Abiogenesis News - Origin Of Complex (Eukarote) Cells - Origin Of The Cell Nucleus

Amoeba infected with a giant virus

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Ushikuvirus: A newly discovered giant virus may offer clues to the evolutionary relationships
Researchers discover a new virus called the "ushikuvirus" that provide evidence for the viral eukaryogenesis hypothesis and reveal virus-host interactions, shaping the evolution of eukaryotic cells.

Professor Masaharu Takemura.

Ushikuvirus: A Newly Discovered Giant Virus May Offer Clues to the Origin of Life | Tokyo University of Science

One of the remaining questions in evolutionary biology is how the complex (eukaryotic) cell acquired its defining feature: a membrane-bound nucleus in which the DNA is stored.

Prokaryotic cells — bacteria and archaea — possess a single circular DNA molecule located in the cytoplasm. By contrast, all eukaryotic cells contain their genetic material within a membrane-bound nucleus. Now scientists at the Graduate School of Science, Tokyo University of Science (TUS), Japan, led by Professor Masaharu Takemura, have provided further evidence that the eukaryotic nucleus may have originated from a giant DNA virus, similar to those that infect certain species of amoeba. Their findings suggest that the origin of the nucleus may be closely linked to the evolutionary history of this class of virus as it adapted to different hosts.

Professor Takemura and Dr Philip Bell, from the Department of Biological Sciences at Macquarie University, Sydney, independently proposed the viral eukaryogenesis theory (a term coined by Dr Bell) in 2001, suggesting that large DNA viruses — such as poxviruses — might represent plausible ancestors. Since then, beginning in 2003, the discovery of several giant DNA viruses has provided more compelling candidates. When these viruses infect a host cell, they establish so-called ‘virus factories’ within the cytoplasm. In some cases these structures are enclosed within membranes that resemble the nuclear envelope.

The hypothesis proposes that, rather than destroying its host, such a virus formed a long-term association with it. Over evolutionary time, it may have incorporated host genes and transitioned from parasite to symbiotic genetic compartment — eventually becoming the nucleus.

For advocates of “irreducible complexity”, the nucleus is often presented as an all-or-nothing structure: a fully formed membrane, nuclear pores, transport machinery, chromatin organisation and regulatory systems supposedly appearing together or not at all. Yet the viral eukaryogenesis model shows how this argument collapses once intermediate stages are recognised. Giant DNA viruses already construct membrane-bound replication compartments inside host cells; they encode components involved in DNA replication, transcription and even elements of translation.

These viral “factories” function as semi-autonomous genetic centres within the cytoplasm — in effect, simplified proto-nuclei. If such a structure entered into a stable symbiotic relationship with a host cell, incremental gene exchange and co-evolution could gradually integrate and refine the system. Each step would confer immediate functional advantages — protection of DNA, separation of transcription from translation, improved regulation — without requiring the simultaneous appearance of a fully modern nucleus. What is claimed to be irreducible instead looks like a product of stepwise evolutionary integration.

Now Professor Takemura’s team report the discovery of a new giant DNA virus infecting amoebae — the ushikuvirus, named after Lake Ushiku where it was isolated — lending further support to the viral eukaryogenesis theory. Their discovery is reported in Journal of Virology.

Refuting Creationism - A Dinosaur With Spikes - 125 Million Years Before 'Creation Week'

Haolong dongi in a Cretaceous forest setting

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Artistic reconstruction of a juvenile Haolong dongi from the Early Cretaceous of China (125 million years ago).

© Fabio Manucci.

A dinosaur with spikes exhibiting unprecedented properties discovered in China | CNRS

Almost eight weeks into the New Year and not a single scientific paper has emerged in support of creationism—or its pseudo-scientific variant, Intelligent Design. Not even a speculative hint of the long-predicted collapse of ‘Darwinism’, nor any sign that Intelligent Design is making inroads into biomedical science. Instead, the steady flow of research continues to do precisely the opposite: quietly and methodically reinforcing evolutionary biology as the indispensable framework through which palaeontology, cell biology, virology and the rest of modern life sciences make coherent, testable sense of the evidence.

Today brings yet another example. An international team led by researchers from the Centre national de la recherche scientifique (CNRS), working at the Université de Rennes, has identified a new species of iguanodontian dinosaur that lived in what is now China around 125 million years ago. Their paper, recently published in Nature Ecology & Evolution, reports that this species was probably covered in hollow spikes, somewhat reminiscent of porcupine quills. The team have named the new species Haolong dongi in honour of Dong Zhiming, a pioneer of Chinese palaeontology.

Using X-ray scans and high-resolution histological sections, the researchers were able to identify preserved skin structures, revealing hollow cutaneous spikes over much of the animal’s body. Although herbivorous, this dinosaur lived in an environment where predation pressure from small carnivores would have been significant, and the spikes likely provided a degree of protection comparable to that of modern porcupines. The structures may also have played roles in thermoregulation and/or sensory perception.

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

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Daniel Fernandes preparing to take a sample.

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

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

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

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

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

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

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

Malevolent Design - Yet More Evidence Of Intelligently Designed Cancer?

