F Rosa Rubicondior: October 2021

Saturday 30 October 2021

Evolution News - Here Be Dragonflies!

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Aeshna cyanea
Source: Wikipedia
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Aeshna grandis
Source: Wikipedia
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Anax junius
Source: Wikipedia
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Ischnura senegalensis
Source: Wikipedia
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Libellula quadrimaculata
Source: Wikipedia
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Sympetrum flaveolum
Source: Wikipedia
Linking the Past and Present: Reconstructing the Dragonfly and Damselfly Family Tree - University of Tsukuba

Scientist from Japan have succeeded in doing what Creationists insist is impossible because it doesn't happen. They have shown the evolution and relationships between the different members of the insect order, Odonata, which includes all living and extinct dragonflies and damselflies, surely amongst the most beautiful of insects. For those unsure of the difference, damselflies tend to be smaller and more dainty and rest with their wings together over their backs, while dragonflies are generally larger, more robust and faster flying, and hold their wings horizontally, like those of an aeroplane when at rest. They are the only insects capable of flying backwards.

The scientists constructed a fanily tree for the order Odorata, by conducting a detailed analysis of the transcriptome - the collection of RNA in cells which are transcriptions of the functional DNA and mapping this onto the fossil record. Because this technique indirectly analyses only the active DNA, it gives a better evolutionary relationship between species and allows detailed timing of species divergence to be estimated.

As the University of Tsukuba research news item explains:

Evolution News - A Newly-Named Species of Archaic Hominin Clarifies our Evolutionary Picture

Artist's rendering of Homo bodoensis
Credit: Ettore Mazza
Experts name new species of human ancestor | University of Winnipeg News

Far from there being no transitional fossils showing the evolution of modern humans from archaic ancestors, as Creationists traditionally claim, there are so many of them that they tend to confuse rather than clarify the picture

Fossils are, of course, an irregular and infrequent snapshot of an evolving species over time, so palaeontologists always have a problem of slotting a new species into existing classifications because there is never a sharp delineation between an ancestral form and a descendant one. It's a bit like trying to determine exactly where one colour changes to another in a rainbow.

Where does the colour change?

So, the tendency has been to name a new find which is significantly different to any others, as a new species, with a name often derived from the place where they were discovered - the scientific equivalent of naming it 'Heidelberg Man' or 'Rhodesia Man'. This is even more problematic if the species is widespread and subject to regional variation, consequently, definitions can be fuzzy and confusing as newer finds are slotted into pre-existing types, each new type broadening and blurring the definition of that species.

Talking about human evolution during this time period became impossible due to the lack of proper terminology that acknowledges human geographic variation.

Naming a new species is a big deal, as the International Commission on Zoological Nomenclature allows name changes only under very strictly defined rules.

Dr Mirjana Roksandic, co-first author
Winnipeg University, Winnipeg, Manitoba, Canada
This international team led by Dr. Mirjana Roksandic from Winnipeg University, Canada has clarified and simplified this muddle in the middle based on latest research and DNA analysis where DNA has been recovered and analysed. They looked especially at specimens that had been classified as Homo heidelbergensis or H. rhodesiensis, both of which carried multiple, often contradictory definitions. European specimens previously classified as H. heidelbergensis have been shown by DNA analysis to be early H. neanderthalensis, while H. rhodesiensis, named when Zimbabwe was still a British colony called Southern Rhodesia, has a name which is too closely associated with Cecil Rhodes and some of the more despicable and brutal aspects of Britain's former imperialism in Africa.

As the Winnipeg University news release explains:

Friday 29 October 2021

Malevolent Designer News - How Creationism's Beloved Malevolence Could Have Made 'Friendly' Acne But Chose Not To.

Acne. Another of the malevolent designer's creations?
Not all acne is equal: scientists reveal strains of C. acnes that promote skin health — Osaka City University

For any teenage Creationist suffering from acne or carrying the facial scars of it, it will come as no comfort at all that their favourite pestilential malevolence, the 'creator' god of the Bible and Qur'an, could have just as easily given them a strain of the bacteria that causes it, Cutibacterium acnes, that not only doesn't cause acne, but which might even protect the skin from another pathogen, Staphylococcus aureus.

It will also come as no comfort to those who have fallen for the Deception Institute's intelligent [sic] design hoax, that a discovery by a Japanese team of scientists from Osaka City University and Okayama University shows how muddled and stupid any intelligence who designed the complex ecosystem that is the human skin and its commensal organisms, would have been.

Using a novel approach where a nematode, Caenorhabditis elegans, was used as a proxy for human skin, the team showed that certain strains, or ribotypes (RT), of C. acnes, based on clades of their ribosomal RNA (rRNA), not only do not cause acne but actually protect the nematode from infection with S. aureus and so possibly help to maintain a healthy skin. RT4 and 8, which are associated with acne also shorten the life of Ce. elegans, while RT6, found on healthy skin, does not.

From the Osaka University News release:

Tuesday 26 October 2021

Creationism and Woolly Thinking

The European Mouflon or Mufflon, Ovis orientalis.

Credit: Jörg Hempel, CC BY-SA 3.0 DE, via Wikimedia Commons

Modern Merino sheep

According to the Bible, God created all animals for mankind, as 'an helpmeet' for Adam (Genesis 2:18-19). Given that this creator god is supposedly omniscient and omnipotent, you would expect any animals so created to be perfectly fitted for purpose and exactly what mankind needs. Yet the reality is that not a single domesticated animal (or plant) has remained unchanged from its wild ancestor. Every single domesticated animal has been improved by selective breeding, to make them bigger, stronger or more productive, or as a food, better flavoured, more versatile or easier to store!

Why would this be? Did this allegedly all-knowing creator not know what mankind would use these animals for or was it just not very good at designing things for a specific purpose?

