F Rosa Rubicondior: March 2022

Monday 28 March 2022

Evolution by Loss of Genetic Information Sends Creationists Batty

The common vampire bat, Desmodus rotundus, feeds exclusively on the blood of other animals. Adaptations to this unique diet are due in part to the loss of genes.
Photo: Brock Fenton
Vampires with genetic defects: MPI-CBG

Sometimes, refuting Creationism is too tempting to resist. The basic problem is that Creationism relies on creationists being fooled into believing things that are, frankly, counter-factual and easily demonstrated to be so.

Take, for example, the latest attempt to make it look like science is wrong about evolution and the facts comply with a literal interpretation of the Bible - Michael J Behe's 'Devolution' nonsense, that basically argues that every mutation is a retreat from the initial perfection of creation, (with the implication that this is due to 'sin' following 'The Fall' - a popular Judeo-Christian myth from the Bronze Age). Following his failure to make any progress in the courts with his and the Deception Institute's 'Intelligent [sic] Design' ploy, he has tried to come up with an alternative that makes Bible-literalist creationism look like real science. Sadly though, the facts are once again against him.

For example, this recent open access publication in Science Advances, by scientists from the LOEWE Centre for Translational Biodiversity Genomics in Frankfurt and the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, which shows that the common vampire bat's ability to live exclusively on a diet of mammalian blood, was made possible by a loss of thirteen genes - mutations which gave them significant advantages so were selected for by natural evolution. It takes some wonderful mental gymnastics to believe that mutations which give an advantage are somehow 'devolutionary' - a meaningless term which implies a 'correct' direction for evolutionary change, so appeals to the childish, teleological thinking of creationists.

Friday 25 March 2022

Evolution News - Science Got it Wrong, But Not The Way Creationists Like to Imagine.

The sand dollar Mellitella stokesii.
Image credit: Rich Mooi (CC BY 4.0)
Study reconsiders early evolution of sea urchins | eLife

In yet another example of how science constantly re-examines, reassesses and revises its understanding, according to an open access paper published in eLife, scientists had got the evolution of sea urchins wrong.

Now, calm down Creationists and don't get over-excited! They didn't get it wrong in the way you've been fooled into believing. There is absolutely no threat to the fundamental biological science of evolution; what they got wrong, according to this paper, is the details. The scientists are in no doubt that the processes involved on evolutionary diversification are as stated in the theory.

As the eLife press release explains:
New insight on the origins and early evolution of echinoids, a group that includes the sea urchins, the sand dollars, and their relatives, has been published today in the journal eLife.

There are still debates among scientists about when the ancestors of echinoids emerged and what role the mass extinction event that occurred between the Permian and Triassic periods may have played in their evolution. We set out to help resolve these debates by combining genomic and paleontological data to disentangle their evolutionary relationships. The extraordinary fossil record of echinoids and the ease with which these fossils can be incorporated in phylogenetic analyses make them an ideal system to explore their early evolution using this approach.

Dr Nicolás Mongiardino Koch, first author
Formerly at Yale University, New Haven, Connecticut, USA.
Now at Scripps Institution of Oceanography
UC San Diego, USA
The study suggests that modern echinoids emerged approximately 300 million years ago, survived the Permo-Triassic mass extinction event – the most severe biodiversity crisis in Earth’s history – and rapidly diversified in its aftermath. These findings help address a gap in knowledge caused by the relative lack of fossil evidence for this early diversification.

There are more than 1,000 living species of echinoids, including sea urchins, heart urchins, sand dollars and sea biscuits, which live across different ocean environments ranging from shallow waters to abysses. Throughout history, the hard spine-covered skeletons of these creatures have left an impressive number of fossils. However, despite this remarkable fossil record, their emergence is documented by few fossil specimens with unclear affinities to living groups, making their early history uncertain.

Our work greatly expands the genomic data available for echinoids and helps resolve some of the long-standing questions around their evolutionary history. Together, the results suggest that we need to re-evaluate the echinoid fossil record, with future studies of overlooked fossil remnants potentially providing further support to our findings.

