Malevolent Design - How The Success Of A Honey Bee Parasite Is Assured - Malevolent Design Or Evolution?

Varroa desructor female.
Dorsal view (top); ventral view (bottom)

By USGS Bee Inventory and Monitoring Lab from Beltsville, Maryland, USA - Varroa destructor, 1_2019-09-06-19.12.07 ZS PMax UDR, Public Domain, Link

Varroa mites on honey bee pupa.

By Unknown author - Kika De La Garza Subtropical Agricultural Research Center
Weslaco, Texas, USA, Public Domain, Link

Varroa mites escape the evolutionary trap of haplodiploidy | Nature Communications

Creationists like to portray living things as products of a single act of creation in which every species was equipped with its characteristic form and method of reproduction from the outset. In that view, reproductive systems should be fixed features of separately created “kinds”, not historically contingent arrangements that can be remodelled by natural selection.

Biology reveals something very different. Even such fundamental characteristics as sex determination, chromosome number and the balance between sexual and asexual reproduction can evolve. Existing developmental mechanisms are modified, discarded or repurposed according to whether the resulting variations leave more descendants. Evolution has no predetermined direction, no obligation to proceed from “simple” to “complex” and no rule forbidding a lineage from reacquiring a feature resembling one possessed by its ancestors.

An international team of researchers has now discovered an especially striking example in Varroa destructor, the globally invasive parasitic mite that feeds on honeybees and transmits damaging viruses between them. Its reproductive system appears to have reversed what was once regarded as an evolutionary one-way street.

Like many mites, bees, wasps and ants, Varroa was believed to be haplodiploid. In conventional haplodiploidy, females develop from fertilised eggs and possess two sets of chromosomes, while males develop from unfertilised eggs and possess only one. Consequently, a haploid male can transmit only the single copy of each gene inherited from his mother.

That should present Varroa with a serious evolutionary handicap. A female mite enters a honeybee brood cell shortly before it is sealed and produces one son followed by several daughters. The siblings mate with one another inside the cell, producing generation after generation of extreme inbreeding. Combined with the population bottlenecks associated with invading new hosts and new geographical regions, this should rapidly erode genetic diversity and limit the parasite’s ability to adapt.

However, by tracing genetic variants through three-generation pedigrees, Nurit Eliash and colleagues discovered that Varroa is not conventionally haplodiploid after all. Its females produce sons parthenogenetically, but those sons initially inherit both copies of their mother’s genome and are effectively genetic clones of her. Although DNA is subsequently eliminated from some of the males’ body cells, their reproductive lineage retains access to both maternal copies, either of which can be transmitted to a daughter.

Creationism Refuted - Recovering DNA from Extinct Galápagos Giant Tortoises

The Pinzón saddleback tortoise, a small giant tortoise species native to Pinzón Island in the Galápagos characterized by a saddle-like curve in its shell.

Credit: Evelyn Jensen

Dome-shelled Galápagos giant tortoise, Chelonoidis nigra

By Mfield, Matthew Field, http://www.photography.mattfield.com - Own work,
CC BY-SA 3.0, Link

Reading the giant tortoise DNA that time forgot | Yale News

Few places are more closely associated with evolutionary biology than the Galápagos Islands. Their isolation has repeatedly divided colonising populations into smaller groups, allowing mutation, genetic drift and natural selection to produce distinct island lineages. Yet their subsequent history has not always resembled a neatly branching tree. Occasional migration—and, more recently, the deliberate movement of animals by humans—has brought formerly isolated populations back into contact, permitting them to interbreed and exchange genes.

The evolutionary radiation of the Galápagos giant tortoises is a particularly striking example. Thirteen living and four extinct lineages are currently recognised within the Chelonoidis complex, each descended from the same ancestral colonisation but subsequently differentiated by geographical isolation. Unfortunately, centuries of exploitation by sailors and settlers devastated many populations, leaving some lineages represented only by bones preserved in museums.

