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.

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]

How Science Works - And Why Religion Doesn't - Changing Its Mind When The Evidence Changes

[left caption]

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Pohlsepia mazonensis PE51727a (part) and PE51727b (counterpart).

Oldest octopus fossil is no octopus at all scans reveal - University of Reading

The excitement creationists may feel on hearing that science has got it wrong yet again because a fossil once classified as the oldest known octopus has now been reidentified, will no doubt be tempered by the awkward fact that the animal it really belonged to lived 300 million years before, according to their beliefs, there was even a universe, let alone life on Earth. As so often, the truth poses no problem for science; it is creationism that stumbles over it.

Far from showing that science is unreliable compared with the supposed ‘eternal truth’ of religion, this revision is a vindication of the scientific method and a demonstration of its self-correcting nature. Unlike religions, which cling to ‘sacred truths’ that, when tested against reality, turn out to be little more than the best guesses and campfire tales of our ignorant and fearful ancestors, science is a method for moving ever closer to the truth. It remains the best tool we have for discovering reality precisely because nothing is sacred except truth itself, and because scientific understanding is always provisional — open to revision whenever new evidence demands it, unlike religions which are doxastically and doctrinally closed to new information.

On this occasion, the fossil re-examined and found not to be what it was once thought to be was the famous Pohlsepia mazonensis, identified as an octopus 25 years ago and even entered in the Guinness Book of Records as the oldest known fossil octopus. Using modern synchrotron imaging to peer inside the fossil and reveal details the original investigators could not see, researchers discovered tiny teeth and other internal features showing that it was not an octopus at all, but a nautiloid — a cephalopod with an external shell. The team recently published their findings in the journal Proceedings of The Royal Society B.

Refuting Creationism - How the Human Eye Evolved

By Rapidreflex - Own work, CC BY-SA 4.0, Link

1:posterior segment of eyeball 2:ora serrata 3:ciliary muscle 4:ciliary zonules 5:canal of Schlemm 6:pupil 7:anterior chamber 8:cornea 9:iris 10:lens cortex 11:lens nucleus 12:ciliary process 13:conjunctiva 14:inferior oblique muscle 15:inferior rectus muscle 16:medial rectus muscle 17:retinal arteries and veins 18:optic disc 19:dura mater 20:central retinal artery 21:central retinal vein 22:optic nerve 23:vorticose vein 24:bulbar sheath 25:macula 26:fovea 27:sclera 28:choroid 29:superior rectus muscle 30:retina

By Chabacano - References: [1] [2] [3] among others, CC BY-SA 3.0, Link

Our modern vision evolved from an ancient one-eyed worm creature

A recently published paper in the Cell Press journal, Current Biology, by four palaeontologists — two from the University of Sussex, UK, and two from Lund University, Sweden — delivers yet another solid rebuttal to creationist misrepresentation. It traces the origin of the vertebrate eye back to a worm-like marine creature that lived around 600 million years ago, neatly demolishing the old creationist claim that something as complex as the eye could never have evolved by natural means.

One of the favourite dishonest tricks in the creationist repertoire is the quote mine: lifting a sentence from an expert, stripping it of context, and presenting it as though it supports the very position the author was arguing against. Few examples are more shameless than their abuse of a passage from Darwin's On the Origin of Species. In typical Darwinian style, he first states what appears to be a serious objection to his theory, then immediately explains why it is not a real objection at all. The part creationists love to quote, from page 100, is this:

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.

Presented on its own, this is supposed to fool the unwary into thinking Darwin admitted defeat — as though he had conceded that evolution could not explain the eye and that modern creationists were right all along with their talk of 'irreducible complexity'. But, as usual, the deception depends entirely on stopping before the very next sentence, where Darwin wrote:

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Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.

Charles Darwin, On the Origin of Species By Means of Natural Selection, or, the Preservation of Favoured Races in the Struggle for Life (p. 100). Public Domain Books. Kindle Edition.

So Darwin was not conceding the point at all; he was doing the exact opposite. He was saying that the apparent absurdity disappears once we recognise that useful intermediate stages can and do exist. In other words, the creationist quote mine works only by concealing Darwin's actual argument.

And now, more than 160 years later, the evidence Darwin lacked has arrived in abundance. He could not have known the developmental genetics, the comparative anatomy, the fossil evidence, or the evolutionary history that modern biology has uncovered. Creationists have no such excuse. They are not merely repeating an old objection; they are repeating one that has been answered again and again, and now answered yet again by evidence tracing the deep evolutionary roots of the vertebrate eye itself.

