Creationism In Crisis - Evolution In Progress As A Familiar Mediterranean Lizard Goes Green

Common wall lizard, Podarcis muralis.
The yellow and orange colour morphs disappeared over time.

Photo: Roberto García Roa

The "Hulk" lizard.

Photo: Roberto García Roa.

“Hulk lizard” knocks out ancient colour palette | Lund University

This lovely example of evolution in progress will no doubt have creationists demanding that science abandon its definition of evolution and adopt their childish “change of kind” parody instead — a caricature which, if it meant one basic type of organism suddenly turning into another, would falsify evolution rather than confirm it.

The example concerns the common wall lizard, Podarcis muralis, a species widespread in the Mediterranean region. For millions of years, populations of this lizard have included three genetically determined throat-colour morphs: white, yellow and orange. These colour forms are not merely superficial differences. They are associated with different strategies for gaining territories, attracting mates and competing with rivals, and their long-term coexistence has been a textbook example of evolutionary balance maintained by natural and social selection.

Now that balance has been disrupted by the spread of a new phenotype: a larger, bright green, aggressive and sexually dominant form, known to science as the green-and-black, white-throated nigriventris phenotype, nicknamed the “Hulk” by the researchers appears to have arisen near Rome several thousand years ago (a mere tick in evolutionary time) and is now spreading through Italy.

As this form spreads through the landscape, the yellow- and orange-throated morphs are disappearing, leaving the white-throated form behind. The change has been so rapid that, had it involved a marked alteration in a structure likely to fossilise, such as teeth or bones, it would appear in the fossil record of the future as a sudden change after a long period of stasis — in other words, exactly the kind of pattern described by punctuated equilibrium. It is, of course, classic evolution: allele frequencies in populations shifting as a newly successful phenotype spreads.

This evolutionary change in progress is the subject of a paper in Science by an international team of researchers led by Professor Tobias Uller of Lund University, Sweden. The team analysed colour data from about 240 populations of P. muralis, comprising more than 10,000 individuals. The results show that the newcomer has significantly altered the long-standing balance within the species, eliminating the yellow and orange morphs as the larger, more aggressive form spreads through the region.

Creationism Refuted - The Complex Origins of Modern Humans Revealed - No Magic Required

AI-generated image (ChatGPT 5.4 Thinking)

View of the village of Kuboes, on the border of South Africa and Namibia. DNA samples were collected from Nama individuals who have historically lived in the region.

Brenna Henn/UC Davis.

New UC Davis Research Using DNA Changes Origin of Human Species | College of Biological Sciences

Research first published in Nature in 2023 shows just how wide of the mark the Bronze Age authors of the Bible’s origin myths were when they guessed at human origins. Of course, in the absence of any knowledge or understanding of the true age of Earth, the history of life on it, or the existence of deep human ancestry, their guesses were no better than we would expect from people trying to explain the world with folklore rather than evidence.

In fact, as the evidence in the 2023 paper by a team co-led by Professor Brenna Henn of the University of California, Davis, and Simon Gravel of McGill University, Montreal, Quebec, Canada, shows, modern humans did not emerge from a single founding couple, or even from one simple, isolated ancestral population. Instead, our origins lie in a complex, dynamic network of human groups that diversified within Africa, evolved in partial isolation, and later exchanged genes as populations moved and merged.

In that respect, human evolution resembles other cases in nature where populations diverge, remain partly distinct, and yet continue to exchange genes — such as the carrion crow/hooded crow Corvus complex, the Eurasian complex of the great tit (Parus major) and its related forms, and the circumpolar herring gull/lesser black-backed gull Larus complex. These examples show evolution not as a neat ladder or a set of separately created “kinds”, but as a branching, reticulating process in which boundaries can be blurred by gene flow.

This process of diversification and later remixing continued in Eurasia, where Homo sapiens interbred with Neanderthals, Denisovans and, possibly, other human populations. Neanderthals eventually disappeared as a distinct population, or were partly absorbed into expanding Homo sapiens populations, around 40,000 years ago.

Far from the single ancestral couple that may have seemed intuitive to parochial Bronze Age pastoralists, modern humanity emerged from a population history that looks less like a single line of descent and more like a tangled bush with cross-linking branches.

The researchers reached this conclusion by analysing DNA sequenced from saliva samples from 44 modern Nama individuals from southern Africa, an Indigenous population known to carry exceptionally high levels of genetic diversity compared with many other modern groups. From that genetic data, the team developed a model suggesting that the earliest detectable split among ancestral human populations occurred between 120,000 and 135,000 years ago, after two or more weakly differentiated Homo populations had already been interbreeding for hundreds of thousands of years.

Even after that split, migration continued between the populations, producing what the researchers describe as a “weakly structured stem” for modern human origins in Africa. Rather than a single stem from which humanity simply sprouted, human evolution is better understood as a reticulated process: branching, merging, and branching again.

Creationism Refuted - 'Doggerland' Was Lush Forest - Over 6,000 Years Before 'Creation Week'

Southern Doggerland, 16,000 years ago

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Southern 'Doggerland' 16,000 years ago.

AI-generated image (ChatGPT 5.4 Thinking).

Warwick Study: Ancient Forests Under North Sea Lost World

More than 16,000 years ago, long before, according to their favourite Bronze Age mythology, creationists' little god created a small flat Earth under a dome centred on the Middle East, people and animals were able to walk from continental Europe into what are now the British Isles. They did so not by walking on water, but across dry land now submerged beneath the North Sea, of which Dogger Bank is one surviving remnant. From this lost landscape, Ice Age fossils such as mammoth teeth and tusks are still regularly dredged up in trawlers' nets.

Whatever hominins left the famous footprints at Happisburgh, Norfolk, almost certainly reached Britain on foot from western Europe, as did, much later, the hominins represented at Swanscombe in Kent and Pontnewydd Cave in Denbighshire, Wales.

