Refuting Creationism - A Denisovan Gene Helped Humans Populate The Americas

An artist's rendering shows the first-ever portrait of a Denisovan woman, recreated from an ancient DNA sample.

Maayan Harel.

The proposed evolutionary history of MUC19.
The Denisovan-like haplotype (in orange) was first introgressed from Denisovans into Neanderthals and then introgressed into modern humans. The introgressed haplotype later experienced positive selection in populations from the Americas. The introgressed MUC19 haplotype is composed of a 742-kb region that contains Neanderthal-specific variants (blue). Embedded within this Neanderthal-like region is a 72-kb region containing a high density of Denisovan-specific variants (orange), and an exonic variable number tandem repeat (VNTR) region (gray). The box below the 742-kb region depicts zooming into the MUC19 VNTR region, in which admixed American individuals carry an elevated number of tandem repeat copies.

Fernando A. Villanea et al. (2025)

Extinct human relatives left a genetic gift that helped people thrive in the Americas | Brown University

Another day; another scientific paper showing the Bible to be wrong — not just slightly wrong, but fundamentally, demonstrably, and irretrievably wrong.

This latest blow comes from researchers at Brown University, who have traced a variant of the gene MUC19, originally identified in the extinct archaic hominins known as Denisovans, and found it alive and well today in modern Latin Americans with Indigenous ancestry. They also detected it in ancient DNA recovered from archaeological sites across both North and South America.

The variant is far too common in modern populations to be a trivial accident. Its persistence screams survival advantage. Natural selection has kept it in play because it helps its carriers thrive in the environments the earliest migrants into the Americas encountered.

What does MUC19 do? It helps build mucus — not glamorous, but life-saving. From the saliva that begins digestion to the mucosal barriers in the gut and respiratory tract that fend off infection, this gene equips its owners with a stronger shield against disease.

And where did it come from? The Denisovans. But it likely reached us by way of Neanderthals, with whom Homo sapiens also interbred. In other words, modern humans are not some isolated “special creation” freshly minted out of clay a few thousand years ago; we are a patchwork of lineages, woven together by repeated episodes of interbreeding over tens of thousands of years.

For creationists, this paper is a nightmare. First, the scientists are explicit: the explanation rests entirely on Evolution and the blind, natural processes that drive it. Second, the mere fact that extinct species like Denisovans and Neanderthals could successfully mate with our ancestors drives a stake through the heart of biblical literalism. Instead of Adam and Eve, what we see is gradual emergence — modern humans arising by incomplete speciation across a broad geographical spread, with genes flowing back and forth whenever populations met again. This pattern repeats itself throughout hominin history, and it unfolds on a timeline that makes the biblical six-thousand-year fantasy look laughably naïve.

The MUC19 Gene

• What it is:
  
  MUC19 belongs to the mucin family of genes. Mucins are large, heavily glycosylated proteins that make up mucus — the slimy, protective coating that lines our respiratory, digestive, and reproductive tracts.
• Function:
  
  MUC19 helps produce the gel-like consistency of mucus, contributing to:
  • Lubrication of food in the mouth (via saliva).
  • Protection of epithelial surfaces from pathogens.
  • Formation of mucosal barriers that trap microbes and particles before they can cause infection.
• Evolutionary origins:
  • The mucin gene family is ancient, with roots stretching back hundreds of millions of years in vertebrates.
  • MUC19 itself arose by gene duplication and diversification within this family. Different mucins have been recruited for specialised roles — for example, MUC2 in the gut and MUC5 in the lungs.
  • The Denisovan variant of MUC19 is one such adaptation, likely honed in Ice Age Eurasia where pathogens and harsh environments placed strong selective pressures on immune defences.
• Human inheritance:
  • Genetic evidence suggests that Homo sapiens acquired this variant of MUC19 through introgression — the flow of genes from Denisovans (probably via Neanderthals) into the modern human gene pool.
  • The variant persisted at high frequencies in the Americas because it provided a survival advantage against local environmental challenges.
• Why it matters:
  
  The story of MUC19 illustrates how evolution works not only through slow accumulation of mutations, but also by horizontal gene transfers from related species. Human biology today is a mosaic assembled from many ancestral sources.

The research team, led by Professor Emilia Huerta-Sánchez of Brown University’s Department of Ecology, Evolution, and Organismal Biology, have published their findings in Science, with further details explained in a Brown University news release by Kevin Stacey.

Another brick out of the crumbling wall of creationist delusion; another win for science.

Extinct human relatives left a genetic gift that helped people thrive in the Americas

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A new study found that a gene passed down from extinct archaic humans provided an adaptive advantage for Indigenous people of the Americas and is still common today in people of Indigenous descent.

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A new study provides fresh evidence that ancient interbreeding with archaic human species may have provided modern humans with a genetic variant that helped them adapt to new environments as they dispersed across the globe.

The study, published in Science, focused on a gene known as MUC19, which is involved in the production of proteins that form saliva and mucosal barriers in the respiratory and digestive tracts. The researchers show that a variant of that gene derived from Denisovans, an enigmatic species of archaic humans, is present in modern Latin Americans with Indigenous American ancestry, as well as in DNA collected from individuals excavated at archeological sites across North and South America.

The frequency at which the gene appears in modern human populations suggests the gene was under significant natural selection, meaning it provided a survival or reproductive advantage to those who carried it. It’s not clear exactly what that advantage might have been — but given the gene’s involvement in immune processes, it may have helped populations fight off pathogens encountered as they migrated into the Americas thousands of years ago.

From an evolutionary standpoint, this finding shows how ancient interbreeding can have effects that we still see today. From a biological standpoint, we identify a gene that appears to be adaptive, but whose function hasn’t yet been characterized. We hope that leads to additional study of what this gene is actually doing.

Professor Emilia Huerta-Sánchez, senior author.
Department of Ecology, Evolution, and Organismal Biology
Brown University, Providence, RI, USA.

Not much is known about the Denisovans, who lived in Asia between 300,000 and 30,000 years ago, aside from a few small fossils from Denisova cave in Siberia, two jaw bones found in Tibet and Taiwan, and a nearly complete skull from China found this year. A finger fossil from Siberia contained ancient DNA, which has enabled scientists to look for common genes between Denisovans and modern humans. Prior research led by Huerta-Sánchez found that a version of a gene called EPAS1 acquired from Denisovans may have helped Sherpas and other Tibetans to adapt to high altitudes.

For this study, the researchers compared Denisovan DNA with modern genomes collected through the 1,000 Genomes Project, a survey of worldwide genetic variation. The researchers found that the Denisovan-derived MUC19 gene is present in high frequencies in Latino populations who harbor Indigenous American genetic ancestry. The researchers also looked for the gene in the DNA of 23 individuals collected from archeological sites in Alaska, California, Mexico and elsewhere in the Americas. The Denisovan-derived variant was present at high frequency in these ancient individuals as well.

The team used several independent statistical tests to show that the Denisovan MUC19 gene variant rose to unusually high frequencies in ancient Indigenous American populations and present-day people of Indigenous descent, and that the gene sits on an unusually long stretch of archaic DNA — both signs that natural selection had boosted its prevalence. The research also revealed that the gene was likely passed through interbreeding from Denisovans to another archaic population, the Neanderthals, who then interbred with modern humans.

Huerta-Sánchez said the findings demonstrate the importance that interbreeding had in introducing new and potentially useful genetic variation in the human lineage.

Typically, genetic novelty is generated through a very slow process, but these interbreeding events were a sudden way to introduce a lot of new variation.

Professor Emilia Huerta-Sánchez.

