Refuting Creationism - Evolution Of Immunity, Longevity And Cancer Resistance In Bats - No Magic Needed

Myotis bats

Little Brown Bat, Myotis lucifugus. Can live up to 35 years, immune to most viruses and rarely develops cancers

Photo © Michael Durham,
Illinois Department of Natural Resources

Clues to longevity may reside in the genomes of long-lived bats - Berkeley News

Creationists routinely claim that mutation cannot produce new genetic information and that complex biological systems must have been separately designed for their allotted purposes. Yet living genomes bear little resemblance to collections of independently engineered components. Genes are duplicated, deleted, rearranged and modified; the resulting variants are tested by natural selection; and the same molecular machinery is repeatedly recruited for several different functions. A new study of bats provides a particularly revealing example of this evolutionary improvisation.

Viruses and their hosts have been engaged in evolutionary arms races for hundreds of millions of years. Viruses evolve ways to enter cells, evade immune responses and appropriate cellular machinery for their own replication, while their hosts evolve countermeasures. From a creationist perspective, this requires an intelligent designer simultaneously to design the viruses, their means of attacking their hosts and the defensive systems needed to resist them. Evolution provides the far simpler explanation: each side imposes selection on the other, with no foresight, overall plan or concern for the suffering caused along the way.

In a paper published in Nature, an international team of researchers assembled near-complete genomes for eight closely related species of Myotis bat and established primary cell lines with which to test some of the genomic findings. The comparison revealed abundant structural variation—including inversions, translocations and gene duplications—within an otherwise strongly conserved arrangement of chromosomes.

The researchers found that bats have responded differently to different classes of virus. Proteins interacting with DNA viruses showed an unusually strong signature of positive selection, whereas genes interacting with RNA viruses were especially prone to gains and losses of copies. One antiviral gene, EIF2AK2, better known as PKR, occurs in one, two or, in one lineage, three copies. The original duplication appears to have arisen near the base of the Myotis radiation, with duplicated and unduplicated forms persisting across species for tens of millions of years. This is new genetic material arising through mutation and subsequently being retained, modified or lost according to its effects—not information supplied fully formed by an external intelligence.

Refuting Creationism - How We Know The Bible Was Written By Ignorant People - Sex Determination In Geckos

Various Geckos

Source: Wikipedia

XY or ZW? Geckos Reveal Evolution's Hidden Playbook

The simplest way to test the claim that the Bible is the inerrant work of an omniscient creator is to compare its account with observable reality. When that is done, its creation stories reflect the limited biological knowledge of their human authors, not omniscience. Genesis 1:27 presents “male and female” as divinely ordained categories for humans, while the wider biblical narrative assumes the familiar arrangement of sexually reproducing males and females among animals; indeed in Genesis 6:19 the Bible unambiguously states all the animals on the Ark were male and female.

Real biology is much less tidy. Many animal species are simultaneous or sequential hermaphrodites; some lineages consist entirely of females and reproduce by parthenogenesis; and many organisms reproduce without sex at all. The biblical authors displayed only the knowledge expected of people living in an ancient pastoral society. An omniscient creator would have known better.

Nor are the mechanisms that determine sex fixed systems established in a single act of creation, with organisms thereafter reproducing only “after their kind”. They are themselves products of evolution. The new gecko study indicates that different lineages have switched repeatedly between genetic sex determination and environmental sex determination, in which conditions such as egg-incubation temperature influence the offspring’s sex. Even genetic sex determination has repeatedly been reinvented, with different ordinary chromosomes recruited independently to become X and Y or Z and W chromosomes. Instead of one immutable system imposed by a designer, geckos exhibit an evolutionary patchwork assembled and repeatedly modified over millions of years.

The familiar mammalian arrangement in which females are XX and males XY is sometimes treated as though it were the inevitable—and therefore designed—way of determining sex. But nature displays no such uniformity. Birds generally use a ZW system, in which females are ZW and males ZZ, while many reptiles dispense with specialised sex chromosomes altogether and allow environmental conditions, particularly incubation temperature, to influence whether an embryo develops as male or female.

Geckos exhibit all three arrangements, sometimes among relatively closely related species. This extraordinary diversity makes them a natural experiment in how sex-determination mechanisms originate, change and disappear during evolution.

In a new study published in *Science*, Yang Zhou and colleagues compared chromosome-level genomes from geckos representing all seven living families. Their reconstruction indicates that gecko lineages have switched between environmental and genetic sex determination at least 23 times. The researchers identified 22 distinct sex-chromosome systems and traced them to 17 different chromosomes in the ancestral gecko genome. Some of those ancestral chromosomes were recruited independently on several separate occasions.

Refuting Creationism - Now It's A Transitional Early Insect - From 324 Million Years Before 'Creation Week'

Palaeoecological reconstruction of the Carboniferous stem-insect Chosha praecursor

From: Tihelka, E., Vásquez, C., Engel, M.S. et al (32026)

Amphibious stem-insect rewrites the evolutionary history of insect terrestrialization---- Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences

A favourite creationist debating tactic is to point to a gap in the fossil record and pretend that the absence of a known transitional form is evidence that no transition occurred. When a suitable fossil is eventually found, the manoeuvre simply creates two smaller gaps on either side of it—or the fossil is arbitrarily declared to be “fully formed” and therefore not transitional. A simple trick which exposes the ignorance and disingenuity of creationism, is to ask them to describe exactly what they would expect a transition fossil to look like. They tend to abruptly break off the debate, because to answer it would violate two unwritten rules of creationism - never consider being wrong and never state what evidence would cause you to change your mind in case it's produced.