Now, evidence presented in Proceedings of the National Academy of Sciences (PNAS) by a team led by Professor Robin G. Allaby of Warwick University's School of Life Sciences shows that southern Doggerland was not a bleak, barren wasteland but supported temperate woodland more than 16,000 years ago. The team reached this conclusion from a detailed analysis of 252 sediment samples from 41 marine cores taken along the prehistoric Southern River in southern Doggerland, where exceptionally well-preserved deposits preserve an environmental record from the Late Pleistocene into the Holocene.

For creationists, the problem is not merely the age of this drowned landscape, awkward though that is for biblical chronology. It is the existence of the evidence itself: well-preserved, datable layers laid down over vast spans of time, preserving a coherent ecological history that can be tested, checked and verified. If biblical mythology were true, those layers should not exist in anything like this form. But they do, and they tell a story utterly at odds with Genesis.

In science, evidence that contradicts a hypothesis counts against it. A theory that repeatedly fails is supposed to be revised or abandoned. Creationism works the other way round. Evidence against it is treated not as a reason to change one's mind, but as a test of faith. By that twisted logic, the more decisively reality refutes it, the more convinced its followers become that they must be right. That is not intellectual strength. It is simply a refusal to let evidence matter.

An interesting aspect to this work, and one that may upset creationists, is the fact that the team used two different, unrelated methods for dating - carbon dating and optically stimulated luminescence (OSL) dating which converged on the same dates.

Refuting Creationism - More on the Domestication of Dogs - Long Before 'Creation Week'

Artist’s impression of a human and their canine companion near a settlement in Ice Age Switzerland.

Credit: Oliver Uberti, Nature.

Cover picture for The Way of the Wolf: A Stone Age Epic

Canine companions: revealing the genetic history of our first friends | Crick

This is the second of my posts on the domestication of dogs and on why the facts are so awkward for creationists. It concerns research by a team led by Anders Bergström and Pontus Skoglund of the Francis Crick Institute, London, working with colleagues from the Max Planck Institute for Evolutionary Anthropology and a large international network of collaborators.

The team have shown that the domestication of dogs had already begun well before the invention of farming, when humans in Europe still lived in nomadic bands of hunter-gatherers. At that stage, dogs would have been hunting companions, sentinel guards for encampments, and perhaps even family pets, long before they were adapted for the many tasks later associated with farming, such as herding livestock and guarding flocks. Their findings are published in Nature.

This establishes dogs as the first domestic animals and suggests that the human-dog relationship may have helped lay the groundwork for later animal husbandry and selective breeding.

The story of the domestication of dogs from wolves is something in which I have long taken a special interest, and it was that interest which led me to write two books with fictionalised accounts of how it may have happened - The Girl and the Wolf and its sequel, The Way of the Wolf: A Stone Age Epic.

Biologically, of course, this evolved symbiotic relationship between two species is exactly the sort of outcome the Theory of Evolution leads us to expect. But, embarrassingly for creationists, it also tells a story rooted in deep time, for which creationism has no credible explanation. Worse still for biblical literalists, it makes a mockery of the claim that God created all animals for the benefit of humankind, because that claim presupposes that animals created by an omniscient, omnipotent designer would already be fit for purpose and would not need extensive modification by human selective breeding.

The researchers reached their conclusions by analysing DNA from 216 canid skeletal remains, including 181 pre-Neolithic samples - that is, from before approximately 10,000 years ago. These remains came from sites across Europe and nearby regions, including Switzerland, Germany, Belgium, the Netherlands, Turkey, Sweden, Denmark and Scotland.

Creationists previously had a little wriggle room when the earliest indisputable domestic dog was thought to date to about 10,900 years ago. They could at least pretend that dogs appeared during their imaginary ‘Creation Week’ or shortly afterwards. That pretence is now no longer sustainable. This study shows that the ancestry of later dogs was already established before 14,200 years ago, and probably earlier still.

Creationism Refuted - Earliest Domestic Dogs - 6,000 Years Before 'Creation Week'

Cover picture for The Girl and the Wolf

Oldest genetic evidence for domestic dogs identified in Europe and Türkiye | University of Oxford

Artistic reconstruction of Pınarbaşı c. 15,800 years ago based on evidence from archaeological excavations by University of Liverpool.

(c) Kathryn Killackey

This is the first of two blog posts on a pair of recent papers published in Nature on the earliest known domestic dogs and what they tell us about when grey wolves first entered into a domestic relationship with humans. Together, these studies push the earliest firm genetic evidence for dogs back[1] about 10,900 years ago, showing that dog populations were already present in western Eurasia during the Late Upper Palaeolithic. For creationists committed to a young Earth and to the simplistic Bronze Age origin myths of the Bible, that is yet another awkward fact: dogs were already on their way to becoming humanity’s first domestic animal long before their preferred chronology even allows for the Earth to exist. [1.1]

Since then, of course, dogs have been systematically modified by selective breeding to suit the many roles humans have found for them. That alone sits uneasily with the claim that a perfect creator made all animals ready-made for human benefit. But what makes these papers especially interesting to me is not only that they create yet another problem for creationist superstition, but that they touch directly on the background to two novels I have recently published, in which the domestication of wolves forms part of the story.

The first of these books, The Girl and the Wolf, tells the story of Almora, a child of the Drognai clan, who is raised alongside a wolf cub, Sharma, who becomes her inseparable companion. When Almora meets one of the last Neanderthals, Tanu, and they fall in love, Sharma plays a crucial part in bringing them together. The kindness of Almora’s mother, Shana, in rescuing and raising the starving cub becomes the small act from which a much larger change in human history begins.