Those remains retain a record of their evolutionary history, but reading it is difficult. DNA begins to fragment and chemically deteriorate after death, while contamination from microorganisms and people can overwhelm the surviving genetic material. In some of the museum specimens examined in a new study, researchers could read less than one per cent of the original genome—far too little for many conventional methods of genomic comparison.

However, a team led by researchers at Yale University has now developed a computational approach capable of extracting reliable evolutionary information from such exceptionally incomplete genomes. As described in Proceedings of the Royal Society B, the researchers analysed dried bones from five historical specimens and placed their surviving DNA fragments upon a reference phylogeny constructed from high-quality genomes belonging to living and other historical tortoises.

Importantly, the researchers did not manufacture plausible sequences to fill the gaps. Their analytical pipeline was designed to recover the phylogenetic and population-genetic signal present in ultra-low-coverage genomes without imputing the missing genotypes. Even at sequencing depths as low as 0.008 times the genome, the surviving fragments contained enough mutually consistent information to reveal where the specimens belonged.

The results confirmed that the bones represented two evolutionarily distinct, now-extinct lineages: the former tortoises of Santa Fe and an extinct San Cristóbal lineage different from the population still living on that island. These were not merely unusual individuals belonging to surviving populations but genetically distinguishable branches of the wider Galápagos tortoise radiation.

Creationism Refuted - Eurasian Homo sapiens Stopped Eating Insects - Thousands Of Years Before 'Creation Week'

Insects in Chang Moi, Mueang Chiang Mai District, Chiang Mai, Thailand.

Credit: mohigan. Licence: CC BY-SA 3.0, via Wikimedia Commons.

European Homo sapiens ate fewer insects than Neanderthals and tropical populations - Institut de Biologia Evolutiva - CSIC UPF (UPF)

Humans are strange creatures. While we recoil at the thought of tucking into a dish of sautéed maggots, fried grasshoppers or other insects, we happily eat their close arthropod relatives, crabs, lobsters and prawns, and yet the evidence is that this has only been so for Northern Eurasians for about the last 9,000 year.

People are also strange in another way: despite all the evidence to the contrary and with no supporting evidence at all, there are people who believe the whole of history can be compressed into a few thousand years and that animals can be created by magic without ancestors.

For biblical literalists, every human who has ever lived must be squeezed into the few thousand years since the supposed creation of the first couple. Yet evidence preserved in something as commonplace as calcified plaque on ancient teeth tells a very different story: one of several human lineages, changing diets, inherited genetic variation and adaptation to contrasting environments over tens of thousands of years.

In a paper published in Science Advances, Manuel Piñero and Pablo Librado of the Institute of Evolutionary Biology in Barcelona combined two independent sources of evidence to investigate the history of human insect-eating, or entomophagy. They searched ancient dental calculus for insect DNA and examined genetic variants affecting our ability to digest chitin—the tough polysaccharide forming much of an insect’s exoskeleton.

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 - 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 - 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.

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 - 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 - Rapid Evolution In Andean Potato Eaters

Andean Quechua speaker

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

Quechua woman and child in the Sacred Valley

By quinet - Mother and Child, CC BY 2.0, Link

Indigenous Andeans have a digestive superpower; researchers think it may be linked to potatoes  | UCLA

The results of a study co-led by researchers at UCLA and the University at Buffalo, published in Nature Communications in May 2026, provide another straightforward counterexample to the creationist claim that natural processes cannot add genetic material to a genome without the intervention of their particular magic creator. They also show how relatively recent human evolution can be detected, reconstructed and quantified from the DNA of living populations.

What cannot be observed is the intelligently designed caricature of evolution that creationists are conditioned to mistake for the scientific theory: a single dramatic event in which one species suddenly transforms into an unrelated form. There is no plausible biological mechanism for such a transformation, which is why evolutionary biologists have never proposed one. Biological evolution is a change in the frequency of heritable variants within a population over successive generations; larger differences, including those associated with speciation, accumulate through many such changes.

Young-Earth creationists are nevertheless prepared to invoke evolution at an absurdly accelerated rate when their mythology requires it. To squeeze the present diversity of life into the few millennia supposedly available after their genocidal global flood, a small number of vaguely defined ancestral “kinds” would have needed to diversify into hundreds of thousands of beetle species and countless other forms almost overnight. Yet the same creationists baulk at evidence that human populations have undergone much more modest evolutionary changes over thousands of years.