Professor Greg Rouse, senior author
Professor of Marine Biology
Scripps Institution of Oceanography
UC San Diego, USA
Mongiardino Koch and the team built upon available molecular resources with 18 novel genomic datasets, creating the largest existing molecular matrix for echinoids. Using this dataset, they were able to reconstruct the phylogenetic relationships and divergence times of the major lineages of living echinoids and place their diversification within broader evolutionary history. They did so by applying a ‘molecular clock’ technique to their dataset, whereby the rate at which mutations accumulated in the echinoid genomes is translated into geological time with the use of fossil evidence, allowing researchers to determine when different lineages first diversified.

Their analyses suggest that the ancestors of modern echinoids likely emerged during the Early Permian, and rapidly diversified during the Triassic period in the aftermath of a mass extinction event, even though this evolutionary radiation does not seem to have been captured by the fossil record.

Additionally, the results suggest that sand dollars and sea biscuits likely emerged much earlier than thought, during the Cretaceous period about 40 to 50 million years before the first documented fossils of these creatures. The authors say this result is remarkable, as the tough skeleton of the sand dollars, their buried lifestyles, and their extremely distinct morphologies imply that their fossil record should faithfully reflect their true evolutionary history.
This is just another example of how the study of DNA and genetics has confirmed Darwin's basic idea and extended our understanding of how species evolved and diversified from common ancestors. Darwin knew nothing of how information was passed to the next generation but he knew that it must be and that it included small variations of which natural selection could favour or disfavour, giving rise to ever-greater adaptation and fitness to survive and reproduce in the selective environment.

The scientists explain more in the abstract to their eLife paper, as does the journal editor in the editor's evaluation:

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace – a multidimensional representation of node ages – and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

Editor's evaluation

The study by Mongiardino Koch et al., presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 18 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.
Incidentally, if anyone is in any doubt about peer-review and imaging it's some sort of formality that waves any scientific papers through on the nod, provided they conform to some assumed dogma, like creationist articles, it is worth scrolling down to the Decision letter section, where unusually for a scientific paper the reviewers' comments appear in full, together with the authors' responses. Peer-review is not a process to ensure compliance to some assumes party line, but a constructive, critical process by experts in the field that ensure the highest standards of scientific integrity and accuracy are maintained in the articles published by scientific journals, so readers can rely on the accuracy and validity of the findings.

For examples (reviewer's comments in italics and the authors' response to them):
Reviewer #2 (Recommendations for the authors):
I found the text long in places and thus tedious to read. Particularly the introduction and the discussion. The intro could have a tighter narrative more focused on the discrepancies of the fossil record and divergence times, and on discrepancies in topology without the needed to review so much echinoid biology. The discussion appears too long. Too much effort is made on justifying the chronospace approach. This perhaps does not need to be justified at all beyond a sentence or two.
The issue of the length of the introduction and the extent to which echinoid background is developed seems to be a discrepancy between reviewers. We have decided not to modify its length, as we believe the present version is already a good compromise, as is suggested by Reviewer #1 as well. We have however reduced the length of the justification of chronospaces.
Because the clock model has such an impact, you should explore this further. PhyloBayes provides the ability to test for the various rate models using Bayes factors and you should try this. Because this analyses are computationally expensive, you can do them on a reduced amount of data. MCMCtree also allows you to test for various clock models with Bayes factors.
Given the computational burden of running a Bayes factor analysis on PhyloBayes, we had explored CorrTest instead, a different approach for selecting among competing clock models. The results of this were not reported before, but are now incorporated as Reviewer #1 also suggested this. Given that these methods did not eliminate uncertainty in terms of which clock model should be preferred, we have taken the position of exploring and reporting the sensitivity of results to all factors. All conclusions drawn in the manuscript regarding echinoderm diversification are robust even to the large effects introduced by the choice of clock models. We don’t feel the need to restrict the analyses or results to a subset of conditions when this would not modify our insights.