Many domesticated animals and plants have been so highly modified that their wild ancestors, where these still exist, are barely recognisable as the ancestors of their domestic descendants. Take as an example, the different breeds of domestic sheep, farmed for their wool as well as for their meat. They are believed to be descended from the mufflon, also spelled 'Mouflon', (Ovis orientalis). Once indigenous to Eastern Europe and Western Asia it is now only common in the Caucasus, Anatolia, northern Iraq and north-western Iran. It is also found on the Mediterranean islands of Elba, Sardinia, Corsica and Cyprus but these may be the descendants of feral forms of early domestic sheep, introduced in the Bronze Age.

Monday 25 October 2021

Evolution News - Yet another of Those Pesky 'Non-Existent' Transitional Forms!

Cretapsara athanata Luque gen. et sp. nov., a modern-looking eubrachyuran crab in Burmese amber.(A to D) Holotype LYAM-9. (A) Whole amber sample with crab inclusion in ventral view. (B) Close-up of ventral carapace. (C) Whole amber sample with crab inclusion in dorsal view. (D) Close-up of dorsal carapace. White arrows in (B) and (D) indicate the detached left fifth leg or pereopod.

Photos by L.X. Figure by J.L.
International team of researchers discover first dinosaur era crab fully preserved in amber | Department of Organismic and Evolutionary Biology.

Another favourite Creationist article of faith was shattered again today with the publication of an open access article in Science Advances by a Chinese team of researchers, describing a Cretaceous crab that shows incomplete transition between an aquatic and a terrestrial existence.

The crab is beautifully preserved in amber and shows an amazing level of detail of soft tissues that are rarely fossilised, even down to the fine hairs on its mouth-parts. It has the gills of an aquatic crab, and lacks the lung-like adaptations of gills characteristic of terrestrial crabs, yet it is clearly terrestrial hence becoming trapped in amber. It thus represents a transition between marine and terrestrial crabs.

The team used micro-CT technology to examine the crab, Cretapsara athanata. At 100 million years old it is the oldest modern-looking crab ever described and is from the Cretaceous era when crabs were diversifying - the so-called Cretaceous Crab Revolution - when the modern crabs originated. According to the Harvard University Department of Organismic & Evolutionary Biology (OEB) press release:
The specimen is spectacular, it is one of a kind. It’s absolutely complete and is not missing a single hair on the body, which is remarkable.

The more we studied the fossil, the more we realized that this animal was very special in many ways.

Now we were dealing with an animal that is likely not marine, but also not fully terrestrial. In the fossil record, nonmarine crabs evolved 50 million years ago, but this animal is twice that age.

Dr Javier Luque, Lead author
Postdoctoral researcher
Department of Organismic and Evolutionary Biology,
Harvard University.
True crabs, or Brachyura, are an iconic group of crustaceans whose remarkable diversity of forms, species richness, and economic importance have inspired celebrations and festivals worldwide. They’ve even earned a special role in the pantheon of social media. True crabs are found all around the world, from the depths of the oceans, to coral reefs, beaches, rivers, caves, and even in trees as true crabs are among the few animal groups that have conquered land and freshwater multiple times.

The crab fossil record extends back into the early Jurassic, more than 200 million years ago. Unfortunately, fossils of nonmarine crabs are sparse and largely restricted to bits and pieces of the animal's carapace – claws and legs found in sedimentary rocks. That is until now with the discovery of Cretapsara athanata

A group of scientists led by co-lead author Lida Xing, China University of Geosciences, Beijing, made micro CT scans of the fossil, which is housed in the Longyin Amber Museum in Yunnan, China. The scans created a full three-dimensional reconstruction of the exquisite preservation of the animal allowing Luque, Xing, and their team to see the complete body of the animal including delicate tissues, like the antennae and mouthparts lined with fine hairs. Shockingly they discovered the animal also had gills…

3D mesh of Cretapsara athanata Luque gen. et sp. nov. holotype LYAM-9.(A to E) 3D mesh extracted from reconstructed micro-CT data in VGSTUDIO MAX, remeshed in MeshLab, and visualized using Autodesk Maya: (A) dorsal, (B) ventral, (C) right lateral, (D) oblique postero-dorsal, (E) oblique antero-ventral views, showing the claws of equal size and four pairs of slender legs similar in shape and size, with P5 slightly smaller than the other legs. (F and G) Details of the dorsal (F) and ventral (G) carapace, showing details of the large eyes and orbits, small antennae, and a small, acute outer orbital spine [(F) thick arrow], two small anterolateral spines (F, thin arrows), a posterolateral margin bearing at least four small and equidistant tubercles (F, small arrows), straight posterior margin, slender coxae of the pereopods, a typical heterotreme eubrachyuran sternum (G), and a reduced and folded pleon with the first pleonites dorsally exposed. Left fifth pereopod digitally reattached. bcg, branchiocardiac groove; ca, carpus; cg, cervical groove; cx, coxa; da, dactylus; ib, ischiobasis; ma, manus or palm of claw; P1, claws or chelipeds; P2 to P5, pereopods or walking legs 2 to 5; po, pollex or fixed finger cheliped propodus; pr, propodus.

Images by E.G.C. Figure by J.L.
Cretapsara is remarkably modern-looking – superficially resembling some shore crabs found today – unlike most crabs during the mid-Cretaceous era which looked quite different from modern crabs. Yet, the animal was entombed in Cretaceous amber and the presence of well-developed gills indicated an aquatic to semi-aquatic animal. Aquatic animals are rarely preserved in tree resins that become amber. Crabs previously found in amber are by the handful and belong to a living group of tropical land and tree-dwelling crabs known as Sesarmidae from the Miocene (15 million years ago). How then, the researchers asked, did a 100 million year old aquatic animal become preserved in tree amber, which normally houses land-dwelling specimens?