In this case, she said, that “new reservoir of genetic variation” appears to have helped modern humans as they migrated into the Americas, perhaps providing a boost to the immune system.

Something about this gene was clearly useful for these populations — and maybe still is or will be in the future.

Professor Emilia Huerta-Sánchez.

She’s hopeful that the recognition of the gene’s importance will spur new research into its function to reveal novel biological mechanisms, especially since it involves coding genetic variants that alter the protein sequence.

Huerta-Sánchez co-authored the study with Fernando Villanea, a former postdoctoral researcher at Brown who is now at University of Colorado, Boulder; David Peede, a graduate student at Brown; and an international team of collaborators.

Publication:

Fernando A. Villanea et al.
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science 389, eadl0882 (2025). DOI: 10.1126/science.adl0882

Structured Abstract

INTRODUCTION
Modern human genomes contain a small number of archaic variants, the legacy of past interbreeding events with Neanderthals and Denisovans. Most of these variants are putatively neutral, but some archaic variants found in modern humans have been targets of positive natural selection and may have been pivotal for adapting to new environments as humans populated the world. American populations encountered a myriad of novel environments, providing the opportunity for natural selection to favor archaic variants in these new environmental contexts. Indigenous and admixed American populations have been understudied in this regard but present great potential for studying the underlying evolutionary processes of local adaptation.

RATIONALE
Previous studies identified the gene MUC19—which codes for a mucin involved in immunity—as a candidate for introgression from Denisovans as well as a candidate for positive natural selection in present-day Indigenous and admixed American populations. Therefore, we sought to confirm and further characterize signatures of both archaic introgression and positive selection at MUC19, with particular interest in modern and ancient American populations.

RESULTS
We identify an archaic haplotype segregating at high frequency in most admixed American populations, and among ancient genomes from 23 ancient Indigenous American individuals who predate admixture with Europeans and Africans. We conclude that the archaic haplotype has undergone positive natural selection in these populations, which is tied to their Indigenous components of ancestry. We also find that modern admixed American individuals exhibit an elevated number of variable number tandem repeats (VNTRs) at MUC19, which codes for the functional domain of the MUC19 protein, where it binds to oligosaccharides to form a glycoprotein, a characteristic of the mucins. Remarkably, we find an association between the number of VNTRs and the number of introgressed haplotypes; individuals harboring introgressed haplotypes tend to have a higher number of VNTRs. In addition to the differences in VNTRs, we find that the archaic MUC19 haplotype contains nine Denisovan-specific, nonsynonymous variants found at high frequencies in American populations. Finally, we observed that the Denisovan-specific variants are contained in a 72-kb region of the MUC19 gene, but that region is embedded in a larger 742-kb region that contains Neanderthal-specific variants. When we studied MUC19 in three high-coverage Neanderthal individuals, we found that the Chagyrskaya and Vindija Neanderthals carry the Denisovan-like haplotype in its heterozygous form. These two Neanderthals also carry another haplotype that is shared with the Altai Neanderthals.

CONCLUSION
Our study identifies several aspects of the gene MUC19 that highlight its importance for studying adaptive introgression: One of the haplotypes that span this gene in modern humans is of archaic origin, and modern humans inherited this haplotype from Neanderthals who likely inherited it from Denisovans. Then, as modern human populations expanded into the Americas, our results suggest that they experienced a massive coding VNTR expansion, which occurred on an archaic haplotype background in MUC19. The functional impact of the variation at this gene may help explain how mainland Indigenous Americans adapted to their environments, which remains underexplored. Our results point to a complex pattern of multiple introgression events, from Denisovans to Neanderthals and Neanderthals to modern humans, which may have later played a distinct role in the evolutionary history of Indigenous American populations.

The proposed evolutionary history of MUC19.
The Denisovan-like haplotype (in orange) was first introgressed from Denisovans into Neanderthals and then introgressed into modern humans. The introgressed haplotype later experienced positive selection in populations from the Americas. The introgressed MUC19 haplotype is composed of a 742-kb region that contains Neanderthal-specific variants (blue). Embedded within this Neanderthal-like region is a 72-kb region containing a high density of Denisovan-specific variants (orange), and an exonic variable number tandem repeat (VNTR) region (gray). The box below the 742-kb region depicts zooming into the MUC19 VNTR region, in which admixed American individuals carry an elevated number of tandem repeat copies.

Fernando A. Villanea et al. (2025)

Abstract
We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed American individuals and at highest frequency in 23 ancient Indigenous American individuals, all pre-dating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30–base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in admixed American populations. Finally, we find that some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into modern human populations through Neanderthal introgression rather than Denisovan introgression.

Fernando A. Villanea et al.
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science 389, eadl0882 (2025). DOI: 10.1126/science.adl0882

© 2025 the American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So here we have it yet again: a gene that entered the human lineage not by divine fiat, but by the messy, natural processes of interbreeding, survival, and selection. It is hard to imagine a clearer demonstration of how evolution operates in practice — reshaping our genomes, blending lineages, and preserving whatever works in the long struggle against disease and death.

For creationists, this isn’t just inconvenient; it’s catastrophic. Their worldview depends on a myth of humans created fully formed, apart from and above the rest of nature, a few thousand years ago. But the evidence of MUC19 is another reminder that we are not passengers on a separate track. We are part of the same evolutionary story as Neanderthals, Denisovans, and the countless other hominins who walked the Earth before us.

Science doesn’t just explain our origins better than Genesis — it explains them *at all*. The biblical account collapses under the weight of real data, while evolution continues to weave a coherent, testable, and beautifully messy picture of our past. Each discovery like this adds another nail in the coffin of creationism and another stone in the foundation of our true evolutionary heritage.

The Bible’s story may comfort creationists and make them feel important, but the genome tells the truth.

Refuting Creationism - A Tiny Piece of DNA That's So Unkind To Creationists

A Genetic Twist that Sets Humans Apart

Humans and chimpanzees share about 98–99% of their DNA, so the vast differences between us must lie within that small fraction where we differ.

Humans have no organs or structures that chimpanzees don’t also have; the differences are mainly in relative size and proportion. In other words, they’re quantitative, not qualitative. But that doesn’t stop creationists solemnly declaring that we are a totally different “kind” — a human “kind” — while chimps are lumped with gorillas, bonobos, and orangutans into the “ape kind.” Two bins, job done.

Creationists insist that no “kind” could have evolved from another because that would require brand-new organs and “new genetic information,” something they claim is impossible. Instead, they set up a straw man, accusing scientists of believing new genes and structures simply pop into existence out of thin air, like some sort of Darwinian magic trick, while insisting no one can explain how it works. (Apparently, gene duplication, mutation, and selection don’t count when you’ve decided in advance that the answer must be wrong.)

But when it comes to humans and chimpanzees, their reasoning ties itself in knots. Humans can’t have evolved from a chimp-like ancestor, they say, because that would be “macro-evolution.” Except when it isn’t. Lions, tigers, leopards, cheetahs, and house cats are all just one happy “cat kind,” because in that case there was obviously no “macro-evolution” — only “variation.” So, if evolution produces cats, that’s “micro-evolution.” If it produces humans, it’s “macro-evolution,” and therefore impossible. Heads I win, tails you lose.

In reality, the major differences between humans and chimpanzees aren’t about inventing new bits and pieces, but in how the same components developed. The key lies in relative sizes of bones, muscles, and teeth — and above all in the brain: not new parts, but differences in growth, proportion, and how the brain is wired.

