrestrial habitats.</li>
<li>Enantiornithines had teeth and clawed wings, features not present in modern birds. They also lacked a specialized breastbone (sternum) like that of modern birds.</li>
<li>Fossil evidence suggests that enantiornithines were quite successful and abundant during the Cretaceous, but they went extinct along with non-avian dinosaurs at the end of the Cretaceous period, about 66 million years ago.</li>
</ul></li>
<li><b>Ornithuromorphs:</b>
<ul type="disc">
<li>Ornithuromorphs are another group of birds that lived during the Cretaceous period. They are considered more closely related to modern birds than enantiornithines.</li>
<li>Unlike enantiornithines, ornithuromorphs had a keeled sternum, similar to modern birds, which likely provided a more efficient attachment for flight muscles.</li>
<li>Ornithuromorphs also had a toothless beak, indicating a more specialized diet compared to enantiornithines.</li>
<li>Fossil evidence suggests that ornithuromorphs evolved diverse body forms and lifestyles, including some species that were capable of powered flight over long distances.</li>
<li>Ornithuromorphs survived the mass extinction event at the end of the Cretaceous period and are believed to be the ancestors of modern birds.</li>
</ul></li>
</ol>
The evolution of both enantiornithines and ornithuromorphs represents important stages in the development of avian diversity and flight adaptation. While enantiornithines represent an early radiation of avian forms that ultimately went extinct, ornithuromorphs are thought to have given rise to the lineage that led to modern birds. Further discoveries and research continue to refine our understanding of the evolutionary relationships between these ancient birds and their modern descendants.
</blockquote>
The team of palaeontologists, which included researchers from the Field Museum, University of Chicago, IL, USA and the Institute of Geology and Paleontology, Linyi University, Linyi, China, who discovered this early bird have published their results in Cretaceous Research and explain it in a Field Museum news release:
<blockquote class="blockit">No birds alive today have teeth. But that wasn’t always the case—many early fossil birds had beaks full of sharp, tiny teeth. In a paper in the journal Cretaceous Research, scientists have described a new species of fossil bird that was the first of its kind to evolve toothless-ness; its name, in honor of naturalist Sir David Attenborough, means “Attenborough’s strange bird.”<br>
<br>
<div class="blockl"><p>It is a great honour to have one’s name attached to a fossil, particularly one as spectacular and important as this. It seems the history of birds is more complex than we knew</p>
<div class="creditl">Sir David Attenborough.</div></div>
<br>
All birds are dinosaurs, but not all dinosaurs fall into the specialized type of dinosaurs known as birds, sort of like how all squares are rectangles, but not all rectangles are squares. The newly described Imparavis attenboroughi is a bird, and therefore, also a dinosaur.<br>
<br>
<i>Imparavis attenboroughi</i> was a member of a group of birds called enantiornithines, or “opposite birds,” named for a feature in their shoulder joints that is “opposite” from what’s seen in modern birds. Enantiornithines were once the most diverse group of birds, but they went extinct 66 million years ago following the meteor impact that killed most of the dinosaurs. Scientists are still working to figure out why the enantiornithines went extinct and the ornithuromorphs, the group that gave rise to modern birds, survived.<br>
<br>
<div class="blockl"><p>Enantiornithines are very weird. Most of them had teeth and still had clawed digits. If you were to go back in time 120 million years in northeastern China and walk around, you might have seen something that looked like a robin or a cardinal, but then it would open its mouth, and it would be filled with teeth, and it would raise its wing, and you would realize that it had little fingers.</p>
<p>[But] Attenborough’s strange bird [bucked this trend]. Scientists previously thought that the first record of toothlessness in this group was about 72 million years ago, in the late Cretaceous. This little guy, <i>Imparavis</i>, pushes that back by about 48 to 50 million years. So toothlessness, or edentulism, evolved much earlier in this group than we thought.</p>
<div class="creditl">Alexander D. Clark, corresponding author.<br>
Committee on Evolutionary Biology<br>
University of Chicago, Chicago, IL, USA.</div></div>
<br>
The specimen was found by an amateur fossil collector near the village of Toudaoyingzi in northeastern China and donated to the Shandong Tianyu Museum of Nature. Clark’s advisor and co-author on the paper, Field Museum associate curator of fossil reptiles Jingmai O’Connor, first noticed something unusual about this fossil several years ago, when she was visiting the Shandong Tianyu Museum’s collections.<br>
<br>
<div class="blockl"><p>I think what drew me to the specimen wasn’t its lack of teeth—it was its forelimbs. It had a giant bicipital crest—a bony process jutting out at the top of the upper arm bone, where muscles attach. I’d seen crests like that in Late Cretaceous birds, but not in the Early Cretaceous like this one. That’s when I first suspected it might be a new species.</p>
<div class="creditl">Jingmai K. O'Connor, co-author<br>
Negaunee Integrative Resource Center<br>
Field Museum of Natural History<br>
Chicago, IL, USA.</div></div>
O’Connor, Clark, and their coauthors in China, Xiaoli Wang, Xiangyu Zhang, Xing Wang, Xiaoting Zheng, and Zhonghe Zhou, undertook further study of the specimen and determined that it did indeed represent an animal new to science.<br>
<br>
The unusual wing bones could have allowed for muscle attachments that let this bird flap its wings with extra power.<br>
<br>
<div class="blockl"><p>We’re potentially looking at really strong wing beats. Some features of the bones resemble those of modern birds like puffins or murres, which can flap crazy fast, or quails and pheasants, which are stout little birds but produce enough power to launch nearly vertically at a moment’s notice when threatened.</p>
