Creationism Refuted - How Humans Acquired Their Pathogens From Their Animals - No Magic 'Sin' Involved

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We’ve long suspected that the transition to farming and animal husbandry opened the door to a new era of disease – now DNA shows us that it happened at least 6,500 years ago,” says Professor Eske Willerslev, author of the new study.

Illustration: William Brøns Petersen

Large-scale DNA study maps 37,000 years of disease history – University of Copenhagen

Young Earth creationist mythology has it that sin, shortly after the magical creation of two adult humans, caused death and disease to enter the world. Until then, so we are expected to believe, there had been no disease and nothing ever died — not even, apparently, the plants Adam, Eve and the other animals ate.

Reality, of course, is materially different from the mythology produced by scientifically ignorant ancient pastoralists and later scribes who knew nothing of bacteria, viruses, parasites, epidemiology or evolution, and who interpreted misfortune in magical terms. Disease was not a supernatural punishment introduced at a single moment by a talking snake, a disobedient couple and an irritable god. It was, and remains, a biological process involving organisms evolving, spreading, adapting and, sometimes, crossing from one host species into another.

And the evidence now shows that at least 6,500 years ago, diseases were passing from animals into the humans who lived alongside them. The domestication of animals, the growth of settled farming communities and the rise of pastoralism brought humans, livestock, waste, parasites and pathogens into much closer proximity than before. This has long been thought to explain why humans suffer from so many infectious diseases. It is also a point Jared Diamond made in Guns, Germs and Steel: The Fate of Human Societies, where he argued that Eurasia’s abundance of domesticable animals, and Europeans’ long exposure to the diseases associated with them, helped Europeans to dominate other populations, often with their pathogens acting as an advance guard against peoples with no previous exposure or immunity.

That view of the zoonotic origin of many human diseases has now been strongly supported by the work of researchers led by Professor Eske Willerslev, of the University of Copenhagen and the University of Cambridge, in a study published open access in Nature in July 2025. The team analysed DNA from more than 1,300 prehistoric individuals, some up to 37,000 years old. Their bones and teeth provided an extraordinary archive of ancient microbial DNA, revealing traces of bacteria, viruses and parasites that infected humans across deep Eurasian history.

The results suggest that close cohabitation with domesticated animals, together with large-scale migrations of pastoralists from the Pontic Steppe, played a major role in the spread of zoonotic diseases. The researchers found that identifiable zoonotic pathogens first appear in their data from around 6,500 years ago, became more widespread after about 6,000 years ago, and peaked roughly 5,000 years ago — precisely the sort of pattern expected if lifestyle, animal husbandry, mobility and population contact were driving disease transmission.

This is especially awkward for creationists because the evidence does not point to a sudden, supernatural transformation of the world’s biology. It does not show disease appearing overnight as the result of a mythical “Fall”. Instead, it shows a long, historical and evolutionary process, unfolding through early Eurasian human history as changing human behaviour created new ecological opportunities for pathogens.

Malevolent Design - The Complex Mechanism That Helps Bacteria Make Us Sick

Clockwise: A bacterium retracts its pili, reeling in a piece of DNA in the environment. This action facilitates “natural transformation,” a process by which bacterium acquire new genetic traits, including antibiotic resistance.

Image courtesy the Dalia Lab, Indiana University

IU biologists uncover a molecular mechanism that helps bacteria spread antibiotic resistance genes: College of Arts + Sciences : Indiana University

Creationists have a problem of their own making. The same evolutionary processes they try to rebrand as evidence for a creator god are also the processes that produce parasites, pathogens and the molecular machinery by which they exploit their hosts. If Michael J. Behe wants to claim “irreducible complexity” as evidence of design, and William A. Dembski wants to claim “complex specified information” as the signature of an intelligent designer, then they cannot confine those arguments to the parts of biology they find theologically convenient. The same kinds of complexity and genetic information are also found in organisms that make us sick and increase the suffering in the world.

