Refuting Creationism - How Complex Organs Evolve

Using the placenta to understand how complex organs evolve

Recently, a new creationist member of a Facebook group resorted to the familiar tactic of presenting the placenta as a complex organ that could not possibly have evolved. As so often with creationist arguments, this was little more than an argument from personal incredulity dressed up as a challenge. In place of scientific evidence, he relied on a god-of-the-gaps argument and a false dichotomy, implying that if he could not imagine a natural explanation, the only alternative must be magic performed by his preferred deity.

The new member appears to have left the group soon after replies began to appear in the comments, complete with links to articles and papers explaining exactly how the problem can be approached scientifically.

This paper in Nature by Oliver W. Griffith and Günter P. Wagner of Yale University provides precisely the sort of answer that exposes the weakness of this common creationist tactic on social media. Their argument amounts to little more than: “I do not know how this could have evolved, therefore God did it.” That is not an explanation; it is simply ignorance masquerading as evidence, and tells us more of the parochial ignorance of the creationist than they probably intended. The paper uses the evolution of the placenta to explain some basic principles of how complex organs evolved. Needless to say, no magic is involved anywhere in the process.

One of the authors, Oliver W. Griffith, has also written an article in The Conversation explaining their research and what it tells us about the evolution of complex organs in vertebrates. His article is reproduced here under a Creative Commons licence, reformatted for stylistic consistency.

First, a short explanation of the role of the placental in placental mammals:

Refuting Creationism - Ancestral Mammals Laid Eggs - Over 200 Million Years Before 'Creation Week'

Impression of Lystrosaurus in natural setting

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Lystrosaurus embryo within its partially preserved shell, reconstruction of the animal

Pictures - Professor Julien Benoit Drawing - Sophie Vrard.

Embryo fossil found in South Africa is world’s oldest proof that mammal ancestors laid eggs

It is well established in evolutionary biology that mammals arose from within the synapsid lineage, the ancient group that includes the therapsids - stem-mammals that long predate true mammals. What had remained uncertain, however, was whether those early synapsids still reproduced by laying eggs, as modern monotremes such as the platypus and echidnas do, or whether live birth had evolved much earlier in the mammalian line.

That gap in our knowledge has now been narrowed dramatically and, no doubt to the acute discomfort of creationists, the evidence shows that about 250 million years ago - roughly 244 million years before young-Earth creationists believe the Earth was created - a therapsid was still reproducing by laying eggs. The evidence comes from a fossil embryo discovered in South Africa in 2008 by palaeontologist John Nyaphuli. Even more awkward for creationists, their mythology requires animals to have been created as separate, unrelated ‘kinds’, yet here we have direct evidence from the stem-mammal lineage showing a reproductive stage inherited from deep evolutionary ancestry rather than sudden, magical creation without predecessors.

Now Julien Benoit and Jennifer Botha of the University of the Witwatersrand, South Africa, together with Vincent Fernandez of the European Synchrotron Radiation Facility in Grenoble, France, have used high-resolution CT and synchrotron imaging to examine the curled-up embryo inside the rock and identify it as a young Lystrosaurus, a dicynodont therapsid from the Early Triassic. Crucially, the specimen preserves features consistent with an unhatched embryo, including a tightly curled in ovo posture and an unfused lower jaw symphysis. No calcified eggshell was preserved, so the egg was probably soft and leathery, as expected for a very early synapsid. Their findings are reported in an open access paper in PLOS One.

The authors have also co-authored an article in The Conversation explaining the discovery and its significance. Their article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency.

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]

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

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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.

Malevolent Design - How Brain Cells Promote Brain Cancer

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Scientists uncover hidden cells fuelling brain cancer — and a drug that could stop them - McMaster News

Scientists at McMaster University and The Hospital for Sick Children have discovered how a type of brain cell that normally supports healthy brain function can instead go rogue, helping glioblastoma grow and spread. Their findings were recently published in the Cell Press journal Neuron. The prognosis for glioblastoma remains grim, with survival often measured in months.

As putative examples of intelligent design, cells like these should be acutely embarrassing for any creationist willing to follow the evidence where it leads, because within the ID creationist paradigm the only logical conclusion is that the designer is malevolent. By contrast, as examples of how evolution produces workable but imperfect, error-prone systems, they are entirely consistent with the Theory of Evolution and yet another vindication of the science.