<div class="creditl">Alexander D. Clark.</div></div>
<br>
Meanwhile, the bird’s toothless beak doesn’t necessarily tell scientists what it was eating, since modern toothless birds have a wide variety of diets. Like its fellow enantiornithines, and unlike modern birds, it does not appear to have a digestive organ called a gizzard, or gastric mill, that helped it crush up its food.<br>
<br>
While Clark notes that “an animal is more than the sum of its parts, and we can’t fully know what an animal’s life was like just by looking at single components of its body,” he and his coauthors have been able to hypothesize about some of <i>Imparavis’s</i> behavior and ecology, based on the details of its wings, feet, and beak together. “I like to think of these guys kind of acting like modern robins. They can perch in trees just fine, but for the most part, you see them foraging on the ground, hopping around and walking,” says Clark.<br>
<div class="block"><p>It seems like most enantiornithines were pretty arboreal, but the differences in the forelimb structure of <i>Imparavis</i> suggests that even though it's still probably lived in the trees, it maybe ventured down to the ground to feed, and that might mean it had a unique diet compared to other enantiornithines, which also might explain why it lost its teeth.</p>
<div class="credit">Jingmai K. O'Connor</div></div>
<br>
In the paper, the researchers also revisited a previously described fossil bird, <i>Chiappeavis</i> (which O’Connor named eight years ago after her PhD advisor), and suggest that it too was an early toothless enantiornithine. This finding, along with <i>Imparavis</i>, indicates that toothlessness may not have been quite as unique in Early Cretaceous enantiornithines as previously thought.<br>
<br>
Clark said that nature documentaries by Sir David Attenborough, in which the renowned British naturalist narrates the behavior of different animals, were pivotal to his own interest in science. "I most likely wouldn't be in the natural sciences if it weren’t for David Attenborough’s documentaries,” says Clark, explaining why he chose to name the new fossil after Attenborough.<br>
<br>
Clark and O’Connor noted the importance of Attenborough’s messaging that not only celebrates life on earth, but also warns against the mass extinction the planet is undergoing due to human-caused climate change and habitat destruction.<br>
<div class="block"><p>Learning about enantiornithines like <i>Imparavis attenboroughi</i> helps us understand why they went extinct and why modern birds survived, which is really important for understanding the sixth mass extinction that we’re in now. The biggest crisis humanity is facing is the sixth mass extinction, and paleontology provides the only evidence we have for how organisms respond to environmental changes and how animals respond to the stress of other organisms going extinct.</p>
<div class="creditl">Jingmai K. O'Connor</div></div>
</blockquote>
<blockquote class="blockit"><span class="t2">Abstract</span><br>
<br>
Among Mesozoic birds, enantiornithines exhibit great morphological variation, which likely reflects their species diversity, range, and overall success throughout the Cretaceous. The majority of enantiornithines come from the Lower Cretaceous Jehol deposits (130–120 Ma) in northeastern China. In contrast to living birds, most enantiornithines were fully toothed. However, the rostral lengths, appendicular proportions, and pedal morphologies of extant birds can still inform on possible diet, flight mode, and ecology. Both partial (e.g., Longipterygidae) and complete tooth loss (e.g., <i>Yuornis</i>, <i>Gobipteryx</i>) are observed among enantiornithines, with edentulous rostra previously restricted to Upper Cretaceous taxa. Here, we describe the first edentulous enantiornithine from the Lower Cretaceous, <i>Imparavis attenboroughi</i> gen. et sp. nov., indicating a toothless beak evolved in this group 48 Ma earlier than previously recognized. Additionally, we reinterpret <i>Chiappeavis</i> as edentulous which together with the discovery of <i>Imparavis</i> indicates the complete loss of teeth in enantiornithines was not uncommon although still less frequent than observed in ornithuromorphs. The absence of gastroliths in all known enantiornithines suggests that the loss of teeth evolved under different pressures in these two ornithothoracine clades. Differences in rostral occlusion between <i>Imparavis</i> and <i>Chiappeavis</i> suggest they utilized different foraging strategies and possibly diet. Appendicular morphology in <i>Imparavis</i> suggest the capacity for relatively high wing beat frequency and powerful take-off capabilities. Together with the morphology of the hindlimb, we suggest <i>Imparavis</i> was primarily a terrestrial forager that could utilize sudden bursts of flight to escape into arboreal settings as a prey evasion strategy.<br>
<br>
<div class="creditl"><a href="https://www.sciencedirect.com/science/article/pii/S0195667124000405" target="_blank">Wang, Xiaoli; Clark, Alexander D.; O'Connor, Jingmai K.; Zhang, Xiangyu; Wang, Xing; Zheng, Xiaoting; Zhou, Zhonghe<br>
First Edentulous Enantiornithine (Aves: Ornithothoraces) from the Lower Cretaceous Jehol Avifauna
Cretaceous Research (2024) <b>159</b> 105867; DOI: 10.1016/j.cretres.2024.105867</a><br>
<br>
© 2024 Elsevier Ltd.<br>
Reprinted under the terms of <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">s60</a> of the <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">Copyright, Designs and Patents Act 1988</a>.</div>
</blockquote>
So much more interesting an informative about the origins of life on Earth today, than putting your hands over your eyes and ears, diving into the creationist cult rabbit hole and eschewing learning in order to retain a childish belief in magic, in case an invisible mind-reading sky thug gets angry if you know too much.