Now, researchers at the University of California San Diego School of Medicine have shown that part of that small genetic difference — specifically a stretch of DNA called HAR123 — acts as an enhancer controlling brain growth and development. In other words, the real evolutionary leap wasn’t the conjuring up of brand-new organs from nowhere, but changes in how existing genes fine-tuned brain development. The decisive shift came not from what parts the brain has, but from how large they grew and the ratio of cell types — glial cells and neurons — within them.

Refuting Creationism - How Denisovans Created Modern Non-African Humans

A reconstruction of the hominin source of the ‘Dragon Man’ cranium in his habitat. The fossil has now been identified as coming from a Denisovan.

Chuang Zhao

An artist's rendering shows the first-ever portrait of a Denisovan woman, recreated from an ancient DNA sample.

Maayan Harel.

New insights into the Denisovans – the new hominin group that interbred with modern day humans - News & Events | Trinity College Dublin

There is increasing evidence that the human evolutionary story is far richer and more complex than was once assumed, back when many expected a neat series of fossils showing a linear descent from a single African ancestor.

It is also becoming increasingly clear that the Bronze Age human-origin myth in the Bible has about as much historical credibility as Enid Blyton’s Noddy’s Adventures in Toyland — and at least Blyton never claimed her stories were literal truth or the basis of moral authority. Unlike creation myths, Noddy’s adventures were always meant for the nursery, not the classroom.

We now understand that hominin populations frequently split into regional varieties which diversified as more or less isolated groups, only to merge again later into a single population. This process appears to have begun even as we were diverging from the common ancestor we share with chimpanzees. For around a million years after that split, interbreeding remained possible, with chimpanzee genes entering the hominin genome and vice versa.

The interbreeding that most shaped modern, non-African Homo sapiens occurred when African H. sapiens encountered Neanderthals—or their immediate ancestors—during successive waves of migration, permitted by changes in climate and geography. These contacts culminated in the last and only successful migration between roughly 60,000 and 40,000 years ago.

The Neanderthals themselves were descended from an earlier migration that had followed H. erectus into Eurasia, later splitting into Neanderthals in western Eurasia and Denisovans in eastern and south-eastern Eurasia. Modern genomics now shows that it was the Denisovans who contributed even more to the ancestry of non-African H. sapiens than the Neanderthals did. The Denisovans—likely to be reclassified as H. longi, the name given to a skull found in China—appear to have diversified into populations adapted to environments as varied as the Tibetan Plateau and the subtropical coasts of Southeast Asia, Oceania, and Austronesia.

Creationism Refuted - Common Origins of Alcohol Metabolism In Humans And African Apes

Scrumped fruit key to chimpanzee life and a major force of human evolution | University of St Andrews news

(b) Scrumping of Pentadesma butyracea (Clusiaceae) by a western gorilla.

Photograph: MMR.

(c) Scrumping of Gambeya albida (syn. Chrysophyllum albidum; Sapotaceae) by an eastern chimpanzee.

Photograph: CH.

The human ability to consume and metabolise alcohol efficiently may trace back to our ape ancestors, who regularly ate overripe and fermented fruit with a naturally high alcohol content. This is according to researchers from the University of St Andrews, Scotland, and Dartmouth College, USA.

The bad news for creationists is that this discovery strongly supports the common ancestry of modern apes and humans. The researchers are in no doubt that the Theory of Evolution explains the presence of the same genetic mutation in African apes — including humans — which allows us to metabolise alcohol around 40 times more efficiently than orangutans, which lack the mutation.

This mutation enables African apes to consume fermented fruit — often as a social activity — in a pattern of alcohol consumption strikingly similar to that seen in humans.

To describe this behaviour in wild chimpanzees, the researchers have borrowed the term scrumping — a familiar UK English word for the (often illicit) picking and eating of apples, particularly by children. The word derives from the Middle Low German schrimpen, meaning ‘shrivelled or shrunken’ (to describe over-ripe fruit). It also survives in the name of the traditional West Country cider known as scrumpy.

Refuting Creationism - A Diverse Human Population in China - 290,000 Years Before 'Creation Week'

Members of the research team.

A study reveals the human diversity in China during Middle Pleistocene | CENIEH

A study recently published in the Journal of Human Evolution reports the discovery of a mixture of archaic and modern traits in the dentition of 300,000-year-old hominin fossils unearthed at the Hualongdong site in Anhui Province, China.

These fossils predate the migration of anatomically modern humans (Homo sapiens) out of Africa by around 250,000 years. They indicate that hominin populations in East Asia were already diversifying and possibly interbreeding with archaic humans, such as Homo erectus, to form lineages distinct from both Neanderthals and Denisovans.

The research, led by Professor Wu Xiujie, director of the Hualongdong excavations, is the result of a longstanding collaboration between scientists from the Dental Anthropology Group at CENIEH — María Martinón-Torres, Director of CENIEH and corresponding author of the paper, and José María Bermúdez de Castro, researcher ad honorem at CENIEH — and the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing.

The findings reveal a rich and complex picture of human evolution in East Asia, wholly at odds with the simplistic biblical narrative still clung to by creationists. That account, written by ancient people with no knowledge of the broader world, reflects a worldview in which Earth was small, flat, covered by a dome, and located at the centre of the universe.

Creationism Refuted - There May Have Been Two Or More Species Of the Hominin Paranthropus That Interbred

Parathropus robustus

© Roman Yevseyev.

New clues from 2 million-year-old tooth enamel tell us more about an ancient relative of humans

Where exactly the archaic hominin, Paranthropus robustus fits into the human evolutionary tree remains a subject of debate among palaeontologists. This species lived in southern Africa around 2 million years ago. They walked upright, indicating a shared ancestry with the Australopithecus and the later Homo genus. However, their comparatively small brains and massive jaws and teeth suggest a distinct evolutionary path, likely adapted for processing tough, fibrous plant material.

Determining their precise place in our evolutionary history would ideally require DNA analysis—but DNA does not survive long in the warm African climate. To overcome this limitation, a team of African and European researchers from the fields of molecular science, chemistry, and palaeoanthropology turned to a cutting-edge technique known as palaeoproteomics. By analysing proteins recovered from ancient tooth enamel, they were able to infer aspects of the underlying DNA, since the amino acid sequence in proteins is directly determined by the nucleotide sequence in DNA.

Their findings suggest that the story of early hominins is more complex than previously thought. There may have been more than one closely related species, with evidence of interbreeding or genetic divergence followed by remixing — patterns that would later come to characterise the tangled branches of the hominin family tree.

The research team included three postdoctoral scientists from the University of Copenhagen — Palesa P. Madupe, Claire Koenig, and Ioannis Patramanis — who have written about their work and its significance in the open-access magazine The Conversation.

Their findings are also published in Science.

Their article in The Conversation is reproduced here under a Creative Commons licence, reformatted for stylistic consistency:

Refutiing Creationism - How Environmental Variability in Africa Produced Co-operative, Intelligent Humans

This article is best read on a laptop, desktop, or tablet

Between 300,000 and 30,000 years ago, Africa experienced intense, local environmental variation.

Environmental Variability Promotes the Evolution of Cooperation Among Humans: A Simulation-Based Analysis | Research News - University of Tsukuba

In a compelling example of how environmental change can drive evolutionary development, two researchers, Masaaki Inaba and Eizo Akiyama, of the University of Tsukuba, Japan, have used computer simulations grounded in evolutionary game theory to demonstrate how intensified environmental variability in Africa during the Middle Stone Age may have promoted the evolution of cooperative behaviour and enhanced cognitive abilities in archaic hominins.

Fundamental to this research is the scientific consensus that Darwinian evolution is the only credible framework for explaining the patterns observed in the fossil record and the genomic evidence for natural selection.