The new research concerns AMY1, the salivary amylase gene. Salivary amylase begins the digestion of starch in the mouth, and people differ considerably in the number of AMY1 copies they carry. An early duplication of the gene occurred in the hominin lineage at least 800,000 years ago, after which repeated duplications, deletions and inversions generated numerous structural variants containing different numbers of copies. These are mutations that change the amount and arrangement of genetic material in the genome — precisely the sort of naturally arising variation that creationists insist cannot occur.

Crucially, cultivating potatoes did not cause the ancestors of Indigenous Andeans to acquire additional AMY1 copies because they needed them. High-copy variants were already present in the population. When potatoes and other starch-rich crops became dietary staples, people carrying more copies probably produced more salivary amylase and obtained a reproductive or survival advantage. Natural selection then increased the frequency of those pre-existing variants — evolution acting as a filter, not as a designer working towards a predetermined goal.

The researchers analysed AMY1 copy numbers in 3,723 people representing 85 populations. Indigenous Peruvian Andeans had among the highest numbers found, with the Quechua participants carrying a median of ten copies, compared with six among the closely related Maya comparison group and seven across the worldwide sample. The genetic evidence indicates that a high-copy haplotype increased in frequency among Andeans from about 2 per cent to approximately 45 per cent after around 10,000 years ago, coinciding with permanent settlement of the high Andes and the domestication of potatoes between about 10,000 and 6,000 years ago.

Refuting Creationism - Ancient Hunters Targeted Female Mammoths - 20,000 Years Before 'Creation Week'

Mammoth bone accumulation site, Kraków Spadzista, Poland

Photo: Jarosław Wilczyñski

Excavation in Langmannersdorf, Austria, 2025.

Photo: Marc Händel/Austrian Academy of Sciences

Ancient DNA reveals Ice Age hunter-gatherers preferentially targeted female mammoths - Stockholms universitet

A heap of ancient bones does not come with a label explaining how it was formed. When large accumulations of woolly mammoth remains are found at Upper Palaeolithic sites, archaeologists must determine whether the animals were killed by people, scavenged after natural deaths, or accumulated through entirely natural processes such as floods, landslides or animals becoming trapped in bogs.

Cut marks, deliberately broken bones and stone projectile points embedded in mammoth remains show that humans sometimes hunted and butchered these enormous animals. But such evidence is not present on every bone, leaving open the possibility that some of the great mammoth bonebeds of Eurasia resulted largely from natural mortality rather than sustained human exploitation.

Now an international team led by researchers at the Centre for Palaeogenetics in Stockholm has approached the problem from an ingenious new direction: instead of asking only what happened to the bones, they used ancient DNA to determine whether the mammoths were male or female.

As described in a newly published paper in Current Biology, the researchers analysed genome data from 521 woolly mammoths, Mammuthus primigenius, recovered across Eurasia and North America. These included 448 animals sequenced for the first time, making this one of the largest palaeogenomic studies yet undertaken on an extinct species.

The contrast was striking. Among 421 mammoths recovered as dispersed remains from natural depositional settings, 66 per cent were male and only 34 per cent female. That male bias is consistent with the behaviour of modern elephants: adult males commonly leave their natal herds and live alone, making them more likely to take risks or become caught in natural traps such as bogs, sinkholes and landslides.

However, among 100 mammoths from large bone accumulations associated with Upper Palaeolithic people, the ratio was almost exactly reversed: 70 per cent were female and only 30 per cent male. As the researchers explain, this substantial difference provides population-scale evidence that human activity, rather than natural mortality alone, was the principal force creating these bone accumulations.

That does not necessarily mean that hunters deliberately selected females simply because they were smaller than adult males. If mammoths lived like modern elephants, females and their young would have travelled in matriarchal herds capable of mounting a formidable collective defence. However, such herds may also have followed more predictable routes than solitary males, making them easier for hunter-gatherers to locate repeatedly. People may have hunted them, scavenged animals that died along those routes, or—most probably—used a combination of both strategies.