Although professional creationists, including fellows of the Discovery Institute such as Behe and Dembski, are careful to avoid naming their putative designer, their audience invariably identifies it with the supposedly omnibenevolent god of the Bible, Torah and Qur’an. But that creates an obvious problem: using their own criteria, this creator god must be credited not only with designing humans and other animals, but also with designing the bacteria, viruses, parasites and molecular mechanisms that infect, disable and kill them.

The significance of this is often lost on creationists because it requires a basic understanding of biology and a willingness to follow an argument to its logical conclusion. When they cite Behe’s favourite examples, such as the E. coli flagellum or anti-malarial drug resistance in Plasmodium falciparum, as evidence for their god, they are in effect crediting that god with designing mechanisms that help microbes move, invade, survive and evade our attempts to stop them. Point this out, however, and the same evidence that was allegedly scientific evidence for intelligent design is suddenly reinterpreted as evidence for “The Fall” and “Original Sin”. The pretence that creationism is science is abandoned in a hasty retreat into fundamentalist theology, where the same facts are repurposed to reach a more comfortable conclusion.

In addition to the two examples I recently discussed here and here, another example has now been reported — and this one involves a powerful molecular motor that should, by creationist standards, look very much like the sort of thing they would normally call “designed”. It is the type IV pilus retraction system, recently reported in Proceedings of the National Academy of Sciences of the USA (PNAS), which many bacteria use to retract tiny hair-like surface structures called pili. These pili act like microscopic grappling hooks, helping bacteria attach to surfaces and tissues, form antibiotic-resistant biofilms, and pull in fragments of DNA from their surroundings, including genes for drug resistance acquired from other bacteria.

Malevolent Design - How SARS-CoV-2 Was Cleverly Designed to Jump From Bats To Humans - Evolution Or Malevolence

A Single Molecular Change May Help Viruses Jump from Bat to Human | UC San Francisco

Two recent papers should delight admirers of creationism's putative intelligent designer, because both show the sort of biochemical ingenuity they normally rush to claim as evidence of design. One, published in Cell Host & Microbe in May 2026 and reported by UCSF in June, shows how a single molecular change can alter the way a coronavirus interacts with bat and human immune systems, helping to explain how viruses related to SARS-CoV-2, the virus that caused the COVID-19 pandemic, can cross the species barrier. The other, published in October 2025 in Nature Communications, which will be the subject of my next blog post, shows how influenza A virus can exploit the remnants of dying cells to help spread infection to neighbouring healthy cells.

However, that excitement is likely to be tempered somewhat when it dawns on them that, if these systems are the products of intelligent design, their designer can only be regarded as malevolent, since the result is an increase in the sum total of suffering in the world. But this does not seem to trouble ID proponents who cite Michael J. Behe's favourite examples — the Escherichia coli flagellum and anti-malarial drug resistance in Plasmodium falciparum — as evidence of irreducible complexity and hence of intelligent design, while ignoring the awkward fact that these supposed examples of design help microorganisms survive, move, infect, or evade human attempts to control them.

This puts creationists in a familiar bind. On the one hand, they like to claim any useful biological complexity as evidence of their Biblical god. On the other, when the same logic points to a designer of pathogens, parasites, immune evasion, drug resistance and viral spread, they retreat into vague claims about 'Sin', 'The Fall', or some mysterious corruption of nature, thereby absolving their god of responsibility for the very mechanisms they were praising as designed only moments earlier.

The first paper, in Cell Host & Microbe, was by a large team of researchers from the University of California San Francisco (UCSF) Quantitative Biosciences Institute, the Icahn School of Medicine at Mount Sinai, the Institut Pasteur and the Fred Hutchinson Cancer Center. It showed that a single amino-acid change in a viral protein can alter how coronaviruses interact with bat and human immune systems, changing the host's response to infection.

Bats are important viral reservoirs because their immune systems and physiology can allow them to tolerate viruses that might cause serious disease in other mammals. They can therefore harbour viruses for long periods, providing opportunities for viral lineages to persist, diversify and acquire mutations that may matter greatly when those viruses encounter a new host species. The UCSF-led study helps to explain how relatively small genetic differences can make the difference between a virus that remains associated with a bat reservoir and one that is better able to evade human immune defences.