Scientists Uncover Key Driver of Treatment-Resistant Cancer

These images show the beginnings of chromothripsis in colorectal cancer cells. The N4BP2 enzyme (green) infiltrates a micronucleus (zoomed in square selections), where it induces DNA damage (red). Blue represents the main cell nucleus.

Credit: UC San Diego Health Sciences

At the risk of labouring the point I made in my post yesterday — that the exact same arguments ID creationists use as ‘proof’ of intelligent design can also be applied to cancers, parasites, pathogens, and genetic diseases, thereby ‘proving’, in ID terms, that these too were intelligently designed by the same deity — we have yet another example of complex specified genetic information driving the evolution of cancers as they rapidly develop resistance to treatments.

This is reported in a research paper in Science by researchers at the University of California, San Diego (UC San Diego).

The researchers discovered an enzyme responsible for breaking up a chromosome in cancer cells and rearranging it into a scrambled version, enabling the tumour to evolve rapidly. The process is quite simple and closely mimics evolution by natural selection, or the development of antibiotic resistance in bacteria. Shuffling genes in this way increases the likelihood that a small number of cancer cells will survive the treatment aimed at destroying them. The tumour then regrows from these resistant cells, producing a treatment-resistant cancer.

This ability, known as chromothripsis, is found in about 24% of human cancers.

The key to this process is the protein enzyme N4BP2, and the complex, specified gene that produces it. The process begins when an error in DNA replication causes individual chromosomes to become trapped inside tiny, fragile structures called micronuclei. When these micronuclei burst, the chromosome is exposed to nucleases — enzymes capable of breaking DNA.

Within the ID creationist paradigm, there are no such things as mistakes: everything works exactly as it was designed to work. So we are left to assume that these fragile micronuclei, with their entrapped chromosomes, are a deliberate design feature.

The researchers showed that N4BP2 is uniquely capable of entering micronuclei and breaking the trapped chromosome.

To test the hypothesis that N4BP2 is the culprit, they eliminated it in brain cancer cells and observed a reduction in chromothripsis. They then introduced it into healthy cell nuclei and found that it caused chromosomes to break even in otherwise normal cells.

This is, of course, just as much compelling evidence of intelligent design as anything traditionally cited by ID creationists as proof of an intelligent designer. By contrast, the theory of evolution provides an explanation with none of the problems that force creationists to retreat into contradictory theology, Bronze Age origin myths, and appeals to ‘mystery’.

Malevolent Design - More Evidence Of Intelligently Designed Cancer?

Pancreatic cancers co-opt nerve cells to assist them to develop.

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Let’s get on pancreatic cancer’s nerves | Cold Spring Harbor Laboratory

Creationists seem to have pinned all their hopes of justification for their evidence-free beliefs on a false dichotomy and a classic “god of the gaps” fallacy: the claim that complex specified information and irreducible complexity are proof of design by an intelligent entity. This argument relies heavily on the parochial ignorance of its intended audience, who are expected to assume that this “designer” must be the Christian god of the Bible — or, depending on geography and cultural background, the god of the Qur’an — and that therefore those holy books must be the inerrant word of the supposed creator.

However, the problem this raises for creationists is an obvious one: who or what, within their framework, designed all the many examples of irreducible complexity and complex specified information that cause suffering, sickness, and death?

Another striking example has just been published in Cancer Discovery by Professor Jérémy Nigri and colleagues from Cold Spring Harbor Laboratory, New York, USA.

In this paper, the researchers use advanced 3D imaging to show how, even before tumours form, tumour-promoting fibroblasts — known as myCAFs — send out signals that attract nerve fibres. The myCAFs and nerve cells then work together within pancreatic lesions to create a microenvironment favourable for cancer growth. Embarrassingly for Intelligent Design advocates, this system depends entirely on the genetic capacity of myCAFs to send the correct molecular signals, and for nerve fibres to respond appropriately — a finely tuned interaction requiring precisely the sort of “irreducible complexity” they insist can only arise through intentional design.

Within the ID paradigm, these facts should be indisputable evidence of their god’s involvement — but only when the outcome is something they find beneficial, such as eyes, blood clotting, or a brain capable of abstract thought. When the very same logic points instead to cancers, parasites, and congenital diseases, it is suddenly no evidence at all, and certainly not evidence of malevolent intent on the part of the designer. The argument collapses into childish special pleading: design is invoked when convenient, but denied when morally awkward.

Creationism Refuted - Poisoned Arrows 50,000 Years Before 'Creation Week'

Preparing poison arrowheads, 60,000 years ago at the Umhlatuzana Rock Shelter in KwaZulu-Natal, South Africa

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Both sides of one of the arrowheads analysed. The left-hand image shows the organic remains in which the arrowhead residues were identified.

Photo: Marlize Lombard.