In the sequel, The Way of The Wolf: A Stone Age Epic, Almora and Sharma have become the stuff of legend, their story spreading far beyond the lands of the Drognai. When Almora’s daughter, Shana — herself of mixed Neanderthal and modern human ancestry — chooses to leave the clan because of the tensions her family’s presence has caused, Almora, Tanu and a small band of Drognai go with her to a distant land. There they discover a people who have taken the legend of Almora and Sharma to heart and formed a close relationship with a pack of tame wolves, a relationship that has helped carry them through hardship into a period of hunting success and prosperity.

These books are fiction, of course, because we cannot know exactly how wolves became domesticated. What we can say is that the current evidence points to a long and complex process rather than a single moment of “invention”. The broad consensus is that some wolves probably began by exploiting scraps around human camps, while humans gradually came to recognise their value as sentinels, scavengers and hunting partners. The rest, as they say, is history.

And according to the first of these two new papers, that history was already under way deep in the Late Ice Age. One study generated nuclear and mitochondrial genomes from canid remains from Pınarbaşı in Türkiye, dated to 15,800 years ago, and from Gough’s Cave in Somerset, dated to 14,300 years ago, and concluded that a genetically homogeneous dog population was already widely distributed across Europe and Anatolia by at least 14,300 years ago. The second study analysed 216 canid remains from Europe and found its oldest dog genome in a 14,200-year-old specimen from Kesslerloch in Switzerland, showing that European dogs were already genetically distinct by then. [1.1]

Refuting Creationism - How Humans Caused 'Warrior' Wheat to Evolve.

Early farming unintentionally bred highly competitive "warrior" wheat, study finds | Biosciences | The University of Sheffield

One of the more embarrassing questions you can ask a creationist is this: if an omniscient, perfect god created all living things for the benefit of humankind, as the biblical creation myth claims, why have humans had to modify almost all our domesticated animals and cultivated crops to make them fit for purpose? In many cases, we have altered them so extensively that they are barely recognisable as the same species as their wild ancestors.

The story of how humans domesticated wild species and gradually modified them is, in effect, a textbook example of evolution in progress. Sometimes this happened through conscious selective breeding, but often it was an unintended consequence of domestication itself. Wheat, for example, evolved grains that were more firmly attached to the stalk. This meant fewer grains were lost when harvested and carried back to camp for communal use, so the plants whose seeds stayed attached were more likely to have those seeds planted again, whether deliberately or accidentally, around early hunter-gatherer encampments.

Another example in wheat is the evolution of taller plants with more upright leaves. As humans began planting wheat more densely, they created an environment in which the more aggressive plants literally overshadowed their neighbours and captured a greater share of the sunlight. In this struggle for existence, the plants best suited to the human-made environment were the ones most likely to survive and become the parents of the next generation.

That is the conclusion of a research group led by Dr Yixiang Shan and Professor Colin Osborne of the University of Sheffield, working in collaboration with colleagues from the Autonomous University of Madrid, Rey Juan Carlos University in Spain, and Wageningen University in the Netherlands. Their findings are published in Current Biology.

Malevolent Design - How Epigenetics Helps Pancreatic Cancer To Spread

Representation of KLF5 expression patterns in lab-grown human pancreatic cancer cells (left) and their patterns of migration from the primary tumor (right). Credit: Andrew Feinberg laboratory, Johns Hopkins Medicine. Originally published in Molecular Cancer.

Growth of Spreading Pancreatic Cancer Fueled By “Under-Appreciated” Epigenetic Changes | Johns Hopkins Medicine

A new paper in Molecular Cancer from Johns Hopkins Medicine describes yet another discovery that should be deeply uncomfortable for Intelligent Design creationists. The researchers found that the spread of pancreatic cancer is driven not chiefly by fresh mutations in DNA sequence, but by epigenetic reprogramming — changes in chromatin organisation and gene activity. In particular, they identified KLF5 as a major driver of metastatic growth, with higher expression in most metastatic lesions than in the matched primary tumours. The paper in Molecular Cancer shows that KLF5 promotes metastatic proliferation through epigenetic modifier genes including NCAPD2 and MTHFD1, helping switch on programmes involved in migration, plasticity and invasion. [1]

What makes this especially important is that epigenetics is not some magical extra layer of “specified information” inserted into life by a supernatural designer. Its roots are ancient. In bacteria, DNA methylation is a major form of epigenetic regulation, involved in gene expression, chromosome replication and DNA repair. In archaea, histone-based chromatin already exists in a form strikingly similar to that of eukaryotes, and studies show that chromatin architecture and its role in regulating gene expression long predate complex multicellular life. In other words, the basic machinery was already there in simpler organisms, doing ordinary cellular housekeeping long before animals and plants ever appeared. [2]

Multicellular organisms did not receive a brand-new control system from an intelligent agent; they inherited this ancient molecular toolkit and elaborated it. As multicellularity evolved, epigenetic regulation expanded and became central to cell differentiation, allowing cells with the same DNA to adopt different stable identities by opening some regions of the genome and closing others. Work on the transition from unicellular to multicellular states in Dictyostelium, for example, shows that chromatin reorganisation and histone modifications are closely tied to the shift into multicellularity, while evolutionary reviews note that epigenetic diversity expanded rapidly with multicellular life and that epigenetic marks are crucial in development and long-lived cell lineages. [3]

And that is exactly why this Johns Hopkins work is such bad news for ID creationists. The same ancient, repurposed system that multicellular organisms rely on for cell specialisation can also be subverted to drive one of the deadliest features of cancer: metastasis. That is what evolved systems do. They are modified from older parts, good enough to work, but never perfect and never immune to catastrophic failure. What this study reveals is not elegant, flawless engineering, but the vulnerability of a historically evolved regulatory system — one that natural selection adapted for development and tissue specialisation, but which disease can hijack with lethal consequences. That is entirely consistent with evolution, and profoundly at odds with the notion of a competent, benevolent designer. [1]

Refuting Creationism - Origin Of Western Europeans - Thousand Of Years Before The Mythical Flood

The Hunter-gatherer life-style persisted in Netherlands and Belgium until about 2,500 BCE

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Map indicating hunter-gatherer ancestry proportions across Europe 4500–2500 BCE. Darker is more.