This 'god of the gaps' rhetorical game depends upon treating an inevitably incomplete geological record as though it ought to contain a specimen from every generation of every evolving lineage - something that if it were true, would be hard for science to explain, given what we know of the circumstances in which fossils are formed, which actually predicts that the record will be discontinuous.

The early history of insects has offered particularly fertile ground for this tactic. Molecular-clock studies indicate that hexapods diverged from aquatic crustacean relatives hundreds of millions of years ago, yet their small, delicate bodies were poorly suited to fossilisation, especially in the environments through which they were making the transition onto land. Consequently, there has been a conspicuous interval—the so-called “hexapod gap”—between the earliest evidence of hexapods and the abundance of unmistakable insects in later Carboniferous rocks.

Now, an international team led by Erik Tihelka and Chenyang Cai has described a remarkable fossil that helps to narrow that gap while illustrating how the familiar insect body plan was assembled. The approximately 324-million-year-old animal, named Chosha praecursor, came from the Late Mississippian Tesnus Formation of western Texas. Collected in 1985 and long misidentified as a juvenile crustacean, it remained in a museum collection until examination under cross-polarised light revealed anatomical details that had previously been almost invisible. The findings are reported in Nature.

Refuting Creationism - A Road-Map Of Evolution Over 600 Million Years - From A Common Ancestor

The ever-branching tree of animal Evolution

AI-generated image (ChatGPT 5.6 SOL)

Roadmap of animal biodiversity: largest-ever comparison of chromosome-scale genomes

Words such as rules, pathways and highways can become treacherous when scientific findings pass through the hands of religious apologists. A rule, in ordinary speech, suggests someone who made it; a highway suggests an engineer who decided where it should lead. It is therefore easy to anticipate claims that a major new study of animal chromosomes has discovered evidence that evolution follows rules—and that rules must imply a rule-maker directing evolution towards a predetermined goal.

That, however, is not what the researchers have found.

In the largest comparison of chromosome-scale animal genomes yet undertaken, Darrin Schultz and colleagues analysed 5,821 genomes representing 4,454 species in 19 animal phyla. Their study, published in Science Advances, developed what they call “evolutionary genome topology”: a way of mapping the enormous variety of animal genomes according to the organisation and shared ancestry of their chromosomes. The results reveal recognisable, partly irreversible patterns extending back more than 600 million years to the common ancestor of living animals.

The accompanying University of Vienna press release describes these patterns as “evolutionary highways” and says that genomes evolve according to a limited set of “rules”. Those are useful metaphors, but they describe constraints and consequences—not commands, intentions or a plan.

Animal chromosomes can split, fuse and exchange material, but these processes are not free to produce every imaginable arrangement with equal probability. Existing chromosome structure limits what can happen next, while every change becomes part of the starting conditions inherited by subsequent generations. In particular, when ancestral chromosomes fuse and their genes subsequently become intermingled, the original arrangement cannot simply be reconstructed by reversing the fusion. The researchers call this process “fusion-with-mixing”. It makes chromosome evolution path-dependent: where a lineage can readily go next depends partly upon where it has already been.

This is what “rules” means in this context. It no more implies a supernatural rule-maker than the regular formation of crystals implies a crystal designer, or the course taken by a river implies that someone planned its route. Physical and chemical processes have consistent properties; biological structures impose constraints; and inherited history restricts the range of subsequent possibilities. Regular outcomes can emerge from those natural conditions without foresight or intention.

Nor does the statement that genomes “do not change at random” mean that their future has been prescribed. Mutations and chromosome rearrangements can occur without regard to what an organism needs, but randomness does not mean that every conceivable event is equally likely—or even physically possible. Some rearrangements are more readily produced than others; some are lethal or reduce fertility; some survive genetic drift or natural selection; and every surviving arrangement alters the possibilities available to its descendants. Chance operates within constraints, producing statistical patterns rather than fulfilling a programme.

Refuting Creationism - The Slow Evolution and Extinction Of African Megafauna - Over 23 Million Years

Modern African megafauna

A selection of extinct African megaherbivores

AI-Generated image (ChatGPT 5.6 Sol)

Scarce emergence of new species drove the decline of African megaherbivores | Museo Nacional de Ciencias Naturales

Africa’s elephants, rhinoceroses and hippopotamuses are surviving representatives of a much richer assemblage of giant herbivores that once included such animals as Deinotherium, an elephant relative with downward-curving tusks, and the pig-like anthracotheres, relatives of modern hippopotamuses. These animals were not merely conspicuous members of their ecosystems. As “ecosystem engineers”, megaherbivores—here defined as herbivorous mammals weighing at least one tonne—alter vegetation, disperse seeds, open pathways, create water holes and redistribute nutrients.

Why so much of this diversity disappeared has usually been approached as a question of extinction. Large animals reproduce slowly, require extensive habitats and comparatively large quantities of food, so it seems intuitively reasonable to assume that they must have been especially vulnerable when climates and environments changed. Human hunting has also figured prominently in explanations of the much more recent global disappearance of large mammals.

But the diversity of any group depends upon two processes, not one. Extinction removes species, while speciation produces new ones. Even a lineage with a comparatively modest extinction rate will decline if its species disappear faster than evolutionary divergence can replace them. Conversely, a group can withstand relatively frequent extinctions if new species continue to arise sufficiently rapidly.