The study also directly challenges a common creationist misrepresentation: that Richard Dawkins’ metaphor of the “selfish gene” implies that evolution inherently favours selfishness and therefore cannot account for altruism or cooperation. This flawed interpretation ignores the fact that evolutionary processes often favour cooperative strategies—especially in complex, fluctuating environments—without invoking supernatural causes.

Severe environmental change can fragment populations into small, isolated groups, where genetic drift plays a significant role in evolution. In such settings, beneficial mutations can rapidly drift to fixation, potentially giving the group a competitive advantage over neighbouring populations when contact is re-established. This process can produce a pattern in the fossil record that resembles 'punctuated equilibrium', with the apparent 'sudden' appearance of a major innovation.

Refuting Creationism - Common Origins - Like Humans, Chimpanzees Use Engineering Skills to Make Tools

A Gombe chimpanzee using a termite fishing tool to fish termites.

Credit: Dr Alejandra Pascual-Garrido

A Gombe chimpanzee using a termite fishing tool to fish termites.

Credit: Dr Alejandra Pascual-Garrido

Research into chimpanzee ‘engineers’ has implications for understanding human technological evolution | University of Oxford

Not so long ago, it was commonly claimed that humans were exceptional due to their supposedly 'unique' ability to make and use tools. This assertion was often used to reinforce the idea that humans occupied a special position at the pinnacle of creation, justifying the biblical concept of human dominion over the rest of nature.

However, this claim was never credible to anyone observing nature carefully. It was largely promoted by religious authorities to foster a sense of human uniqueness and importance. This, in turn, reinforced belief in a creator god, supported the authority of religious institutions and their clerics, and justified their claims to the right to create laws governing human behaviour.

Scientific research has increasingly exposed the fallacy of this notion of human exceptionalism. Tool-making and tool use in humans are indeed more sophisticated than in other animals, but this ability is far from unique. Many other species demonstrate these abilities, notably chimpanzees—our closest living relatives. The widespread occurrence of tool use in nature strongly suggests this trait was present in a common ancestor we share with other primates. Furthermore, the independent evolution of tool use in species as diverse as birds, bees, and octopuses demonstrates that this capability is not unique to humans but rather a result of natural evolutionary processes.

Another human characteristic, traditionally cited by religious authorities as evidence for special creation and human exceptionalism, has, once again, been shown by science to be better explained as evidence of our evolutionary heritage within the natural world.

And today we have evidence that chimpanzees not only make and use tools but employ sophisticated 'engineering' skill in their choice of the right materials for their construction. It comes in the form of a paper published, open access, in iScience by a team of researchers led by Dr Alejandra Pascual-Garrido, of the School of Anthropology and Museum Ethnography, University of Oxford, UK.

Refuting Creationism - Our Ancesters Were Vegetarian, 3 Million Years Before 'Creation Week'

'Little Foot' from the Sterkfontein Cave, South Africa

Witwatersrand University

Three million years ago, our ancestors were vegetarian - Wits University

The Australopithecus genus is widely regarded as the immediate ancestor of the Homo genus that includes modern humans, Homo sapiens, but, from new evidence revealed by a team of researchers from the Max Planck Institute for Chemistry in Germany and the University of the Witwatersrand in South Africa, it appears that meat did not become part of our immediate ancestors' diet until after Homo species emerged.

The evidence comes from an isotope analysis of the enamel from the fossilised teeth of seven Australopithecus individuals is strongly indicative of a vegetarian diet with little or no meat consumption.

How they discovered this is the subject of a paper in Science and a new item from Witwatersrand University. Creationists should note that the isotopes of nitrogen on which this analysis is based are stable, so the traditional excuse that radioactive decay rates have changes over time is not relevant here. Besides, they are not the basis of dating these fossils, but of working out where in the food chain these Australopithecines were:

Refuting Creationism - Ability to Perform Complex Tasks Had Already Evolved Before Chimps and Hominins Split

Male chimp cracking nuts.

Photo: Dora Biro.

Study shows that chimpanzees perform the same complex behaviours that have brought humans success | University of Oxford

Time and again, science is showing that characteristics which were once considered uniquely human, and therefore, according to creationists, evidence that humans are a special creation, distinct from all other animals, are in fact shared with other animals.

Instead of being evidence of unique creation, they are evidence of common origins and descent with modification.

On such human characteristic is the ability to perform complex tasks, involving tool use, in organised sequence, and adapt those sequences if necessary to complete the task. In other words, to plan a strategy for achieving a specific goal.

However, a new study has shown that chimpanzees also have this ability, suggesting it was present in the common ancestor before chimps and Hominins diverged some 6 million years ago.

Common Origins - How The Mammalian Outer Ear Evolved - From Our Ancestral Fish Gills

An earful of gill: USC Stem Cell study points to the evolutionary origin of the mammalian outer ear | USC Stem Cell

I'm sorry if this spoils a creationists new year, but a bunch of scientists from the Stem Cell Lab of the University of Southern California have just published a paper showing an ancient ancestor of mammals, including of course us humans, was a fish.

It comes in the form of evidence that our outer ear develops from the same tissues in the embryo as the gills of fish. These tissues have been exapted by evolution for many new structures, one of which is the outer ear of mammals.

Refuting Creationism - How the 'Lizard' Part of Your Brain Influences Your Thinking

In a new Northwestern Medicine study, scientists sought to better understand how humans evolved to become so skilled at thinking about what’s happening in other peoples’ minds.

Amygdala is the organ in the limbic system (inner mind) —though a tiny little one is significantly responsible for our emotions which falls in the bracket of implicit memories.

Overthinking what you said? It’s your ‘lizard brain’ talking to newer, advanced parts of your brain: For Journalists - Northwestern University

Few things upset creationists more than evidence that they are not only apes and share a common ancestor with the other African apes, but that they also share a common ancestor even with non-mammals such as reptiles, and yet, as the American evolutionary biologist, Theodosius Dobzhansky reminds us, nothing in biology makes sense without the Theory of Evolution (TOE).

And one thing that does make sense is how the human brain is the result of an evolutionary process with ancestry in those common ancestors, including lizards.

A second thing that creationists who have deluded themselves into believing that mainstream biomedical scientists are giving up on the TOE and adopting the childish notion of intelligent design, will find distressing, is the news that the team who did this piece of research are firmly convinced that the structure of our brain and the way it works is the result of evolution, not magic.

The third thing is how this explains empathy, of which creationists often feign ignorance, claiming they get their sense of right and wrong from their invisible friend and have a handbook to tell them how to behave. The curious belief that even influenced supposed Christian intellectual 'giants' such as the smugly self-satisfied, C.S. Lewis, is despite the fact that one of the Golden Rules of human society, that even the founder of Christianity, Jesus, allegedly told his followers to apply - "Do unto others what you would they do unto you" or words to that effect, depend entirely on having the empathetic ability to know what someone else would want.

The research explains how this ability in humans comes from an ancestral ability to read social signals and form relationships, including an understanding of social hierarchies, possessed even by lizards.

Common Origins - Marmoset and Human Brain Development

Common marmoset, Callithrix jacchus

Peterwchen, CC BY-SA 4.0,
via Wikimedia Commons

As in humans, infants of common marmosets interact with several caregivers from birth and are thus exposed to intensive social interaction.

Image: Judith Burkart/UZH

Brain Development Marmosets | | UZH

Creationists like to pretend there is nothing in common between humans and the rest of the animal kingdom because humans were magically created as the special creation of a god who made all the 'lower' animals for our use, then gave us dominion over everything. This makes creationists feel really important.