Either way, the result opens a remarkable window onto human behaviour between about 30,000 and 20,000 years ago. Mammoths supplied meat and fat for food, hides for clothing and shelter, bones for construction, and ivory for tools, ornaments and works of art. By combining genetics with archaeology and knowledge of elephant social behaviour, scientists can now reconstruct something of how Upper Palaeolithic people located and exploited this critically important resource.

And all this human ingenuity, accumulated ecological knowledge and repeated interaction with mammoth herds was taking place tens of thousands of years before creationists believe their god created Earth and everything upon it. Once again, the evidence reveals not a recently created world interrupted by a global flood, but a deep and richly documented human past—one preserved not merely in tools and bones, but in fragments of ancient DNA surviving within those bones.

Creationism Refuted - The Neanderthal Genes We Inherited Are Still Making A Difference.

We carry the legacy of our ancestors interbreeding with Neanderthals

AI-generated image (ChatGPT 5)

Shana - the daughter of a Neanderthal father and a Homo sapiens mother
Cover illustration for my book The Way of the Wolf

AI-generated image (ChatGPT 5.2)

Neandertal growth hormone receptor increases muscle mass in people today | Max-Planck-Gesellschaft

Evolutionary history is often represented as a neatly branching tree: an ancestral population divides, its descendants diverge, and each resulting lineage continues along its own independent path. Real evolution, however, is frequently much less tidy.

As I explained in my previous post on the Hawaiian honeycreepers, lineages that have begun to diverge can subsequently meet again and exchange genes through hybridisation. The result is reticulated evolution: an evolutionary history that is partly tree-like but also contains connecting branches where genes have passed between related populations.

The same principle applies to our own ancestry.

Modern humans, Neanderthals and Denisovans were not separately created, genetically sealed “kinds”. They were closely related human lineages produced by population separation and divergence, but that separation was never absolute. When populations encountered one another again, they sometimes interbred, allowing genes from one evolutionary branch to enter another—a process known as introgression.

Much of the resulting Neanderthal-derived DNA carried by people today may have little or no detectable effect. Some introgressed variants, however, continue to influence human biology. An international team led by Philipp Kanis of the Max Planck Institute for Evolutionary Anthropology and Hugo Zeberg of Karolinska Institutet has now investigated one particularly interesting example: the Neanderthal version of the growth-hormone receptor.

Their peer-reviewed paper in Current Biology examines two amino-acid substitutions in the receptor that were characteristic of Neanderthals. The growth-hormone receptor sits on the surface of cells and transmits the signal produced when growth hormone binds to it, helping to regulate the growth of bone, muscle and other tissues.

In laboratory-grown cells, the Neanderthal form of the receptor produced a stronger response to growth hormone than the common modern-human version. Under the experimental conditions used, cells carrying it grew by about 40 per cent more, with most of the increase attributable to one of the two Neanderthal-derived substitutions.

Refuting Creationism - Evolutionary Radiation Of Hawaiian Honeycreepers

Hawaiian honeycreepers

Source: Wikipedia (various contributors)

Loxiodes bailleui

By Jack Jeffrey, USGS - gallery.usgs.gov, Public Domain, Link

Smithsonian Scientists Resolve the Hawaiian Honeycreeper Family Tree | Smithsonian's National Zoo and Conservation Biology Institute

Only a few days after writing about Darwin’s famous Galápagos finches and how the Galápagos daisy had parallelled their evolutionary radiation, another group of island birds provides an even more spectacular example of adaptive radiation.

This time the setting is the Hawaiian archipelago, and the birds are the Hawaiian honeycreepers — an extraordinary collection of finches that evolved an assortment of beaks, diets and ways of life from a shared ancestral population.

More than 60 species of Hawaiian honeycreeper are known, ranging from thick-billed seed-eaters and nectar-feeders to birds with long, curved beaks for probing flowers or extracting insects from beneath bark. Some became so anatomically different that, before their evolutionary relationships were understood, naturalists found it difficult to believe that they could all be related.