Glioblastoma is not simply a mass of malignant cells, but an organised ecosystem sustained by a network of interacting cells. In that sense, it is indistinguishable from the sort of irreducibly complex system that Michael J. Behe claims is evidence of intelligent design. What the researchers found is that a type of cell called an oligodendrocyte, normally responsible for supporting and insulating nerve fibres, can switch roles and actively support tumour growth. These helper cells communicate with cancer cells through a specific signalling system, creating conditions in which the tumour can flourish.

The team discovered that a crucial part of this communication system involves cell-surface receptors called CCR5. By blocking this receptor, tumour growth can be significantly slowed. CCR5 is already the target of the anti-HIV medication Maraviroc, a drug that has already been clinically tested and approved, so it offers a potentially promising treatment for glioblastoma, even if not yet a cure.

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.

Malevolent Design - A Parasitic Fly With All Creationism's Hall Marks for Intelligent Design Is Heading For The USA

Lava of the New World screwworm, Cochliomyia hominivorax.

By John Kucharski - via Wikipedia

The New World screwworm, Cochliomyia hominivorax.

Judy Gallagher, CC BY

An article in The Conversation by Richard Wall, Emeritus Professor in the School of Biological Sciences at the University of Bristol, should remind creationists—if they had the wit to understand why—of the theological quagmire into which their favourite leaders have led them.

The Discovery Institute and its fellows, with their reliance on notions such as irreducible complexity and complex specified genetic information, have taken creationism to a point where the only escape lies in three almost equally unacceptable options:

• They can abandon the very arguments they present as proof of intelligent design, and so admit that they have no proof at all.
• They can accept that the designer god they traditionally equate with the god of the Bible and Qur'an is in fact an evil god, relentlessly designing ever more ingenious ways to increase suffering in the world.
• Or they can retreat into theology and Bible-literalist fundamentalism, abandoning any pretence that intelligent design is genuine science rather than simply rebranded creationism, by blaming everything on 'The Fall'. But in doing so they must also admit the existence of some other creative force with powers sufficient to rival their creator god—one to which their god is either powerless or indifferent. That, of course, destroys the basic principle of Judeo-Christian monotheism: a single omnipotent ruling deity. Ironically, the Discovery Institute was established for the very purpose of persuading US legislators and state education officials that intelligent design is real science.

This problem for creationism arises because the notions of irreducible complexity and complex specified genetic information apply just as well—if not better—to parasites and pathogens as they do to those aspects of nature that creationists like to present as evidence of their god's existence and benevolence; in other words, anything that happens to benefit them.

Professor Wall's article concerns a parasitic fly, the New World screwworm, Cochliomyia hominivorax, whose larvae feed on open wounds in cattle and sometimes humans, often with fatal consequences. The fly is currently extending its range northwards through Mexico and has now reached states bordering Texas. His article is reproduced here under a Creative Commons licence, reformatted for stylistic consistency:

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]

Creationism Refuted - A Possible Ancestor Of All The Apes - From Egypt

Masripithecus moghraensis in Early Miocene Egypt

AI-generated image (ChatGPT Latest) based on artist's reconstruction.

Masripithecus: A new Miocene ape from Egypt sheds light on the origins of modern apes

Another piece of the rich and complex story of human evolution may have come to light, and it is not quite what researchers had expected. Competing theories have placed the ancestral home of the common ancestor of African and Asian anthropoid apes either in Eurasia or in Africa. This discovery, however, points instead to Egypt, and more broadly to North Africa and the Middle East, as the region in which the pivotal transition from Old World monkeys to the lineage that gave rise to the modern apes may have occurred.

News that this distant ancestor of humans came from Egypt and the wider Middle East may briefly gladden the hearts of creationists desperate for support for the biblical myth of a special creation of humans in that region. That enthusiasm is unlikely to survive contact with the details, however, because this animal lived 17–18 million years ago and was not a human at all, but part of the lineage leading to the common ancestor of humans, chimpanzees, gorillas and the Asian apes. Like so much palaeontological evidence, it therefore stands not in support of the Genesis creation myth, but as evidence for Darwinian evolution.

The discovery is described in a recent paper in Science by a research team from the Mansoura University Vertebrate Paleontology Center in Egypt and the University of Southern California in the USA, led by Mansoura University palaeontologist Hesham Sallam.

The fossil, belonging to a species the team have named Masripithecus moghraensis, was discovered at Wadi Moghra. The generic name combines Masri, the Arabic word for “Egyptian”, with the Greek píthēkos, meaning “ape”, so the name can be read as “Egyptian ape from Moghra”.