The truth however is that we have very much in common with other animals and particularly with the species to which we are most closely relates and with whom we share the most recent common ancestor as we and they evolved and diversified over the same period of time to arrive at our present state.

This is reflected in the nested hierarchies into which the different branches of the evolutionary tree can be arranged in, anatomy, physiology and DNA and in the way our bodies develop through embryology and continued into childhood.


And yet creationists insist we are not only a different species, but a different 'kind' of animal, even a different category of life altogether, even though none of the difference they insist apply to different taxons as evidence of evolution apply to humans in respect of the other great apes.

The common marmoset, Callithrix jacchus, and their evolutionary relationship to humans. The common marmoset (Callithrix jacchus) is a small primate species native to the forests and scrublands of northeastern Brazil. Known for its expressive face, tufted ears, and squirrel-sized body, it’s a popular species for scientific research, primarily because it shares some interesting genetic and behavioural traits with humans. Here’s an overview of its characteristics, behaviour, and evolutionary relationship with humans.

Physical Characteristics

• Size: Common marmosets are small, weighing only about 300-400 grams, with a body length of 7-10 inches (18-25 cm) and a long, bushy tail.
• Appearance: They have a distinctive look with white ear tufts, a small face, and wide eyes. Their fur is mostly brownish-grey with a mix of white and black, allowing them to blend into their arboreal habitat.
• Hands and Feet: Like other New World monkeys, they have claws on most fingers (rather than flat nails like humans), which helps them cling to trees.

Habitat and Diet

• Environment: Marmosets thrive in forests, especially in areas with dense foliage where they can find food and avoid predators. They’re highly adaptable and can be found in both natural and urbanized settings in Brazil.
• Diet: They’re omnivores, feeding on tree sap, insects, fruits, and small animals. They use their specialized incisor teeth to gouge tree bark and access sap, which is a key component of their diet.

Social Structure and Behaviour

• Social Groups: Marmosets live in family groups typically led by a dominant pair. Groups consist of 5-15 individuals, often including multiple generations, with cooperative care of young by both parents and other group members.
• Communication: Marmosets are highly social and communicate through vocalizations, scents, and body language. They produce different calls depending on the context, and some sounds are ultrasonic, beyond human hearing range.
• Reproduction: These primates have a unique reproductive system, where dominant females can suppress the reproduction of other females in the group. They often give birth to twins, and group members assist in raising the young, a rare behaviour in mammals that echoes human familial cooperation.

Relationship to Humans

Marmosets belong to the infraorder Simiiformes, which includes all monkeys and apes, meaning they’re more distantly related to humans than other primates like chimpanzees and gorillas, who are part of the hominoid lineage. However, they still share significant genetic similarities with humans—about 92% of their DNA. They’re one of the smallest primates often studied for insights into human aging, neurological diseases, and genetics because of several interesting parallels:

• Brain and Behaviour: While their brains are much smaller than humans', they share many structural and functional aspects, including similar regions that govern emotions, memory, and sensory processing.
• Lifespan and Aging: Marmosets age quickly for a primate, with a lifespan of around 12-16 years. They exhibit aging patterns similar to humans, including changes in the immune system, body mass, and cognitive abilities, which is valuable in studying aging processes.
• Social and Parenting Behaviours: Cooperative parenting and close social bonds within groups mirror certain aspects of human social structures.

Conservation Status

The common marmoset is currently listed as "Least Concern" by the IUCN, though habitat loss and pet trade are concerns. They adapt well to different environments, which has helped their survival, but their populations are still vulnerable to ecological changes.

In summary, while common marmosets diverged from humans over 40 million years ago, their unique traits and social behaviours make them a valuable species for understanding certain aspects of human biology and psychology, providing insight into genetic, neurological, and social characteristics that bridge the gap between humans and other primates.

Now, as though to drive another nail into the coffin of that primitive superstition, scientists have just shown how the brains of humans and the common marmoset monkey follow parallel development, demonstrating their common origins.

Common marmosets and humans have similar prolonged periods of childhood where child care is shared amongst several adults, so the children experience intense socialisation as they develop juts as human children do, and because their brains are fundamentally the same as human brains, the same areas develop in the same way and at the same stage in their development:

Similarities in Brain Development Between Marmosets and Humans

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In common marmosets, the brain regions that process social interactions develop very slowly, extending until early adulthood, like in humans. During this time, all group members are involved in raising the infants, which contributes to the species’ strong socio-cognitive skills.

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The development of primate brains is shaped by various inputs. However, these inputs differ between independent breeders, such as great apes, and cooperative breeders, such as the common marmoset (Callithrix jacchus) and humans. In these species, group members other than the parents contribute substantially to raising the infants from birth onwards.

A group of international researchers led by Paola Cerrito from the University of Zurich’s Department of Evolutionary Anthropology studied how such social interactions map onto brain development in common marmosets. The study provides new insights into the relationship between the timing of brain development and the socio-cognitive skills of marmosets, in particular their prosocial and cooperative behaviours.

Prolonged learning from social interactions

The research team analysed brain development using magnetic resonance data and showed that in marmosets, the brain regions involved in the processing of social interactions exhibit protracted development – in a similar way to humans. These brain regions only reach maturity in early adulthood, allowing the animals to learn from social interactions for longer.

Like humans, immature marmosets are surrounded and cared for by multiple caregivers from birth and are therefore exposed to intense social interaction. Feeding is also a cooperative business: the immature animals are fed by group members and as they get older they have to beg for food because their mothers are already busy with the next offspring. According to the study, the need to elicit care from several group members significantly shapes brain development and contributes to the sophisticated socio-cognitive motivation (and observed skills) of these primates.

A model for human evolution

Given their similarities with humans, marmosets are an important model for studying the evolution of social cognition.

Our findings underscore the importance of social experiences to the formation of neural and cognitive networks, not only in primates, but also in humans. This insight could have an impact on various fields, ranging from evolutionary biology to neuroscience and psychology.

Paola Cerrito, first author
Department of Evolutionary Anthropology
University of Zurich, Zürich, Switzerland.

The early-life social inputs that characterize infants’ life in cooperatively breeding species may be a driving force in the development of humans marked social motivation.

Publication:

Paola Cerrito, Eduardo Gascon, Angela C. Roberts, Stephen J. Sawiak, Judith M. Burkart.
Neurodevelopmental timing and socio-cognitive development in a prosocial cooperatively breeding primate (Callithrix jacchus). Science Advances, 30 October 2024. DOI: 10.1126/sciadv.ado3486

Abstract
Primate brain development is shaped by inputs received during critical periods. These inputs differ between independent and cooperative breeders: In cooperative breeders, infants interact with multiple caregivers. We study how the neurodevelopmental timing of the cooperatively breeding common marmoset maps onto behavioral milestones. To obtain structure-function co-constructions, we combine behavioral, neuroimaging (anatomical and functional), and neural tracing experiments. We find that brain areas critically involved in observing conspecifics interacting (i) develop in clusters, (ii) have prolonged developmental trajectories, (iii) differentiate during the period of negotiations between immatures and multiple caregivers, and (iv) do not share stronger connectivity than with other regions. Overall, developmental timing of social brain areas correlates with social and behavioral milestones in marmosets and, as in humans, extends into adulthood. This rich social input is likely critical for the emergence of their strong socio-cognitive skills. Because humans are cooperative breeders too, these findings have strong implications for the evolution of human social cognition.