A new study published open access in Nature Communications. has now examined both sides of that evolutionary balance. Juan L. Cantalapiedra and colleagues analysed 3,327 African fossil occurrences representing 396 species of herbivorous mammals. Using neural-network models, they reconstructed changes in speciation and extinction over the past 23 million years while considering body size, tooth-crown height, evolutionary relationships and environmental change. Their results challenge the apparently obvious assumption that Africa’s largest herbivores declined because they were inherently more prone to extinction.

In fact, the models indicate that extinction rates were generally somewhat lower among the largest species. High-crowned teeth, which better withstand abrasive diets, were also associated with a reduced risk of extinction. The underlying problem for megaherbivores was that their already low speciation rates could not compensate for the species that were lost.

The imbalance developed over millions of years. As Africa became increasingly arid from about 7.2 million years ago, both speciation and extinction initially accelerated as changing vegetation and expanding open habitats reorganised its ungulate communities. Speciation then levelled off after about 3.6 million years, while extinction continued to rise and increased sharply with the beginning of the Pleistocene, about 2.58 million years ago. During the driest intervals, smaller herbivores generated new species at substantially higher rates, whereas speciation among megaherbivores was suppressed still further. The resulting decline was already well under way long before humans possessed the technology needed to hunt such enormous animals systematically.

This does not mean that humans played no part in the most recent losses, nor that climate alone explains every extinction. Rather, it places recent events within a much longer evolutionary history in which changing climate, declining ecosystem productivity, extinction and unequal rates of speciation gradually transformed the African fauna.

Refuting Creationism - Why Sex Evolved

Recombination by sexual reproduction drives adaptive diversity in yeast

AI-generated image (ChatGPT 5.6 Sol)

The why behind sex — Harvard Gazette

For creationists, who typically know little or nothing about evolution and so have no understanding that it is a process that takes place in a population, not an event that happens to individuals, sexual reproduction is a fertile source of disinformation and misunderstanding with which to attack the Theory of Evolution.

For instance, they frequently argue that the probability of the 'first man' and 'first woman' evolving together is so highly unlikely that their myth of the spontaneous creation out of dirt of a man and the cloning of a woman by magic is a far more rational alternative explanation. The science is attacked because when they try to force fit their childish myth of every species having a single ancestral male and female couple into the science of evolution, it doesn't fit well. The possibility of the myth being wrong must never be contemplated, because that would risk having to change their mind.

However, science works by addressing questions, not by throwing stones at infantile straw-man parodies of alternative ideas and declaring victory by default.

For science, sexual reproduction presents evolutionary biology with a different long-standing puzzle. An asexual organism can pass on its entire genome without finding a mate, competing for one or investing energy in courtship. In species with separate sexes, there is also the familiar “twofold cost of males”: only females produce offspring, whereas every member of an asexual population can potentially reproduce.

All else being equal, an asexual lineage should therefore increase more quickly than a sexual one, and indeed there are a few examples of where this is true - a single female vine weevil can quickly populate a window box or plant pot with devastating consequences for the owner as I have found to my cost; a single marbled crayfish can rapidly spread through a new river system, out-competing any native species.

Yet sexual reproduction is widespread among eukaryotes and has persisted for hundreds of millions of years. This does not imply that evolution requires foresight or that sex was introduced by a designer for some future purpose. It means that, under many circumstances, the descendants of organisms that exchange and recombine genetic material must acquire advantages sufficient to offset the immediate costs.

One important advantage is that sex reshuffles the genome. In an asexual lineage, genes are inherited together as a largely indivisible package. A beneficial mutation can therefore carry neighbouring neutral or mildly harmful mutations with it as it spreads through a population—a process known as genetic hitchhiking. Sexual reproduction and recombination can break up these associations, separating advantageous mutations from some of the damaging evolutionary baggage accompanying them.

Creationism Refuted - The Simple Mutation That Made Grasses So Successful - 100 Million Years Before 'Creation Week'

Joinvillea ascendans, a close relative of grass plants. Used in the Study

Photo: Sarah Friedrich.

Maeda and his collaborators sequenced the slow-growing Joinvillea ascendans plant, a close relative of grasses, to compare genomes and learn what makes grass plants unique.

Photo: Sarah Friedrich.

Molecular “bypasses” improve grass plants’ synthesis of lignin and starch, laying the early groundwork for evolutionary success – Department of Biology – UW–Madison

Creationists routinely claim that mutations can only damage genetic “information” and can never produce anything genuinely new. The claim depends partly upon leaving information conveniently undefined and partly upon ignoring the many well-understood processes by which genomes acquire new functions. Gene duplication, mutation and natural selection can preserve an existing function while a spare copy accumulates changes, sometimes enabling it to perform an additional task or participate in a new biochemical pathway.

A new study published in Science provides an unusually clear example. Rather than merely showing that related organisms possess different enzymes, Yuri Takeda-Kimura and colleagues reconstructed how two important metabolic innovations arose during the ancestry of grasses: additional routes for producing starch and lignin. They did this by comparing the genomes of grasses with those of several of their closest non-grass relatives, including Joinvillea, Ecdeiocolea, Pharus and Typha.

Abiogenesis News - How RNA Droplets Could Have Preceded The First Cells - No Magic Required

RNA condensates forming in an early-Earth mineral pool

AI-generated image (ChatGPT 5.6 Sol)

RNA droplets may have helped start life on Earth. A new study explains why they form - University at Buffalo

One of the enduring questions in origin-of-life research is how the first biologically useful molecules could have become sufficiently concentrated to interact before cells, complete with enclosing membranes, had evolved. Dispersed throughout an ocean or pond, relatively fragile molecules such as RNA would have been unlikely to encounter one another often enough to sustain complex chemical reactions and would have remained exposed to environmental degradation. Some form of compartmentalisation therefore appears to have been an important intermediate stage between unorganised prebiotic chemistry and the first true cells.