So this discovery matters not simply because it adds another detail to the history of life, but because it exposes the intellectual bankruptcy of the creationist argument. The eye is not a problem for evolution. It is a triumph of evolution — a structure whose history is precisely the sort of gradual, functional modification Darwin predicted. The real problem lies not with evolutionary theory, but with those who continue to misquote Darwin and mislead their audiences in the hope that no one will bother to read past the sentence they have carefully amputated from its context.

An account of how the researchers arrived at their conclusion is given in an article in The Conversation by two of the four scientists involved. Their article is reproduced below under a Creative Commons licence, reformatted for stylistic consistency:

Refuting Creationism - Transitional Fossils From Before The Cambrian 'Explosion'

A newly-discovered fossil from the Jiangchuan biota.

Credit: Gaorong Li.

Reconstruction of Jiangchuan biota

Credit: Xiaodong Wang.

Spectacular fossil treasure trove pushes back origins of complex animals | University of Oxford

A paper just published in Science by a team of palaeontologists from Oxford and Yunnan universities should, if creationists were honest enough and sufficiently knowledgeable to understand it, finally lay to rest two favourite canards they use to attack Darwinian evolution: the so-called Cambrian Explosion and their misrepresentation of Stephen Jay Gould’s idea of punctuated equilibrium.

The Cambrian Explosion is a favourite target for creationists, who exploit the word “explosion” to misrepresent it as the sudden appearance of multicellular life with multiple body plans, supposedly without ancestry, and therefore as a single act of supernatural creation. The fact that it happened some 535 million years ago is usually dismissed with the standard creationist repertoire: claims that scientists are inventing the dates, relying on “flawed” dating techniques, or, more bizarrely still, failing to take account of some unspecified change in radioactive decay rates that just happens to make 6,000–10,000 years look like 535 million.

But that fallacy was based on very limited data, especially the fossils from the Burgess Shale, which provided only a narrow snapshot of living organisms at one time and place. From evidence such as this, Stephen Jay Gould and Niles Eldredge developed the idea of punctuated equilibrium, in which long periods of relative stasis in the fossil record are interrupted by comparatively short episodes of more rapid evolutionary change. Creationists eagerly seized on this, dishonestly presenting it as though Gould had somehow replaced Darwinism and proved Darwin wrong. In reality, it did no such thing. It was not a rejection of evolution, nor of common descent, nor of natural selection, but a discussion within evolutionary biology about the pattern and tempo with which evolutionary change appears in the fossil record.

Darwin, of course, never claimed that evolution must proceed at a constant, steady rate. On the contrary, his theory makes it clear that changing environments drive evolutionary change, so more rapid evolution during periods of environmental upheaval is entirely consistent with Darwinian evolution and, indeed, a vindication of it. The appearance of long stasis followed by apparently abrupt change can also be exaggerated by the incompleteness of the geological record, in which spans of thousands of years may appear almost instantaneous when compressed into a thin layer of rock.

However, the notion that the Cambrian Explosion was a sudden event without ancestry has been steadily dismantled by discoveries pushing the origins of Cambrian-type biota back towards the Ediacaran, together with evidence that some Ediacaran organisms were already capable of movement. What emerges is not a miraculous burst of creation, but a clear evolutionary progression from the Ediacaran into the Cambrian.

Now this new paper strengthens that case by showing that complex body plans existed much earlier than previously thought, and by presenting evidence of gradual Darwinian evolution from the Ediacaran into the Cambrian.

The evidence comes from a treasure trove of fossils, the Jiangchuan Biota in Yunnan Province, southwest China, where more than 700 fossil specimens were recovered from rocks dated to between 554 and 539 million years old. Among the more surprising finds is a deuterostome — part of the broad group that includes vertebrates such as fish and humans.

Refuting Creationism - The Oldest Known Ancestor of Spiders - 500 Million Years Ago

Head of Megachelicerax cousteaui

Credit: Rudy Lerosey-Aubril.

Close up of chelicera

Credit: Rudy Lerosey-Aubril.