INTRODUCTION
Strong social cognition and prosociality are, from a very young age, hallmarks of the human mind compared to the closest living relatives, the nonhuman great apes (1). Because of our peculiar life history, characterized by early weaning and extensive allomaternal care starting from very early in infancy, human development is embedded in a world filled with other individuals, including parents, siblings, and other family members. Thus, this is the context in which human toddlers’ strong social cognition and prosociality develops (2). It is this same period that is also the most important for the formation of the neural bases of higher-order social, emotional, and communicative functions (3). Not unexpectedly then, several independent lines of evidence, spanning neuroscience, pediatrics, primatology, and psychiatry, point to the fundamental role that the relative timing of brain development and social interactions have for the acquisition of social cognition and prosocial behaviors (4).

During ontogeny, total brain volume increases until reaching its adult levels. This volumetric increase is the product of gray matter (GM) volume (GMV) increase until a peak value is reached in childhood, after which it decreases concurrently with synaptic pruning and white matter volumetric increase (5). In addition, the ontogenetic trajectories of cerebral GM are heterochronous, such that both maximum GMV and GM reduction rate vary across brain regions. The importance of the temporal patterns of brain development in shaping the adult phenotype becomes apparent, for example, in the case of autism spectrum disorder (ASD). Deviations from the normal range of developmental timing of the cortex can profoundly affect socio-cognitive skills and are one of the main factors linked to the occurrence of ASD (3). Specifically, several studies have found that early brain overgrowth during the first years of life strongly correlates with ASD [e.g. (6)] and a meta-analysis of all published magnetic resonance imaging (MRI) data by 2005 revealed that the period of greatest brain enlargement in autism is during early childhood (7), with about a 10% volume increase compared to controls during the first year of life. Hence, individuals affected by ASD present an accelerated early-life brain growth and achieve a final brain volume that is not different from that of controls, but they achieve it earlier than controls. Recent works with human brain organoids has confirmed the accelerated maturation of the cortex in the ASD phenotype, especially interneurons (8, 9). Consequently, given this accelerated early-life brain development, fewer social inputs are available during the period when the GMV reduces to adult size and differentiates via experience-dependent pruning. Accelerated development of functional connectivity between certain brain areas [e.g., amygdala–prefrontal cortex (PFC)] can also be a consequence of early-life stress, which, in turn, can cause adverse physiological conditions such as increased anxiety and cortisol levels (10). Unfortunately, so far, nothing is known regarding the impact of changes in brain developmental timing within nonhuman species. That is, we do not know if, within a given nonhuman species, alterations in ontogenetic trajectories of the brain have an impact on the adult behavioral phenotype. However, comparative studies across species with different ontogenetic trajectories and social behaviors can help us shed light on the relationship between the two.

The importance of social inputs occurring during prolonged brain maturation and slow developmental pace has also been highlighted in the context of human evolutionary studies. The remarkable brain growth and development occurring postnatally in humans arguably allows the brain to be influenced by the social environment outside of the uterus to a greater extent than that seen in other great apes (11), who are not cooperative breeders (12). Hawkes and Finlay (13) show that, in addition to weaning our infants earlier than expected (based on allometric scaling with other life-history variables), human neonates have an especially delayed neural development, which is likely correlated with the energetic trade-offs stemming from the large size and high caloric demand of our brain (14). In addition, we observe that, in humans, compared to other great apes, myelination is much prolonged and continues well into adulthood (15).

Common marmosets (Callithrix jacchus) are cooperatively breeding platyrrhine monkeys. Like humans, but unlike other great apes (12), they rely on extensive allomaternal care and share many life-history traits (e.g., short interbirth intervals and a hiatus between menarche and first reproduction) with humans (16). They also show remarkable prosociality (4, 15) [much more than great apes (16)] and strong socio-cognitive abilities, which have been argued to correlate with cooperative breeding (17–20). However, the neurobiological features underlying the socio-cognitive abilities promoting the prosocial behavior are poorly understood. Moreover, experimental research has shown that, in common marmosets (hereafter marmosets), there is a critical period for the development of social behaviors (21), although the relationship between developmental timing of the brain and these early-life social interactions is poorly understood.

Given these similarities with humans, marmosets are becoming an ever-more important model in neuroscience (22–25) and particularly in research investigating the neurobiological and neurodevelopmental bases of social cognition. As in humans, immature marmosets are surrounded and cared for by multiple caregivers from the first day on. The entire family is typically present during birth, and oxytocin levels increase not only in mothers but also in all group members (26). Group members contribute appreciably to carrying the infants and, once infants start eating solid food, frequently share food with them. After a peak provisioning period, adults are increasingly less willing to share food with them (27–29). During this period, intense and noisy negotiations over food are frequent, with immatures babbling and begging and adults eventually giving in—or not. Intriguingly, when doing so, immatures appear to take into account how willing individual adults are to share and will insist in more and longer attempts with adults who are generally less likely to refuse them. Soon after, immatures have to compete for attention and food not only with their twin sibling but also with the next offspring that are born far before they themselves are independent because, like in humans, marmosets are weaned early and mothers have their next offspring soon after (30). By now, the immatures still have not reached puberty; this only happens shortly before yet another set of younger siblings is born. Typically, with these new arrivals, the immatures start to act as helpers themselves and thus face the developmental task of switching from being a recipient of help to becoming a provider of help and prosocial acts (31). This is thus the developmental context in which marmosets’ socio-cognitive skills develop.

The goal of this study is to map these behavioral milestones specific to a cooperatively breeding primate to its region-specific brain development to better understand the social interactions in which infants engage during the differentiation period of brain regions selectively implicated in processing social stimuli. Our working hypothesis is that, like in humans, social interactions with several caregivers during this critical period profoundly contribute to the co-construction of the marmoset brain, the maturation of socially related associative areas, and therefore the emergence of prosocial behaviors. For that purpose, we sought to determine if there is a relationship between the temporal profile of the developing marmoset brain and the early-life social interactions that may help explain their sophisticated socio-cognitive skills at adulthood.

To compare the timing of brain development to that of these behavioral milestones and developmental tasks of attaining nutritional independence, we focused on brain regions that, in adult marmosets, are selectively activated by the observation of social interactions between conspecifics but not by multiple but independently behaving marmosets, as identified by Cléry et al. (32). We tested if these brain regions share similar developmental trajectories based on the developmental patterns of regional GMV. To potentially reveal a coordinated ontogenetic profile underlying the “tuning” of the social brain in marmosets, we then compared these neurodevelopmental patterns to longitudinal data of infant negotiations with caregivers in relation to food (as measured by the frequency of food begging). Last, because it is known that brain regions whose activations correlate with performance on a given task strengthen and get fine-tuned with age (33, 34), we assessed if there is stronger connectedness between areas that develop according to similar developmental trajectories and share similar response to social interaction stimuli.

We thus combined several types of previously published data from marmosets to provide a unified picture of structural brain development alongside the development of social interactions between infants and multiple caregivers necessary to ensure survival (infant provisioning). These included structural MRI (sMRI) data of GM of 53 cortical areas and 16 subcortical nuclei acquired from a developmental cohort (aged 13 to 104 weeks) of 41 male and female marmosets (35), functional MRI (fMRI) data mapping the brain areas activated by the observation of social interactions in marmosets (32), food sharing interactions in five family groups of marmosets including a total of 26 adults and 14 immatures [from 1 to 60 weeks of age (27)], and cellular-resolution data of corticocortical connectivity in marmosets obtained via 143 retrograde tracer injections in 52 young adult marmosets of both sexes (36).