Creationists routinely present this and other unanswered questions about abiogenesis as though they were evidence for supernatural intervention. The familiar argument is that, because scientists have not yet reconstructed every step between simple chemistry and the earliest life, an unexplained creator must have supplied whatever is missing. This is merely the false dichotomy and the god-of-the-gaps fallacy masquerading as an explanation. A gap in current scientific knowledge is not evidence that magic occurred inside it, and the history of science is largely a history of such gaps being progressively narrowed by evidence.

Research led by physicist Priya R. Banerjee of the University at Buffalo has now identified a potentially important natural mechanism that could have helped solve the problem of pre-cellular compartmentalisation. In a paper published in Nature Communications, Gable M. Wadsworth and colleagues compared the behaviour of RNA with that of single-stranded DNA carrying essentially equivalent nucleotide sequences. They found that RNA was markedly more inclined to gather spontaneously into microscopic, liquid-like droplets known as biomolecular condensates.

These condensates are not cells and are not enclosed by lipid membranes. Nevertheless, they could perform part of the function later assumed by cellular compartments: bringing molecules together in a confined space, increasing the likelihood of interactions and potentially providing some protection from hostile surroundings. The experiments showed that RNA began forming droplets at temperatures about 10 °C lower than the corresponding DNA and was also more prone to developing interconnected, gel-like molecular networks. Such networks might have retained and protected RNA more effectively than freely dispersed molecules could have done. The researchers used temperature-controlled microscopy, small-angle X-ray scattering and molecular-dynamics simulations to investigate the effect.

Remarkably, much of the difference can be traced to a very small chemical distinction between RNA and DNA. The ribose sugar in RNA carries a hydroxyl group at its 2′ position—the 2′-OH group—which is absent from the deoxyribose sugar of DNA. The experiments and computer simulations indicated that this group alters RNA’s interactions with magnesium ions and the surrounding water, helping RNA strands to associate with one another. When the researchers chemically modified the 2′-OH group, RNA’s tendency to condense weakened and the physical properties of the resulting droplets changed. A single chemical group on each sugar unit can therefore influence the emergence of structures many times larger than the individual molecules themselves.

Unintelligent Design - The Evolutionary Compromises That Made The Human Female Pelvis - No Intelligence Involved

Virtual reconstructions of the Neanderthal pelvises of a 1.5-year-old infant from Dederiyeh Cave, Syria (left), and a young adult female from Sima de las Palomas de Cabezo Gordo, Spain (right). Age- and sex-matched modern human pelvises are superimposed in transparency to highlight form differences.

Image credit: Marcia Ponce de León
and Christoph Zollikofer
(University of Zurich)

A Neanderthal woman and Baby. Her Pelvis is the result of the same evolutionary processes as that of Homo sapiens women.

AI-generated image (ChatGPT 5.6 Sol).

Rethinking Birth and Bipedalism - School of Science University of Tokyo

The human pelvis is a particularly poor candidate for anyone wishing to argue that the human body was intelligently designed from scratch. It must support the upper body, anchor muscles used in standing and locomotion, protect internal organs, maintain the pelvic floor and— in females—provide a passage through which a large-bodied, large-brained infant can be born. The result is not an ideal solution to a single engineering problem, but an evolutionary compromise assembled by modifying an inherited structure while several competing selection pressures acted upon it.

For much of the past century, one influential explanation for its shape has been the “obstetrical dilemma”. According to the simplest version of this hypothesis, the female pelvis represents a compromise between a birth canal wide enough to accommodate a large-brained baby and hips narrow enough to permit efficient bipedal walking. Childbirth pushes pelvic evolution in one direction, in other words, while locomotion pushes it in the other.

That explanation has never been beyond dispute. Studies have questioned whether wider hips necessarily impose the assumed energetic penalty on walking or running, while alternative hypotheses have emphasised maternal metabolism, infant development and the need for a stable pelvic floor capable of supporting the abdominal organs. The pelvis is involved in too many functions for its evolution necessarily to be reduced to a single contest between walking and childbirth.

Refuting Creationism - Observed Evolution Of Live Birth in the European Common Lizard

European common lizard, Zootoca vivipara

Image credit: Meredith Kimble

European common lizard, Zootoca vivipara

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

University of Glasgow - University news - Scientists uncover the evolutionary process behind live birth in lizards

Live birth is not a simple characteristic that could be produced by switching a single gene on or off. Retaining embryos inside the mother until they are sufficiently developed to survive requires coordinated changes in gestation length, uterine physiology, eggshell formation, gas exchange, nutrient transfer, hormonal control and the maternal immune response. To creationists, this is just the sort of complex biological system that must supposedly have appeared complete and fully functional in a single act of creation.

But that is not what the genomes of living animals show.

In a study recently published in Current Biology, an international team led by Dr Hongxin Xie of the University of Glasgow has reconstructed how live birth evolved in the Eurasian common lizard, Zootoca vivipara. The transition did not depend upon one miraculous genetic leap, or even upon one or two mutations of exceptionally large effect. It arose through natural selection acting upon numerous genetic changes distributed across the genome and accumulated over an extended period.

Refuting Creationism - Denisovans Show Why Scepticism Is The Stuff Of Good Science, But Toxic To Creationism

The Harbin cranium

From: Fu Q, Cao P, Dai Q (2025)

Reconstruction of Homo longi from the Harbin cranium, now identified as that of a Denisovan.

© Nobu Tamura, CC BY-SA 3.0, via Wikimedia Commons.