New research into ancient DNA sheds light on key phase in European prehistory - University of Huddersfield

This second post on discoveries made by international teams of palaeontologists and geneticists, including scientists from the University of Huddersfield’s Archaeogenetics Research Group, examines the genetic evidence for the ancestry of modern western Europeans. As so often happens in research into human origins and archaeology, the findings are not what creationists keep hoping for: not a scrap of evidence that the creation myths in the Bible contain even a grain of historical truth. Instead, the team’s findings, published in Nature, add yet more evidence for a deep, complex and thoroughly non-biblical human past.

As usual, the evidence sits squarely at odds with those childish fairy tales of magical creation and a recent global population reset caused by a genocidal flood. The study shows that farming practices were reaching parts of western Europe long before biblical chronology allows for such events, and that there is no sign of the extreme genetic bottleneck such a story would require. On the contrary, both the archaeological and genetic evidence point to continuity across the period, with farming introduced unevenly into the region and with women of Early European Farmer ancestry from the Near East marrying into local hunter-gatherer communities.

Nor are these findings any comfort to far-right white supremacists who fantasise about Europeans as some sort of ancient “pure race”. Research led by scientists including Dr Maria Pala, Professor Martin B. Richards and Dr Ceiridwen J. Edwards of the University of Huddersfield shows that modern Europeans carry ancestry from multiple distinct populations: indigenous hunter-gatherers, Neolithic farmers ultimately derived from the Near East, and later pastoralist groups associated with the Eurasian steppe. In other words, the population history of Europe is one of movement, mixture and cultural exchange, not racial purity.

The team also found that the hunter-gatherer way of life persisted in what are now Belgium and the Netherlands for thousands of years longer than in most other parts of Europe. Rather than being rapidly replaced, these communities retained high levels of hunter-gatherer ancestry well into the Neolithic, apparently because the wetland, riverine and coastal environments allowed them to adopt some farming practices without abandoning their existing lifeways.

Refuting Creationism - Modern Humans Reached Australia 50,000 Years Before 'Creation Week'

AI-Generated imaginative reconstruction of first humans arriving in Sahul

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The migration of the first settlers to Sahul 60,000 years ago.

Photo: Helen Farr and Erich Fisher.

New genetic research supports “long chronology” for first settlement of Sahul - University of Huddersfield

Two recent papers by teams that included members of the Archaeogenetics Research Group at the University of Huddersfield, UK, show how modern DNA extraction and sequencing techniques are adding yet another independent line of evidence in support of the Theory of Evolution and against creationism. Together, they reveal the ancient and complex origins of modern humans, in stark contradiction to the simplistic Bronze Age origin myths of the Bible.

The first of these papers, published last November (2025), and available open access in Science Advances, examines human migration into Australia and lends support to the ‘long chronology’ hypothesis for the earliest settlement of Sahul, the Ice Age landmass that united Australia, New Guinea and nearby islands.

The second paper examines the more recent population history of Western Europe. That will be the subject of my next blog post.

According to the long chronology hypothesis, humans first reached Sahul around 60,000 years ago, whereas the short chronology hypothesis places their arrival between about 45,000 and 50,000 years ago. Either date is, of course, utterly incompatible with the childish notion of magical creation just 6,000-10,000 years ago. And unlike geochronological dating methods, which creationists routinely dismiss as fraudulent, flawed or unreliable whenever the results embarrass them, this evidence comes from genetic analysis of mitochondrial DNA (mtDNA). Because mtDNA is inherited through the female line, it can be used to reconstruct maternal ancestry in remarkable detail.

Refuting Creationism - How New Genetic Information Can Arise Rapidly, Naturally

Lake Malawi cichlids

Source: Wikipedia

A small selection of Lake Malawi cichlids

How ‘supergenes’ help fish evolve into new species | University of Cambridge

Creationists like William A. Dembski constantly reassure their fellow believers that new genetic information cannot arise naturally and therefore requires divine intervention. This claim depends on a misrepresentation of the laws of thermodynamics and a deliberate confusion of information with energy. It is clung to despite the obvious and overwhelming evidence to the contrary, with the same tenacity that creationists bring to their insistence that evolution either does not happen at all or, if it does, must somehow have occurred at an impossibly rapid rate after the Flood to produce such enormous variation within their invented ‘kinds’ from just a single surviving pair.

So now we have yet more contrary evidence for creationists to ignore, this time in the form of an explanation for how the cichlid fishes of Lake Malawi in East Africa were able to evolve into more than 800 species in a fraction of the time it took humans and chimpanzees to diverge from a common ancestor. Readers of this blog with long memories may recall that, back in 2012, I described these fish as a particularly powerful argument against creationism.

The fact of this rapid adaptive radiation, taking place on a timescale that could be independently verified, was already indisputable. What we lacked at the time was a clear understanding of the underlying mechanism that made it possible. That gap has now been filled by researchers from the Universities of Cambridge and Antwerp, who have shown that the source of this new genetic information lies in genetic inversions, where an entire section of DNA is inserted in reverse orientation. They have recently published their findings in the journal Science.

During the normal process of meiosis, in which reproductive cells are formed, crossing-over reshuffles genes to produce new combinations in offspring. But when a segment of DNA has been inverted, that section cannot take part properly in the crossing-over process. As a result, the genes within it remain linked together as an intact block, forming what geneticists call a ‘supergene’. These supergenes can then be inherited largely unchanged across generations. The effect is to create barriers to hybridisation much more quickly than would otherwise be possible, effectively isolating a new gene pool within the wider population and allowing new species to evolve far more rapidly than usual, instead of having novel gene combinations continually diluted by interbreeding across the whole population.