This is precisely the sort of thing creationists should, by their own logic, have to call 'complex specified information'. The change is functional; it affects a specific biological outcome; and it is beneficial from the point of view of the viral lineage. The problem, of course, is that creationists usually smuggle in the assumption that 'beneficial' must mean beneficial to humans. If it benefits a virus, a bacterium, a parasite or a cancer cell, they suddenly decide it does not count.

Comparing SARS-CoV-2 with a related bat coronavirus, RaTG13, the researchers found that a viral protein called ORF9b was a key factor. The SARS-CoV-2 and RaTG13 versions of ORF9b are very similar, but behave very differently. In human cells, the SARS-CoV-2 version helped disable an innate immune alarm system, allowing the virus to multiply more effectively. In bat cells, the RaTG13 version interacted with a restriction factor that helped suppress infection.

The team found that changing just one of ORF9b's roughly 100 amino acids reversed its ability to evade the immune response. In creationist thinking, if the phrase is to mean anything at all, this would be new functional genetic information. Yet the actual explanation requires no magic, no designer and no supernatural intervention: a mutation changed an amino acid; that change altered protein interactions; and the result affected viral fitness in different host-cell environments. In other words, ordinary chemistry and physics, operating through mutation, selection and host-virus interaction, produced exactly the kind of functional change creationists insist cannot happen naturally.

The paper in Cell Host & Microbe was accompanied by a news item from UCSF by Levi Gadye:

Refuting Creationism - Two Ancient Eurasians Carried Human Papillomavirus (HPV16) - Long Before 'Creation Week' and 'The Fall'

A facial reconstruction of Ötzi the Iceman.

Image credit: Reconstruction by Kennis © South Tyrol Museum of Archaeology, Foto Ochsenreiter

Ötzi the Iceman mummy carried a high-risk strain of HPV, research finds | Live Science

Palaeontologists at the Federal University of São Paulo, Brazil have analysed the DNA recovered from two ancient humans and discovered that they were both carriers of the Human Papillomavirus HPV16, a virus implicated in several cancers. They have presented their evidence, ahead of peer-reviewed publication in the pre-print server, bioRxiv.

The interesting thing from the point of view of virology is that this discovery shed considerable light on when HPV entered the human virome and commenced co-evolving with us, with one theory being that we acquired them from Neanderthals. From the point of view of creationists however, the news could scarcely be worse.

The first sample, obtained from the famous 'Ötzi the Iceman', the 5,300 year-old mummified body recovered from a glacier on the Italian-Austrian border, is probably not too much of a problem for creationists as it just about falls within the timeline of the Bible mythology, apart from the little problem of it being from before they believe the was a general reset of Earth's biosphere in a genocidal flood which would have destroyed the glacier and everything in it, so Ötzi should not have been there.

But, the second is a massive problem, since it was recovered from a leg of a man, Ust'-Ishim man, recovered from western Siberia and dated to 45,000 years BP - way before creationists believe Earth existed, and tens of thousands of years before the mythical 'Fall', when creationists believe viruses didn't exist. This specimen provided the oldest complete human genome so far recovered and the DNA contains the unmistakable genome of HPV16. Creationist mythology just keeps getting further and further from reality as exposed by science using real-world evidence.

Traditionally, creationists claim Earth is 6,000 - 10,000 years old and was created perfect in every way, with no deaths or diseases, so no viruses, parasites or pathogens, bodies that always functioned perfectly and genomes that never failed to replicate perfectly. Then, along came 'sin' which, by some mysterious process, was able to thwart the omnipotent creator god's perfect plan and create viruses and other pathogens and make perfect physiology begin to malfunction and genomes to fail to replicate perfectly, causing variations and genetic weaknesses, etc.

Why a reputedly omnipotent creator failed to anticipate the effects of 'sin' and make its creation robust enough to resist them is never explained, although, apparently, it provided immune systems in preparation for something that, although omniscient, and even claimed to have created 'evil' (Isiah 45:7), it then failed to anticipate. But, as though those myths aren't too ridiculous for any adult with even a basic education to believe, creationists have to continually think of ways to ignore the evidence and continue holding plainly absurd beliefs, under the child-like delusion that their ability to do so is a sign of strength.