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<center>If you've enjoyed my blog please show your appreciation
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0tag:blogger.com,1999:blog-7583674511519808833.post-53905172509308896702024-03-06T12:15:00.001+00:002024-03-06T12:15:54.036+00:00Creationism in Crisis - Giant Sea Lizards From 66 Million Years Before 'Creation Week'<div class="title-box" style="height: 600px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left; flex: 2"><i>Khinjaria acuta</i> was around the length of an orca, (7-8 metres).</div>
<div class="right-column" style="text-align: right; flex: 1">Credit: Andrey Atuchin</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6uvSas9Yg7UewcSsOEI5O-7MWsf3v8OWixcyq3aQIvX7v_hxCT4HSh1MOuKnGj-Y2tqethlE4Q-xkUuOSqUWsefzrV3lF4rzwHGhP4K_r3KWcd3vBpbY9xQAIw5tHPEFCb_gsbJ7I5J8ChxHvCY84cgcSanpp0SDYWATb94ofCpmmkv02OO1KcrUDuVoq/s1600/53567672518_a3792c6cbc_b.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6uvSas9Yg7UewcSsOEI5O-7MWsf3v8OWixcyq3aQIvX7v_hxCT4HSh1MOuKnGj-Y2tqethlE4Q-xkUuOSqUWsefzrV3lF4rzwHGhP4K_r3KWcd3vBpbY9xQAIw5tHPEFCb_gsbJ7I5J8ChxHvCY84cgcSanpp0SDYWATb94ofCpmmkv02OO1KcrUDuVoq/s1600/53567672518_a3792c6cbc_b.jpg"/></a></div>
<div class="rpanel450plain">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLDDgH7Pa7AcqQxitNBykDfj6sDwiT1FGJ0QHSA5SIJdFMVbVuTtm3svnXkpLMPEM5EaQAUuwbh2iP13TR9hhcafTZDRiB2QyDg7GIrsMWbaa8EoT2FK4-yffoVA8FIionqbAAuNdtG2NWqPczgF3BxE9bQvVKsFUycNk2jn_I5tgmZHZ7Wme6jP5sGXAQ/s1600/Khinjaria+skull.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLDDgH7Pa7AcqQxitNBykDfj6sDwiT1FGJ0QHSA5SIJdFMVbVuTtm3svnXkpLMPEM5EaQAUuwbh2iP13TR9hhcafTZDRiB2QyDg7GIrsMWbaa8EoT2FK4-yffoVA8FIionqbAAuNdtG2NWqPczgF3BxE9bQvVKsFUycNk2jn_I5tgmZHZ7Wme6jP5sGXAQ/s1600/Khinjaria+skull.jpg"/></a>
<div class="captionc">Fossil skull of <i>Khinjaria acuta</i></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG0ajEWMo-DD_RXIiNqwGvrHqtIIMn_uCwVADBzGmt1dY65dIZRmR85jRuTu6N0HDmDMyp9NID6Bfep_FjZ28rbApYB-F0lO7rHmfA0d4_-F4nnDM6_lOi_M6lsmyeQ5Own562iOo22xCDKntudpyYdoACE0mGTkMfmLFlzpi0xyblgiCeMaTy8rauM4rN/s1600/Khinjaria+skull+reconstruction+by+Nick+Longrich.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjG0ajEWMo-DD_RXIiNqwGvrHqtIIMn_uCwVADBzGmt1dY65dIZRmR85jRuTu6N0HDmDMyp9NID6Bfep_FjZ28rbApYB-F0lO7rHmfA0d4_-F4nnDM6_lOi_M6lsmyeQ5Own562iOo22xCDKntudpyYdoACE0mGTkMfmLFlzpi0xyblgiCeMaTy8rauM4rN/s1600/Khinjaria+skull+reconstruction+by+Nick+Longrich.jpg"/></a>
<div class="captionc">Reconstruction of the skull of <i>Khinjaria acuta</i><br><div class="credit">Dr. Nicholas R. Longrich</div></div>
</div>
<a href="https://www.bath.ac.uk/announcements/fossils-of-giant-sea-lizard-show-how-our-oceans-have-fundamentally-changed-since-the-dinosaur-era/">Fossils of giant sea lizard show how our oceans have fundamentally changed since the dinosaur era</a><br>
<br>
Creationists only have themselves to blame. By insisting that Earth is only 6-10 thousand years old, they are consigning the vast majority of Earth’s 3.8-billion-year history to the pre-'Creation Week' period, before they believe Earth Existed. <br>
<br>
So, they then need to perform the most ludicrous of intellectual gymnastics to avoid dealing with all the evidence that they are wrong about the age of Earth and wrong about their denial of what else that evidence shows. For example, there is no way a 66-million-year-old fossil of a marine lizard could be assimilated into creationist superstition, so their only recourse is to devise a way to dismiss it. Favorite tactics are straight denial; bear false witness against the scientists by impugning their honesty and professional integrity; claim, without any evidence to support it, that the dating methods were so flawed they somehow made 10,000 or less look like 66 million.<br>
<br>
But the fact remains, no matter that creationists stamp their feet and cover their eyes and ears and demand the Universe changes to conform to their requirements, there were orca-sized marine lizards in the seas 66 million years ago.<br>
<br>
This is explained in a recent paper by researchers from the University of Bath in the UK, the Marrakech Museum of Natural History, Morocco, the Museum National d’ Histoire Naturelle (NMNH) in Paris, France, Southern Methodist University in Texas, USA, and the University of the Basque Country, Bilbao, Spain. Their paper is published in <i>Cretaceous Research</i> and explained in a Bath University news release.<br>
<br>
First, a little background on the dating of the phosphate deposits in Morocco where the fossils were found:
<a name='more'></a>
<blockquote class="ai">Do you have any information on the dating of fossil-bearing the Late Cretaceous phosphate deposits in Morocco?
Yes, the Late Cretaceous phosphate deposits in Morocco are well-known for their rich fossil content, particularly of marine organisms. These deposits have been dated using various methods, including radiometric dating of associated volcanic rocks and biostratigraphy, which involves correlating the fossils found in the deposits with known fossil assemblages from other regions and time periods.<br>
<br>
One of the key methods used for dating these deposits is radiometric dating, particularly using isotopes such as uranium-lead (U-Pb) dating of zircons found in volcanic ash layers interbedded with the phosphate deposits. Additionally, biostratigraphy, which relies on the identification of index fossils and their temporal ranges, has been crucial for establishing the age of these deposits.<br>
<br>
Studies have indicated that the Late Cretaceous phosphate deposits in Morocco date to the Campanian and Maastrichtian stages of the Late Cretaceous period, roughly between 83 to 66 million years ago. These deposits have yielded a diverse array of marine fossils, including ammonites, bivalves, gastropods, sharks, fish, marine reptiles such as mosasaurs, and even some dinosaur remains.<br>
<br>
Overall, the dating of these phosphate deposits in Morocco provides valuable insights into the geological history and evolution of marine ecosystems during the Late Cretaceous period.