Although the find consists only of a lower jaw, it preserves several features not seen in any contemporaneous apes, including exceptionally large canine and premolar teeth, and molars with rounded, heavily textured chewing surfaces, all set in a robust mandible. Taken together, these features suggest a flexible feeder able to eat both fruit and harder foods such as nuts, an adaptation that may have helped it cope with the increasingly seasonal climate of Early Miocene Egypt.

In addition to the sophisticated Bayesian methods that placed Masripithecus earlier in ape evolutionary history than any other known fossil anthropoid, the researchers point out that during the Early Miocene the Egyptian region lay at a geographical crossroads between Eurasia and Africa. At that time, the African and Arabian plates were still moving northwards towards Eurasia, while fluctuating sea levels periodically opened migration routes between the continents. As so often in palaeontology, multiple independent lines of evidence converge on the same conclusion.

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

AI-generated image (ChatGPT Latest)

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 - Archaic Hominins In Spain - 390,000 Years Before 'Creation Week'

Homo antecessor working at the Gran Dolia butchery site

AI-generated image (ChatGPT Latest)

The Gran Dolina site at Atapuerca reveals an almost exclusive use of local chert 400,000 years ago | CENIEH

In stark contrast to the simplistic Bronze Age mythology of the Bible, in which all humanity is supposedly descended from a single magically created couple with no ancestors just a few thousand years ago, followed by a biological reset in a global genocidal flood a mere 4,000 years ago, archaeology continues to reveal a far richer and more complex human story. Instead of a single recent origin, the evidence shows a deep evolutionary history stretching back hundreds of thousands of years, involving multiple related human species and regional populations, with occasional interbreeding. Part of that long history was played out in Eurasia.

A study led by scientists from the Spanish Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), just published in Quaternary International, has identified 400,000-year-old human artefacts at the Gran Dolina site in Atapuerca, Burgos, Spain, together with what may be the earliest evidence of communal hunting. The findings show the sophisticated manufacture of stone tools from locally available chert. The site is also associated with the remains of 60 bison, strongly suggesting a communal butchering site that implies strategic planning, cooperation, and large-scale social coordination.

What makes this especially striking is that these activities took place before the hominin lineage had diversified into Neanderthals, Denisovans, and modern humans. Taken together with other evidence from Atapuerca, including discoveries from Sima de los Huesos (‘Cave of Bones’), the findings indicate that archaic hominins such as Homo antecessor had established themselves in Iberia long before Homo sapiens entered Eurasia.

Refuting Creationism - A Reptile That Looks Like A Cross Between a Greyhound And A Crocodile - From 215 Million Years Ago

Life reconstruction of Galahadosuchus jonesi n. gen. n. sp. The morphology of regions of the body that are not currently known for Galahadosuchus jonesi (i.e., not preserved in NHMUK PV R 10002) is inferred from comparison with Terrestrisuchus gracilis (Spiekman et al., 2023, 2024) due to the high degree of morphological similarity between these two taxa. Scale bar represents 100 mm.

Artwork by M. Dempsey.

New species of ancient crocodile named in honour of Welsh school teacher | Natural History Museum

A newly named, 215-million-year-old species of crocodile-like reptile, discovered in Gloucestershire, UK, and described in The Anatomical Record, looks rather like the sort of creature creationists imagine a transitional fossil should be: half of one modern species and half of another from an unrelated group. That, of course, is the ridiculous parody of evolution that the creationist cult teaches its followers to believe is what those crazy scientists think the Theory of Evolution describes.

In reality, this discovery is nothing of the sort. What it actually reveals is a species that raises interesting questions about the environmental pressures that shaped its evolution. It was a long-legged, fast-running crocodylomorph, resembling a greyhound with scales and a crocodile’s head and jaws. It probably lived its entire life on land, using its speed to hunt small animals. That, in turn, suggests its prey were also fast-moving, rather like the relationship between cheetahs and gazelles, which have co-evolved speed in an evolutionary arms race: one to catch fast prey, the other to escape a fast predator. It is exactly the sort of process that refutes the notion of intelligent design, yet is entirely predictable under the Theory of Evolution by natural selection.

This animal lived in what was then an area of high ground overlooking hot, arid plains during the Late Triassic. That was a period of major diversification, brought to an end by a mass extinction caused by intense volcanic activity. It was followed by the Jurassic, so comparing animals from before and after that extinction event can help us understand how life responded to those dramatic environmental changes. Among the creatures that survived were the ancestors of the dinosaurs, and later, birds and mammals.