But related they are. According to research published in the Proceedings of the National Academy of Sciences (PNAS) by Michael G. Campana and colleagues at the Smithsonian’s National Zoo and Conservation Biology Institute and National Museum of Natural History, the honeycreepers form a single adaptive radiation whose history includes not only repeated branching into new species but also genetic exchange between some of those emerging lineages.

Creationism in Crisis - Speciation in Progress? - Genetic Isolation In A British Dolphin.

Risso's dolphin Grampus griseus.

Credit: Nicola Hodgins

Risso's dolphin, Grampus griseus

© Nicola Hodgins.

British Risso’s dolphins belong to single population - University of Exeter News

According to newly published research in the Journal of the Marine Biological Association of the United Kingdom (JMBA), Risso’s dolphins, Grampus griseus, around the British Isles appear to form a single, genetically connected population. At the same time, their mitochondrial DNA distinguishes them from dolphins sampled elsewhere in the Atlantic and Mediterranean, suggesting that the British population has experienced relatively little genetic exchange with more distant populations.

The research was conducted by an international team whose joint first authors were Nicola K. Hodgins, a visiting researcher at the University of Exeter, UK, and Ing Chen of National Taiwan Normal University, with Michael Krützen of the University of Zurich as corresponding author.

At first sight, describing the British dolphins as both a single population and genetically distinct might seem contradictory, but the two findings concern different geographical scales. Within British waters, the dolphins appear to interbreed freely enough to prevent significant regional genetic divisions from developing. Compared with populations farther afield, however, reduced gene flow has allowed the British population to acquire a distinctive genetic signature.

Creationism In Crisis - After Darwin's Finches It's Darwin's Daisies - Evolution In Progress

Serrated leaves of Scalesia affinis (radiate-headed scalesia)

Photo: Michael Martin, NTNU University Museum

Botany’s answer to Darwin’s finches shows evolution in real time

The Galápagos Islands occupy an iconic place in the history of evolutionary biology. The animals and plants Darwin encountered there during the voyage of HMS Beagle contributed important evidence to the theory he developed after returning to England: that living species are not fixed and immutable but are the products of a long historical process.

Darwin eventually realised that natural selection acting upon inherited variation could produce organisms that appeared designed for their environments, without foresight, planning or divine intervention. Individuals possessing variations that gave them an advantage in their particular circumstances tended to leave more descendants, causing those variations to become more common over successive generations.

Like the uniformitarian geologists—particularly Charles Lyell—Darwin recognised that the world as we see it is not a fixed unchangeable result of a single act of perfect creation, but is the product of natural processes operating over immense periods of time. The processes that shaped the past are still operating today and will continue to shape the future.

The familiar story that Darwin saw the Galápagos finches and immediately conceived his theory is, however, an oversimplification. During the voyage, he believed he had collected birds belonging to several different groups, including finches, grosbeaks, blackbirds, wrens and warblers. Only after the ornithologist John Gould examined the specimens in England did it become apparent that these apparently disparate birds belonged to a distinctive group of closely related species—what we now call Darwin’s finches, although taxonomically they are members of the tanager family.

Darwin then appreciated the evolutionary significance of their shared characteristics and striking differences. Their varied body sizes and beaks could be understood as modifications of a common ancestral form, associated with different diets and ecological niches throughout the archipelago. One ancestral population had diversified into numerous related forms: a process now known as adaptive radiation.

The standard creationist response is to dismiss Darwin’s finches as evidence for evolution because they remain recognisably finch-like. This objection depends upon the childish parody of evolution in which one species should turn suddenly into an entirely different and supposedly unrelated species. Such an event would not demonstrate evolution; it would contradict the branching process of descent with modification. Descendants necessarily remain related to their ancestors and inherit modified versions of ancestral structures.

This misconception lies behind such familiar creationist “Gotchas!” as “Why do we never see evolution happening?” and “Why has evolution stopped?” Evolution has not stopped. What creationists demand to see is not evolution but an instantaneous transformation that evolutionary biology neither predicts nor requires.