Gills allow aquatic animals to breathe in water. But crabs have successfully and independently conquered land, brackish water, and fresh water at least twelve times since the dinosaur era. In doing so their gills evolved to include lung-like tissue allowing them to breathe both in and out of the water. Cretapsara however, had no lung tissue, only well-developed gills indicating the animal was not completely land dwelling.

The team’s phylogenetic studies show that carcinization (the evolution of true crab-looking forms) had actually already occurred in the most recent common ancestor shared by all modern crabs more than 100 million years ago. Cretapsara bridges the gap in the fossil record and confirms that crabs actually invaded land and fresh water during the dinosaur era, not during the mammal era, pushing the evolution of nonmarine crabs much further back in time.
In their open access paper published in Science Advances the authors say:

Amber fossils provide snapshots of the anatomy, biology, and ecology of extinct organisms that are otherwise inaccessible. The best-known fossils in amber are terrestrial arthropods—principally insects—whereas aquatic organisms are rarely represented. Here, we present the first record of true crabs (Brachyura) in amber—from the Cretaceous of Myanmar [~100 to 99 million years (Ma)]. The new fossil preserves large compound eyes, delicate mouthparts, and even gills. This modern-looking crab is nested within crown Eubrachyura, or “higher” true crabs, which includes the majority of brachyuran species living today. The fossil appears to have been trapped in a brackish or freshwater setting near a coastal to fluvio-estuarine environment, bridging the gap between the predicted molecular divergence of nonmarine crabs (~130 Ma) and their younger fossil record (latest Cretaceous and Paleogene, ~75 to 50 Ma) while providing a reliable calibration point for molecular divergence time estimates for higher crown eubrachyurans.

The great thing about these frequent transitional forms and so incidental refutations of a basic article of faith of the Creationist cult, is the way Creationists and the frauds who live off their gullibility, studiously ignore them and continue to insist they don't exist. It's as though they live in some sort of weird parallel Universe in which reality obediently conforms to their requirements.

Sunday 24 October 2021

Evolution News - The Difference Between Information and Meaning

I. sakaiensis grown on poly(ethylene terephthalate) (PET) accumulates poly(3-hydroxybutyrate) (PHB).
How a bacterium may help solve the plastic pollution crisis|NARA Institute of Science and Technology

One key concept in genetic evolution that Creationists, either wilfully, or because of genuinely limited critical thinking ability, find hard to grasp, is the difference between genetic information and the meaning of that information in the context of the prevailing environment. This makes them especially susceptible to professional frauds in the Deception Institute and others in the Creation Industry, to false claims about mutation always involving a loss of information, when what changes in most forms of mutation is simply a change in the meaning of the information.

Certain bacteria harbor the necessary enzymes to degrade PET, the most problematic plastic environmentally. Our research has shown that the bacterium Ideonella sakaiensis converts PET into poly(3-hydroxybutyrate) (PHB), a type of poly(hydroxyalkanoate) (PHA) plastic that is biodegradable.

We believe that this discovery could be significant in tackling plastic pollution, as we show that the PET-degradation and PHB-synthesis pathways are functionally linked in I. sakaiensis. This might provide a novel pathway where a single bacterial species breaks down difficult-to-recycle PET plastics and uses the products to make biodegradable PHA plastics.

Shosuke Yoshida, senior author
Institute for Research Initiatives,
Nara Institute of Science and Technology, Nara, Japan
This is illustrated neatly by the discovery that the 201-F6 strain of the bacterium Ideonella sakaiensis can not only degrade petroleum-based plastics but can also sustainably produce biodegradable plastics from otherwise non-biodegradable poly(ethylene terephthalate) (PET), a plastic widely used for disposable containers such as drinks bottles as well as textiles and food wrappers. This discovery was made by scientists at the Nara Institute of Science and Technology (NAIST), Kansai Science City, Japan. Their findings are published, open access, in Scientific Reports.

This ability depends on the presence of two enzymes, PET hydrolase (PETase) and mono(2-hydroxyethyl) terephthalic acid (MHET) hydrolase (MHETase) which together hydrolyse PET into terephthalic acid (TPA) and ethylene glycol (EG) monomers, both of which are readily biodegraded by other organisms.

In this strain of bacteria, genetic information has mutated to produce these two enzymes which, in the context of an environment highly polluted by man-made plastics, has given them the ability to exploit an abundant food source, unlike their ancestral form. Had this mutation arisen in pre-plastic times, it would have been utterly useless and might even have been detrimental in taking up resources to produce useless enzymes. In other words, the change in information now has a highly beneficial meaning in the context of a modern Earth, where once it had none.

In their paper published a few days ago in Scientific Reports the team say:

Poly(ethylene terephthalate) (PET) is a widely used plastic in bottles and fibers; its waste products pollute the environment owing to its remarkable durability. Recently, Ideonella sakaiensis 201-F6 was isolated as a unique bacterium that can degrade and assimilate PET, thus paving the way for the bioremediation and bioconversion of PET waste. We found that this strain harbors a poly(hydroxyalkanoate) (PHA) synthesis gene cluster, which is highly homologous with that of Cupriavidus necator, an efficient PHA producer. Cells grown on PET accumulated intracellular PHA at high levels. Collectively, our findings in this study demonstrate that I. sakaiensis can mediate the direct conversion of non-biodegradable PET into environment-friendly plastic, providing a new approach for PET recycling.

What has changed in not the quantity of genetic information but the contextual meaning of it and that meaning has changed over time with the invention, use and environmental accumulation of vast quantities of non-biodegradable man-made plastic.