Were Denisovans tall compared to other ancient humans? We should be sceptical

One of the most important differences between science and creationism is not that science possesses absolute certainty while creationism does not. It is that science has procedures for recognising uncertainty, testing assumptions and preventing an interesting possibility from being promoted prematurely into an established fact. Creationism, by contrast, begins with an asserted certainty and then selects, distorts or dismisses the evidence according to whether it supports the required conclusion.

That distinction is illustrated particularly well by the recent suggestion that Denisovans may have been exceptionally tall. The claim originated in a preprint by Yousuke Kaifu and colleagues describing an incomplete femur and tibia recovered by dredging from the Penghu Channel between Taiwan and mainland China. Ancient proteins preserved in the bones identify them as Denisovan, giving scientists the first known Denisovan leg bones and potentially valuable information about the bodies of these enigmatic archaic humans.

Penghu 2 and Penghu 3 hominin leg bones.
Anterior (a), medial (b), and distal (c) views of the Penghu 2 right femoral shaft. Anterior (d), lateral (e) and distal (f) views of the Penghu 3 right tibia. Symbols: m=medial, p=posterior. Scale bar=10cm.

Kaifu, Y., et al.(2026)

Reconstructions suggest that the owner of the femur, known as Penghu 2, may have stood about 1.8 metres tall and weighed approximately 83 kilograms. The owner of the Penghu 3 tibia may have been about 1.9 metres tall and weighed around 91 kilograms. These were undoubtedly large individuals by Pleistocene standards, and their estimated dimensions compare with those of some of the largest ancient humans known from Africa and Europe.

But two large individuals do not establish that Denisovans as a population were exceptionally tall. Modern humans vary considerably in height, and no responsible anthropologist would attempt to calculate the average stature of the entire species from two people selected from a crowd. The problem is even greater when dealing with two incomplete bones recovered by trawling rather than from a documented archaeological excavation. Their exact discovery locations and original geological contexts are unknown, while large, robust bones are more likely than small or fragile ones to survive, become caught in fishing nets and be recognised as scientifically interesting.

This is the point made by palaeoanthropologist Sally Christine Reynolds in an article in The Conversation. The height estimates may be perfectly reasonable for the two individuals concerned, but extending those estimates to Denisovans generally would require a much larger and more representative sample. At present, “two Denisovans were tall” is a defensible conclusion; “Denisovans were a tall species” remains an intriguing but weakly supported generalisation.

This is evolutionary population thinking in practice. Species are not collections of identical specimens conforming to an ideal form. They are variable populations in which individuals differ because of their genes, sex, nutrition, health, environment and developmental history. Treating one or two specimens as definitive representatives of an entire species is a remnant of the typological thinking that sits much more comfortably with the creationist notion of separately manufactured and essentially unchanging “kinds”.

Creationists habitually misrepresent scientific disagreements about details as evidence that scientists are abandoning evolution. Nothing of the sort is happening here. Reynolds is not questioning whether Denisovans existed, whether they shared common ancestry with Neanderthals and Homo sapiens, or whether they interbred with the ancestors of some living people. She is questioning whether two bones provide sufficient evidence for one proposed characteristic of the Denisovan population.

Indeed, identifying these bones as Denisovan depended upon evolutionary science. Proteins change through inherited mutations, so similarities and differences in their amino-acid sequences retain evidence of common ancestry. Even when recoverable DNA and diagnostic skeletal features are unavailable, palaeoproteomics can place a fossil within an evolutionary family tree. Creationism supplies no corresponding method for predicting those nested molecular relationships and no explanation for why the history recorded by fossil proteins should agree with that reconstructed from DNA and anatomy.

One qualification should be added to the account in The Conversation. Reynolds states that neither bone has been dated directly. However, a companion preprint reporting radiocarbon and stable-isotope analyses gives Penghu 3 a direct radiocarbon age of approximately 45,575–44,522 calibrated years before the present. Penghu 2 remains undated, and the lack of stratigraphic provenance still prevents the two individuals from being assumed to have lived together or even during the same period. Both studies are also preprints and have yet to complete peer review.

Scientific scepticism therefore does not weaken the evolutionary account; it protects it from exaggeration. Scientists can accept that the bones belonged to two large Denisovans, recognise the importance of their molecular identification and direct dating, and nevertheless withhold judgement on whether Denisovans generally were unusually tall. That willingness to make the conclusion no larger than the evidence can support is one of the defining strengths of science—and the antithesis of a creationist doctrine in which the conclusion was declared infallible before any evidence was examined.

Sally Christine Reynolds's article in The Conversation is reprinted here under a Creative Commone License, reformatted for stylistic consistency:

Refuting Creationism - Rationalising The Complex Hominin Taxonomy

Evolution is a process not an event

AI-generated image (ChatGPT 5.6 Sol)

Where does red become blue?

Why it might be time to rethink the human family tree.

Taxonomy is an indispensable tool for organising the living world, but it can also create a misleading impression of nature divided into sharply separated compartments. The familiar Linnaean hierarchy was devised in a pre-evolutionary age, principally to classify organisms as distinct types. It was not designed to accommodate fragmentary snapshots of populations undergoing continuous change over millions of years.

That problem becomes particularly acute in palaeoanthropology. Fossils do not come with labels identifying their species and genus, and palaeoanthropologists cannot test whether their owners could have interbred. They must infer relationships from incomplete and often distorted remains, sometimes consisting of little more than a few teeth or part of a jaw. They must then assign those remains to discrete taxonomic boxes, even though evolution within each lineage was continuous, while populations were also branching, diverging, coexisting and sometimes exchanging genes.