Darwin knew nothing of Mendelian genetics or DNA, of course. Modern genomic research has confirmed the common ancestry of his finches while revealing a history more complicated than a simple, neatly branching tree. Rapidly diverging lineages can retain genetic variants inherited from their common ancestor and can occasionally exchange genes through hybridisation.

Now, genomic research into a family of plants—the genus Scalesia, commonly known as the Galápagos giant daisies—has provided a botanical counterpart to Darwin’s finches. In only about one million years, the founding lineage has diversified into 15 recognised species occupying habitats ranging from dense, humid highland forests to hot, dry and exposed lowlands. They vary from low-growing shrubs to trees, with leaves ranging from large and unlobed to small, deeply lobed and intricately serrated.

Refuting Creationism - The Complex Origins of Modern Humans - No Just A Single Couple - Not Even A Single Species

Interwoven Human ancestry

AI-Generated image (ChatGPT 5.6 Sol)

New technique pinpoints human DNA inherited from ‘ghost’ ancestors - Berkeley News

Using genealogical relationships in DNA, UC Berkeley researchers have uncovered hidden contributions from extinct human populations that left no sequenced genomes.

Meaghan Marohn

The evolutionary ancestry of modern Homo sapiens is far more complex than anything the authors of the Bible’s absurdly simplistic origin myths could have imagined. We already know that populations of our species migrating out of Africa interbred with Neanderthals and Denisovans, and that these two archaic lineages also exchanged genes with one another. Consequently, most people with ancestry outside Africa carry some Neanderthal DNA, while many Asian and especially Oceanian populations also carry Denisovan DNA.

Now, according to a paper just published in Science, our ancestry is even more complicated. A team led by researchers at the University of California, Berkeley, with colleagues at Johns Hopkins University and 54Gene, has identified genetic material inherited from two previously unknown archaic hominin lineages. These are described as “ghost” lineages because no sequenced genome from either population is available: their existence must be inferred from the traces they left in the genomes of living people.

The researchers developed a computational method called TRACE — TRacking Archaic Contributions via ARG Estimation — which reconstructs genealogical relationships among segments of DNA. By identifying regions whose ancestry extends unusually far back in time, TRACE can detect contributions from extinct populations without requiring DNA recovered from their bones.

Creationism Refuted - How Humans Modified Wild Rice - Because 'The Creator' Didn't Know What We Needed?

Paddy fields in Vietnam with people transplanting rice.

Dave Mckay/Alamy Stock Photo

Different varieties of rice grown today

By IRRI Images - originally posted to Flickr as IMG_2039-77,
CC BY 2.0, Link

One grain to rule them all: the history of rice as a global food

A point made several times in these blog posts is that the creationist interpretation of Genesis presents the living world as having been deliberately created for human use. That raises an obvious question: why have humans needed to modify virtually every domesticated animal and cultivated plant to make it more useful?

In many cases, selective breeding has altered organisms so extensively that modern breeds and crop varieties are barely recognisable as descendants of their wild ancestors. Did the supposed creator fail to anticipate how humans would use them, or was it simply incapable of finishing the job and obliged to leave the improvements to us?

Creationists have never produced a satisfactory, evidence-based answer. Instead, they appeal to “mystery”, “unknowable intentions” or some other form of theological evasion — ways of avoiding the question while pretending to have answered it. Alternatively, they simply ignore the problem and continue asserting that Genesis provides an accurate account of history and the origins of living species.

Rice, of course, doesn't get a mention in the Bible, the cultural origins of whose authors were primarily the Tigris-Euphrates rivers of Mesopotamia and later the Nile in Egypt, where wheat and barley were the staple crops, so they knew nothing of the origins or cultivation of rice, nor of India or China for that matter. Wheat by contrast is mentioned in the Bible 51 times and barley, 37.

Science, by contrast, allows us to reconstruct increasingly detailed and testable histories of domesticated animals and cultivated plants. Genetics, archaeology and the study of ancient plant remains show how humans selected heritable variations and gradually changed wild populations through artificial selection, hybridisation and the movement of crops between regions. One particularly fascinating example is the origin and cultivation of Asian rice, Oryza sativa, which now provides sustenance for more than 3.5 billion people.