</blockquote>
Creationists might like to ignore the fact that those dreaded zircons in volcanic deposits were dated using <a href="https://rosarubicondior.blogspot.com/2024/01/creationism-in-crisis-something-for.html#UPb" target="_blank">Uranium-Lead (U-Pb)</a> dating which is about the most accurate available dating methods with very few sources of error and very precise results.<br>
<div class="panelplain" style="margin: 1em auto">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyAk7yY9KImLBfc6Bfyol1y0MbcRI2SButZwTj963EOL8JzmaCbdakZL6meTaMFEwidr-hPcHBroboGxzn1d5TS-6f5pRO1hM8mOm_espIN5ys-ryeJzm3VYS-0o6AGTFFS3OPzHi7vsN1fXPYz7NZbyUlkOAJ88b1PtHxqahCIvg7VNr4hpH6EEkSc7N5/s1600/70+Ma+Moll+_Late-Cret-GPT.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyAk7yY9KImLBfc6Bfyol1y0MbcRI2SButZwTj963EOL8JzmaCbdakZL6meTaMFEwidr-hPcHBroboGxzn1d5TS-6f5pRO1hM8mOm_espIN5ys-ryeJzm3VYS-0o6AGTFFS3OPzHi7vsN1fXPYz7NZbyUlkOAJ88b1PtHxqahCIvg7VNr4hpH6EEkSc7N5/s1600/70+Ma+Moll+_Late-Cret-GPT.jpg"/></a>
<div class="captionc">Earth during the Late Cretaceous, when sea levels were higher and North Africa was under water.<br><br><div class="credit">Source: <a href="https://www.nicklongrich.com/blog/yet-another-terrifying-predatory-mosasaur-from-morocco" target="_blank">Dr Nicholas Longrich; Yet another terrifying predatory mosasaur from Morocco</a></div></div>
</div>
<blockquote class="blockit">Paleontologists have discovered a strange new species of marine lizard with dagger-like teeth that lived near the end of the age of dinosaurs. Their findings, published in <a href="https://doi.org/10.1016/j.cretres.2024.105870" target="_blank">Cretaceous Research</a>, show a dramatically different ocean ecosystem to what we see today, with numerous giant top predators eating large prey, unlike modern ecosystems where a few apex predators – such as great white sharks, orca and leopard seals – dominate.<br>
<br>
<i>Khinjaria acuta</i> was around the size of an orca (7-8 metres) and a member of the family Mosasauridae, or mosasaurs. Mosasaurs weren’t dinosaurs, but giant marine lizards, relatives of today’s Komodo dragons and anacondas, which ruled the oceans 66 million years ago, during the era of <i>Tyrannosaurus</i> and <i>Triceratops</i>.<br>
<br>
<i>Khinjaria</i> had powerful jaws and long, dagger-like teeth to seize prey, giving it a nightmarish appearance. It was part of an extraordinarily diverse fauna of predators that inhabited the Atlantic Ocean off the coast of Morocco, just before the dinosaurs went extinct.<br>
<br>
The study is based on a skull and parts of the skeleton collected from a phosphate mine southeast of Casablanca. The study involved researchers from the University of Bath in the UK, the Marrakech Museum of Natural History, the Museum National d’ Histoire Naturelle (NMNH) in Paris (France), Southern Methodist University in Texas (USA), and the University of the Basque Country (Bilbao).<br>
<div class="block"><p>What’s remarkable here is the sheer diversity of top predators. We have multiple species growing larger than a great white shark, and they’re top predators, but they all have different teeth, suggesting they’re hunting in different ways. Some mosasaurs had teeth to pierce prey, others to cut, tear, or crush. Now we have <i>Khinjaria</i>, with a short face full of huge, dagger-shaped teeth. This is one of the most diverse marine faunas seen anywhere, at any time in history, and it existed just before the marine reptiles and the dinosaurs went extinct.</p>
<div class="creditl">Dr Nicholas R. Longrich, lead author<br>
Department of Biology and Biochemistry<br>
University of Bath, Bath, UK.</div></div>
Morocco’s diverse marine reptiles lived just before an asteroid struck the Yucatan Peninsula in Mexico. Dust and fine particles shot into the high atmosphere blocked out the sun for months, causing darkness and cooling, which drove most of the planet’s species to extinction.<br>
<br>
Dinosaurs were wiped out on land, and a handful of surviving species of mammals, birds, and lizards diversified to take their place. Meanwhile, the same happened in the oceans.<br>
<br>
Mosasaurs, plesiosaurs and giant sea turtles disappeared, along with entire families of fish. This opened the way for whales and seals, and fish like swordfish and tuna appeared. However, the ecosystem that evolved after the impact was different.<br>
<div class="block"><p>There seems to have been a huge change in the ecosystem structure in the past 66 million years. This incredible diversity of top predators in the Late Cretaceous is unusual, and we don’t see that in modern marine communities.</p>
<div class="creditl">Dr Nicholas R. Longrich</div></div>
Modern marine food chains have just a few large apex predators, animals like orcas, white sharks, and leopard seals. The Cretaceous had a whole host of top predators.
<div class="block"><p>It’s not just that we’re getting rid of the old actors and recasting new ones into the same roles. The story has changed dramatically. Modern ecosystems have predators like baleen whales and dolphins that eat small prey, and not many things eating large prey. The Cretaceous has a huge number of marine reptile species that take large prey. Whether there’s something about marine reptiles that caused the ecosystem to be different, or the prey, or perhaps the environment, we don’t know. But this was an incredibly dangerous time to be a fish, a sea turtle, or even a marine reptile.</p>
<div class="creditl">Dr Nicholas R. Longrich</div></div>
<div class="block"><p>The phosphates of Morocco deposit in a shallow and warm epicontinental sea, under a system of upwellings; these zones are caused by currents of deep, cold, nutrient-rich waters rising towards the surface, providing food for large numbers of sea creatures and, as a result, supporting a lot of predators. This is probably one of the explanations for this extraordinary paleobiodiversity observed in Morocco at the end of the Cretaceous.</p>
<div class="creditl">Professor Nathalie Bardet, co-author.<br>
Centre de Recherche en Paléontologie de Paris<br>
Muséum National d'Histoire Naturelle, Paris, France</div></div>
<div class="block"><p>The phosphates of Morocco immerse us in the Upper Cretaceous seas during the latest geological times of the dinosaurs’ age. No deposit has provided so many fossils and so many species from this period. After the ’titan of the seas’, <i>Thalassotitan</i>, the ‘saw-toothed’ mosasaur <i>Xenodens</i>, the ‘star-toothed’ mosasaur, <i>Stelladens</i> and many others, now there is <i>Khinjaria</i>, a new mosasaur with dagger-like teeth. The elongation of the posterior part of the skull which accommodated the jaw musculature suggests a terrible biting force.</p>
<div class="creditl">Professor Nour-Eddine Jalil, co-author<br>
Centre de Recherche en Paléontologie de Paris<br>
Muséum National d'Histoire Naturelle, Paris, France</div></div>
</blockquote>
<div class="panelplain" style="margin: 1em auto"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvTK6dqL7ynhnw6deCM_KkY3DMGiujDC-s-CyHBsQiO17ff-9SWFudnZN5OZ2M9ylr_vKVX2bUhW8YC_5HLz_obJXUVmgs7-JRp2ZGVSneumndWaEKHCqcUiVSWN1Msvh2FXpOYiI8vaGWX8q_E1i3EiOtiDfqj_vVAjpo2rsE0rY0yAoQtesekG9Y8tv9/s1600/Khinjaria+silhouette+by+Nick+Longrich.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvTK6dqL7ynhnw6deCM_KkY3DMGiujDC-s-CyHBsQiO17ff-9SWFudnZN5OZ2M9ylr_vKVX2bUhW8YC_5HLz_obJXUVmgs7-JRp2ZGVSneumndWaEKHCqcUiVSWN1Msvh2FXpOYiI8vaGWX8q_E1i3EiOtiDfqj_vVAjpo2rsE0rY0yAoQtesekG9Y8tv9/s1600/Khinjaria+silhouette+by+Nick+Longrich.jpg"/></a>