The boundary traditionally drawn between Australopithecus and Homo has always seemed especially arbitrary. It gives the impression that, at some point between the two, evolution took a sudden stride and produced something qualitatively different: a creature sufficiently human to be admitted into our genus. In reality, the characteristics once used to define Homo did not appear together as a package. Bipedalism preceded substantial brain enlargement by millions of years; tool use is no longer regarded as the exclusive preserve of Homo; and fossils repeatedly present mosaics of supposedly “primitive” and “advanced” features.

Nor is there a universally objective amount of anatomical difference that separates one genus from another. A genus is a humanly constructed rank, not something that can be excavated from the ground alongside the fossil. Drawing a firm boundary across a gradually changing lineage can therefore exaggerate the differences on either side of it, artificially turning a succession of small evolutionary changes into an apparent leap.

This is the problem addressed by Monash University palaeoanthropologist Dr Ian Towle in a new paper, Clades, grades, and the genus problem: A case for revising hominin taxonomy, published in the American Journal of Biological Anthropology. Towle proposes expanding the genus Homo to include the species currently assigned to Australopithecus and Paranthropus—in effect placing the closely related hominins of the past four or five million years within one broadly defined genus.

Refuting Creationism - How Flightless Beetles Evolved On Japanese Islands

Carabus blaptoides

By Adan - Photo taken by Adan at Sendai Miyagi, Japan., CC BY-SA 3.0, Link

Reach in or crush the shell? A flightless snail-hunting beetle evolved different body shapes even without a sea barrier | EurekAlert!

Montage created by AI (ChatGPT 5.6 Sol)

Phylogenetic relationships and geographic distribution of Carabus blaptoides

Junji Konuma

Islands have repeatedly provided some of the clearest demonstrations of evolution in action. The most famous example is, of course, Darwin’s finches, whose differently shaped beaks reflect adaptation to different foods in the Galápagos. More recently, as I described in an earlier article about “Darwin’s daisies”, the Galápagos plant genus Scalesia has diversified from a common ancestor into forms with different growth habits and leaf shapes suited to different island environments.

Now scientists studying the Japanese Archipelago have uncovered another striking example of the same fundamental evolutionary process—this time involving flightless beetles and the land snails they eat.

In a paper published in the Biological Journal of the Linnean Society, Junji Konuma of Toho University, Nobuaki Nagata of Japan’s National Museum of Nature and Science, and Teiji Sota of Kyoto University describe the evolutionary diversification of the snail-eating ground beetle Carabus blaptoides. The species is distributed across the Japanese islands and has diversified into eight recognised subspecies.

Because the beetles’ hindwings are reduced, they cannot fly and must disperse on foot. Seas therefore isolate populations on different islands, while sheer distance, topography and environmental variation can restrict movement even between populations on the same large island. This reduced gene flow allows populations to respond independently to local ecological conditions—the familiar starting point for adaptive divergence and, eventually, speciation.

The principal selective pressure appears to be sitting on the beetles’ dinner plate—or, more accurately, retreating into its shell. Different regions of Japan contain different assemblages and sizes of land snails, particularly species of Euhadra and Satsuma. Beetles living where large snails predominate tend to have long, narrow heads and thoraxes. This slender form allows a beetle to push its head deeply into a large shell and reach the animal inside.

Refuting Creationism - How Death Stalked South America In The Form Of Giant Crocodylians - Over 10 Million Years Before 'Creation Week'

[caption]

[credit]

Reconstruction of Purussarus neivensis attacking Pericotoxodon platignathus.

Image: Miguel Hernandez.

Giant crocodylians dominated the food chain in Miocene South America | University of Helsinki.

If the Young-Earth creationist claim that there was no death, suffering or predation before Eve’s supposed ‘sin’ were true, four fossil specimens preserved in museum collections in Colombia should not exist. They are the remains of large herbivorous mammals bearing punctures and other damage attributed to the teeth of a giant crocodylian—and they are between approximately 10.5 and 16 million years old.

In other words, these fossils are not merely the remains of animals that lived and died millions of years before there were humans to commit any biblical ‘sin’. They preserve physical evidence of animals attacking—or, at the very least, feeding upon—other animals in a functioning predator–prey ecosystem more than a thousand times older than the entire universe imagined by Young-Earth creationists.

The evidence is described by Oscar E. Wilson of the University of Helsinki and Jorge W. Moreno-Bernal in a paper recently published in the Journal of Vertebrate Paleontology. The researchers examined four specimens belonging to three species of large, now-extinct South American ungulates from the celebrated La Venta fossil assemblage of Colombia: the toxodontid Pericotoxodon platignathus and the astrapotheres Xenastrapotherium kraglievichi and Granastrapotherium snorki.

The skulls and jaws bear puncture marks and, in some cases, substantial deformation caused by a powerful bite. From the size and shape of the marks, together with the force apparently needed to produce the damage, Wilson and Moreno-Bernal identify the most likely culprit as Purussaurus neivensis, an enormous relative of modern caimans that may have reached about seven metres in length and weighed approximately 1,800 kilograms.

Middle Miocene South America contained an ecosystem unlike anything living today. The continent’s long geographical isolation had allowed native mammals—including toxodontids, astrapotheres, ground sloths and glyptodonts—to diversify independently. Around the immense tropical wetlands lived giant snakes, flightless predatory ‘terror birds’, terrestrial crocodyliforms and several kinds of aquatic crocodylian. Because large mammalian carnivores were comparatively scarce, reptiles such as Purussaurus occupied the major apex-predator niches.