The evidence traces this history across a timescale wholly incompatible with the creationist belief in a 6,000–10,000-year-old Earth. Wild rice ancestral to modern cultivated rice was growing in the lower Yangtze region of China about 100,000 years ago. Humans began gathering and processing it approximately 24,000 years ago, and evidence of pre-domestication cultivation appears about 13,000 years ago. By around 11,000 years ago, plant remains show a rapid increase in characteristics associated with domestication, as generations of human selection transformed wild rice into a recognisably cultivated crop.

There is also evidence of rice cultivation in the Ganges valley of northern India as early as 6500 BCE—about 8,500 years ago. The details remain a subject of legitimate scientific debate, particularly whether Indian rice was domesticated independently and how much the eventual development of indica rice owed to hybridisation between local rice and japonica introduced from China. What is not in dispute is that modern rice emerged through a prolonged history of cultivation, selection, migration and hybridisation — not through an instantaneous act of creation.

The history of rice is the subject of an article in The Conversation by Garritt C. Van Dyk, Senior Lecturer in History at the University of Waikato, New Zealand. His article is reprinted below under a Creative Commons licence and reformatted for stylistic consistency:

How Evolution Works - The Founder Effect

The brown tree snake, Boiga irregularis

Photo: USGS

Photo: USGS

Study: Hidden genetic diversity may have helped inbred brown tree snakes take over Guam - University at Buffalo

Biological invasions present evolutionary biologists with an apparent paradox. A newly established population may begin with only a handful of individuals and therefore contain only a small sample of the genetic variation present in its parent population. The resulting population bottleneck should increase inbreeding, reduce its capacity to adapt and expose harmful recessive mutations to natural selection. In extreme cases, the population should succumb to what population geneticists call an “extinction vortex”, in which declining genetic diversity and declining population size reinforce one another.

And yet some introduced species do precisely the opposite. They survive, proliferate and overwhelm the ecosystems into which they have been introduced. Few examples are more spectacular—or more ecologically destructive—than the brown tree snake, Boiga irregularis, on the Pacific island of Guam.

Native to Australia, Papua New Guinea and other parts of the western Pacific, brown tree snakes probably reached Guam as accidental stowaways in military cargo sometime after the Second World War. The invading population is believed to have been founded by only a handful of snakes. Nevertheless, their descendants multiplied until, in some parts of the island, densities reached an extraordinary 30,000 snakes per square mile.

The consequences for Guam’s wildlife have been catastrophic. As nocturnal, generalist predators encountering abundant prey that had evolved without such a snake, they devastated the island’s native birds, causing several species to disappear from the wild on Guam. They have also disrupted food webs, preyed upon reptiles and small mammals and caused hundreds of power cuts by climbing electricity infrastructure.

But how did a population founded by so few individuals avoid collapsing under the burden of inbreeding?

A new paper in Science Advances by Christopher A. Osborne of the University at Buffalo and colleagues from Buffalo and the US Geological Survey suggests that the answer lies partly in a form of genetic variation that earlier sequencing methods tended to miss.

The snakes did not, in fact, avoid the bottleneck. Their genomes retain compelling evidence of it. The researchers found that roughly half of each snake’s genome consisted of long “runs of homozygosity”—regions in which the copies inherited from the mother and father were almost identical. This is a genomic signature of intense inbreeding, comparable with that seen in some endangered species of conservation concern.

However, genetic diversity is not confined to changes in individual DNA letters. Using long-read sequencing, which can detect much larger differences, the researchers found nearly 19,000 structural variants. These included sections of DNA that had been duplicated, deleted, inserted or rearranged. Together, these structural variants affected almost eight times as much of the genome as the single-nucleotide variants upon which conventional estimates of genetic diversity have largely relied.

More importantly, the surviving variation was not distributed randomly. Structural variants were especially abundant around gene promoters and in genes associated with adaptive immunity and olfaction. Variation in immune genes could help the snakes respond to pathogens, while variation affecting their highly developed sense of smell could influence their ability to recognise prey, exploit different foods and distinguish closely related snakes from potential prey. In other words, a population can be genetically impoverished overall while retaining disproportionately important variation in precisely those parts of its genome that influence survival and adaptability.