World’s oldest arrow poison – 60,000-year-old traces reveal early advanced hunting techniques - Stockholms universitet

Creationism’s Biblical narrative has just become even harder to defend, with news that researchers from South Africa and Sweden, led by Professor Sven Isaksson of the Archaeological Research Laboratory at Stockholm University, have identified the oldest traces of arrow poison yet discovered. These were found on 60,000-year-old quartz arrowheads from Umhlatuzana Rock Shelter in KwaZulu-Natal, South Africa.

That is a full 50,000 years before creationist mythology claims the world was created, but entirely consistent with the palaeontological and archaeological evidence that fully modern humans had already evolved in Africa and were developing increasingly sophisticated technologies.

The discovery is reported open access in Science Advances.

The significance of this find is two-fold. Firstly, it shows that early humans had invented the bow and arrow as a hunting weapon much earlier than previously thought. Secondly, it demonstrates that they also understood how to exploit natural toxins — specifically the alkaloids buphanidrine and epibuphanisine — found in the plant Boophone disticha, commonly known as gifbol or “poison onion”. Traces of these compounds had previously been identified on arrowheads only around 250 years old, so this remarkable discovery reveals that the knowledge and use of such poison technology persisted among hunter-gatherer groups for tens of millennia.

Creationism Refuted - The Oldest Known Human Remains in Northern Britain Are From 1,000 Years Before 'Creation Week'!

A Mesolithic burial, 11,000 years ago

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Figure 3. View facing west over the surface of the deposits in the main chamber at the start of the current fieldwork, showing the paint markings made by Mr Redshaw.

Photo by Martin Stables.

DNA analysis reveals Northern Britain’s oldest human remains are of a young female child

A good thousand years before creationism’s god allegedly created the first two humans, the body of a young girl was being buried in a cave in Cumbria, northern England.

This unwelcome news for creationists comes from an international team led by archaeologists at the University of Lancashire, who have just published their findings in Proceedings of the Prehistoric Society.

The girl’s remains were discovered about three years ago in Heaning Wood Bone Cave by local archaeologist Martin Stables, from the nearby village of Great Urswick. The University of Lancashire team have now succeeded in extracting enough DNA to determine that she was between about 2.5 and 3.5 years old when she died.

Jewellery in the form of a deer tooth pendant and pierced beads has been radiocarbon dated to around 11,000 years ago, strongly suggesting this was a deliberate burial. This raises the question of why the cave held such significance as a burial site. Modern hunter-gatherer groups often regard caves as gateways to a spirit world, so it is possible that Mesolithic hunter-gatherers in northern Europe held similar beliefs.

The team also showed that at least eight other individuals were buried in the cave over a period spanning roughly 4,000–11,000 years ago, from the Early Neolithic to the Early Bronze Age — ironically, the latter being the period when the creation myths of the Bible were being invented. The authors of those Bronze Age stories, of course, would have known nothing whatever of hunter-gatherer societies in northern Europe, their cultural history, or their spiritual traditions.

No doubt we will see the traditional creationist misrepresentation of this evidence, with unfounded assertions that radiocarbon dating “doesn’t work” and that scientists simply make things up to conform to some notional Darwinian narrative. Making things up to fit a pre-existing story is something creationists themselves routinely do. It seems to be characteristic of those who set out to deceive that they accuse others of doing exactly what they themselves practise.

Abiogenesis News - A Small Self-Copying RNA Molecule That Could Easily Arise Spontaneously

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Bridging the gap from chemistry to life: discovery of a tiny RNA that can copy itself | MRC Laboratory of Molecular Biology

A paper by Philipp Holliger’s group in the MRC Laboratory of Molecular Biology’s Protein and Nucleic Acid Chemistry (PNAC) Division, Cambridge, UK, announces the discovery of a self-replicating small RNA molecule that can also synthesise its complementary strand. It was published yesterday in Science Advances.

This effectively resolves one of the few remaining major questions in explanations of abiogenesis: the origin of a simple self-catalysing replicator. Such a molecule must have existed at the very beginning of life’s emergence, and for decades RNA has been the leading candidate, because it can function both as an enzyme and as an information store — capable of copying that information repeatedly, provided there is a supply of nucleotides from which to build itself.

The question of where such a replicator first arose — in Darwin’s “warm little pond”, at a deep-ocean hydrothermal vent, or on wave-splashed rocks providing a steady supply of raw materials — is secondary to the more fundamental question of what could have initiated self-replication in the first place. Once replication began, occasional copying errors would inevitably generate variation, giving natural selection something to act upon. From that point, it is difficult to avoid the conclusion that progressively more efficient replicators would emerge, eventually dominating and monopolising the available resources.

Although various RNA molecules are known that can also act as catalysts (ribozymes), most are far too large to self-catalyse, or plausibly to have arisen spontaneously under prebiotic conditions. This newly discovered RNA molecule, at a mere 45 nucleotides long, neatly plugs that gap.

Creationists will no doubt reach for their usual “astronomical improbability” trope, but it only works by assuming the wrong problem. It treats abiogenesis as if one exact, predetermined sequence had to assemble by perfectly random chance in a single step. Real chemistry is biased, real environments concentrate and cycle materials, and—most importantly—the target was never one unique sequence but any of a potentially vast number of small RNAs with even modest replicative activity.