Overall, we make the following predictions:

1. P1: Cortical regions that show significantly stronger activation during the observation of social interactions (32) share similar structural neurodevelopmental profiles, which are distinct from those regions showing significantly stronger activation during the observation of nonsocial activities.
2. P2: That those same brain regions showing a significantly stronger activation during the observation of social interactions exhibit a protracted development, reaching their adult volume later than the other regions.
3. P3: The developmental trajectory of infant negotiations with caregivers in relation to food (as measured by the frequency of food begging) is more similar to that of brain regions responding more strongly to the observation of social interactions than to the other regions.
4. P4: Functional connectivity is stronger between regions with similar developmental timing and response strength to the observation of either social or nonsocial behaviors and weaker between regions with different developmental timing and response strength.

If the brains of humans an marmosets are fundamentally similar and develop the same way, perhaps a creationist could explain in what way, apart from their tail and their claws in place of human flat finger nails, marmosets are a different 'kind' to humans, and then explain why the same reasoning doesn't place the great apes in the same 'kind' as humans.

Creationism Refuted - How We Inherrited Part Of Our Anti-Viral Immune Response From A Microbial Ancestor

Credit: Pedro Leão.

A comparison of immune proteins called viperins from Asgard archaea (left) and from a group of more complex life that includes humans, called eukaryotes (right). The three-dimensional shapes (a.k.a. structures) are strikingly similar, suggesting they also function similarly.

Credit: Pedro Leão.

Next Time You Beat a Virus, Thank Your Microbial Ancestors | College of Natural Sciences

Multicellular organisms are collections of specialised eukaryote cells, which are themselves collections of prokaryote cells that have been around for several billion years before getting together to form more complex cells.

And those prokaryote cells - bacteria and archaea - had had to cope with viruses which arose as soon as there were replicating assemblages of DNA for them to parasitize and co-opt the replication mechanism to make more copies of themselves.

The result was one of the first evolutionary arms races as the prokaryotes evolved ways to prevent themselves being parasitised and viruses evolved ways to overcome the microbes defences.

And, or course, the later eukaryote, complex cells that were to form the multicellular organisms inherited these antiviral defences and carried on the arms race with viruses, so it makes sense to find some of the remnants of these microbial defences, probably modified, inside our own cells, and forming a first line of defences.

This is a simple prediction of the Theory of Evolution and the resulting descent with modification from a common ancestor from billions of years ago.

What information do you have on the anti-viral proteins, Asgard Viperin and Eukaryote Viperin? Asgard Viperin and Eukaryote Viperin are both antiviral proteins that play crucial roles in the innate immune response, particularly in targeting and neutralizing viral infections. They belong to a broader family of proteins called Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible). Viperin is a well-known antiviral protein that is highly conserved across various species, including archaea, bacteria, and eukaryotes. Here's a breakdown of what is known about Asgard Viperin and Eukaryote Viperin:

1. Asgard Viperin
   • Origin: Asgard Viperin is derived from the Asgard archaea, a group of microorganisms that are thought to be closely related to the last common ancestor of archaea and eukaryotes. These archaea were discovered in deep-sea hydrothermal vent environments and are considered important in studying the evolution of complex life forms.
   • Function: Asgard Viperin has been identified as an antiviral protein that provides insights into the ancient mechanisms of immune defense. Its function is similar to that of Viperin in eukaryotes, where it inhibits viral replication by targeting viral components or the cellular machinery viruses depend on for replication.
   • Structure and Mechanism: Like other Viperins, Asgard Viperin is likely to have a radical SAM (S-adenosylmethionine) domain, which is critical for its antiviral activity. This domain allows the protein to produce a reactive radical species, which can interfere with viral processes, such as the synthesis of nucleotides that viruses require for replication.
   • Evolutionary Significance: The discovery of Asgard Viperin highlights the ancient origins of antiviral defense mechanisms. It suggests that the strategies used by modern eukaryotic cells to combat viruses may have deep evolutionary roots.
2. Eukaryote Viperin
   • Origin: Eukaryote Viperin is found in eukaryotic organisms, including humans. It is one of the interferon-stimulated genes (ISGs) that are upregulated in response to viral infection. This protein is highly conserved across various species, from simple eukaryotes like algae to complex organisms like mammals.
   • Function: In eukaryotes, Viperin is a key player in the innate immune response. It exerts its antiviral effects through multiple mechanisms, depending on the type of virus. For example:
     • Inhibition of Viral Replication: Viperin can interfere with the replication of viruses by altering lipid metabolism or disrupting the assembly of viral particles.
     • Interaction with Cellular Machinery: It can inhibit viral RNA polymerase, thereby preventing the replication of RNA viruses.
     • Modulation of Immune Response: Viperin can enhance the production of other antiviral molecules and modulate the signaling pathways involved in the immune response.
   • Mechanism of Action: The radical SAM domain is crucial for the antiviral activity of Viperin in eukaryotes. This domain facilitates the formation of a radical species that can interfere with the function of viral proteins or the host cell machinery that viruses exploit.
   • Clinical Relevance: Understanding the role of Viperin in the immune response has significant implications for developing antiviral therapies. Since Viperin is involved in the response to a wide range of viruses, enhancing its activity could be a potential strategy for treating viral infections.

Comparative Insights

• The study of Asgard and Eukaryote Viperin provides valuable insights into the evolution of antiviral defense mechanisms. The presence of similar antiviral proteins in both archaea and eukaryotes suggests that these defense strategies are ancient and have been conserved throughout evolution.
• While both Asgard and Eukaryote Viperin share functional similarities, their specific roles and mechanisms may differ due to the differences in their cellular environments and the types of viruses they encounter.

Research Significance

• The discovery and study of Asgard Viperin contribute to our understanding of the origin of eukaryotic cells and their immune systems. It also opens up new avenues for research into the evolution of antiviral defenses and the development of new antiviral strategies based on ancient mechanisms.

Understanding these proteins, particularly in the context of their evolutionary history and their function in modern organisms, is crucial for advancing our knowledge of immune responses and the development of antiviral therapies.

And this is precisely what researchers in the College of Natural Science at The University of Texas at Austin have found. They have shown that the proteins Asgard Viperin from the Asgard archaea and the Eukaryote viperin, possessed by eukaryotes including humans are structurally (and functionally) very similar.

Next Time You Beat a Virus, Thank Your Microbial Ancestors

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Two of our key defenses against viruses have persisted for billions of years, arising before complex life.

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When you get infected with a virus, some of the first weapons your body deploys to fight it were passed down to us from our microbial ancestors billions of years ago. According to new research from The University of Texas at Austin, two key elements of our innate immune system came from a group of microbes called Asgard archaea.

Specifically, viperins and argonautes, two proteins that are known to play important roles in the immune systems of all complex life — from insects to plants to humans — came from the Asgard archaea. Versions of these defense proteins are also present in bacteria, but the versions in complex life forms are most closely related to those in Asgard archaea, according to the new scientific study published in the journal Nature Communications.

This research bolsters the idea that all complex life, called eukaryotes, arose from a symbiotic relationship between bacteria and Asgard archaea.

It adds more support to the fact that the Asgards are our microbial ancestors. It says that not only did eukaryotes get all these rich structural proteins that we’ve seen before in Asgards, now it’s saying that even some of the defense systems in eukaryotes came from Asgards.

Associate Professor Brett J. Baker, senior author
Associate professor of integrative biology and marine science
Department of Integrative Biology
University of Texas at Austin, Austin, TX, USA.

The researchers identified for the first time a large arsenal of defense systems in archaea that were previously known only in bacteria.