Creationism Refuted - 100 Million Years Of Cuttlefish and Squid Evolution

Top Left: Pygmy squid. Idiosepius sp.
Photo by Keishu Asada
Bottom left: Ram’s horn squid, Spirula spirula. Photo by Dr. Victor Tuset

Top right: Ryukyuan bobtail squid, Euprymna brenneri Photo : Jeff Jolly
Bottom right: Common cuttlefish, Sepia sp.
Photo by Keishu Asada

The intricate ram’s horn squid shell is only about the size of a fingernail. Compared to other cephalopod species, the shell structure has not degraded over time. As part of this study, researchers used transcriptomics which revealed genes supporting biomineralization and regeneration of the shell.

Credit: Catherine Hodges/OIST

100 million years ago, an ‘evolutionary fuse’ was lit in the deep ocean, sparking squid diversification | EurekAlert!

Another day, another gap in evolutionary history closed by scientists doing what scientists do: following the evidence wherever it leads. This time, the gap concerns the origins and diversification of squid and cuttlefish, the decapodiform cephalopods.

An international team led by the Okinawa Institute of Science and Technology (OIST) has now reconstructed a much clearer picture of their history, and their findings are published, open access, in Nature Ecology & Evolution. The study supports a rapid mid-Cretaceous diversification of the major decapodiform lineages around 100 million years ago, followed much later by expansion into coastal habitats after the K–Pg mass extinction. [1]

That is, of course, disastrous for creationism. Creationists need the history of life to be short, simple, and static: a few thousand years, separate acts of special creation, and only trivial shuffling of variation within rigidly defined “kinds”. What this study shows instead is exactly what evolutionary biology has long predicted - deep ancestry, branching descent, ecological change over immense spans of time, and major radiations triggered by changing environmental conditions. In other words, not magic, not fixity, and not “kinds”, but evolution. [1]

The researchers conclude that the ancestors of modern squid and cuttlefish probably originated in the deep ocean, where oxygenated refugia may have allowed them to survive while shallow marine environments became increasingly hostile. Ocean acidification in shallower waters would likely have damaged shell-bearing forms, and the later recovery of coastal ecosystems and coral reefs after the K–Pg event opened up new ecological opportunities. What followed was not the survival of a few immutable “created kinds”, but the adaptive expansion of lineages into newly available habitats. [2]

That matters because it gives the lie to one of creationism’s central evasions: the claim that organisms merely vary within fixed boundaries. The history uncovered here is not one of minor tinkering around the edges. It is one of common ancestry, divergence, persistence through catastrophe, and later radiation into new environments. It is precisely the sort of deep, branching history that creationists have to deny, ignore, or misrepresent because their belief system simply has no room for it. [1]

The team reconstructed this history using genome-scale data, including newly sequenced genomes that helped fill key phylogenetic gaps. Together with data from the Aquatic Symbiosis Genomics Project and other existing resources, this allowed the researchers to produce a robust evolutionary tree covering nearly all recognised decapodiform lineages. Because cephalopod genomes are often very large, this kind of work has only recently become practical with modern sequencing technology and computing power. [1]

So, once again, creationism is refuted not by some special anti-creationist project, but as an incidental consequence of real scientific research. Scientists set out to understand the evolutionary history of a fascinating group of animals, and in doing so they uncovered yet more evidence for common descent, ancient Earth history, and the power of evolution to generate biological diversity. Reality, as usual, has no respect for creationist dogma. [1]

The Fallible Bible - How We KNow The Bible's Is Not The Inerrant Word Of A Creator God

Leopard Gecko, Eublepharis macularius

Researchers discover leopard gecko produces females at cooler incubation temperatures and mostly males at warmer ones. This clear sex-determination pattern of leopard gecko has established it as a key model for studying environmental effects on development.

Credit: Professor Shinichi Miyagawa from Tokyo University of Science, Japan.

New study clarifies how temperature shapes sex development in leopard gecko | EurekAlert!

Bible literalists insist that every word in the Bible is true and without error, yet the text itself contains statements that cannot all be true at the same time, so at least one of them must be false*. The Bible also contains factually incorrect statements, such as the assertion in Genesis 6:19 and 7:15–16 that males and females of every ‘kind’ were brought onto the Ark, reflecting the same assumption found in Genesis 1:27 that living creatures were created as male and female.

We now know, unlike the authors of Genesis, that not all species exist as fixed male–female pairs. There are many examples of hermaphrodite creatures that are both male and female; some species that are entirely female, such as the New Mexico whiptail lizard and the marbled crayfish; many aphids and some beetles such as the vine weevil; and species that can change sex during their lifetime, such as certain fish. And, as a recent paper in the journal Developmental Biology by a team of researchers led by Professor Shinichi Miyagawa from the Department of Biological Science and Technology, Tokyo University of Science, Japan, shows, there are also species such as the leopard gecko, Eublepharis macularius, in which sex is not determined by inherited chromosomes at all but by the temperature at which the embryo develops in the egg.

In other words, in some species the difference between male and female is not fixed at conception at all, but depends on something as mundane as the temperature of the nest.

The team showed that there is a discrete window, known as the temperature-sensitive period, during which temperature triggers temperature-dependent sex determination (TSD), activating specific sets of genes that control the development of either testes or ovaries, thereby determining the sex of the developing embryo.

Malevolent Design - Why Autism Refutes Intelligent Design - Or Is the Designer Incompetent?

Evolution's well-tinkered machine.

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Autism Research Breakthrough Discovered by Hebrew University Researchers | en.new.huji

Researchers at the Hebrew University of Jerusalem have uncovered a mechanism that leads to autism. If this is the product of intelligent design then the designer is either incompetent or malevolent, but as so often with diseases that arise when systems go wrong, it is exactly what we expect of an evolved process. Their paper has just been published open access in the journal Molecular Psychiatry.