<div class="captionc"><i>Khinjaria acuta</i> with a human for scale. <br><div class="credit">Dr Nicholas Longrich, 2024.</div></div>
</div>
Technical details are given in the team's research paper in <i>Cretaceous Research</i>:
<blockquote class="blockit"><span class="t2">Abstract</span><br>
<br>
The Upper Maastrichtian of Morocco has produced a remarkably diverse fauna of mosasaurids, the most diverse known for any time or place. As apex predators, Mosasauridae provide a picture of the marine ecosystem just before the end-Cretaceous mass extinction. Here we describe a bizarre new plioplatecarpine mosasaurid, <i>Khinjaria acuta</i>, characterized by enlarged, dagger-like anterior teeth, short, robust jaws, and posterior elongation of the skull. <i>Khinjaria</i> is related to <i>Goronyosaurus nigeriensis</i> from Nigeria and Niger, and <i>Gavialimimus almaghribensis</i> from Morocco. These species form a distinct clade of specialized mosasaurids so far unknown outside of Africa. Mosasaurids show high endemism in the Maastrichtian, with different lineages occurring in different regions, implying that mosasaurid diversity is underestimated because of limited geographic sampling. The large size, robust jaws, akinetic skull, and bladelike teeth of Khinjaria suggest it was an apex predator, but the unusual skull and jaw differ from those of contemporary predators like <i>Hainosaurus</i>, <i>Thalassotitan</i>, and <i>Mosasaurus</i>, suggesting a distinct feeding strategy. Mosasaurids became increasingly specialized in the latest Cretaceous, repeatedly evolving to occupy the apex predator niche, suggesting a diverse marine ecosystem persisted up to the K-Pg boundary. Late Cretaceous marine ecosystems differ from modern marine ecosystems in the high diversity of large predators.<br>
<br>
<div class="creditl">Longrich, Nicholas R.; Polcyn, Michael J.; Jalil, Nour-Eddine; Pereda-Suberbiola, Xabier; Bardet, Nathalie<br>
A bizarre new plioplatecarpine mosasaurid from the Maastrichtian of Morocco<br>
<i>Cretaceous Research</i> (2024),105870, doi: 10.1016/j.cretres.2024.105870.<br>
<br>
© 2024 Elsevier Ltd.<br>
Reprinted under the terms of <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">s60</a> of the <a href="https://www.legislation.gov.uk/ukpga/1988/48/section/60" target="_blank">Copyright, Designs and Patents Act 1988</a>.</div>
</blockquote>
Why on Earth creationists believe the people who made up the childish origin myths in the Bible knew everything, when they were manifestly completely oblivious to the vast history of Earth and life on it, is anyone's guess. It take a special mixture of intellectual dishonesty, careful scientific illiteracy avoidance of logic and terror of the consequences of doubt, to maintain a belief in the fairytales they were fed as children, that normal people grow out of by the age of about 10 when they stop believing in Santa and the Tooth Fairy. If the same Bronze Age ignorami the wrote Genesis had included fairies at the bottom of the garden, creationists would be making up excuses for believign in them despite the lack of any evidence for them.
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Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com1tag:blogger.com,1999:blog-7583674511519808833.post-58048750732351515942024-03-05T20:21:00.004+00:002024-03-05T21:19:16.596+00:00Abiogenesis News - New Evidence For The 'RNA World' Hypothesis<div class="title-box" style="height: 1000px; display: none">
<div class="postTitle"></div>
<div class="horizontalBox">
<div class="left-column" style="text-align: left; flex: 3">Hammerhead sequences copied by the lower-fidelity polymerase drift away from their original RNA sequence (top) and lose their function over time. Hammerheads catalyzed by the higher-fidelity polymerase retain function and evolve fitter sequences (bottom).</div>
<div class="right-column" style="text-align: right; flex: 1">Credit: Salk Institute</div>
</div>
</div><br>
<div class="rpanel450plain" style="display: none"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioIr1928uiIaY2GCXwVoP-vtACSmng5YxBjc6YuqjS2guGvj2gjh4UzBcWZsYsM650JM0KOuy9EK7WgG-wbCJXZXZncj8v2BIp1OZ5A4f9AKPuENaUj4YqHacxLNvjEvVaebDyrWfP5ZuGfLiIxQPKJ9t5dgTBy40PJZvxAjn8oh1XNvnHhkrCjY6AS6PD/s1600/PNAS_Joyce_RNA.jpg" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" data-original-height="1250" data-original-width="961" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioIr1928uiIaY2GCXwVoP-vtACSmng5YxBjc6YuqjS2guGvj2gjh4UzBcWZsYsM650JM0KOuy9EK7WgG-wbCJXZXZncj8v2BIp1OZ5A4f9AKPuENaUj4YqHacxLNvjEvVaebDyrWfP5ZuGfLiIxQPKJ9t5dgTBy40PJZvxAjn8oh1XNvnHhkrCjY6AS6PD/s1600/PNAS_Joyce_RNA.jpg"/></a></div>
<div class="rpanel450plain"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi41zWG_FksJo8G01npd3Vj6hk5LL76OT1wm5ZdquAaDWy5zQy-5kr93Segfr63WeweTpbP_pyzVKNGztECEjvobbZKT-qoMUc5DQXxWZahOSERRpR5HHLrYM_-iAVFtd2iNBGw4w_Edc6X1o3j2ZT_oU1Uz_ht12XmuUKmJKPTPivzhMkWx1eTBcv62LQS/s1600/Hammerhead_ribozyme_ribbons.png"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi41zWG_FksJo8G01npd3Vj6hk5LL76OT1wm5ZdquAaDWy5zQy-5kr93Segfr63WeweTpbP_pyzVKNGztECEjvobbZKT-qoMUc5DQXxWZahOSERRpR5HHLrYM_-iAVFtd2iNBGw4w_Edc6X1o3j2ZT_oU1Uz_ht12XmuUKmJKPTPivzhMkWx1eTBcv62LQS/s1600/Hammerhead_ribozyme_ribbons.png"/></a>
<div class="captionc">Stylized rendering of the full-length hammerhead ribozyme RNA molecule<br><div class="credit">Source: <a href="https://en.wikipedia.org/wiki/Hammerhead_ribozyme#/media/File:Hammerhead_ribozyme_ribbons.png" target="_blank">Wikipedia</a></div></div>
</div>
<a href="https://www.salk.edu/news-release/modeling-the-origins-of-life-new-evidence-for-an-rna-world/">Modeling the origins of life: New evidence for an “RNA World” - Salk Institute for Biological Studies</a><br>
<br>
On way of looking at cellular life is that it is based on RNA, not DNA. In that model, DNA is RNA's data store. All the functional processes that DNA codes for are first transcribed into RNA and short lengths of RNA still regulate some of the cell processes. RNA can even act as a catalyst playing the role normally performed by protein enzymes - proteins that are themselves transcriptions of RNA triplet codes for amino acid sequences.<br>
<br>
On that model, early self-replicating systems were based on RNA, and DNA was late to the game.<br>
<br>
Now three researchers at the Salk Institute for Biological Studies, La Jolla, California, USA, have shown how such a system could have bootstrapped from simple, self-catalysing lengths of RNA which not only self-replicate but can continue to do so even when there are variations stemming from faulty replications. This system would have created the variation needed for Darwinian evolution by natural selection as some variant performed better in terms of competing for resources and ultimately making more copies, so coming to predominate in the pool of RNA-based organisms.<br>
<br>
How the scientists discovered this is the subject of a research paper in PNAS which sadly is behind a paywall with only the abstract and statement of significance freely available. It is also the subject of a news release from the Salk Institute.<br>
<br>
Since the team refer to an RNA structure known as the 'hammerhead ribozyme', it might help to understand a little about it first:<br>
<a name='more'></a>
<blockquote class="ai">Do you have any information on the 'hammerhead ribozyme'?