Additional points:
The y-axis (Δ likelihood) of panel C in Figure 2 needs to be explained in the legend. What is the benchmark likelihood?
Panel C of Figure 2 is better explained now in the caption. There is no benchmark likelihood, values larger than 0 mean support for one topology, those below 0 for the alternative.
In the figure legends, the program/models used to infer the tree and times should be indicated. From the methods it's clear that many many different methods were tested, but from the main text and the figure legends is not clear what is being summarised in the figures.
Software are now mentioned in the captions of Figures 2 and 4.
Please remove the p-value for the multivariate analysis in line 198. This is not a replicated stochastic experiment. You are simply changing priors and substitution models and hence the posterior changes. This is a deterministic mapping between data/prior and posterior.
We agree with this comment and have removed the mention to p-values.
Panel C of Figure 4: please mention in the legend the scale of the x-axis tickmarks (10 My?).
Lines 359 to 367 have little substance. There are no figures in this paper showing the correlation structure among branch lengths. For example, figure 4 shows stacked posterior distributions, like those in previous works, so isn't this work a victim of its own criticism? There is indeed a correlation structure among branches and times, which is not shown, and which is discarded in the plots shown here. To emphasise this point, here is paper's text edited: "The sensitivity of inferred ages is commonly explored by running analyses under different settings and summarizing the results in tables or by stacking chronograms in order to visualize the relative position of nodes (see for example Figure 4C here and the supplementary material figures)."
We agree with the reviewer and have removed all of the text mentioned here, as well as other parts referring to the chronospace approach. Correlation plots were shown in a previous version of the manuscript, but we agree that these sentences do not add much after these have been removed.

Tuesday 22 March 2022

Why The Pandemic Is Not Over and Why You Should Get Vaccinated and Boosted

The folowing article is taken from The Conversation under a Creative Commons licence.

Most COVID patients in NZ’s Omicron outbreak are vaccinated, but that’s no reason to doubt vaccine benefits

Hannah Peters/Getty Images
Thomas Lumley, University of Auckland

New Zealand’s Omicron wave may be peaking, but we’ll continue to record thousands of new cases each day and most people who test positive or are hospitalised with COVID will have been vaccinated.

This is exactly what we should expect and it’s no reason to doubt vaccine effectiveness.

The principal reason why a lot of COVID cases are vaccinated is because most New Zealanders are now vaccinated. As of today, about 94% of people 12 years and older have had two or more vaccine doses, and even if their risk of catching COVID is significantly lower than for an unvaccinated person, they vastly outnumber those who aren’t.

In the week ending March 13, about 93% of the 118,000 confirmed cases 12 years and older were in people with two or more doses. But such crude proportions of cases aren’t all that good an indicator of vaccine effectiveness.

Last year, during the Delta outbreak, the proportions were misleading in the other direction. The rate of cases in people who were unvaccinated was about 20 times that in vaccinated people.

Unfortunately, some commentators talked about that ratio as if it was all a real benefit of vaccination. It wasn’t.

The outbreak in Auckland was nearly under control and was spreading among unvaccinated people partly because they had less resistance to infection, but also because they were more likely to come into contact with infected people. Social clustering leads to disease clustering.

What case numbers can tell us

For Delta, two doses of the vaccine produced very good immunity, especially in the short term. The vaccine is less effective for Omicron; two doses give only partial immunity even in the short term, and the effectiveness wears off over time.

About 60% of people 12 years and older have had a booster dose, and in the week ending March 13, only 42% of cases were in people who had been boosted. We can see that boosters help.

Counting cases remains important, because even a non-hospitalised case of COVID can be unpleasant, and because we don’t know how likely a mild case is to lead to long COVID and months or years of disability. We can’t draw strong conclusions from numbers of cases, though.