For proponents of Intelligent Design such as Michael Behe and William Dembski, biological systems are supposed to bear the hallmarks of careful engineering — intricate machines whose parts work together with purpose and precision. But the mechanism uncovered in this study looks nothing like the output of a competent engineer. Instead, it reveals a fragile regulatory network in which a single biochemical modification destabilises a key control protein and sends an entire signalling pathway out of balance. The result is a cascade of downstream effects that ultimately alters brain development and behaviour.

What the researchers have uncovered is not a piece of irreducibly complex machinery but a regulatory system that can be knocked off course by a small perturbation. Nitric-oxide signalling modifies the protein TSC2, leading to its degradation and the subsequent overactivation of the mTOR pathway — a pathway that controls cellular growth and protein synthesis throughout the body. In other words, the pathology arises because a normal biological control system fails to maintain the delicate balance on which it depends.

This is precisely the sort of vulnerability we expect from systems produced by evolution. Evolution does not design organisms from scratch with perfect foresight; it works with what already exists, modifying and repurposing pathways that originally evolved for other purposes. The result is a network of interacting components that usually works well enough to keep organisms alive and reproducing, but which inevitably contains points where the system can fail. When those failures occur, the consequences can be severe.

Far from supporting Intelligent Design, discoveries like this highlight the jury-rigged nature of biological systems. They show that life’s complexity arises not from optimal engineering but from the gradual accumulation of workable solutions over evolutionary time — solutions that function most of the time, yet remain vulnerable to the occasional catastrophic malfunction.

Refuting Creationism - How Sex Selection Between Homo sapiens And Neanderthals Played A Part In Human Evolution

Genetic inheritance in Homo sapiens/Neanderthal hybrids

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How ancient attraction shaped the human genome | Penn Today

What creationist mythology cannot account for is the presence not just of Neanderthals, but of traces of their DNA in almost all people who are not of recent African ancestry.

So imagine the mental gymnastics they will need to perform to cope with the news that new genomic research by members of Sarah Tishkoff’s lab at the University of Pennsylvania has shown how that most Darwinian of evolutionary mechanisms—sexual selection—is responsible for how Neanderthal DNA is distributed in the Homo sapiens genome.

It is enough to send any dedicated creationist into deep denial, with cries of foul and accusations that the scientists involved are somehow deceiving the public—anything to avoid accepting the fact that their primitive beliefs are wrong, even to the extent of betraying the uncomfortable reality that their professed ‘faith’ often functions as a front for a political agenda far removed from the basic teachings they claim to defend.

The findings of the University of Pennsylvania team were recently published in the journal Science.

This subject strikes a particular chord with me because, in my novel, The Way of the Wolf: A Stone Age Epic, Almora—the mother of the central character, Shana—has a Neanderthal partner and they are unable to produce male children, who either die in early infancy or are miscarried. This was in recognition of the fact that no Neanderthal Y chromosomes have ever been discovered in Homo sapiens, suggesting that male offspring of such hybridisation were either non-viable or sterile.

The Pennsylvania team, however, were seeking to explain why Neanderthal DNA is largely absent from the Homo sapiens X chromosome. As is well known, humans, like other mammals, have two sex chromosomes: females have two X chromosomes (one from each parent), while males have an X (from their mother) and a Y (from their father).

The researchers showed that if there was a preference for mating between Neanderthal males and Homo sapiens females, the fact that Homo sapiens contributed two X chromosomes to the hybrid gene pool for every one Neanderthal X chromosome could, over time, have led to the loss of Neanderthal DNA from the X chromosome. This suggests that sexual selection may have played a significant role in shaping human evolution, in addition to natural selection.

They also showed that Neanderthals possessed disproportionately more Homo sapiens DNA on their X chromosome than on their other chromosomes. This can likewise be explained by the influx of predominantly female Homo sapiens X-chromosome DNA into the Neanderthal gene pool, again supporting the hypothesis that hybrid matings occurred predominantly between Homo sapiens females and Neanderthal males, producing this imbalance.

Refuting Creationism - How Deep-Sea Species Evolved

A field of deep-sea mussels (Bathymodiolus sp.) on the Atlantic margin seafloor near a cold methane seep.

Image: Deepwater Canyons 2013 -
Pathways to the Abyss, NOAA-OER/BOEM/USGS.

Into the deep: scientists find two paths | News | Physical Sciences Division | The University of Chicago

A recent paper in Proceedings of the Royal Society B should ring alarm bells for any creationist with the courage and personal integrity to risk reading it. It reports on the findings of a team of three researchers led by scientists at the University of Chicago and including Stewart M. Edie, of the National Museum of Natural History, Smithsonian Institution, Washington DC, that species adapted to deep-sea living evolved to survive in that difficult environment by two different evolutionary pathways.

The first problem for creationists here is that there is no doubt expressed anywhere in the paper that the explanation requires anything other than the Theory of Evolution. There is no sign — as with every other biomedical paper published so far this year — that evolutionary theory is proving inadequate and that biologists are turning instead to creationism, with its unevidenced magic entities and mysteries posing as answers to scientific questions. That narrative exists only in the imagination of creationists.

The second problem arises from the arrogant creationist belief that all living organisms were created especially for humans. If that were so, why ‘design’ some of them to live in the inaccessible depths of the oceans, where for much of human history their existence was entirely unknown? This question has been posed many times in these blog posts, yet not a single creationist has managed to produce anything more convincing than an appeal to ‘mysterious ways’.