Once replication begins, copying errors generate variation and natural selection can take over, amplifying the better replicators. In short: the relevant question is not the odds of one bullseye in 4⁴⁵, but how quickly chemistry can stumble into a broad foothold and let Darwinian processes do what they inevitably do.

Refuting Creationism - Life In A New Zealand Cave - 1 million Years Before 'Creation Week'

Prehistoric New Zealand Cave

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AI generated image of the NZ cave

P Scofield, Canterbury Museum.

1m-year-old 'lost world' discovered – News

About a million years before creationism’s putative designer supposedly fashioned a small flat world beneath a solid dome — the imagined cosmos of Bronze Age pastoralists in the Middle East who authored the Bible’s creation myths — ancient frogs and birds, the ancestors of today’s New Zealand species, lived and died and became fossilised deep in a cave near Waitomo on Aotearoa’s North Island.

Of course, confined as they were to within a few days’ walk of the Canaanite hills, the authors of those myths could have had no inkling of people and places in far-flung regions of a spherical planet. Their tales were based entirely on what they imagined to be the whole universe, and contain nothing that existed beyond their narrow horizons.

How these New Zealand fossils were unearthed, and what they can tell us about Aotearoa’s deep past, is the subject of a paper just published in Alcheringa: An Australasian Journal of Palaeontology, by a research group led by Associate Professor Trevor Worthy of the College of Science and Engineering at Flinders University.

It is, of course, a story vastly different from Biblical mythology — the evidence for which stubbornly refuses to manifest itself, and instead consistently refutes it, revealing it to be the product of parochial ignorance and an attempt to force-fit what little was known into prevailing cultural assumptions: what Christopher Hitchens aptly called “the fearful infancy of our species”.

The findings show that around 33–50% of species went extinct about one million years before humans first arrived on Aotearoa (New Zealand). The cause appears to have been a combination of rapid climate change and catastrophic volcanic activity. The discovery helps fill a fifteen-million-year gap in our knowledge of Aotearoa’s history.

Excavations at St Bathans in Central Otago have allowed palaeontologists and geologists to reconstruct the period between 20 and 16 million years ago, but until now there has been very little information about the long stretch between then and one million years ago.

Among the discoveries was a new species of parrot, Strigops insulaborealis, an ancient relative of the flightless kākāpō, but one that could probably fly; an extinct ancestor of the modern takahē; and an extinct species of pigeon closely related to Australian bronzewing pigeons.

To forestall the traditional creationist attempt to discredit both the discovery and the scientists who made it — by claiming the dating methods are flawed or even fraudulent — the fossils can be dated accurately because they lie between two layers of volcanic ash: one deposited around 1.55 million years ago, and another about one million years ago. Volcanic ash can be dated with a high degree of confidence using Uranium–Lead (U–Pb) dating of zircon crystals.

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

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

© Mikaël Pittet – UNIGE

Immune 'hijacking' predicts cancer evolution - Medias - UNIGE

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

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

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

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

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

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

Refuting Creationism - Bonobos Can Imagine Things Detached From Reality

Apes share human ability to imagine | Hub

A paper published recently in Science should give creationists something to think about. It shows how our close relatives, the bonobos, can imagine things completely detached from physical reality — rather like children playing games of pretend, or creationists pretending they are leading experts on biology and understand the subject better than the actual experts.

In this study, two researchers from Johns Hopkins University demonstrate that bonobos can engage in imaginative “pretend play”, an ability long assumed to be uniquely human. In doing so, they dismantle yet another supposed human-exclusive trait that creationists cite as evidence of special creation.

In one experiment with a captive bonobo, Kanzi — a 43-year-old individual living at Ape Initiative — a researcher pretended to pour juice from an empty jug into a transparent empty cup, and then pour it again into a second empty cup. When asked, “Where is the juice?”, Kanzi correctly identified the second cup.

In a similar experiment, an imaginary grape was taken from an empty bowl and placed into an empty jar. When asked, “Where is the grape?”, Kanzi again correctly pointed to the jar.

These experiments show that Kanzi was able to imagine and successfully track the movement of invisible, non-existent objects — something human children can typically do by the age of about two.

Creationism Refuted - A Football-sized Vegetarian - From 307 Million Years Before 'Creation Week'

A Shoreline scene in the Carboniferous

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A reconstruction of Tyrannoroter heberti, eating a fern.

Illustration by Hannah Fredd.

Football-sized fossil creature may have been one of the first land animals to eat its veggies - Field Museum

We have another example today of how the evidence written into the fossil record — which creationists insist either does not exist, or is at best a lie forged to deceive us — stubbornly refuses to conform to creationist requirements. Instead, it continues to tell the only story it can: of life evolving slowly over deep time on a planet that is billions of years old.

The latest example comes from a paper published in Nature Ecology and Evolution by researchers from the Field Museum of Natural History in Chicago, Carleton University in Ottawa, Ontario, Canada and the Smithsonian Museum. The study was co-led by Arjan Mann, assistant curator of fossil fishes and early tetrapods at the Field Museum.