Evolution News - Observed Rapid Evolution in African Elephants

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Female elephants in Gorongosa National Park in Mozambique evolved to be tuskless in response to intense hunting.
Credit: Joyce Poole/ElephantVoices. Source: Science
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Elephants in Gorongosa National Park, Mozambique, declined by 90% during the 20-year civil war because of ivory poaching. This spurred the rapid evolution of tuskless females, such as this female Loxodonta africana.
Credit: ElephantVoices. Source: Science
Civil war drove these elephants to lose their tusks—through evolution | Science | AAAS

Since evolution by natural selection is driven primarily by the selecting environment, rapid change in the environment can produce rapid evolution. If the selection pressure is strong enough, this intense selection can also result in a linked deleterious gene increasing in the population by being dragged up the fitness landscape by a strongly advantageous gene to which it is linked by close proximity on a chromosome.

This was the case in Mozambique, where during a 15-year-long civil war when there was intense poaching of elephants for their ivory to finance the armies of both sides and because any wild-life protection was largely absent or non-functional. In the Gorongosa National Park for example, the elephant population fell by 90% in 20 years with predation heavily selecting against those with tusks. Consequently, the gene for tusklessness in females increased in the population. Over a period of 28 years which included the 15 years of civil war, the proportion of tuskless females increased from 18.5% (n = 52) to 50.9% (n = 108), but so did the proportion of females in the population and the pre-term deaths of male calves!

This was due to an increase in the genes AMELX and MEP1a, which are associated in mammals with normal tooth formation. AMELX is linked by its proximity on the X chromosome to a dominant male-lethal syndrome in humans that also diminishes the growth of maxillary lateral incisors (homologous to elephant tusks). In other words, as AMELX increases in the population, so does a male-lethal gene that also reduces the growth of tusks in elephants. The result is an absolute increase in the proportion of live births of females and of tuskless females in particular.

In the abstract to their recent paper, a team led by Princeton scientists Shane C. Campbell-Staton of the Department of Ecology and Evolutionary Biology and Brian J. Arnold of Department of Computer Science, Princeton University, Princeton, NJ 08540, USA. said:

Understanding the evolutionary consequences of wildlife exploitation is increasingly important as harvesting becomes more efficient. We examined the impacts of ivory poaching during the Mozambican Civil War (1977 to 1992) on the evolution of African savanna elephants (Loxodonta africana) in Gorongosa National Park. Poaching resulted in strong selection that favored tusklessness amid a rapid population decline. Survey data revealed tusk-inheritance patterns consistent with an X chromosome–linked dominant, male-lethal trait. Whole-genome scans implicated two candidate genes with known roles in mammalian tooth development (AMELX and MEP1a), including the formation of enamel, dentin, cementum, and the periodontium. One of these loci (AMELX) is associated with an X-linked dominant, male-lethal syndrome in humans that diminishes the growth of maxillary lateral incisors (homologous to elephant tusks). This study provides evidence for rapid, poaching-mediated selection for the loss of a prominent anatomical trait in a keystone species.
Over the short term, this attrition of males is not overly detrimental to elephants because herds are matriarchal with a single male able to serve multiple females and 'spare' males forming non-breeding 'batchelor' herds, so the population can remain stable or even increase with relatively few males.

What we can observe in this population then is a rapid evolution of a strong advantageous gene, in that tusklessness makes females less likely to be poached, with the 'opportunistic' increase in a deleterious gene which kills pre-term male calves by being linked physically to a strongly advantageous one, the deleterious effect in the population being more than compensated for by the overall advantageous effect.

Over the longer term, and with control of poaching, whatever environmental pressures led to the evolution of tusks in females originally is likely to reassert itself and the balance should shift back towards tusked females and more male live births. An beautiful example of how a changing environment changes the meaning of the same genetic information without any change in that information itself. And no magic deities involved anywhere in that process.

Saturday 23 October 2021

Evolution News - Savana Chimpanzees are Showing us How Humans Evolved

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Chimpanzees walking in the savanna of Fongoli (Senegal).
Photo: U. Villalobos-Flores.
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Savanna chimpanzees in a cave in Sabe (Guinea).
Photo: Jane Goodall Institute Spain and Senegal.
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Chimpanzees at Fongoli in Senegal drink polluted water in mining pits.
Photo: J. Pruetz.
savanna chimpanzees, a model for the understanding of human evolution - Universitat de Barcelona

An international group of primatologists, co-directed by Adriana Hernández, of the University of Barcelona, Catalunya, Spain and Stacy Lindshield of Purdue University, West Lafayette, Indiana, USA, has studied the behaviour of savanna chimpanzees as a model for how the chimpanzee ancestors of hominids would have behaved at a key stage in their diversification from their common ancestor.

Although savanna chimpanzees (Pan troglodytes) are genetically identical to their forest-dwelling counterparts, they have several cultural differences that have enabled them to survive in a savanna environment which it hotter, drier and more seasonal than a forest environment. These are exactly the environmental challenges that early pre-hominid apes would have had to cope with in south and east Africa as climate change firstly isolated them in diminishing forests then stranded them in a relatively treeless landscape in which only those able to adapt would survive.

Like their modern counterparts, at least a substantial part of that adaptation was to evolve cultures which enabled them to adopt survival strategies. This in turn would then have facilitated the genetic changes which now distinguish us from our close cousins.
From the Barcelona University news release:
The study of chimpanzees in the savanna and what we call the effect of the savanna environment has important implications in reconstructing the behavior of the first humans who lived in similar habitats and therefore helps us to better understand our own evolution.

We know that early hominins adapted to savanna environments similar to those found by chimpanzees, and it is thought that savanna conditions caused adaptations in our ancestors, such as brain expansion or tolerance to high temperatures, therefore, understanding how our genetically closest relatives adapt to a dry, hot, seasonal and open environment, very similar to those where early hominins lived, helps us to analyze how our ancestors might have adapted and how the characteristics that define us as humans could have emerged.