The research team set out to understand how organisms living on the abyssal plain — where temperatures hover just a few degrees above freezing, pressures are immense enough to crush all but the most robust submersibles, sunlight never penetrates, and food is scarce — managed to adapt to such extreme conditions. Clearly, they had to undergo substantial evolutionary change, which is probably why relatively few lineages have made the transition, including certain bivalve molluscs such as mussels, oysters, scallops and clams.

The scientists examined the lineages of two groups of bivalves that successfully inhabit the deep sea. They found that one group, already adapted to harsh conditions, moved into the deep-sea environment and adjusted to those conditions without diversifying greatly. A second group, by contrast, radiated into a swarm of new species from a single ancestral lineage.

Refuting Creationism - Why There Are No fossils Of The Early Sponges From 650 Million Years Before 'Creation Week'

Sponges in the Ediacaran

AI-generated image (ChatGPT 5.2)

A giant barrel sponge from Indonesia. Sponges were the first reef builders and maintain a fundamental role in modern marine ecosystems.

January: Bristol scientists discover early sponges were soft | News and features | University of Bristol

Creationists have a massive gap to try to close; a gap so wide it makes the Grand Canyon look like a mere ditch. It is the gap between the earliest signs of life in the fossil record and the timeline a literal reading of the Bible allows. And that gap just got a lot wider.

Creationists could once take comfort from the fact that there was little solid fossil evidence of multicellular life much before the Cambrian, when organisms with hard body parts that fossilise begin to appear in the record. That gap was closed, not by fossils as we normally understand the term, but by chemical fossils contained in ancient rocks, as I explained in my last blog post. This evidence, together with genetic evidence from other work, shows that the common ancestors of multicellular animal life were very probably sea sponges.

But to a creationist, conditioned to believe that the Theory of Evolution is a theory about fossils—so that any gaps in the fossil record must be fatal for the theory—there is still some comfort in the fact that whatever left these chemical fingerprints in ancient rocks left no tangible fossils.

Now a team of palaeontologists, led by the University of Bristol, have shown that the lack of fossil evidence of these ancestral sponges has a simple explanation: they were soft-bodied, having yet to evolve the characteristic skeletons composed of millions of microscopic glass-like spicules. These did not evolve until about 560 million years ago. The team have recently published their findings, open access, in the journal Science Advances.

The Bristol-led team have now pushed back the evolution of these soft-bodied sponges to between 615 and 600 million years ago by using a combination of genetic evidence from 133 protein-coding genes and fossil evidence. This approach also showed that the spicules evolved independently in different sponge groups by convergent evolution.

Refuting Creationism - Creationists Rebutted By Old Irish Goats From Before The Legendary Genocidal Flood

Old Irish Goat carries 3,000 years of Irish history - University College Dublin

If the biblical flood really wiped the slate of life almost clean a few thousand years ago, we should expect to see unmistakable genetic signatures of that event across modern species. Instead, what scientists repeatedly find is exactly the opposite: long, continuous lineages stretching back thousands of years before the supposed catastrophe.

A good example comes from Ireland, where geneticists at University College Dublin, in collaboration with colleagues at Queen’s University Belfast and international partners, have shown that the ‘Old Irish Goat’, an Gabhar Fiáin – the wild goat – is a descendant of goats living in Bronze Age Ireland some 3,000 years ago, and thus ultimately of an older population introduced by Neolithic agriculturalists about 5,900 years ago. Their paper is published open access in the Journal of Archaeological Science.

According to Bible literalists, there was a general reset of Earth’s biology a few thousand years ago when their god supposedly decided to destroy everything in a fit of pique because its creation had gone wrong and, rather than undertaking an entirely new creation, chose instead to start again with a few survivors, hoping the outcome would be different this time. However, time and again we find evidence not of a general reset but of uninterrupted continuity of cultures and ancient species, such as the Old Irish Goat, which existed both before and after the supposed reset.

The problem for creationists is that, although they claim there was a period of miraculous hyper-evolution in which a handful of ‘kinds’ that survived the genocide radiated into all the modern species—an event which appears to have gone unnoticed and unreported by the people who supposedly lived while it was happening, and a belief for which there is no Biblical basis—the Old Irish Goat shares its common ancestry with other goats long before the alleged flood, not within the last few thousand years. Within the creationist paradigm, therefore, it must trace its ancestry to just two survivors. However, although there is evidence of a genetic bottleneck, this is very recent and is due to population collapse brought about by human activity; there is no evidence of the narrow bottleneck of just two individuals about 4,000 years ago.

Creationism Refuted - Genetic Diseases 2,000 Years Before 'Creation Week'

AI-Generated image (ChatGPT 5.2)

Daniel Fernandes preparing to take a sample.

© Adrian Daly

Ancient DNA reveals 12,000-year-old case of rare genetic disease

The standard creationist response to evidence that the human genome is not the perfectly designed blueprint we should expect from a flawless designer is to claim that ‘sin’ somehow caused it to become degraded. Discovery Institute fellow Michael J. Behe even introduced the biologically nonsensical notion of ‘genetic entropy’, which supposedly allows deleterious genes to spread throughout a species’ gene pool by some unexplained process — an idea that only those unfamiliar with how natural selection works could find convincing.

It is, of course, impossible for a genuinely deleterious gene to increase in frequency within a population unless it is linked to an advantageous trait whose benefits far outweigh its harmful effects. And if the genome were originally perfect, as Behe assumes, how could any advantageous mutation arise in the first place?

Behe, unwittingly or otherwise, appears to have abandoned any pretence that Intelligent Design is science rather than fundamentalist Christianity in a lab coat. By invoking an initial perfect creation followed by corruption through ‘sin’, he has simply retreated into theology — especially after his ‘irreducible complexity’ argument collapsed so spectacularly during the Kitzmiller v. Dover trial.