Earlier studies had inferred this ecological role from the animals’ size, anatomy and the composition of the La Venta fauna. The newly reported bite marks provide direct physical evidence that giant crocodylians interacted with—and probably preyed upon—some of the ecosystem’s largest herbivorous mammals. Purussaurus may therefore have helped to regulate herbivore populations, much as large predators influence prey populations in modern ecosystems.

For creationists, the problem could hardly be clearer. These animals lived, competed, killed, fed, reproduced and became extinct millions of years before any known hominin existed, let alone the mythical couple blamed in Genesis for introducing death into the world. Even if an individual bite mark resulted from scavenging rather than an actual attack, that alternative still requires a dead animal, a flesh-eating crocodylian and an established ecological system based partly upon the consumption of carcasses. It offers no refuge for the claim that the pre-Fall world was free from death and carnivory.

Refuting Creationism - Mammals May Have Evolved Live Birth 236 Million Years Before 'Creation Week'

"Triassic Mothers," a life reconstruction of a group of Chiniquodon theotonicus individuals, a pregnant female (left) as well as a female (right) breastfeeding few, relatively large neonates.

Credit: María de los Ángeles Miceli Baro.

New fossil evidence challenges the story of mammalian birth

A newly published study suggests that one characteristic commonly associated with modern mammals—giving birth to live young—may have appeared in the mammalian lineage far earlier than palaeontologists previously realised.

Creationists prefer to imagine the major groups of organisms appearing fully formed, equipped from the outset with complete packages of supposedly defining characteristics. Evolution, however, produces no such conveniently bundled collections of features. Characteristics arise, change and sometimes disappear at different times, producing the mosaic of inherited and modified traits documented throughout the fossil record.

Creationists also rejoice at any suggestion that scientists might have to change their minds because, in their simplistic view of science, if something is not exactly and eternally true, it's wrong; there is no concept in creationism of incomplete truths or provisional conclusions contingent on future discoveries. Unlike creationism, though, changing one’s mind when the evidence changes is the hallmark of intellectual integrity, and what give science it's reliability and great strength as a tool for discovering the truth.

So here, to sow confusion in the minds of creationists, is an example of science changing its collective mind and still refuting creationists mythology, because it happened 236 million years before the mythical 'Creation Week'. Significantly too, the authors readily conceded that their conclusion is only provisional and they identify what additional information is needed to confirm or refute it. No such reasoning is ever advanced by creationist apologists because it must never be conceded that creationism could be falsified with evidence, lest that evidence be found.

Refuting Creationism - How Humans Evolved, Migrated And Interacted In The Nile Valley - 34,000 Years Before Creation Week'

The history of Homo sapiens in Africa between 44,000 and 3,000 years ago was one of isolation, migration, interaction and replacement a shown by characteristic inner ear labyrinth morphologies.

AI-generated image (ChatGPT 5.6 Sol)

Research paper: Bony labyrinth morphology reveals deep population history and isolation among Homo sapiens in prehistoric northeastern Africa (44–3 ka) | Nature Communications

An international team of biological anthropologists has found a novel way to reconstruct tens of thousands of years of human population history in north-eastern Africa: by examining tiny variations in the shape of the bony cavities that once contained people’s inner ears. It's not good news for creationists so it'll be just one more thing for them to ignore one way or another.

The researchers, led by Nicolas Martin and Isabelle Crevecoeur of the PACEA laboratory at the University of Bordeaux and the French National Centre for Scientific Research (CNRS), have published their findings in Nature Communications.

The bony labyrinth is a complex system of cavities within the temporal bone of the skull. It surrounds the cochlea, involved in hearing, and the semicircular canals, involved in balance. Although its shape varies subtly between individuals and populations, much of that variation reflects inherited ancestry. High-resolution micro-CT scanning allows the labyrinth to be reconstructed and measured in three dimensions without damaging the remains.

This makes it especially valuable in regions such as north-eastern Africa, where heat and other environmental conditions have frequently destroyed ancient DNA. When molecular evidence is unavailable, the shape of the inner ear can preserve an anatomical record of biological relationships between ancient populations.

Martin and his colleagues analysed 194 bony labyrinths belonging to 148 individuals. Their sample included people who lived between approximately 44,000 and 3,000 years ago in the Middle Nile Valley, the Horn of Africa and Central Africa, together with comparative specimens from elsewhere in Africa, Europe and the Levant. The researchers applied three different methods of shape analysis, all of which produced the same broad patterns.

Those patterns reveal a long and complicated history of regional continuity, isolation, migration, interaction and partial population replacement. Late Pleistocene and Early Holocene hunter-fisher-foragers from the Middle Nile Valley showed broad morphological similarities both to one another and to still earlier African Homo sapiens. This is consistent with deep regional ancestry and substantial biological continuity extending across many thousands of years.

That continuity was disrupted during the Neolithic transition. Beginning about 8,000 years ago, food-producing populations with distinctly different inner-ear morphologies appeared in the Middle Nile Valley, supporting the conclusion that pastoralism and agriculture arrived with migrating people rather than being adopted solely by the region’s existing foragers.

This was not necessarily a simple or complete replacement. Individuals retaining affinities with the earlier foragers survived for several millennia in areas bordering the Nile Valley, while some remains display combinations of characteristics consistent with limited interaction or admixture between the old and new populations. Samples from the Horn of Africa and Central Africa also showed considerable morphological diversity, indicating population substructure and differing regional demographic histories.