The paper presents evidence of the earliest known herbivorous vertebrate — dating to some 307 million years before creationists believe the Earth was created. Once again, this highlights the fundamental problem creationists face when they begin with a dogmatic belief that the Earth is only a few thousand years old because a handful of Bronze Age pastoralists said so. Having declared in advance that there has been no significant evolution, only minor variation within “kinds”, they are then forced to twist and contort the real-world evidence in a futile attempt to shoehorn it into their absurdly compressed timescale.

The animal, named Tyrannoroter heberti by the researchers, evolved over the tens of millions of years since the first vertebrates transitioned from lobe-finned fish to terrestrial tetrapods around 375 million years ago — perhaps to escape aquatic predators, or to exploit the invertebrate prey that had already colonised the land. Plants, meanwhile, which had begun spreading onto land some 475 million years ago, had also been evolving, and by this time were well established as ferns, horsetails, and other tough early vegetation.

Tyrannoroter heberti, known so far from a single skull, was probably among the largest terrestrial animals alive at the time, reaching around a foot in length — roughly the size of an American football — based on the proportions of close relatives. The fossil was recovered from shoreline cliffs in Cape Breton, Nova Scotia, Canada.

It is thought to represent a stem amniote: part of the lineage of vertebrates that evolved the ability to lay eggs away from water, unlike amphibians which must still return to water to reproduce. This group ultimately gave rise to reptiles, birds, and mammals — in other words, to almost the entire later terrestrial vertebrate world, including ourselves.

Creationism Refuted - Why We Need Our Gut Microbiome To Keep Us Healthy

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Electron microscopic image of rod-shaped gut bacteria.

© Bacteria in the gut. NIH Image Gallery/Donny Bliss, NIH

What gut bacteria like

An open access paper in Proceedings of the National Academy of Sciences of the USA (PNAS) is a stunning example of the ludicrous complexity evolution has produced — the exact antithesis of what an intelligent designer would create, if such a designer were anything more than grossly incompetent. As I explain in my book, The Unintelligent Designer: Refuting The Intelligent Design Hoax, and as I have pointed out repeatedly on this blog, the hallmark of intelligent design should be minimal complexity and maximal efficiency. And yet what we find in humans — and in just about every other bilaterian animal with a gut — is a vast, intricate symbiotic microbiome supplying functions that could far more simply have been provided directly, with even a little forethought on the part of any competent designer.

Instead, in the sort of convoluted complexity that creationists like to attribute to their putative designer god, but which is in reality a hallmark of evolved systems, we see yet another example of a biological arrangement that betrays not intelligence, but its absence.

The paper, by an international team led by Professor Victor Sourjik and colleagues from the Max Planck Institute for Terrestrial Microbiology, the University of Ohio, and Philipps-University Marburg, describes how an interdependent gut microbiome helps to keep both the microorganisms and their host healthy. They show that this complex and dynamic community is governed by countless chemical interactions — not only among the microorganisms themselves, but also between microbes and host tissues. The perception of nutrients and signalling molecules by gut bacteria is therefore crucial in maintaining these relationships.

One key role of this microbiome is in deterring and combating pathological species which would otherwise find the gut — with its warmth and steady supply of pre-digested nutrients — an ideal environment to colonise. This must have been a problem even for the earliest animals with a digestive tract: a vulnerability effectively built into the body plan. The solution, in the form of beneficial commensal organisms, is therefore probably as old as the first tube-like bilaterians themselves.

The problem the human gut faces in this respect can be gauged from the fact that some studies have shown that 50-55% or more of the dry weight of human faces is bacteria, dead and alive[1] , with populations of bacteria in the order of 10¹¹ bacteria per gram![2] Imagine then the opportunities this presents to a potentially pathological bacteria with a generation time in minutes. With a population exploding exponentially, the potential to overwhelm the host in a few days is enormous. This is the scale of the problem, and of the selection pressure to overcome it, that has produced this massively complex solution, because it wasn't solved in the initial 'design' stage.

Since it worked well enough, there has been no evolutionary pressure to replace it with a less vulnerable gut, or one better equipped to cope with infection without relying on an entire ecosystem of different microorganisms to maintain health. In other words, what we have today is the result of more than half a billion years of evolutionary history since this basic body plan first emerged in the Cambrian.

Refuting Creationistm - An Evolutionary Trap That No Intelligent Designer Would Blunder Into

Sceptobius beetles in an ant colony

The evolutionary trap that keeps rove beetles alive

A new study reported in Cell describes an extraordinary example of evolutionary adaptation unfolding right under our noses — and it will make uncomfortable reading for anyone still clinging to the creationist fantasy that living systems were neatly “designed” in their present form a few thousand years ago.

Researchers from the Division of Biology and Biological Engineering, California Institute of Technology, CA. USA, investigating the symbiotic relationship between certain rove beetles and their ant hosts have shown how these beetles have evolved the ability to infiltrate ant colonies by chemically disguising themselves as ants. Far from being “created” to live harmoniously together, this is an evolutionary arms-race in miniature: ants have evolved sophisticated chemical recognition systems to detect intruders, while the beetles have evolved equally sophisticated counter-measures to bypass those defences.