Even that feeble argument, however, has now fallen foul of evidence showing that deleterious variants and genetic disorders existed in the human genome long before the creationist narrative claims that ‘perfect’ humans were created somewhere in Mesopotamia just 6,000–10,000 years ago. A paper recently published in The New England Journal of Medicine by a team of researchers led by the University of Vienna and Liège University Hospital Centre reports the identification of genetic variants associated with a rare disorder in two prehistoric individuals who lived more than 12,000 years ago.

The individuals were discovered in 1963 at Grotta del Romito in southern Italy, buried in an embracing position. There was no sign of trauma. ‘Romito 1’, an adult female, was embracing ‘Romito 2’, an adolescent initially assumed to be male, whose reduced limb length suggested a height of about 110 cm (3 feet 7 inches). Palaeogenomic analysis, using DNA extracted from the petrous part of the temporal bone, has now shown that the adolescent was also female and was homozygous for a variant in the NPR2 gene, which is essential for normal bone growth. The two individuals were first-degree relatives, probably mother and daughter. The adult, Romito 1, was heterozygous for the same variant.

What this study makes clear is that genetic variants capable of causing disease were already present in the human genome thousands of years before the Bronze Age authors of Biblical origin myths imagined a special creation of ‘perfect’ humans without ancestry. These variants did not require some magical ingredient called ‘sin’ to arise — only the ordinary reality of imperfect replication and inheritance.

Malevolent Design - How Cancer Reprograms The Immune System To Work For It, Not Against It - Malevolence or Evolution?

Tumour containing infiltrating neutrophils. In light grey, tumour cells. Among the infiltrating neutrophils, some do not express CCL3 (blue), while others are CCL3 positive (red). CCL3-positive neutrophils are highly conserved across tumour types and promote the growth of growing tumours.

© Mikaël Pittet – UNIGE

Immune 'hijacking' predicts cancer evolution - Medias - UNIGE

A recent research paper in Cancer Cell, published by a team from the Université de Genève (Unige), Switzerland, led by Professor Mikaël Pittet, describes how neutrophils — key cells of the immune system — can be reprogrammed by cancer cells and then co-opted to drive the cancer’s progression.

This process depends entirely on the presence of multiple interacting components and on specific genes being expressed in both the tumour cells and the neutrophils. Without such irreducible complexity and so-called complex specified genetic information, these cancers would fail to progress.

Regular readers of this blog will be aware that, if we accept the Intelligent Design creationists’ argument for design — namely irreducible complexity and complex specified information — then the inescapable conclusion is that this putative designer must also be the evil genius behind cancers, parasites, pathogens, genetic disorders, congenital diseases, and all the suffering they entail, along with the vast medical resources required to combat them.

Far from being the reputedly omnibenevolent and compassionate god of the Bible, creationism’s designer becomes the exact opposite: randomly mendacious and obsessively sadistic, toiling relentlessly to devise ever more ways to increase suffering in the world.

And yet creationists appear to prefer us to adopt that view of their favourite deity rather than accept the evidence that such systems have evolved — and that what we see in cancers, parasites, and pathogens is precisely what the Theory of Evolution predicts, with no supernatural malice or intent involved. For some reason, Intelligent Design creationists often seem more concerned with disproving “Darwinism” for political purposes than with promoting the god of the Bible or Qur’an.

This apparent paradox goes a long way towards explaining why they have so little hesitation in bearing false witness against scientists, misleading their followers with disinformation, and spreading blatant falsehoods. There is no pro-truth agenda in creationism. There is, however, a thinly veiled political agenda: the establishment of theocratic government — first in the USA, then elsewhere — dragging society back towards the pre-Enlightenment world of the so-called Dark Ages, when ignorance, fear, and superstition allowed unelected and unaccountable religious clerics to rule unchecked, and for most people at the lower strata of a hierarchical society, life was nasty, brutish and short.

Refuting Creationism - How The Evidence Refuses To Comply With Creationist Requirements

Reconstruction of life in the Matjes River Rock Shelter, South Africa, 100,000 years ago

Ai-generated image (ChatGPT 5.2)

Ten-thousand-year-old genomes from southern Africa change picture of human evolution – Uppsala University

The story emerging from the latest palaeogenomic research reads like a science fiction epic — only it’s real, deep, and immutably ancient. A new study published in Nature reports that prehistoric humans in southern Africa lived in virtual genetic isolation for tens of thousands of years, diverging so far from other branches of Homo sapiens that their genomes fall “outside the range of genetic variation” seen in any living people. These weren’t minor differences; the DNA of individuals who lived south of the Limpopo River for much of the last 100,000–200,000 years retains an astonishing reservoir of variation, some of which has since vanished from other populations.

This isn’t an update to a dusty side-note in human history. It’s a profound rewriting of our origin story. Instead of a simple, uniform lineage emerging neatly from a single place and time, the evidence shows a complex mosaic of populations, genomes and adaptations evolving in parallel, sometimes in long-term isolation, sometimes intermingling. What we once thought of as the “standard” range of human genetic diversity was simply a tiny slice of a much richer prehistoric past.

For those committed to a literal reading of ancient texts like the Bible, discoveries like this pose a stark challenge. The creationist narrative — anchored in a literal six-day creation a few thousand years ago, followed by the dispersion of humankind from a single family — simply cannot grapple with human populations that were genetically distinct for hundreds of millennia before any traditionally assumed timeline. And yet, even here, one predictable excuse will surface: “God planted the evidence as a test of faith.”

That response, however, collapses under the very theological claims it purports to defend. The Bible repeatedly asserts that God is truthful and incapable of deceit — that “God cannot lie” (Titus 1:2; Numbers 23:19; Hebrews 6:18). If we accept those texts at face value, it follows that the Creator would not embed misleading evidence in the earth’s deepest strata as a cosmic trap for intellect. Instead, what we see in the genetic record is precisely what natural processes — mutation, isolation, selection, drift and admixture — predict and what evolutionary theory models with remarkable fidelity.