Understanding how they cope with the heat can help us understand how the strategies that humans have to cope with the heat came about. Some are probably the same for chimpanzees and hominins, such as using caves or diving into water to cool off.

The early hominins also had to face water shortages for part of the year.

R. Adriana Hernández, Co-senior author
Department of Social Psychology and Quantitative Psychology
Faculty of Psychology
University of Barcelona, Barcelona, Spain
According to the researchers, the environmental conditions of these places would provoke a specific type of behaviors and physiological responses in these chimpanzees - such as resting in caves or digging to extract water - that do not occur in those of their congeners that live in wooded areas, where they do not they face such extreme environmental conditions.


The closest living genetically evolutionary relative to humans

Chimpanzees ( Pan troglodytes ) are the closest living evolutionary relatives of our species, sharing 98.7% of their DNA with humans and sharing an ancestor with them that lived approximately 4.5 to 6 million years ago. years. Despite this closeness, they lack some of the biological and cultural traits that humans possess to adapt to extreme heat, such as the numerous eccrine sweat glands, the relative lack of hair, or the ability to create artifacts such as containers of water. and sun hats that mitigate dehydration and heat stroke.

Chimpanzees that live in the savanna are taxonomically indistinguishable from other chimpanzees. For this reason, comparisons of behavior, morphology and ecology with those living in more forested landscapes provide key information for generating hypotheses or testing theories about how early humans were able to adapt millions of years ago as forests Africans were retreating and giving way to the savannas.


Strategies to adapt to high temperatures

Among the characteristics collected by the study, the strategies of savanna chimpanzees to tolerate high temperatures stand out… Another example that the researcher highlights are the ways in which these chimpanzees try to hydrate during the late dry season, such as digging for water when it is reduced to only a few points on the ground.
Geographic distribution of chimpanzees (Pan troglodytes)54 in savanna and forest landscapes across Africa relative to the minimum threshold of annual rainfall (Worldclim)11, 54, 264, and indicating potential new sites for future research on savanna chimpanzees.

Modified from Reference 11 under a Creative Commons Attribution 4.0 International License
As well as adapting their behaviour to cope with high temperatures and seasonal water supplies, there is another adaptive cultural change. Instead of living in small bands occupying a relatively small, densely-populated territory where essential resources are in good supply, the savanna chimpanzees have had to expand their territory from the usual 3-30 km2 to about 100 km2 with a much lower population density. Larger territories are naturally harder to defend.

The group's findings are published, open access, in the journal Evolutionary Anthropology.

Chimpanzees (Pan troglodytes) are the only great apes that inhabit hot, dry, and open savannas. We review the environmental pressures of savannas on chimpanzees, such as food and water scarcity, and the evidence for chimpanzees' behavioral responses to these landscapes. In our analysis, savannas were generally associated with low chimpanzee population densities and large home ranges. In addition, thermoregulatory behaviors that likely reduce hyperthermia risk, such as cave use, were frequently observed in the hottest and driest savanna landscapes. We hypothesize that such responses are evidence of a “savanna landscape effect” in chimpanzees and offer pathways for future research to understand its evolutionary processes and mechanisms. We conclude by discussing the significance of research on savanna chimpanzees to modeling the evolution of early hominin traits and informing conservation programs for these endangered apes.

Once again, we see biomedical scientists in no doubt that the difference between modern and ancient hominins, and how we diversified from our common ancestor with the modern chimpanzees, has an evolutionary explanation, with no hint whatsoever of a loss of confidence in the TOE to explain the processes involved in this transition that Creationists fantasise over. Consequently, we can observe bands of chimpanzees, subject to the same environmental forces that shaped our remote ancestors several million years ago and put hominins on the path that eventually led to Homo sapiens, and draw conclusions based on those observations. Also, what we can observer here is the beginnings of gene-meme co-evolution which has been a major factor in the evolution of modern humans.

Friday 22 October 2021

Malevolent Designer News - Another Blow for Creationism

Bacteriophage caspids can carry extra DNA that the virus can tinker with.

Credit: Kristina Dukart/iStock via Getty Images Plus
Viruses are both the villains and heroes of life as we know it

Here is an article by Ivan Erill, associate professor of Biological Sciences, University of Maryland, in The Conversation, that would have those few intelligent [sic] design Creationists who have found the courage to read a scientific article punching the air with joy - until they read on and find it contradicts all they think they know about how their divine creative malevolence works.

The problem for these Creationists is, as I have repeatedly pointed out in this blog and in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good, that whilst they continue to insist that only their putative designer god is capable of designing things like viruses and bacterial pathogens and bringing about change in its creations, they are portraying it as a pestilential, sadistic monster obsessively determined to make its creations suffer in ever more imaginative ways. A case in point being the SARS-CoV-2 virus that, at the time of writing, according to Johns Hopkins University has killed nearly 5 million people, made almost a quarter of a billion sick and is wrecking economies worldwide.

So, it will come as a relief to those Creationists who can understand this problem, that there is at least one scientist who can see a positive benefit in at least some viruses, particularly bacteriophage viruses or phages for short - until they discover that this benefit is in how it can help humans defend themselves against some of the nastier of their beloved malevolence's creations. To make matters worse for Creationists, the science, because it's written by a biologist, not a theologian who is mostly ignorant of this subject, is of course based on evolutionary biology, not Bronze Age superstition. He says:

Monday 18 October 2021

Evolution News - How Lizard's Teeth Fatally Bite Creationism

3D reconstruction of the skull of an Amazon racerunner (Ameiva ameiva) captured through an X-ray micro-CT scan. Complex teeth with multiple tips ("cusps") are visible on the jaws. This feature—also seen in the dentition of early mammals—evolved many times in independent lizard groups.
Image: Fabien Lafuma
Plant-eating lizards on the cusp of tooth evolution | University of Helsinki

A couple of Creationist articles of faith have taken a beating with another biology paper that refutes them without even trying, as usual. This time it is the evidence of transition from simple to complex teeth in multiple lineages of lizard in response to the advantages that a vegetarian diet had over an insectivorous diet, and then the evidence that this evolution towards increasing complexity sometimes went into reverse.