And the details are exactly the sort of thing intelligent design advocates never seem to anticipate. The beetles do not simply possess some magical, pre-installed “ant colony access” trait. Instead, evolution has shaped them into something far stranger and far less tidy: they suppress their own scent production and acquire the colony’s chemical signature directly from the ants themselves. In effect, they become living imposters — accepted not because the ants were “meant” to host them, but because natural selection has honed the beetles’ ability to exploit a biological loophole.

Malevolent Design - The Malaria Parasite Is Irreducibly Complex And Has Complex Specified Genetic Information - Oops!

Blood smear showing P. falciparum parasites.

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Malaria: Newly Identified “Crown” Stage Controls Parasite Reproduction

Researchers from the Hebrew University of Jerusalem have uncovered yet another layer of exquisite molecular sophistication in one of humanity’s most persistent and lethal parasites, Plasmodium falciparum, the chief cause of malignant malaria. Their findings, reported in a recent press release and published in the peer-reviewed Journal of Cell Biology, describe a newly identified regulatory “crown” checkpoint that controls parasite reproduction with remarkable precision.

It is difficult to imagine a discovery more awkward for Intelligent Design creationists, because Plasmodium falciparum is precisely the sort of organism that embodies everything Michael Behe and William Dembski insist cannot arise by evolution. Here is complex specified genetic information, tightly regulated developmental choreography, and interlocking biochemical machinery operating across multiple life stages — the very definition, we are told, of “irreducible complexity”.

Unfortunately for the Discovery Institute, this irreducible complexity does not produce a bird’s wing, a human eye, or some uplifting example of divine craftsmanship. It produces malaria — a parasite responsible for immense suffering and hundreds of thousands of deaths every year, mostly children. If complexity is meant to be a hallmark of intelligent design, then the designer’s portfolio includes some rather grim specialities.

The problem is compounded by the fact that Michael Behe has already made malaria central to his arguments. In The Edge of Evolution, he famously pointed to the parasite’s resistance to anti-malarial drugs as an example of the supposed limits of Darwinian evolution, claiming that multiple coordinated mutations were beyond the reach of natural selection. Yet malaria has since become one of the clearest demonstrations that evolution not only occurs, but does so rapidly and repeatedly, exploiting enormous population sizes and intense selection pressures to produce exactly the adaptations Behe claimed were improbable.

As Kenneth Miller pointed out, Behe's mathematical sleight of hand was to assume resistance had to evolve as a single event in a single cell, not across a large population over time - a fallacy of which any good microbiologists should have been aware.

This newly described “crown” stage is simply the latest reminder that biological complexity is not evidence of supernatural design. Evolution predicts complexity wherever it confers survival advantage — including in parasites, pathogens, and diseases. The only real surprise is that creationists continue to present complexity as a theological virtue, when nature so often deploys it in the service of exploitation rather than benevolence.

As ever, none of this will deter creationists from repeating their familiar articles of faith. Faced with an organism whose life cycle resembles a biochemical symphony — regulated checkpoints, specialised invasion machinery, host-cell remodelling, immune evasion, and reproductive stages split between mosquito and human — they will insist that this is not evidence for evolution but evidence against it. The argument, such as it is, runs that complexity must have been present from the start, because it could not have arisen gradually.

But this is simply the old “irreducible complexity” claim in a new disguise: the assertion that because creationists personally cannot imagine intermediate stages, no such stages could have existed. Science, of course, is not obliged to conform to the limits of anyone’s imagination. Evolution does not require that complex systems appear in a single leap. It proceeds by modification of what already exists — co-option, duplication, repurposing, and incremental refinement over deep time — producing the layered complexity we observe today.

Another common retreat is the insistence that this is merely “microevolution”, the trivial shuffling of genes within some mythical created “kind”. Yet Plasmodium falciparum is not merely adjusting the colour of its spots. It is evolving novel biochemical strategies, repeatedly acquiring drug resistance, fine-tuning developmental regulation, and exploiting host environments with extraordinary efficiency. If this is “only microevolution”, then the term has been drained of all meaning.

Refuting Creationism - A Gap-Filling Miniature Dinosaur from 120 Million Years Before 'Creation Week'

Paleo art reconstruction of Foskeia pelendonum.

Credit: Martina Charnell

Tiny new dinosaur Foskeia pelendonum reshapes the dinosaur f | Vrije Universiteit Brussel

Researchers from the Vrije Universiteit Brussel (VUB), working with colleagues in Spain and elsewhere in Europe, have just described a remarkable new species of dinosaur from the Early Cretaceous of northern Spain. Their findings are the subject of a read-only paper in Papers in Palaeontology.

The tiny herbivore, named Foskeia pelendonum, lived around 125 million years ago, yet it is already forcing palaeontologists to rethink part of the ornithopod family tree. The discovery provides another striking example of how the fossil record continues to grow in detail, resolution, and explanatory power.