These results independently support earlier research by Martin and many of the same colleagues, which detected a similar Neolithic population discontinuity from the internal structure of ancient teeth. A CNRS account of that earlier study explains how enamel–dentine junctions revealed population replacement and continuing interaction along the Nile and its Saharan margins. Now two independent anatomical systems—teeth and inner ears—have produced compatible reconstructions of the region’s population history.

This presents creationists with the familiar problem of evidence that should not exist if their mythology were true. According to the young-Earth version of the biblical story, the entire human population was reduced to Noah’s family only a little over 4,000 years ago. Every population on Earth must therefore have descended from that tiny group after an extraordinarily rapid dispersal from somewhere in the Middle East.

Unintelligent Design - The Perpetual Evolutionary Arms Race In Your Gut

Certain bacteriophages found in the human gut have mutation hotspots scattered throughout their genomes that help them modify key defense genes, researchers report.

Credit: Sundharraman Subramanian and Alaina Pabbathi
Cryo-EM Core Facility
Michigan State University

Mutation hotspots help 'friendly' viruses outmaneuver the bacteria in your gut

One of the more persistent creationist falsehoods is the claim that mutations can only damage or destroy genetic information and can therefore provide none of the variation needed for evolution. The claim is usually protected from contrary evidence by leaving “information” conveniently undefined or by dismissing every beneficial mutation as merely a “loss of function”.

However, a new study by Jasper B. Gomez, Jeffrey E. Barrick and Christopher M. Waters of Michigan State University provides an especially clear demonstration of mutation generating heritable variation on which natural selection can act. Their findings were published in Nature Microbiology.

The researchers found that the genomes of the bacteriophages T2 and T4 — viruses that infect bacteria such as Escherichia coli — contain regions of repetitive DNA called contingency loci. These are mutational hotspots in which the DNA-copying machinery is particularly liable to slip while copying a run of repeated bases. It may insert or omit one of the repeats, changing the way the remainder of a gene is read and consequently altering the protein it produces.

Such replication errors occur in these regions thousands of times more frequently than mutations across the rest of the phage genome. Far from producing a population of genetically identical copies, therefore, phage replication continually generates a mixture of variants with different inherited characteristics.

The discovery arose from experiments involving a bacterial antiviral system called TgvAB, normally found in Vibrio cholerae, the bacterium that causes cholera. The researchers transferred the genes for this defence system into laboratory E. coli and exposed the bacteria to T2 phages. Although the defence initially restricted the phages, the viral population began overcoming it within hours.

Refuting Creationism - How the Earliest Cells Evolved Not Once But Twice - 4 Billion Years Before 'Creation Week'

Shared metal-catalysed metabolic network within a primordial hydrothermal vent, diverging into the bacterial and archaeal lineages.

AI-generated image (ChatGPT 5.6 Sol)

Early Evolution of Life: Publication in Science Advances

A paper recently published in Science Advances by an international team led by researchers at Heinrich Heine University Düsseldorf (HHU) will make disappointing reading for any creationist with enough courage to read a scientific paper—especially those pinning their hopes on science never closing their favourite gap: the gap between geochemistry and the first living systems.

Leaving that gap permanently open would allow them to declare, “God did it!”, without providing a scrap of supporting evidence or explaining how their preferred god supposedly made chemistry and physics behave in ways that they could not have done unaided. This combination of the god-of-the-gaps argument and a false dichotomy—either science already has a complete explanation, or magic must have been responsible—is standard creationist fare in the absence of positive evidence for a creator.

The new research does not, as some headlines might suggest, show that abiogenesis occurred twice independently. Instead, it presents evidence that the genetic code and a core metabolic network had a single origin before the ancestral lineage divided into Bacteria and Archaea, but that the two lineages subsequently completed the transition to free-living cells independently. As senior author William F. Martin expressed it, the findings point to “one origin of the genetic code, but two origins of life”—with “life” here referring specifically to autonomous, free-living cellular life.

The findings therefore do not overturn universal common ancestry. Both Bacteria and Archaea still trace their ancestry to the last universal common ancestor, or LUCA. What the researchers propose is that LUCA was not yet a fully independent cell equipped with enzymes for every essential metabolic reaction. It remained partly dependent on inorganic catalysts supplied by the hydrothermal environment in which its metabolism had evolved. Only after the bacterial and archaeal lineages had diverged did each independently evolve the remaining enzymes needed to become free-living.

Unintelligent Design - How Badly-Designed Mitochondria Can Make Us Sick - When They Behave Like Their Ancestral Bacteria

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Refuting Creationism - How Dogs And Humans Co-Evolved Naturally - No Magic Involved

A selection of dogs with a common ancestry. Creationists need to explain why this is not macro-evolution even though the scale of the differences between them and wolves is at least as great as that between humans, chimpanzees and gorillas

Various Internet sources

Eurasian grey wolf (Canis lupus lupus)

By User:Mas3cf, CC BY-SA 4.0,Link

How dogs evolved differently across the globe to match human traits - Taylor & Francis Newsroom

The story of how wolves became domestic dogs is one to which I have returned several times, for both scientific and personal reasons. It is one of the most remarkable examples of two species forming a relationship that changed the evolutionary future of one and the cultural history of the other.

It also provided the inspiration for two of my novels, The Girl and the Wolf and its sequel, The Way of the Wolf: A Stone Age Epic. These are, of course, works of fiction, not proposed reconstructions of an event for which the details will probably never be known. In them, however, I tried to imagine a biologically plausible way in which the process might have begun: not with people deciding suddenly to “invent” the dog, but with individual wolves and humans discovering that tolerance, cooperation and mutual protection could benefit both.