This reversal is contrary to creationist dogma that says evolution always involve increasing complexity and new information and that any loss of information (and so loss of complexity) is invariably detrimental.

The paper is by a team of researchers from the Universities of Helsinki and Lyon and the Geological Survey of Finland, led by associate professor, Nicolas Di-Poï of the Institute of Biotechnology, University of Helsinki, and is published open access in Nature Communications. The Helsinki University news release explains:

Sunday 17 October 2021

Malevolent Designer News - How The Flesh-Eating Bug Was Created.

Vibrio vulnificus ("the flesh-eating bug")
Pictures of the damage it does are too distressing to show!
Clues Emerge: How Harmless Bacteria Go Rogue Turning into Deadly Flesh-eating Variants | University of Central Florida News

Creationist mode:

As any intelligent [sic] design creationist will tell you, nothing evolves, so all changes in a species are the result of direct, intentional design by their putative designer, who, depending on the particular creationist cult, is either the omnibenevolent god of the Bible, or the omnibenevolent god of the Qur'an. Either way, this putative creator only wants a maximally good world for its favourite creation - humans - to live in.

From COVID to V. vulnificus the emergence of human pathogens is one of the most concerning public health issues facing us but we know surprisingly very little about what triggers the change from harmless to deadly. We want to answer that question using aquatic pathogens such as the agent of cholera or V. vulnificus as model systems. Our study is a big step in understanding this emergence phenomenon, and will hopefully help us predict, prevent and manage future outbreaks.

Our results indicate how ecosystems may be generating pressures that facilitate the emergence of specific strains with pathogenic potential within a natural population. We now have evidence that the environment plays a most critical role in shaping the emergence of this pathogen. Nonetheless, we are pathogen hunters and there is much more research to conduct. But this is a critical starting point in solving the mystery of what are the elements/ingredients that make a pathogen?

Assistant professor Salvador Almagro-Moreno, Lead author
Burnett School of Biomedical Sciences,
College of Medicine,
University of Central Florida, Orlando, FL, USA
Curiously though, they also insist that the pathogens that make us sick and die are reputedly intelligently designed, making this creator god look like quite the opposite of an all-loving creator. Nevertheless, they will look at the results of this piece of research as evidence of the design ability of their god, and still insist that it can't be the result of a natural process in which no god(s) were involved.

The research in question was carried out by scientists from the University of Central Florida, led by assistant professor Salvador Almagro-Moreno, of the Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA. They investigated the difference between pathological and non-pathological strains of the bacterium, Vibrio vulnificus, found in the Indian River Lagoon in East Central Florida, where the organism is endemic. This bacterium can cause necrotizing fasciitis, so is also called the 'flesh-eating bug'. If ingested in oysters, for example, it can cause life-threatening septicaemia in patients with underlying health conditions such as diabetes mellitus. It is one of the fastest killing organisms with a mortality rate of over 50%.

The team investigated samples of organisms obtained from two different sites in the lagoon, one of which contains a population of potentially pathogenic V. vulnificus and the other a population of a non-pathogenic strain. They had previously identified a set of genetic markers that identify the pathogenic strain. They also examined the environmental factors that could account for the two distinct local populations - salinity, other bacterial communities in the environment, water pollutants, dissolved organic matter or the presence of algal blooms, etc.

Of course, being scientists, they were looking for environmental factors that could have driven the evolution of distinct local populations and produced pathogenic strains, but as any creationist will claim - this was all designed by their particular god, in full and omniscient knowledge of the effects it would have on its human victims.

Creationist mode:

Back in the real world now, where sadly, the team's paper, published a few days ago in PNAS is behind a paywall, but the abstract can be read here. In it, the team say:

Wednesday 13 October 2021

Evolution News - What makes us Different to the Chimpanzees and Why it Should Bother Creationists

What makes us human? The answer may be found in overlooked DNA | Lund University.

Sometimes you just have to laugh at Creationists, the knots they have to tie themselves into to try to make their childish superstition match what real-world evidence shows.

This paper, for example, which argues that the functional genetic difference between humans and the chimpanzees is to be found, not so much in the 2% of the genes by which we differ from them, but in how the 'junk' DNA is used by the them and us.

Creationists, of course, hate the statistic about us sharing 98% of our DNA with chimpanzees, and the intelligent [sic] design cult hates the fact that so much of our DNA is junk and so evidence against design, intelligent or otherwise. They would normally be jubilant over a finding like this that shows at least some of it might make a functional difference, so is not strictly junk after all - until they realise that that function is all that separates us from the chimpanzees.

The open access paper in the on-line journal, Cell Stem Cell is by a team of scientists led by Johan Jakobsson, professor of neuroscience at the Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Sweden, together with colleagues from Washington University, USA and Ecole Polytechnique Fédérale de Lausanne, Switzerland. Lund University's news item explains:

Monday 11 October 2021

Power at Any Price - The Lengths Christian Extremists Will Go To To Grab Power

Michael P Farris, Conservative Christian President and CEO of Trump-supporting Alliance Defending Freedom
How Michael P. Farris Tried to Block 2020 Election Outcome - The New York Times.

As students of Early 20th Century European history will be aware, the Christian churches were often amongst the most enthusiastic supporters of the extreme right-wing parties that overthrew democracy and installed odious, racist, misogynist and criminal fascist government in countries such as Portugal, Spain, Italy, Hungary and Germany. Not surprisingly then, they are amongst the most enthusiastic supporters of attempts by the extreme right-wing in the USA to overthrow democracy, reverse the stunning victory of the Democrats and reinstall the odious racist, misogynist and criminal Donald J. Trump in the Oval Office.