The research team, led by PhD student Ewart H. Bodenham of University College London, with colleagues from UCL, the Natural History Museum, London, and the Staatliches Museum für Naturkunde Stuttgart, Germany, carried out a detailed analysis of this and other fossils from fissure deposits on either side of the Bristol Channel, in South Wales and South-West England. They concluded that this specimen represented a species new to science.

Unintelligent Design - Men Lose Their Y Chromosome - And Why It Matters

Men lose their Y chromosome as they age. Scientists thought it didn’t matter – but now we’re learning more

Creationists who point to the supposed 'perfection' of the human body as evidence of intelligent design have yet more evidence to ignore if they are to retain that belief. In my book, The Body of Evidence: How the Human Body Refutes Intelligent Design, I listed many of the conditions and vulnerabilities from which humans suffer precisely because our bodies are the products of evolution, not intelligent design. Viewed objectively, rather than through the rose-tinted lens of creationism, the human body is one of the strongest arguments against intelligent design and in favour of evolution.

We now have additional evidence of this. As men age, increasing numbers of their cells lose the Y chromosome — the chromosome that males normally possess alongside a single X chromosome, while females usually have two X chromosomes. It is becoming increasingly clear that this loss is implicated in several diseases that affect men disproportionately, including cardiovascular disease, Parkinsonism, and some cancers such as ocular melanoma. Together, these help to explain men's lower life expectancy.

According to the ID creationist paradigm, the human body is the supreme achievement of their god's design. So, if we assume, as they do, that this designer is the omniscient and omnibenevolent god of the Bible and Qur'an, then this male-specific vulnerability must either have been intended or be the accidental result of incompetence and lack of foresight. Traditionally, of course, ID creationists try to absolve their designer of responsibility for such flaws by blaming them on some other entity supposedly capable of thwarting the divine plan, with humans bearing the guilt because of the 'sin' of a mythical ancestral couple. This merely exposes Intelligent Design for what it really is: not science, as the Discovery Institute and its allies insist, but biblical literalism in a lab coat, forced to rely on fundamentalist superstition to explain away the failures of its own claims when the facts are examined.

How scientists are discovering this age-related loss of the Y chromosome in men's cells, and the damaging effects it has on male health, is the subject of an article in The Conversation by the distinguished geneticist Jenny Graves, Distinguished Professor of Genetics and Vice-Chancellor's Fellow at La Trobe University, Australia. Her article is reproduced here under a Creative Commons licence, reformatted for stylistic consistency.

First, some background information on the origins and function of the Y chromosome:

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.

Unintelligent Design - The DNA Design Blunder That Causes Cancers and Dementia - Malevolence, Incompetence or Evolution?

New research discovers dementia-linked protein’s role in DNA mistakes | Houston Methodist Newsroom

Scientists have discovered that a protein responsible for regulating DNA repair can itself become a source of genomic instability, contributing to cancers and neurodegenerative diseases. The finding provides another example of the fragile and failure-prone complexity that characterises biological systems shaped by evolutionary tinkering rather than the work of a competent designer.

The research, reported in an open access paper published in the journal Nucleic Acids Research, was carried out by a team led by Professor Muralidhar L. Hegde, PhD, professor of neurosurgery at the Houston Methodist Research Institute's Center for Neuroregeneration and Department of Neurosurgery. The team describe how a key regulatory protein, TDP43, which controls the genes involved in DNA repair, can itself become a major cause of genomic instability.

When the regulation of TDP43 fails, the consequences can include cancers, amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). The difficulty is that this protein can either be absent or overproduced, and both conditions cause the DNA repair genes it regulates to become overactive, resulting in a destabilised genome. This sort of delicate regulatory balance is exactly what evolutionary biologists expect from systems assembled gradually through natural selection, where new control mechanisms are added to existing processes rather than engineered from scratch.

This presents an awkward problem for creationists who claim that biological complexity is evidence of intelligent design. For those with the intellectual integrity to confront the implications, the findings present a difficult choice. Either accept that evolution provides a coherent explanation for such biological paradoxes, or accept that what is claimed to be evidence of intelligent design instead suggests a designer who is incompetent, malevolent, or possibly both—certainly nothing like the allegedly omnibenevolent god of the Bible and Qur'an.

There are also a couple of additional problems here for ID creationists. First, well-designed DNA should not require an additional layer of complexity in the form of a suite of repair genes, followed by yet another regulatory system to control them. Secondly, a well-designed repair mechanism should not itself require such delicate regulation, and the regulatory system should certainly not fail—let alone fail catastrophically. Within the ID creationist paradigm, this is difficult to reconcile with the idea of a competent and benevolent designer.

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.