A 500-Million-Year-Old Clawed Predator Rewrites the Origin of Spiders and Horseshoe Crabs | Department of Organismic and Evolutionary Biology

Another day, another piece of evidence for creationists to ignore, misrepresent or simply lie about — anything, in fact, except honestly acknowledge that it shows they are wrong. This discovery strikes at the heart of creationism. It not only refutes the notion that Earth is just 6,000–10,000 years old, but also demolishes two favourite creationist misrepresentations: that there are no transitional fossils, and that the Cambrian Explosion was some sudden, magical appearance of multiple body plans with no evolutionary ancestry. Of course, creationists can always fall back on the familiar claim that scientists invented the dates to lure people away from God and convert them to “Darwinism”.

The evidence, published in Nature, is a 500-million-year-old transitional fossil showing that arthropods had already diverged to produce the chelicerate subphylum — the lineage that would eventually give rise to spiders, scorpions and horseshoe crabs. This pushes the earliest known chelicerates back by some 20 million years from the previous oldest example, dated to about 480 million years ago from the Early Ordovician Fezouata Biota of Morocco.

The crucial evidence was the presence of the defining chelicerae, identified by research scientist Rudy Lerosey-Aubril of Harvard University while microscopically cleaning a fossil arthropod that the scientists have named Megachelicerax cousteaui. Chelicerae are the pincer-like, sometimes venomous, foremost appendages that define chelicerates, in contrast to the antennae that are the foremost appendages in insects and many other arthropods.

This shows that chelicerae evolved before chelicerates acquired their later, more familiar body plan with a two-part body and the reduced head appendages that became the eight walking legs of spiders and their relatives. In other words, this fossil captures an intermediate stage between the earlier, multi-segmented arthropods and the later chelicerate body plan. It is, therefore, precisely the sort of transitional form creationists keep claiming does not exist — right up until one is found, at which point they are forced to deny, distort or ignore it.

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]

Holy Cow! - Clever Veronika Refutes Creationism

This cow uses tools like a primate—and scientists are stunned | ScienceDaily

If humans evolved intelligence, why are there still creationists?

This is a question that evolutionary biologists struggle to answer, with the best attempt probably by Francis Collins, who explained that "Young Earth Creationism has reached a point of intellectual bankruptcy, both in its science and in its theology". (Francis Collins - The Language of God).

Paradoxically though, creationists often cite human intelligence as evidence for the special creation of mankind, separate from the other animals, who, according to creationist mythology, don't display what they define as evidence of intelligence - love, aesthetic appreciation, creativity, etc, as opposed to science which includes things like tool selection, adaptation and use, as characteristics of intelligence and cognitive ability.

So, it will be interesting to see how creationist explain the following video evidence of intelligence in a cow - namely, the ability to select a tool for an appropriate task and its ability to adapt how it uses that tool for maximal effectiveness.

This evidence comes in the form of a paper in Current Biology by Antonio J. Osuna-Mascaró and Alice M.I. Auersperg of the University of Veterinary Medicine, Vienna, Austria:

Refuting Creationism - Hominin Diversity In Middle Pleistocene China

Middle Pleistocene humans in China

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A new study places China at the center of the debate on human evolution | CENIEH

1 million-year-old stone tools from the Nihewan Basin

Continuing the theme from my last post, that the human evolutionary story is vastly richer and more complex than the childishly simplistic fairy tale in the Bible, this paper by a team led by the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing, together with researchers from the Spanish Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), and published in Nature Ecology & Evolution, argues that East Asia may have been a major centre of evolution within the genus Homo outside Africa.

At the heart of the study is a systematic reassessment of the so-called ‘transitional’ hominin fossils from the Chinese Middle Pleistocene. These fossils show intriguing mixtures of primitive and derived traits, and refuse to fit neatly into the tidy, linear progression that older models liked to assume between Homo erectus, Homo neanderthalensis and Homo sapiens. In other words, the human story in Asia was not a simple ladder of progress but a tangled evolutionary bush, with several populations, overlapping traits, and probably more than one lineage sharing the landscape at different times.

Some of these fossils may represent Denisovans, while recently proposed species such as Homo longi and Homo juluensis hint at an even greater diversity of archaic humans than had previously been recognised. It is also entirely possible that there were other hominin groups in East Asia that remain unidentified. As so often in palaeoanthropology, the more evidence scientists uncover, the less plausible the old cartoon version of human evolution becomes — and the more absurd the Biblical fantasy of humanity springing fully formed from a single magically created couple just a few thousand years ago appears by comparison.

This work also resonates with the recent findings from Atapuerca in Spain, where Homo antecessor has been interpreted as representing a basal population from around a million years ago, potentially close to the ancestry of later human lineages. Far from showing a simple, straight-line march toward modern humans, the fossil evidence increasingly suggests a deep and branching history, with different populations spreading, diverging, mixing, and adapting across Eurasia over hundreds of thousands of years.