Refuting Creationism - The Unbroken History of China

Carving stone at Shimao city.

Image by IVPP.

The landscape of Shimao city.

Image by IVPP.

New DNA Study Unlocks Origins, Social Structure of Neolithic Shimao Civilization----Chinese Academy of Sciences

In my last blog post, I pointed out that ancient Egypt’s archaeological and written record extends continuously from long before the date young-Earth creationists assign to Noah’s Flood, through that supposed catastrophe and into biblical times. Nowhere is there any sign that Egypt was destroyed by a global flood and subsequently repopulated by migrants from Mesopotamia. I also showed that the biblical writers who set stories in Egypt possessed only a tenuous understanding of its real history and culture.

Ancient China presents creationists with much the same problem. Its archaeological record contains long regional sequences extending across the supposed date of the Flood, with local populations, cultures and economies continuing to develop. If every human outside Noah’s immediate family had been exterminated, the existing peoples of East Asia should disappear from the record and be replaced by a rapidly expanding population of recent Mesopotamian origin. That is not what archaeology shows—and ancient DNA now provides an especially clear test of the claim.

The evidence comes from a paper published in Nature in November 2025 by an international team led by Professor Qiaomei Fu of the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) at the Chinese Academy of Sciences, working with researchers from several other Chinese institutions.

The team analysed genome-wide data from 169 ancient individuals recovered from Shimao and surrounding settlements in northern China. Population analyses were conducted using 144 unrelated individuals, while the remaining close relatives enabled the researchers to reconstruct pedigrees extending across as many as four generations.

Shimao, in northern Shaanxi Province, was one of the largest fortified settlements in Late Neolithic China. Occupied from approximately 2300 to 1800 BCE, it covered about four square kilometres and contained massive stone walls, separate inner and outer enclosures, specialised craft production, elite cemeteries and unmistakable evidence of a highly stratified society. Its occupation therefore began at about the very time when, according to the conventional young-Earth creationist chronology, the world should have been struggling to recover from a global extermination and repopulation by Noah’s immediate descendants.

Instead, the genomes showed that the people associated with Shimao were predominantly descended from populations already living in northern Shaanxi at least 1,000 years earlier. Those earlier inhabitants were associated with the Yangshao cultural tradition of the Yellow River’s Loess Plateau. The researchers found regional genetic continuity from the Middle to the Late Neolithic—continuity extending from before the supposed Flood into the centuries following it.

This was not a completely isolated or genetically static population. The researchers detected continuing contact with Yumin-related people from Inner Mongolia, close connections with the contemporary Taosi population farther south, and some ancestry from southern East Asian populations, possibly associated with the northward spread of rice cultivation. These were the ordinary movements, exchanges and intermarriages expected among neighbouring prehistoric farming and pastoral communities. They did not interrupt the dominant local ancestry, and there was no sign of wholesale population replacement by descendants of a family recently arrived from Mesopotamia.

The genetic evidence also revealed much about the organisation of Shimao society. Pedigrees reconstructed from elite burials indicated a predominantly patrilineal system in which status and wealth commonly passed from high-ranking men to their sons. Male members of these lineages showed relatively little diversity in their Y-chromosome ancestry, whereas the women displayed much greater mitochondrial diversity. This is consistent with women frequently marrying into communities dominated by established male lineages, although the evidence for strictly patrilocal residence remains suggestive rather than conclusive.

The study also uncovered a possible sex-related pattern in Shimao’s practice of human sacrifice. Nine of the ten sampled victims buried beneath the East Gate were male, contradicting earlier identifications based on skeletal anatomy. In contrast, most sampled sacrificial victims accompanying elite burials were female: six of seven at Hanjiagedan and fourteen of nineteen at Huangchengtai. This suggests that male and female victims may have been selected for different rituals conducted in different places, although the researchers caution that the number of genetically sexed victims remains too small to establish the pattern conclusively.