One such would-be autocratic theocrat, is lawyer, Michael P. Farris, President and CEO of Christian extremist organization, Alliance Defending Freedom [sic].

Friday 8 October 2021

Late Persistence of Human Ancestors at a Site in India.

Map illustrating the location of the study site, Singi Talav, in relation to the world’s youngest Acheulean sites from other key regions. Made with Natural Earth: Free vector and raster map data at naturalearthdata.com.

© Jimbob Blinkhorn
Late Persistence of Human Ancestors at the Margins of the Monsoon in India | Max Planck Institute for the Science of Human History

More evidence published recently that an archaic hominin spread far and wide out of Africa into Eurasia, many thousands of years before Homo sapiens migrated out of Africa.

This evidence is from the youngest Acheulean site so far discovered, at Singi Talav, in the Thar Desert, Rajasthan, India, dated to 177,000 years ago. This shows that stone tools were used there for over 1 million years and may have persisted until the arrival of H. sapiens. This stone tool-making technology is believed to have arisen in Africa about 1.5 million years ago and reached India, presumably by being taken there by migrants, about 1.2 million years ago.

This new dating was done by researchers led by Dr. James Blinkhorn of the Max Planck Institute for the Science of Human History. According to to their news release:

How Religion Keeps the Poor Poor.

Religious belief really does seem to draw the sting of poverty | The Economist

The problem with religion is that it teaches poor people to accept their 'place' in society and not to aspire to something better. This is the obvious conclusion to be drawn from a piece of research carried our recently by a group of sociologists and psychologists led by Jana B. Berkessel of the Mannheim Centre for European Social Research, University of Mannheim, Mannheim, Germany.

The team found that, contrary to accepted ideas, people with a low socioeconomic status (SES) in a developed country carry a higher psychological burden than their counterparts in developing countries. The assumption had been that the psychological burden would ease as society developed and became more prosperous. However the research showed that there was an inverse relationship between the psychological burden of SES and the religiosity of the society and there was a similar relationship between religiosity and economic development.

In other words, as society develops economically, so religiosity falls, removing the religious norms that ease the burden of low SES.

This conclusion came as a result of statistical analysis of three surveys covering 3.3 million people in 156 countries.

This teaching to accept your place is not confined to Christianity either but can be found in almost all major religions. The team say:
Among the religious norms that enable cultural groups to thrive is a set relevant for SES. That set eases the burden of lower SES (“The poor are admitted into Paradise before the rich, by five hundred years;” Vol. 5, Book 37, Hadith 4261, The Qur’an; “For those who are poor and destitute; May I turn into all things they could need;” Ch. 3, Verse 10, Bodhisattvacharyavatara) and it does so in part by casting a bad light on higher SES [“It is easier for a camel to go through the eye of a needle than for a rich man to enter the kingdom of God;” Matthew 19:24, The Bible, “The demoniac person thinks: So much wealth do I have today, and I will gain more;” Ch. 16, Verse 13, Bhagavad-Gita (16, 29)]
Their open access paper is published in PNAS:
According to a fundamental assumption in the social sciences, the burden of lower socioeconomic status (SES) is more severe in developing nations. In contrast to this assumption, recent research has shown that the burden of lower SES is less—not more—severe in developing nations. In three large-scale global data sets, we show that national religiosity can explain this puzzling finding. Developing nations are more religious, and most world religions uphold norms that, in part, function to ease the burden of lower SES and to cast a bad light on higher SES. In times of declining religiosity, this finding is a call to scientists and policymakers to monitor the increasingly harmful effects of lower SES and its far-reaching social consequences.

Lower socioeconomic status (SES) harms psychological well-being, an effect responsible for widespread human suffering. This effect has long been assumed to weaken as nations develop economically. Recent evidence, however, has contradicted this fundamental assumption, finding instead that the psychological burden of lower SES is even greater in developed nations than in developing ones. That evidence has elicited consternation because it suggests that economic development is no cure for the psychological burden of lower SES. So, why is that burden greatest in developed nations? Here, we test whether national religiosity can explain this puzzle. National religiosity is particularly low in developed nations. Consequently, developed nations lack religious norms that may ease the burden of lower SES. Drawing on three different data sets of 1,567,204, 1,493,207, and 274,393 people across 156, 85, and 92 nations, we show that low levels of national religiosity can account for the greater burden of lower SES in developed nations. This finding suggests that, as national religiosity continues to decline, lower SES will become increasingly harmful for well-being—a societal change that is socially consequential and demands political attention.

It looks as though both Seneca and Napoleon were right in that religion is used by the ruling class to keep the poor happy and contented so they never aspire to anything better. The priesthoods are complicit in this deception in return for protection and special status within the state.

This much was evident in the repose of religions to a Pew Research forecast a few years ago that support for religions will grow in coming years as the populations of third-world and developing countries is set to increase. They were jubilant at the though that the number of poor people in the world was going to increase and that they would benefit from this growth, part of which, with their teachings against contraception and family planning and for female subservience, they were responsible for.

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Thursday 7 October 2021

Malevolent Designer News - Is Creationism's Divine Malevolence Trying Something New

The study suggests that the Yezo virus, a type of orthonairovirus, transmits between animals and humans via ticks and causes fever and other symptoms in humans.
Emerging infectious disease caused by a new nairovirus identified in Japan | Hokkaido University

Creationist mode:

Here's some great news to thrill worshippers of Creationism's favourite malevolence, the putative designer god responsible for all living things and any changes they undergo over time.