The study also re-examines the evidence for the arrival of Homo sapiens in China, suggesting that our species may have been present there as early as 100,000 years ago, rather than only around 50,000 years ago as often assumed. If that interpretation is correct, then modern humans were dispersing across Asia earlier, and in a much more complex pattern, than traditional models allowed. That would mean repeated movements of populations, interaction with other human groups, and probably episodes of interbreeding — all of it part of a dynamic evolutionary process that creationists are forced either to ignore or grotesquely misrepresent.

Taken together, the evidence points to East Asia as an important arena in human evolution, occupied by adaptable and innovative hominin populations capable of surviving in a wide range of environments. This increasing adaptability, associated with larger brains and behavioural flexibility, helped lay the foundations for the eventual spread of Homo sapiens across the globe. Once again, the real story of human origins turns out to be not the childish simplicity of myth, but the far more fascinating complexity of evolution.

Refuting Creationism - Rapid Evolution After The Dinosaur Extinction - 66 Million Years Before 'Creation Week'

An artist’s interpretation of life and death after the asteroid impact that wiped out the dinosaurs. The three hair-covered forms (left) represent species of plankton found inside the crater made by the impact. The geometric form (bottom left) is a species of algae. The bones belong to an extinct marine reptile.

The University of Texas at Austin Jackson School of Geosciences/John Maisano.

Evidence of ‘Lightning-Fast’ Evolution Found After Dino-Killing Asteroid Impact | Jackson School of Geosciences | The University of Texas at Austin

That life on Earth eventually recovered after the Chicxulub impact—the asteroid strike that wiped out the non-avian dinosaurs and much of the planet’s megafauna—is hardly surprising. If it had not, mammals and birds would not be the dominant land vertebrates today. What may be more surprising is how quickly that recovery appears to have begun, according to new research led by Assistant Professor Chris Lowery of the University of Texas Institute for Geophysics (UTIG) at the Jackson School of Geosciences.

Their findings have just been published in the journal Geology.

For creationists, the study presents yet another awkward problem. Not only did these events occur 66 million years ago — tens of millions of years before primates evolved, let alone the humans that some creationists insist lived alongside dinosaurs — but the results also show evolution proceeding exactly as evolutionary theory predicts.

Refuting Creationism - The Evolution of Our Ancestral Fish

Illustration of the Paleolophus swimming in ancient Asian seas.

Credit: Dr Brian Choo (Flinders University)

New pieces link fish puzzle – News

Today we have not one but two papers which together help fill a gap between the bony fishes and the first fish to venture onto land and evolve into the terrestrial tetrapods from which all land vertebrates subsequently evolved. It is a gap that presents creationists with a dilemma: it would have been a perfect god-shaped gap into which to insert their designer; however, it dates to some 410 million years ago, far too distant for their preferred timeline of 6,000–10,000 years, into which they need to try to compress the entire history of the universe.

One of these papers, just published in Canadian Journal of Zoology, is by a team from Flinders University, led by Dr Alice Clement, who have reassessed a mysterious fossil from the Late Devonian Gogo Formation in Western Australia using the latest technology, including CT scanning and computed tomography.

This work adds to our understanding of lungfish evolution from a key Australian fossil site that contains a diversity of lungfish fossils, including some poorly preserved specimens.

Meanwhile, Flinders University researcher Dr Brian Choo and colleagues at the Chinese Academy of Sciences, led by the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, have described a new fossil, Paleolophus yunnanensis (‘old crest from Yunnan’). This team's work has just been published in Current Biology.

Paleolophus helps fill the gap between ancestral lungfish and their diversification a few million years later; in other words, it is one more example of the sort of transitional form that creationists insist does not exist: yet another so-called 'missing link'.

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 - Evidence For Earliest Large Land Predators - 280 Million Years Before 'Creation Week'

New study finds earliest evidence of big land predators hunting plant-eaters | EurekAlert

Contradicting creationist claims that death entered the world when Eve's sin somehow transformed a previously perfect world into a fallen one—with the creator god apparently powerless to prevent some other magical entity interfering in its creation—we now have evidence of predation; that is, the killing and eating of one living organism by another. Needless to say, like 99.975% of the history of life on Earth, this all occurred 280 million years ago, during that long pre-“Creation Week” period before the creationist god supposedly decided to create his small flat planet with a dome over it and call it perfect.