Yes, the hammerhead ribozyme is a small catalytic RNA molecule that cleaves other RNA molecules in a sequence-specific manner. It is one of the best-characterized ribozymes and has been extensively studied in the field of RNA biochemistry and molecular biology.<br>
<br>
The hammerhead ribozyme gets its name from its secondary structure, which resembles the head of a hammer. It consists of three helical regions connected by loops, with a conserved catalytic core formed by conserved sequences within the loops. This core region contains the catalytic residues responsible for RNA cleavage.<br>
<br>
The hammerhead ribozyme functions by binding to a target RNA molecule through Watson-Crick base pairing interactions with its substrate-binding arms. Once bound, the ribozyme catalyzes the cleavage of the target RNA at a specific site, typically a purine-pyrimidine dinucleotide sequence.<br>
<br>
The discovery and study of hammerhead ribozymes have contributed significantly to our understanding of RNA catalysis and have potential applications in biotechnology and gene therapy. Researchers have engineered hammerhead ribozymes for various purposes, including the specific cleavage of target RNA molecules for gene silencing or as tools for studying RNA structure and function.
</blockquote>.
<blockquote class="blockit"><span class="t2">Modeling the origins of life: New evidence for an “RNA World”</span><br>
<br>
<b>Salk scientists unveil RNA capabilities that enable Darwinian evolution at a molecular scale, and bring researchers closer to producing autonomous RNA life in the laboratory</b><br>
<br>
Charles Darwin described evolution as "descent with modification." Genetic information in the form of DNA sequences is copied and passed down from one generation to the next. But this process must also be somewhat flexible, allowing slight variations of genes to arise over time and introduce new traits into the population.
<div class="rpanel450plain" >
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8EU4Dx8v9DYxonOoEuObTED9yVglHTJ4iEJqz73vkScZo2qLV4Tq49H30cMTLqJB5i5f0EKCtMEXCBEKGqeCB_brSk031O0jQHkyckGC5mk0MVCcn4-xfueXl_NRUp_8-djgNO8PmIFHBu-pco-YqeJjPJOHPCJ-RT4SSCK05XStWYqwdcB516XGcNtOx/s1600/Joyce-PR-20240212-551A6842.jpg"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8EU4Dx8v9DYxonOoEuObTED9yVglHTJ4iEJqz73vkScZo2qLV4Tq49H30cMTLqJB5i5f0EKCtMEXCBEKGqeCB_brSk031O0jQHkyckGC5mk0MVCcn4-xfueXl_NRUp_8-djgNO8PmIFHBu-pco-YqeJjPJOHPCJ-RT4SSCK05XStWYqwdcB516XGcNtOx/s1600/Joyce-PR-20240212-551A6842.jpg"/></a><br>
<div class="captionc">From left: David Horning, Gerald Joyce, and Nikolaos Papastavrou.</div>
</div>But how did all of this begin? In the origins of life, long before cells and proteins and DNA, could a similar sort of evolution have taken place on a simpler scale? Scientists in the 1960s, including Salk Fellow Leslie Orgel, proposed that life began with the “RNA World,” a hypothetical era in which small, stringy RNA molecules ruled the early Earth and established the dynamics of Darwinian evolution.<br>
<br>
New research at the Salk Institute now provides fresh insights on the origins of life, presenting compelling evidence supporting the RNA World hypothesis. The study, published in Proceedings of the National Academy of Sciences (PNAS) on March 4, 2024, unveils an RNA enzyme that can make accurate copies of other functional RNA strands, while also allowing new variants of the molecule to emerge over time. These remarkable capabilities suggest the earliest forms of evolution may have occurred on a molecular scale in RNA.<br>
<br>
The findings also bring scientists one step closer to re-creating RNA-based life in the laboratory. By modeling these primitive environments in the lab, scientists can directly test hypotheses about how life may have started on Earth, or even other planets.<br>
<br>
<div class="lpanel48plain">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyMtVuzb9D7eCxN4YJpbK-K8l6TJ4EmQgfCM8skznDzzF46iAffShsajMb0OW_aVOqbTpAQoYaR-3_NC9OpehdE8VJ2y3ElOKl1tVdrOA5YpoHzj25Tt5OOkpcWJ29_W1DpM9ozPvqAIchUWuATVpDXfIbwzrLiEEKiCximFWtRzUDO6PD1iMy-dVYkuPp/s1600/PNAS_Joyce_RNA.jpg" ><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyMtVuzb9D7eCxN4YJpbK-K8l6TJ4EmQgfCM8skznDzzF46iAffShsajMb0OW_aVOqbTpAQoYaR-3_NC9OpehdE8VJ2y3ElOKl1tVdrOA5YpoHzj25Tt5OOkpcWJ29_W1DpM9ozPvqAIchUWuATVpDXfIbwzrLiEEKiCximFWtRzUDO6PD1iMy-dVYkuPp/s1600/PNAS_Joyce_RNA.jpg"/></a>
<div class="caption">Hammerhead sequences copied by the lower-fidelity polymerase drift away from their original RNA sequence (top) and lose their function over time. Hammerheads catalyzed by the higher-fidelity polymerase retain function and evolve fitter sequences (bottom).<br><br><div class="credit">Credit: Salk Institute</div></div></div>
<div class="blockr"><p>We're chasing the dawn of evolution. By revealing these novel capabilities of RNA, we're uncovering the potential origins of life itself, and how simple molecules could have paved the way for the complexity and diversity of life we see today.</p>
<div class="creditl">Gerald Joyce, senior author<br>
President<br>
Salk Institute for Biological Studies<br>
La Jolla, California, USA.</div></div>
Scientists can use DNA to trace the history of evolution from modern plants and animals all the way back to the earliest single-celled organisms. But what came before that remains unclear. Double-stranded DNA helices are great for storing genetic information. Many of those genes ultimately code for proteins—complex molecular machines that carry out all sorts of functions to keep cells alive. What makes RNA unique is that these molecules can do a bit of both. They’re made of extended nucleotide sequences, similar to DNA, but they can also act as enzymes to facilitate reactions, much like proteins. So, is it possible that RNA served as the precursor to life as we know it?<br>
<br>
Scientists like Joyce have been exploring this idea for years, with a particular focus on RNA polymerase ribozymes—RNA molecules that can make copies of other RNA strands. Over the last decade, Joyce and his team have been developing RNA polymerase ribozymes in the lab, using a form of directed evolution to produce new versions capable of replicating larger molecules. But most have come with a fatal flaw: they aren’t able to copy the sequences with a high enough accuracy. Over many generations, so many errors are introduced into the sequence that the resulting RNA strands no longer resemble the original sequence and have lost their function entirely.<br>