This will come as an unwelcome development for creationists, who still cling to the claim that evolution is “just speculation” and that the fossil record contains no meaningful evidence of transitional relationships or evolutionary diversification. On the contrary, finds like Foskeia show exactly what evolutionary science predicts: new lineages appearing in the right strata, in the right environments, with a mixture of ancestral and derived traits that help clarify how later forms evolved.

Creationists will, of course, respond in the usual way. Some will insist that this dinosaur is “just another dinosaur”, as though classification and evolutionary relationships are irrelevant. Others will retreat to the vacuous assertion that it represents merely “variation within a kind”, without ever defining what a “kind” is or explaining why such variation produces a nested hierarchy that maps so precisely onto geological time. And as always, the more committed will simply dismiss the evidence altogether, because no amount of fossil discovery can compete with a belief system that must remain true regardless of what the rocks contain.

Yet the significance of Foskeia pelendonum lies precisely in the details. This was not simply a juvenile form of a larger dinosaur, but a genuinely small-bodied species, confirmed by bone histology to have reached adulthood. Even more intriguingly, it possessed unexpectedly specialised skull and dental features, showing that evolutionary change does not always follow the simplistic “bigger and more advanced” caricature imagined by creationists, but often proceeds through ecological experimentation, miniaturisation, and adaptation to local conditions.

Far from undermining evolutionary theory, discoveries like this strengthen it. They refine the dinosaur family tree, help fill long-recognised gaps in the ornithopod record, and demonstrate once again that the history of life is written not in Bronze Age mythology but in the sedimentary archive of deep time — an archive that continues to contradict creationism with every new fossil unearthed.

Unintelligent Design - A Bacterium That Goes Wrong And Self-Destructs

SAR11 bacteria comprise some 40% of marine bacterial cells, making them an essential part of our ocean ecosystems.

Image source: Smithsonian / Xiaowei Zhao.

One of Earth’s most abundant organisms is surprisingly fragile

Microbiologists at the University of Southern California (USC) have discovered that one of Earth’s most abundant species, the SAR11 bacterium, has a fundamental — and potentially fatal — ‘design’ flaw. They have just published their findings in Nature Microbiology, and it should make grim reading for any creationists with sufficient courage to read it.

When you have trillions of copies, what does it matter to ‘selfish’ genes if a few billion go wrong and end up destroying the organisms they travel through time in? For an evolved organism, it matters not one tittle or jot to its genes, because they can always produce more copies. So long as there is a sufficiently large population to keep replicating, they will continue to exist and reproduce — and they have no other ultimate function. This is all they evolved to do.

But could we say the same for an organism designed by an omniscient, intelligent designer? What would be intelligent about creating an organism that, under particular but entirely predictable conditions, attempts to reproduce but succeeds only in making repeated copies of its DNA, fails to divide, and enters a runaway cycle of replication until it becomes so disorganised that it can no longer survive and effectively self-destructs?

SAR11 dominates the surface waters of the world’s oceans and accounts for around 40% of marine bacterial cells. As such, it is a vital component at the base of the marine food chain, and is so successful partly because of a process known as genetic streamlining — the evolutionary loss of genes to reduce energy demands in nutrient-poor environments. This alone is not the main problem for creationists to explain, although it does raise the obvious question of why a designer would burden an organism with a genetic load it does not need in the first place.

The real problem is that this streamlining, as an evolved process, comes at a cost. In shedding a load of mostly surplus genes, some essential ones are lost too — including genes that regulate the cell cycle. The result is a failure to divide after genome replication, with the cell instead entering an uncontrolled loop of DNA replication without division.

How on Earth can that be regarded as intelligent design? The organism does exactly what it is ‘designed’ to do under conditions of low nutrient stress, but in doing so falls into an inescapable trap. The consequence is that populations continue to decline even when nutrients later become available again — with potentially serious knock-on effects for other species higher up the food chain.

Malevoent Design - Has Creationism's Divine Malevolence Been Up To Its Old Tricks? - Another Bat Virus Modified To Infect Humans.

Pteropine orthoreovirus (PRV)

Illustration of a Nipah virus.

Photo: AFP / Ruslanas Baranauskas / Science Pho

Bats Identified as Origin of Unexplained Acute Respiratory Illness and Encephalitis in Bangladesh | Columbia University Mailman School of Public Health

paper just published in Emerging Infectious Diseases by a team led by Nischay Mishra, of the Columbia University Mailman School of Public Health, shows that Pteropine orthoreovirus (PRV) — a bat-borne orthoreovirus — has crossed the species barrier into humans in Bangladesh, causing a Nipah-like illness that is difficult to distinguish clinically from Nipah virus infection. The disease presents primarily as an acute respiratory infection, sometimes accompanied by encephalitis.

It has long been known that bats possess a markedly more effective antiviral immune system than humans. This fact alone presents a problem for creationists who insist that humans — and, conveniently, themselves — are the special creation of an omnibenevolent deity. There is no coherent reason why such a deity would equip bats with a superior immune system while leaving humans comparatively vulnerable, unless the intention were for humans to suffer more infectious disease than is strictly necessary.