The nonsensical idea that there were no deaths before “The Fall” has always defied logic because all living things require a supply of energy in the form of food. Even if that food is plants, plants must die in the process. But then the Bible’s mythologies were written by people who confused “living” with “breathing”, so assumed plants were not living. Presumably, Bible literalists today believe the same biologically nonsensical idea.

The evidence for the earliest large land predators comes from three palaeontologists led by Professor Robert R. Reisz of the Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada, who have just published their findings, open access, in the journal Scientific Reports. The group studied tooth marks on the fossilised skeletons of three young herbivores from the Permian of Texas. Two hundred and eighty million years ago was relatively soon after the first terrestrial tetrapods had crawled out of the sea and evolved into amphibians and the earliest proto-reptiles. The evolution of predation would have been a major driver of evolution due to the resulting arms races in which predators became more efficient hunters and prey became better at avoiding being eaten—a process that hardly fits the description “intelligent design”.

Refuting Creationism - Earth - Fine Tuned For Catastrophe

Impact-formed glass evidence of cosmic collision in Brazil about 6 million years ago

Geologists led by Professor Álvaro Penteado Crósta of the Institute of Geosciences at the State University of Campinas, Brazil (IG-UNICAMP), in collaboration with researchers from Brazil, Europe, the Middle East and Australia, have discovered evidence of an impact by a large extraterrestrial body at least 6.3 million years ago.

They have recently published their findings in the journal Geology. This impact joins the long list of such collisions in Earth’s history — not merely the one that marked the Cretaceous–Paleogene (K–Pg) mass extinction that eliminated the non-avian dinosaurs.

Creationists like to imagine they live in some sort of wonderland, specially created with them in mind — perfectly designed for human existence. Of course, this ignores the fact that much of the Earth is uninhabitable and even actively hostile to human life without specialised equipment. They often refer to Earth as existing in a ‘Goldilocks zone’ where everything is “just right”, forgetting that life could only have evolved on a planet where conditions permitted it. Our existence does not demonstrate improbability; it simply confirms that the necessary conditions were present.

Away from the tropics, ordinary human life is only possible with clothing, heating and buildings — or at least some form of shelter and a means of making fire. None of us would survive for more than a few hours naked outdoors in mid-winter at northern or southern latitudes.

Much of the planet is covered by deep oceans, and large areas of land consist of high plateaus or arid deserts where human life would again be impossible without specialised technology.

It also ignores the fact that, throughout its history, Earth has endured catastrophe after catastrophe. Mass extinctions have often been triggered by plate tectonics, which alter ocean currents and weather patterns, or by volcanic activity that disrupts the balance between CO₂ production and its removal by plants. Earth exists within a cosmos capable of bombarding it with the debris left over from planetary formation — from microscopic dust grains to vast bodies of rock that release enough energy on impact to devastate regions hundreds of kilometres across. Such collisions can inject enormous quantities of dust and aerosols into the stratosphere, blocking sunlight for years and plunging the planet into prolonged global cooling, with devastating ecological consequences.

Refuting Creationism - Cleaner Wrasse Have Mammal-Like Cognitive Abilities

Cleaner wrasse, Labroides dimidiatus

By Diego Delso, CC BY-SA 4.0, Link

Cleaner wrasse with giant moray eel client

By Silke Baron - originally posted to Flickr as Giant Moray Eel getting cleaned,
CC BY 2.0, Link

Cleaner fish show intelligence typical of mammals | Osaka Metropolitan University

A central dogma of creationism—indeed one reason why it persists and is clung to in the face of contrary evidence, massaging the egos of creationists—is the claim that humans were uniquely created, separate from and superior to other animals. Until the middle of the 20th century, humans were believed to possess unique abilities to make and use tools, to learn and design, and above all to be self-aware—qualities that religious people believed placed us next to God in possessing these abilities because we had been created in its image.

Since then, one formerly unique human ability after another has been shown to be possessed by other animals, mainly, but not exclusively, mammals and birds. Many species are now known to use tools and some are even known to make them. And many have been shown to be self-aware, using the 'mirror test' in which an animal can identify the image in the mirror as itself—see the information in the side panel for many examples of other animals with these formerly 'unique' human abilities.