Many cases, probably most cases, are not being diagnosed at the moment. Unvaccinated people will be less likely to get tested, especially in mild cases of the disease, either because of poor access to the health system or because they don’t think COVID is important. We can’t really tell how much bias this introduces into the numbers.

Hospitalisations and deaths are much more reliably counted than cases. Results from clinical trials and careful population studies of COVID vaccines consistently show the vaccines to be more effective in preventing more serious disease, especially with the new variants. There are plausible biological explanations for this, based on different parts of our immune response.

Antibodies against the COVID virus seem to be affected more by differences between strains than T-cells are; antibodies are probably more important for preventing initial infection and less important for fighting serious disease.

More benefit in protecting from serious disease

When we look at hospitalisations and deaths, the difference between vaccinated and unvaccinated people is much more dramatic. In the week ending March 13, 65% of people over 12 hospitalised were vaccinated, compared to 94% in the population; 32% had a booster dose, compared to 60% in the population. The 5% of unvaccinated people over 12 contributed 20% of hospitalisations.

The number of deaths is, fortunately, too small for the Ministry of Health to publish detailed weekly breakdowns, but vaccinated people are a minority over the period since August.

The relatively small number of deaths in New Zealand’s Omicron wave also shows the effectiveness of the vaccine. Hong Kong had largely eliminated COVID until Omicron; they are now getting a large outbreak similar to New Zealand’s, but only in the number of cases. Over the past week, Hong Kong averaged 280 deaths per day, in a population less than twice that of New Zealand.

The vaccination rate in Hong Kong is much lower. About 71% are fully vaccinated and only 30% have had a booster. Among elderly people, who are at much greater risk from COVID, the vaccination rate is especially lower, with two-thirds of people over 80 and more than a third of those aged 70-80 having been unvaccinated when Omicron hit.

Towards fair comparisons

Comparing across whole populations this way gives some indication of the vaccine benefit, but it is very imprecise. We don’t choose randomly who gets the vaccine and who doesn’t.

In New Zealand, for example, essentially everyone over 75 has been vaccinated. Since people over 75 are much more likely to need hospital care than younger people, the higher vaccination rate in people over 75 makes the vaccine look less effective than it really is.

Statisticians call this “confounding by indication”. Auckland has always had more exposure to new outbreaks and had higher vaccination rates than the rest of the country; this again tends to make the vaccine look less effective that it really is.

More reliable comparisons require either random allocation of vaccine to people, as in the clinical trials performed before the vaccines were approved, or careful statistical matching of vaccinated and unvaccinated groups to get a fair comparison.

Omicron is too recent to have useful clinical trial data, but peer-reviewed statistical analyses of individual case data from the United Kingdom, the United States, and South Africa all agree the vaccines are beneficial.

There’s some evidence vaccination also reduces the risk and severity of long COVID, the most likely bad outcome for healthy people. But there obviously hasn’t been time to do this sort of comparison specifically for the Omicron variant.

Overall, the most reliable comparisons between vaccinated and unvaccinated people have consistently shown a benefit of vaccination. The effectiveness of the vaccines does wear off over time, and the effectiveness is lower against Omicron than it was against Delta or the original COVID strain, but it still improves your chances of avoiding infection, keeping out of hospital and making a full recovery.

Thomas Lumley, Professor of Biostatistics, University of Auckland

This article is republished from The Conversation under a Creative Commons license. Read the original article.

The Conversation
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Religious War Crimes News - How the Russian Orthodox Church Backs Putin's War on Women & Children

Patriarch Kirill and Vladimir Putin.

War on Ukraine is "an active manifestation of evangelical love for neighbours" - Patriarch Kirill
How Putin's invasion became a holy war for Russia

Fulfilling the Christian Churchs' historic roll of supporting right-wing totalitarian nationalism, the Russian Orthodox Christian Church is backing Putin's murderous and unprovoked attack on Ukraine and the territorial ambitions of Vladimir Putin.