However, the bat immune system appears to have a significant evolutionary trade-off. Rather than eliminating viruses entirely, it often suppresses their pathological effects while allowing persistent infection. As a result, bats function as biological incubators in which viruses can circulate, diversify, and evolve. Inevitably, some of these variants acquire the ability to cross species barriers and infect humans. This remains the most parsimonious explanation for the emergence of SARS-CoV-2, the virus responsible for COVID-19 — the pandemic of 2020–2022 that killed tens of millions of people and inflicted severe damage on the global economy.

Creationists argue that complex, specified genetic information must be supplied by their putative intelligent designer and then, by a glaring act of circular reasoning, claim that the mere existence of such information constitutes evidence for that designer. This line of argument has no more merit than insisting that tins of baked beans can only be made by magic pixies, and therefore that the existence of tins of baked beans proves the existence of magic pixies. It is a form of reasoning that functions only for those who lack even a basic grasp of logic.

An additional difficulty for creationists is that PRV could only become infectious to humans if it possessed the precise genetic features required for that capability. Within the internal logic of intelligent design apologetics, the zoonotic PRV must therefore count as the product of deliberate design — and hence as evidence for a malevolent intelligent designer. The usual response is to abandon any pretence that intelligent design is science rather than religion in disguise, and to retreat into Christian fundamentalism, invoking “the Fall” and claiming that some other supernatural entity was empowered to interfere with creation and design its own suite of pathogens and parasites. This claim borders on blasphemy even within Christian theology, which traditionally reserves the creation of living things exclusively to their deity.

Unintelligent Design - The Prolific Waste Of Baby Dinosaurs as Food - 150 Million Years Before 'Creation Week'

Ecosystem reconstruction of the Late Jurassic Dry Mesa Dinosaur Quarry around 150 million years ago in Colorado, the United States

Credit: Sergey Krasovskiy and Pedro Salas

Life in Late Jurassic Colorado.

AI-generate image (ChatGPT5.2)

Baby dinosaurs a common prey for Late Jurassic predators | UCL News - UCL – University College London.

The prolific-waste reproductive strategy of Late Jurassic dinosaurs has been highlighted in a paper published in a New Mexico Museum of Natural History and Science Bulletin by a team of palaeontologists led by Dr Cassius Morrison of University College London’s Department of Earth Sciences.

The team constructed a detailed food web using fossil data laid down around 150 million years ago in the Morrison Formation of the United States. The Morrison Formation is a prominent sequence of Upper Jurassic sedimentary rocks (approximately 156–147 million years old) spanning around 1.5 million square kilometres across the western United States. It is North America’s most prolific source of dinosaur fossils, preserving vast deposits of mudstone, sandstone, and limestone formed in ancient river systems and floodplains.

Their analysis revealed that a major food source for carnivorous dinosaurs consisted of the young of the largest herbivores. These animals followed a reproductive strategy in which large numbers of offspring were produced and then effectively abandoned after hatching. Such juveniles would have been abundant, vulnerable, and easy prey for predators. This strategy is a familiar one in biology and only makes sense as the outcome of evolutionary processes. As an intelligently designed reproductive strategy, however, it is difficult to make sense of at all.

This is yet another example of the prolific waste that characterises living systems and betrays the absence of intelligent foresight in their design. Prolific waste and unnecessary complexity are hallmarks of evolution, whereas minimal waste and minimal complexity are the defining features of genuinely intelligent design — a distinction I explore in detail in my book The Unintelligent Designer: Refuting the Intelligent Design Hoax.

Malevolent Design - How Complex Specified Genetic Information and Irreducible Complexity Cause Pancreatic Cancer

Study reveals protein linked to spread of pancreatic cancer through nerves

A paper just published in Molecular and Cellular Endocrinology shows how precisely the sort of complex specified information and irreducible complexity that Discovery Institute fellows William A. Dembski and Michael J. Behe proclaim as evidence of intelligent design can instead combine to ensure that pancreatic cancer survives, metastasises, and ultimately kills its victims.

This, of course, is true of many diseases, which simply would not exist unless the right combination of genetic information were present and functioning correctly for the disease itself. Yet creationists routinely compartmentalise their beliefs so that harmful “designs” are excluded and blamed on something else, while only those features that appear to benefit humans are credited to a designer.

In the case of parasites, what is harmful to humans is often beneficial to the parasite, but once again the presence of harm causes the logic of creationist arguments to shift. No longer is this evidence of intelligent design, but of something called “sin”, which appears to operate as an autonomous entity capable not only of corrupting creation but of designing living organisms and manipulating their genomes. The formerly omnipotent, omnibenevolent and omniscient designer god now seems strangely impotent, indolent, or indifferent in the face of this alternative “designer”.

This theology also sits uncomfortably alongside another core fundamentalist belief: that God has a plan for everyone, and that everything that happens in a person’s life occurs as part of this divine plan. Presumably, then, that plan must include any diseases they suffer from, including cancer.

It is therefore difficult to see how creationists can escape the conclusion that their god designs and causes cancer as part of this plan, while continuing to cling to the claim that intelligent design is inherently benevolent.