Researchers at Hokkaido University, Japan, have identified a previously unknown, tick-borne virus, a type of orthonairovirus they have named Yezo virus. When infected from a tick bite, victims suffer from a fever, and a reduction in platelets (the circulating cell fragments responsible for blood-clotting following injury) and leucocytes (the blood cells responsible for infection control, etc) and abnormal liver function.

As the news release from Hokkaido University explains:

Tuesday 5 October 2021

Catholic Child Abuse News - Correction: Not 10,000 Victims of French Catholic Priests! It was 216,000 - 330,000!

Éric de Moulins-Beaufort, Archbisop of Reims. Head of the Conference of French Bishops.
Told there were 216,000 French victims of 3000 paedophile Catholic priest since 1950.
Estimated 216,000 children abused by French Catholic priests, report finds | France | The Guardian

A couple of days ago I reported on the leaked report of the French independent commission of enquiry into child abuse by Catholic priest in France since 1950. The reports spoke of 10,000 victims of 3000 priests and other Catholic clerics.

The 10,000 figure was wrong and grossly underestimated the true number. In the report delivered to the Archbishop of Reims, Éric de Moulins-Beaufort, in his position as head of the French Conference of Bishops, which commissioned the report, the true number of abuse victims was estimated to be about 216,000 and possibly as high as 330,000!

Malevolent Designer News - Creationism's Divine Sadist is Not Giving up on Malaria

Plasmodium falciparum parasites amongst red blood cells.
Plasmodium Falciparum Evolving to Escape Malaria Rapid Diagnostics in Africa | Newsroom

Creationist mode:

We saw yesterday how Creationism's favourite malevolence, the putative intelligent designer responsible for all living organisms and how they adapt, is pulling out all the stops in an effort to combat the success human medical science is having with its anti-COVID-19 vaccines, by designing multiple variants and now tweaking the more successful ones so they can kill even more people and make many more sick.

Now we have news that it is also working hard to maintain the suffering caused by another of its brilliantly malevolent designs - Plasmodium falciparum, the parasitic protozoan that caused malaria.

Monday 4 October 2021

Catholic Child Abuse News - Enquiry Confirms - 3000 Paedophiles in the French Catholic Priesthood and 10,000 Victims!

Jean-Marc Sauvé, head of the independent commission
Photograph: Quentin TOP/SIPA/Rex/Shutterstockx
'3000 paedophiles' held positions in French Catholic Church since 1950s — leaked report | Euronews

Another major scandal is about to rock the Catholic Church with the report due out tomorrow into child sexual abuse within the Catholic Church in France.

The report, leaked ahead of publication, will confirm that about 3000 priests and other Catholic clerics, sexually abused some 10,000 children between 1950 and 2018 when the independent commission of enquiry was established. The report runs to about 2,500 pages.

Sunday 3 October 2021

Malevolent Designer News - Creationism's Divine Malevolence is Not Giving up on Covid-19

MU researchers identify mutations of Delta, Delta Plus variants // Show Me Mizzou // University of Missouri

Creationist mode:

There is one thing that Creationism's divine malevolence definitely is not, and that's a quitter.

Having designed one of the nastiest viruses to hit humanity for over a century, it is never going to let a little thing like human medical science stand in the way of killing millions of people, making tens of millions more sick and ruining national economies and private business all over the world, without a fight. Humans might think they are on the verge of defeating it with their vaccines, and natural antibodies but the intelligent [sic] designer still has a few tricks up its sleeve. They are not getting away with that.

So, it's busy looking for a variant that is not only more contagious than its first model, but can get around the antibodies the man-made vaccines produce, as well as the antibodies human immune systems produce naturally when infected. This is, of course, the same immune system that creationists believe their divine malevolence designed to protect us from the viruses and bacteria it designs to harm us, but that's by the by.

Friday 1 October 2021

Unintelligent Design News - Another Arms Race - Between Birds

1 / 5
The common cuckoo lays its eggs in the nests of other bird species, burdening these hosts with the task of raising its young.
Photo by Olda Mikulica
2 / 5
Yellow warblers sometimes abandon their nests when a cowbird lays an egg in them. Another strategy involves building a new nest on top of the old one, sealing off the parasitic egg.
Photo by Pookie Fugglestein
3 / 5
Researchers report that brood parasites, like this common cuckoo, top, have larger eyes than the birds they target – beyond the difference expected as a result of their larger body size. Common cuckoos will parasitize the nests of European robins, bottom left, but not those of European bee-eaters, bottom right.
Photos by Tomas Grim
4 /5
The great reed warbler
sometimes has its nest parasitized by cuckoos.

Photo by Olda Mikulica
5 / 5
An adult common redstart feeds a parasitic cuckoo chick in its nest.
Photo by Tomas Grim
Birds' eye size offers clues to coevolutionary arms race between brood parasites, hosts | Illinois

The existence of arms races is about as good evidence as you can get that there is no intelligence behind life on Earth. After all, what single intelligent entity would indulge in an ultimately futile competition with itself where a solution to a problem is then turned around into another problem to be solved and so ad infinitum, in a futile, never-ending cycle of redesign for no ultimate purpose save possibly to make more parasites?

And this example of one such arms races is a good example. As so often with these arms races, it starts off with one species becoming an obligate parasite on another - and obligate parasites are themselves more evidence of the lack of intelligence since it will inevitably lead to yet another arms race as the parasitised species develops ways to resist or mitigate the parasite and the parasite has to counter those measures or become extinct. Any half-decent biologist will understand this, so it shouldn't be beyond the comprehension of an intelligent designer god.

And let's remind ourselves that Creationism's putative designer god is also normally the supposedly omniscient Abrahamic god of Christianity, Islam and Judaism who should therefore have foreseen that a pointless and ultimately futile arms race would ensue when it allegedly designed an obligate parasite.

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