<br>
Until now. The latest RNA polymerase ribozyme developed in the lab includes a number of crucial mutations that allow it to copy a strand of RNA with much higher accuracy.<br>
<br>
In these experiments, the RNA strand being copied is a “hammerhead,” a small molecule that cleaves other RNA molecules into pieces. The researchers were surprised to find that not only did the RNA polymerase ribozyme accurately replicate functional hammerheads, but over time, new variations of the hammerheads began to emerge. These new variants performed similarly, but their mutations made them easier to replicate, which increased their evolutionary fitness and led them to eventually dominate the lab’s hammerhead population.<br>
<div class="block"><p>We’ve long wondered how simple life was at its beginning and when it gained the ability to start improving itself. This study suggests the dawn of evolution could have been very early and very simple. Something at the level of individual molecules could sustain Darwinian evolution, and that might have been the spark that allowed life to become more complex, going from molecules to cells to multicellular organisms.</p>
<div class="creditl">Nikolaos Papastavrou, first author<br>
Research associate<br>
Salk Institute for Biological Studies<br>
La Jolla, California, USA.</div></div>
<div class="panelplain" style="margin: 1em auto"><iframe style="border-radius: 20px; width: 100%; height:420px" src="https://www.youtube.com/embed/cn_Nh15ufTQ" title="Modeling the origins of life: New evidence for an “RNA World”" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe><div class="caption">Scatterplots show the evolving populations of hammerheads across multiple rounds of evolution. Hammerheads copied by the lower-fidelity polymerase (52-2) drift away from the original RNA sequence (white contours) and lose their function. Hammerheads copied by the new higher-fidelity polymerase (71-89) retain function, with new functional sequences emerging over time.<br><div class="credit">Credit: Salk Institute</div></div></div>
The findings highlight the critical importance of replication fidelity in making evolution possible. The RNA polymerase’s copying accuracy must exceed a critical threshold to maintain heritable information over multiple generations, and this threshold would have risen as the evolving RNAs increased in size and complexity.
Joyce’s team is re-creating this process in laboratory test tubes, applying increasing selective pressure on the system to produce better-performing polymerases, with the goal of one day producing an RNA polymerase that can replicate itself. This would mark the beginnings of autonomous RNA life in the laboratory, which the researchers say could be accomplished within the next decade.
The scientists are also interested in what else might occur once this mini “RNA World” has gained more autonomy.
<div class="block"><p>We’ve seen that selection pressure can improve RNAs with an existing function, but if we let the system evolve for longer with larger populations of RNA molecules, can new functions be invented? We’re excited to answer how early life could ratchet up its own complexity, using the tools developed here at Salk.</p>
<div class="creditl">David Horning, co-author<br>
Staff scientist<br>
Salk Institute for Biological Studies<br>
La Jolla, California, USA.</div></div>
The methods used in the Joyce lab also pave the way for future experiments testing other ideas about the origins of life, including what environmental conditions could have best supported RNA evolution, both on Earth and on other planets.
</blockquote><br>
And more detail is in the abstract to the paper in PNAS:<br>
<blockquote class="blockit"><span class="t2">Significance</span>
<br>
An RNA enzyme with RNA polymerase activity was used to replicate and evolve an RNA enzyme with RNA-cleavage activity. The fidelity of the polymerase is sufficient to maintain heritable information over the course of evolution, with a succession of variants of the RNA-cleaving RNA enzyme arising that have progressively increasing fitness. The RNA-catalyzed evolution of functional RNAs is thought to have been central to the early history of life on Earth and to the possibility of constructing RNA-based life in the laboratory.<br>
<br>
<span class="t2">Abstract</span><br>
<br>
An RNA polymerase ribozyme that was obtained by directed evolution can propagate a functional RNA through repeated rounds of replication and selection, thereby enabling Darwinian evolution. Earlier versions of the polymerase did not have sufficient copying fidelity to propagate functional information, but a new variant with improved fidelity can replicate the hammerhead ribozyme through reciprocal synthesis of both the hammerhead and its complement, with the products then being selected for RNA-cleavage activity. Two evolutionary lineages were carried out in parallel, using either the prior low-fidelity or the newer high-fidelity polymerase. The former lineage quickly lost hammerhead functionality as the population diverged toward random sequences, whereas the latter evolved new hammerhead variants with improved fitness compared to the starting RNA. The increase in fitness was attributable to specific mutations that improved the replicability of the hammerhead, counterbalanced by a small decrease in hammerhead activity. Deep sequencing analysis was used to follow the course of evolution, revealing the emergence of a succession of variants that progressively diverged from the starting hammerhead as fitness increased. This study demonstrates the critical importance of replication fidelity for maintaining heritable information in an RNA-based evolving system, such as is thought to have existed during the early history of life on Earth. Attempts to recreate RNA-based life in the laboratory must achieve further improvements in replication fidelity to enable the fully autonomous Darwinian evolution of RNA enzymes as complex as the polymerase itself.