Now a team of researchers, led by Dr. Shumpei Sogawa and Professor Masanori Kohda of Osaka Metropolitan University, Osaka, Japan, have shown that a fish, the cleaner wrasse, shows evidence of self-awareness according to the mirror test. These small fish specialise in removing parasites from the bodies of larger fish, even entering the mouths of predators to remove food particles and parasites from between the teeth and on the gills of their 'clients'. The Osaka-led team recently published their findings, open access, in the journal Scientific Reports.

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.

Refuting Creationism - Global Spread of Giant Predatory 'Sea Salamanders' - 250 Million Years Before 'Creation Week'

Erythrobatrachus noonkanbahensis (foreground) and Aphaneramma (middle ground)

AI-Generated image (ChatGPT 5.2)

250 million-year-old amphibian fossils from Australia reveal global spread of ‘sea-salamanders’

Since the beginning of 2026, with only a few days spent on other projects, I’ve been able to write one or two articles every day about yet another paper that comprehensively refutes basic creationist dogma and illustrates the strength of the Theory of Evolution as the grand unifying theory of biology, without which little of it would make sense. Over the same period, there has not been the faintest hint of a paper providing peer-reviewed support for ID creationism, or even suggesting that the Theory of Evolution is in crisis and in need of replacement because it cannot explain the facts.

Today is no exception, with the second such paper. The first showed how people were using signs and patterns to communicate ideas 30,000 years before creationists think Earth was created; this one discusses the fossil record from 250 million years ago and what it tells us about the evolution of early marine tetrapods — animals that had returned to the marine environment from which their ancestors had originally emerged and had become apex predators. In this case, the focus is on an amphibian that had converged on a body shape resembling a crocodile.

It also shows how an environmental catastrophe — itself utterly inconsistent with creationist notions of a created perfection ideally suited for life — created opportunities that could be exploited by the evolutionary process, allowing surviving lineages to radiate into new species, exactly as evolutionary theory predicts. Again, this stands in stark contrast to the childish notion of special creation without ancestors by some unexplained magical process.

The paper, by an international team led by Dr Lachlan Hart of the University of New South Wales, has just been published in the Journal of Vertebrate Paleontology. It explains how fossils of a marine amphibian, Erythrobatrachus noonkanbahensis, found in the Blina Shale and originally described in 1972 from material recovered in the 1960s, turn out on re-examination to represent two different species, one of which rapidly achieved a near-global distribution, probably by coastal dispersal around the supercontinent Gondwana.

These species appear to have flourished soon after the ‘Great Dying’, the end-Permian mass extinction event that saw the disappearance of 90–96% of all species (around 96% of marine species and 70% of terrestrial species).

Dr Hart has explained his team’s research and its significance in a University of New South Wales news item. He has also written an article in The Conversation, reproduced below under a Creative Commons licence, reformatted for stylistic consistency. First, background information on the end Permian mass extinction or 'Great Dying':

Abiogenesis News - Origin Of Complex (Eukaryote) Cells - Association With Mitochondria.

Beginnings of symbiosis

Ai-Generated image (ChatGPT 5.2)

A Break in a Longstanding Mystery about Origin of Complex Life | College of Natural Sciences

Here are a couple of papers published today that deal with related aspects of the origins of complex (eukaryotic) cells — all living organisms apart from Bacteria, Archaea and viruses (the prokaryotes). There is little doubt in biology that eukaryotes evolved from symbiotic associations between prokaryotes, despite the regular creationist straw man claim that scientists are naïve enough — or somehow brainwashed by evil “Darwinists” — to believe that the first complex cell arose spontaneously in a single step so fantastically improbable that magical creation becomes an almost plausible alternative.

In reality, as these two papers demonstrate, the precise details of how these symbiotic associations arose remain matters of active research and debate. I will deal with the second paper in a separate blog post. This post concerns the paper by scientists from The University of Texas at Austin, published in *Nature*, which addresses the question of how the oxygen-dependent bacterium that became the mitochondrion came together with a presumed anaerobic (oxygen-intolerant) archaeon, given that the two would not be expected to occupy the same environment.

The team propose that this apparent problem may be resolved by evidence that some archaea of the Asgard group — which today live primarily in the deep sea and other oxygen-free environments — can use, or at least tolerate, oxygen.

The Asgard archaea most closely related to eukaryotic cells are found in shallow coastal sediments or floating in the marine column. Crucially, they possess metabolic pathways that use oxygen. It is therefore possible that their ancestors did as well, meaning they could have cohabited with the bacterial ancestors of mitochondria.

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.