For Putin and the Russian Orthodox Church, the war against Ukrainian democracy is wrapped in the Russian flag and shrouded in religious zeal, since Kiev is the home of Prince Vladimir the Great of Kiev, the legendary founder of the Russian Church who , in about 978 AD, was responsible for making Byzantine Christian Orthodoxy the official religion of Russia, Ukraine and Belarus.

The Hagia Sophia, Istanbul
Legend has it that Prince Vladimir the Great of Kiev was so impressed he adopted the Orthodox Christianity of Byzantium as the state religion for Russia, Ukraine and Belorus.
The legend is that he invited missionaries from Eastern (now Orthodox) Christianity, Western (now Catholic) Christianity, Judaism and Islam to persuade him to adopt their religion. He rejected Islam because of the prohibition on alcohol and pork, saying that the Rus couldn't do without alcohol and Judaism because 'God had allowed the Jews to lose Jerusalem'. He eventually settled on Eastern Christianity when his emissaries reported the magnificence of the Hagia Sophia Church in Constantinople (now Istanbul).

On Russian National Unity Day, 4th November 2016, with Patriarch Kirill, the oleaginous head of the Russian Orthodox Church, at his side, smiling and applauding enthusiastically, Putin unveiled a huge statue of Vladimir the Great outside the Kremlin. On the day that Putin ordered his troops into Ukraine, Patriarch Kirill published a grovelling and nauseatingly obsequious statement which read:

Wednesday 16 March 2022

Malevolent Designer News - Another Design Blunder as a Fungus Prevents a Bacterium From Doing Its Job

UMaine study shows pathogen and drug work together to fight fungal lung infection - UMaine News - University of Maine

Scientists working at the Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA, have discovered a phenomenon that, if you're gullible enough to be a creationist, which admittedly would make it unlikely that you'd be reading, let alone understanding, this blog, must look like the putative intelligent [sic] designer has lost the plot.

The discovery is that when two particular organism occur together to produce a polymicrobial disease, one of the organisms will work against the other. In the presence of an antibiotic, it will not only prevent the other organism developing resistance, but will remove it from the infection site.

The two organisms are the fungus, Candida albicans and the bacterium, Pseudomonas aeruginosa, both of which are opportunistic pathogens that can be found in similar sites of infection such as in burn wounds and most importantly in the lungs of cystic fibrosis and mechanically ventilated patients.

As the University of Maine news release explains:

Monday 14 March 2022

Evolution News - Evolution of Evolvability

Capturing the many facets of evolvability | Science Linx News | Science LinX | University of Groningen

Imagine, if you can, being a creationists who has swallowed the absurd idea that the scientific theory of evolution is a 'theory in crisis' which is about to be overthrown by a superstition from the fearful, ignorant infancy of our species in the Bronze Age, from a time when a bunch of nomadic pastoralists and hill farmers in the Middle East though Earth was small, young, flat and had a dome over it to keep the water above the sky out. You've been waiting excitedly for most of your adult life for this momentous event - the first time an established scientific theory has been replaced by a mystical, supernatural one involving unproven entities and magic - and so proving that you know better than all those clever scientists without having bothered to learn any science!

Then along comes a bunch of those clever scientists from Groningen Institute for Evolutionary Life Sciences at the University of Groningen in the Netherlands and not only presents a detailed discussion paper on how evolution works, but on how evolvability itself evolved, with no hint whatsoever that they have any doubts about evolution being the reason for all the biodiversity.

Copyright: © 2022 The authors. Published by Elsevier Ltd.
Open access
(CC BY-NC-ND 4.0)
And to cap it all, they even explain the notion of 'punctuated equilibrium' that was invented by the evolutionary biologist, Stephen Jay Gould, to try to explain the fossil record which appears to show that many species have long periods of stasis when their morphology changes very little, followed by a burst of rapid evolution, then another period of stasis, etc.