</blockquote>
So, one step close towards closing creationism last remaining refuge for their ever-shrinking little god. All that was needed to get 'RNA world' was the right combination of nucleotides in the RNA molecule from the millions of possible combinations to arise just once and the process could take off to become self-sustaining and subject to improvement and refinement by Darwinian natural selection, just as Darwin had predicted, only at a molecular level he could not have been aware of.<br>
<br>
This of course makes the transition from pre-biotic molecules in solution to self-replicating molecules and eventually metabolising entities enclosed in a cell membrane all a matter of the operation of physics and chemistry, with no need for magic anywhere in the process. Creationism’s soon-to-homeless small god should be packing its bags right now. So, all that will be left by way of a home for it will be the carefully constructed gaps in creationists’ knowledge and understanding.
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styledSentence.innerHTML = firstSentence;
styledSentence.classList.add("t2"); // Add your CSS class here.
const infoText = document.createTextNode("Information current at January 2022");
const br = document.createElement("br");
// Create a new container for the remaining content (excluding the first sentence);
const blockquoteBody = document.createElement("div");
blockquoteBody.innerHTML = content.substring(sentenceEndIndex);
footer.appendChild(br);
footer.appendChild(document.createTextNode("ChatGPT3.5 [Response to user request]"));
footer.appendChild(br.cloneNode());
footer.appendChild(document.createTextNode("Retrieved from "));
footer.appendChild(link);
footer.appendChild(br.cloneNode());
footer.appendChild(br.cloneNode());
footer.appendChild(infoText);
footer.style.fontSize = "x-small";
footer.style.fontStyle = "italic";
// Clear the blockquote content and insert the styled first sentence;
blockquote.innerHTML = "";
blockquote.appendChild(styledSentence);
blockquote.appendChild(br.cloneNode());
blockquote.appendChild(br.cloneNode());
blockquote.appendChild(blockquoteBody);
blockquote.appendChild(footer);
});
// read newtooltips and populate fields if needed
var newtooltips = document.querySelectorAll("a.newtooltip");
var listPos = 0;
var txt = null;
var url = null;
for (var i = 0; i < newtooltips.length; i++) {
var newtooltip = newtooltips[i];
var newtooltipContent = newtooltip.textContent;
// Check if the content of the newtooltip is a number
if (!isNaN(parseFloat(newtooltipContent))) {
// Replace newtooltip content with the integer part
newtooltip.textContent = Math.trunc(parseFloat(newtooltipContent));
var reference = findReferenceByValue(referenceList, newtooltipContent);
if (reference) {
txt = reference.text;
url = reference.url; //=== '' ? '#' : reference.url;
} else {
console.error('Missing tooltip index', newtooltipContent);
}
} else {
// Check if there's a text-based newtooltip available
var listContent = toolTipText[listPos]
txt = listContent.text;
url = listContent.url; // === '' ? '#' : listContent.url;
listPos++
}
url === '' ? '#' : url
url = url !== undefined ? url : '#'; // url is undefined
//console.log(txt);
//console.log(url);
if (txt) {
txt = txt.replace(/–/g, '-'); // replace endash with hyphen
txt = txt.replace(/ /g,' '); // replace thinspace with space
txt = txt.replace(/’/g,"'"); // replace single quote with apostrophe, e.g., O'Sullivan
txt = txt.replace(/“/g,'"'); // replace left double quote with "
txt = txt.replace(/”/g,'"'); // replace right double quote with "
newtooltip.setAttribute("data-tooltip", txt);
newtooltip.setAttribute("href", url);
newtooltip.setAttribute("target", "_blank");
}
}
});
//--------------------------------------
function setTitle() {
postTitle = postTitle.replace("Rosa Rubicondior:","");
postTitle = postTitle.replace("Preview","");
if (postTitle.includes(" - ")) {
postTitle = "<span class='bigTitle'>" + postTitle;
postTitle = postTitle.replace(" - ","</span><br><br>")
postTitle = postTitle.replace(" - "," -<br><br>")
}
postTitle = postTitle.replace(/"/g, '');
postTitle = postTitle.trim();
console.log(postTitle);
titleText.innerHTML = postTitle;
titleText.classList.add('outlined-text');
};
function findReferenceByValue(referenceList, value) {
// Match the tooltip content against the referenceList values
return referenceList.find(ref => ref.n.startsWith(value));
}
function getbgImageUrl() {
// Select the first div element with class "rpanel450plain"
const firstDivElement = document.querySelector('.rpanel450plain');
// Check if the div element exists
if (firstDivElement) {
// Select the first img element within the div
const imgElement = firstDivElement.querySelector('img');
// Check if the img element exists
if (imgElement) {
// Get the value of the src attribute (image URL)
imageUrl = imgElement.src;
// Now you can use imageUrl as needed, for example, setting it as a background image
//console.log('Image URL:', imageUrl);
} else {
console.error('Img element not found within the div.');
}
} else {
console.error('Div element with class "rpanel450plain" not found.');
}
return imageUrl;
};
function formatDate(date) {
var d = new Date(date);
var months = ['January','February','March','April','May','June','July','August','September','October','Novemember','December'];
var days = ['Sunday', 'Monday', 'Tuesday', 'Wednesday', 'Thursday', 'Friday', 'Saturday'];
var day = d.getDate();
var dayName = days[d.getDay()];
var month = months[d.getMonth()];
var year = d.getFullYear();
var hours = d.getHours();
var minutes = d.getMinutes();
var seconds = d.getSeconds();
// Add leading zeros if necessary
day = (day < 10) ? '0' + day : day;
hours = (hours < 10) ? '0' + hours : hours;
minutes = (minutes < 10) ? '0' + minutes : minutes;
seconds = (seconds < 10) ? '0' + seconds : seconds;
var formattedDate = dayName + ', ' + day + ' ' + month + ' ' + year + ' ' + hours + ':' + minutes + ':' + seconds;
return formattedDate;
}
</script>
<div class="blogger-post-footer"><br />
<center>If you've enjoyed my blog please show your appreciation
by giving to a great cause - <a href="http://www.oxfam.org.uk/">Oxfam</a>
<br />
Be Humankind. Feed the world.</center></div>Rosa Rubicondiorhttp://www.blogger.com/profile/06063268216781988588noreply@blogger.com0