When viperins detect foreign DNA, which might indicate a dangerous virus, they edit the DNA so that the cell can no longer make copies of the DNA, which stops the virus from spreading. When argonautes detect foreign DNA, they chop it up, also halting the virus. Additionally, in more complex organisms, argonautes can block the virus from making proteins in a process called RNA silencing.

Viral infections are one of the evolutionary pressures that we have had since life began, and it is critical to always have some sort of defense. When bacteria and archaea discovered tools that worked, they were passed down and are still part of our first line of defense.

Assistant Professor Pedro Leão, lead author
Department of Microbiology - RIBES
Radboud University, Nijmegen, The Netherlands.

The researchers compared proteins involved in immunity across the tree of life and found many closely related ones. Then they used an AI tool called ColabFold to predict whether ones that had similar amino acid sequences also had similar three-dimensional shapes (aka structures). (It’s the shape of a protein that determines how it functions.) This showed that variations of the viperin protein probably maintained the same structure and function across the tree of life. They then created a kind of family tree, or phylogeny, of these sister amino acid sequences and structures that showed evolutionary relationships.

A family tree of immune proteins called viperins from different organisms. Versions of viperin found in complex life forms, called eukaryotes (green), fit within the group of viperins from Asgard archaea (purple).

Credit: University of Texas at Austin.

Finally, the researchers took viperins from Asgard archaea genomes, cloned them into bacteria (so the bacteria would express the proteins), challenged the bacteria with viruses, and showed that Asgard viperins do in fact provide some protection to the modified bacteria. They survived better than bacteria without the immune proteins.

This research highlights the integral role cellular defenses must have played from the beginning of both prokaryotic and eukaryotic life. It also inspires questions about how our modern understanding of eukaryotic immunity can benefit from unraveling some of its most ancient origins.

Emily Aguilar-Pine, co-author Department of Integrative Biology
University of Texas at Austin, Austin, TX, USA.

It’s undeniable at this point that Asgard archaea contributed a lot to the complexity that we see in eukaryotes today, so why wouldn’t they also be involved in the origin of the immune system? We have strong evidence now that this is true.

Assistant Professor Pedro Leão

Other authors, all from UT, are Mary Little, Kathryn Appler, Daphne Sahaya, Kathryn Currie, Ilya Finkelstein and Valerie De Anda.

This work was supported by the Simons and Moore foundations (via the Moore-Simons Project on the Origin of the Eukaryotic Cell) and The Welch Foundation.

Abstract
Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.

Introduction
Organisms across the tree of life contain complex defense systems (DS) to battle viral infections^1,2,3. Over the past decade, dozens of new DS have been identified and characterized in bacteria, sparking a debate about a potential link between these systems and the origins of innate immune mechanisms in eukaryotes. More recently, protein components of bacterial NLR (Nucleotide-binding domain leucine-rich repeat), CBASS (Cyclic oligonucleotide-based antiphage signaling system), viperins (virus-inhibitory protein, endoplasmic reticulum-associated, interferon (IFN)-inducible), argonautes, and other DS have been shown to exhibit homology with proteins involved in the eukaryotic immune system⁴. Most of the research on prokaryotic defense systems has focused on bacteria, with archaea representing <3% of the genomes in these studies^5,6,7. Thus, very little is known about the diversity or evolution of these systems in archaea.

Recently, diverse novel genomes have been obtained belonging to the archaea most closely related to eukaryotes, commonly referred to as “Asgard” archaea, the phylum Asgardarchaeota⁸. In addition to being sister lineages to eukaryotes, these archaea also contain an array of genes that are hallmarks of complex cellular life involved in signal processing, transcription, and translocations, among other processes⁹. The Asgard archaea are descendants of the ancestral host that gave rise to eukaryotic life. One newly described order, the Hodarchaeales (within the Heimdallarchaeia class), shared a common ancestor with eukaryotes⁸. Here, we characterize defense systems in archaea and show that Asgard archaea have a broad array of these DS. We also show that Asgards contributed to the origins of innate immune mechanisms in eukaryotes.

Fig. 2: Evolutionary history and anti-phage activity of Asgard viperins.

A Phylogenetic analysis of viperins. Viperins phylogeny revealed ancestral links of eVip (eukaryotic viperin) with asVip (asgard viperin) (nodes marked in red), particularly those within the Heimdallarchaeia class (including Kariarchaeaceae (2), Heimdallarchaeaceae (3) and Hodarchaeales (5)). The size of the dots on the nodes is proportional to bootstrap values ranging between 60 and 100. B Structure-based homology of viperins. Consistent with the sequence homology-based phylogenetic tree, the eVip structure appears to have been inherited from asVip (red node). The darker green color represents reference sequences predicted experimentally. The size of the dots at the center of the nodes is proportional to bootstrap values ranging between 50 and 100. C Superposition of an eVip structure, predicted by X-ray diffraction (green), and the structural models of an asVip, archaeal viperin (arVip), and bacterial viperin (from left to right). The yellow color in the models emphasizes the high conservation of the viperin catalytic site across the tree of life. The information regarding bacteria, archaea, asgard archaea and eukaryotes in panels (A–C) are represented by the pink, blue, purple and green color respectively. D Anti-T7 phage activity of asVip in E. coli. Nine asVip (asVip 26,11,20,25,16,12,17,23,8) exhibited anti-viral activity as indicated by the p-values (*p < 0.05; **p < 0.01). E Anti-T7 phage activity of asVip after codon optimization for their expression in E. coli. One asVip from a Hodarchaeales organism provided protection against viral infection (asVip 19). The center line of each box plot denotes the median; the box contains the 25^th to 75^th percentiles. Black whiskers mark the 5th and 95^th percentiles. pVip34 is a prokaryotic viperin selected as a positive control from Bernheim et al.¹³. Each experimental condition includes, on average, 53 plaques pooled from three biological replicates. A two-tailed t-test was used to calculate statistical significance in figures (E, D).

Fig. 3: Evolutionary history of Asgard argonaute proteins.

A Phylogeny of long type argonaute proteins from archaea, bacteria, and eukaryotes with cyclases as outgroup (grey). B Structure-based homology of argonautes. C Structural alignment of asAgo5 and 4OLA (eAgo) MID and PIWI domains (left), and the graphic model of the corresponding alignments (right). Salmon regions on the alignment highlight strong conservation (low RMDS values). Red amino acids in the structural alignment, and their respective models represent the 4OLA conserved functional residues in MID and PIWI. The information regarding bacteria, archaea, asgard archaea and eukaryotes are represented by the pink, blue, purple and green color respectively. The size of the dots on the nodes is proportional to bootstrap values ranging between 70 and 100.

Leão, P., Little, M.E., Appler, K.E. et al.
Asgard archaea defense systems and their roles in the origin of eukaryotic immunity.
Nat Commun 15, 6386 (2024). https://doi.org/10.1038/s41467-024-50195-2

Copyright: © 2024 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

A highly-conserved antiviral protein across all eukaryote cells speaks loudly of common ancestry. The fact that a very similar protein is found in an "Asgard" archaea is strongly supportive of the theory that the fist eukaryote cells were alliances of bacteria and archaea and that the "Asgard" archaea contributed antiviral protection on this early eukaryote, showing common ancestry extending back beyond the first eukaryotes.

Of course, the less intelligent creationists will now be chanting 'Common Ancestry', but the more intelligent cultists would realise that that would mean the first eukaryote cells arose after Adam and Eve, because these antiviral proteins wouldn't have been needed until after 'Sin' had allowed viruses to 'devolve' by 'genetic entropy' (© Michael J. Behe), unless they don't understand how having an arms race with oneself is not the sign of an intelligent designer.