Many creationists like to imagine this somehow refutes Darwinian evolution, although Gould never proposed a mechanism for it and other biologists have explained that Darwinian gradualism doesn't imply a constant rate of evolutionary change, especially at the phenotypic level and that what can appear to be a sudden change in phenotype in the geological columns can take tens or hundreds of thousands of years. Or the record simply shows that one species was replaced by another closely related species over that part of its range, as happened in the UK where the more robust introduced grey squirrels have replaced the slighter native red squirrels in less than a hundred years. In the geological column in, say, 10,000 years, this will look like a case of 'punctuated equilibrium' and an unexplained sudden change to a more robust form. The explanation is that newly evolved evolvability enables a species to radiate into new niches to give a relatively sudden increase in new species or to more quickly evolve in response to environmental pressures.

So, what do you do if you're a creationists and a paper like this is published?

Tuesday 8 March 2022

Human Evolution News - Human Cultural and Technological Evolution in Northern China, 40,000 Years Ago

Archaeologists Discover Innovative 40,000-Year-Old Culture in China | Max Planck Institute for the Science of Human History

Of course, they never could have guessed it, so the people who were leaving these remains 40,000 years ago would have been oblivious of the fact that their activities as discovered by modern archaeologist, have utterly refuted the ideas that were to emerge in another part of the world some 37,000 years later.

The fact is, however that this is exactly what they have done insofar as the primitive Bronze Age origins myths of a bunch of Middle Eastern nomadic pastoralists and hill farmers are concerned, because these people who made up these camp-fire tales or elaborated on earlier ones, had no inkling that there had been people much like them around in what is now Northern China, some 37,000 years earlier.

The tales these simple people had been handed down had their origins in a part of the world where people believed Earth was very small and only a couple of thousand years old and had been created just for them by magic beings who lived above the sky-dome and who directed the affairs of man.

For these people, the entire world was a circle bounded by the Eastern Mediterranean to the west, the Black Sea and the Caucasus Mountains to the north, the Arabian desert to the south and the flood plains of Mesopotamia and the Iranian Plateau to the east. These were the tales that eventually got written down and incorporated into the state religion of a desperate, increasingly autocratic, dying Roman Empire and are now, almost unbelievably, still regarded as historical truths by some number of people alive today, albeit a decreasing proportion of the developed world's people.

Sadly for these deluded people, evidence of human habitation and cultural/technological progress in Northern China 40,000 years ago, utterly refutes their primitive beliefs which include a global genocidal flood just 6000 years ago, which, had it really happened, would have swept away the archaeological evidence of this culture, as it does the notion that the entire planet has been repopulated by the descendants of a handful of survivors of this flood.

The findings by an international group of archaeologists including scientists from the Chinese Academy of Science and the Max Planck Institute for the Science of Human History, were published recently in Nature. The artifacts are from a period in Eurasian hominin history when Homo sapiens was coming into contact with the Neanderthals and Denisovans, the descendants of an earlier migration by an archaic hominin such as H. erectus, and interbreeding with them and no doubt sharing ideas and technologies.

Tuesday 1 March 2022

Malevolent Designer News - How The Devine Malevolence Has Turned Our Immune System Against Us.

Roseolovirus particles emerge from an infected immune cell (above). Studying mice, researchers at Washington University School of Medicine in St. Louis have discovered that roseolovirus can trigger autoimmunity in a previously unknown way: by disrupting the process by which immune cells learn to avoid targeting their own body's cells and tissues.
Credit: Bernard Kramarsky
New way viruses trigger autoimmunity discovered – Washington University School of Medicine in St. Louis

Researchers at Washington University School of Medicine in St. Louis have discovered how a virus can probably make our immune system turn against us to create autoimmune diseases such as arthritis, lupus and type I diabetes, long after infection by the virus.

In the wackadoodle world of Creationism, this means that the viruses in question were designed specifically to produce that outcome since, being omniscient, the designer knows exactly what the outcome will be and so designs them for that exact function.

The fact that it does this to use a system it supposedly designed to protect us from the parasites like viruses and bacteria it designs to harm us with, is not seen as a reason to doubt the intelligence or sanity of this supposed designer!

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