The paper itself sets out to address a long-standing question in human virology: how long oncogenic human papillomaviruses have been associated with our species, and whether their origins lie in relatively recent cultural changes or deep evolutionary history.

Malevolent Designer News - How Candida Albicans (Thrush) Is Cleverly Designed to Infect Your Mouth - Evolution Or Malevolent Design?

The yeast fungus Candida albicans (blue) breaks out of human immune cells (red) by forming long thread-like cells called hyphae. The part of the hypha that has already left the immune cells is coloured yellow.

© Erik Böhm, Leibniz-HKI

The dose makes the difference - Leibniz-HKI

As has often been pointed out in these blog posts, the "evidence" offered by Discovery Institute fellows William A. Dembski and Michael J. Behe for an intelligent designer can, by the same logic and using the same evidence, be interpreted as pointing to a theologically awkward malevolent designer. This is a line of reasoning routinely ignored by the "Cdesign proponentcists", who prefer to overlook the many examples of parasites and pathogens—and the evolutionary traits that make them so successful at invading and surviving within their hosts.

A fresh example that creationists will either have to ignore or blame on "The Fall" comes from researchers at the Leibniz Institute for Natural Product Research and Infection Biology. They have shown that the fungus Candida albicans, which causes thrush, has evolved a highly sophisticated and "finely tuned" mechanism for infecting the human mouth while evading the immune system.

The stock creationist response is to shift responsibility onto the biblical myth of "The Fall," retreating into Bible literalism. Yet this is precisely the kind of literalism the Discovery Institute has been at pains to insist is not essential to the notion of intelligent design, which it markets as a scientific alternative to evolutionary theory—or "Darwinism," as they prefer to call it. This rhetorical sleight of hand was central to the Institute’s "Wedge Strategy," devised after the 1987 US Supreme Court ruling in Edwards v. Aguillard, which confirmed that teaching creationism in public schools violated the Establishment Clause of the First Amendment.

The new research reveals that C. albicans produces a toxin called candidalysin in carefully regulated doses that allow it to infiltrate the mucous lining of the mouth. Too little candidalysin, and the fungus would fail to establish itself; too much, and it would trigger an immune response strong enough to destroy it. Normally, C. albicans exists in a round, yeast-like form, but under the "right" conditions it can switch into the filamentous hyphal form typical of fungi. This transformation allows it to penetrate host tissues and, in immune-compromised patients, become life-threatening. It is in this invasive hyphal state that C. albicans produces candidalysin.

The production of hyphae, and therefore candidalysin, is controlled by the gene EED1. By any definition, EED1 would qualify as an example of "complex specified information" according to Dembski’s own formulation — evidence, according to the Discovery Institute, of supernatural intelligent design.

Malevolent Design - How The Poxvirus is 'Intelligently Designed' To Rapidly Multiply

A Survival Kit for Smallpox Viruses - Universität Würzburg

The tRNA ensures the cohesion of the polymerase and the associated factors; without it, they would not arrange themselves in this way.

Image: Clemens Grimm.

Researchers at Julius Maximilian University of Würzburg (JMU) have discovered that poxviruses have developed a unique strategy to multiply rapidly after infecting a host cell. They achieve this by assembling a large protein complex with the help of a transfer RNA (tRNA) molecule. Remarkably, this is the first known example of a ‘chaperone’ function being carried out by a tRNA rather than a protein. Each component of the assembly plays a specific role in the production of new poxviruses. Crucially, the complex only functions when all parts are correctly assembled, and the tRNA is indispensable for this construction.

In other words, the tRNA provides the essential element of the complex, which some might describe—using the Discovery Institute’s own terms—as containing “complex specified information” and forming an “irreducibly complex” system essential to the virus’s success.

By that same logic, it follows that the viruses responsible for smallpox and mpox (monkeypox) must have been intelligently designed. This leaves creationists with an unenviable dilemma:

• Accept the Discovery Institute’s definitions and admit their designer created deadly viruses — theologically awkward.
• Claim another intelligence designs life, beyond their god’s control — even more awkward.
• Abandon the Institute’s “evidence” for intelligent design — politically awkward.