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.

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

Beginnings of symbiosis

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

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

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

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

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

Creationism In Crisis - What Caused Homo Floresiensis (The 'Hobbit') To Go Extinct - 40,000 Years Before 'Creation Week'?

Homo floresiensis hunting a Stegodon

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Reconstruction of Homo floresiensis

By Cicero Moraes et al, Arc-Team Research
CC BY 4.0, Link

The ‘hobbits’ mysteriously disappeared 50,000 years ago. Our new study reveals what happened to their home

Long before anatomically modern Homo sapiens took their first tentative steps out of Africa and established themselves in Eurasia, an archaic hominin, Homo erectus, had already done so about a million years earlier, spreading across Asia into what is now the Indonesian archipelago and diversifying into a number of species and regional variants along the way.

One lineage settled on the island of Flores, where they encountered a miniature species of elephant, Stegodon florensis insularis, which probably became one of their principal sources of meat. By a process known to evolutionary biologists as Foster's Rule or the “island effect”, the descendants of these hominins also became smaller, eventually evolving into Homo floresiensis, popularly known as “The Hobbit” on account of their diminutive stature. Then, quite suddenly, they disappeared from history some 50,000 years ago.

Now an international team of archaeologists, including scientists from the University of Wollongong (UOW), Australia, believe they have found evidence explaining their extinction. It appears to have coincided with the disappearance of Stegodon florensis insularis and to have been driven by extensive climate change that began about 76,000 years ago, culminating in severe summer droughts between 61,000 and 50,000 years ago. The researchers reached this conclusion through analysis of the chemical record preserved in stalagmites from Flores caves, alongside isotopic data from the teeth of Stegodon. Their paper has just been published open access in Communications Earth & Environment.

In addition to the University of Wollongong news release explaining the study, four of the authors have written an article in The Conversation. Their article is reproduced here under a Creative Commons licence, reformatted for stylistic consistency.

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.

© Adrian Daly

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

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

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

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

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

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

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

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’.

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.

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.

Abiogenesis News - The Genes That Predate Life

Scientists describe a window into evolution before the tree of life | Oberlin College and Conservatory | EurekAlert!

In a paper published recently in the journal Cell Genomics, scientists Aaron Goldman (Oberlin College), Greg Fournier (MIT), and Betül Kaçar (University of Wisconsin–Madison) describe how they were able to study evolutionary history even before the last universal common ancestor of all living things (LUCA) emerged, and discovered that some of the genes associated with LUCA may in fact predate LUCA itself.

Creationists determined to misrepresent the process of abiogenesis often present it as a ridiculous parody in which a fully complex cell is supposed to have spontaneously assembled out of inorganic atoms and molecules. This straw-man caricature is far easier to attack than what science actually proposes: that the first population of self-replicating proto-cells arose through gradual chemical and evolutionary processes within a large and diverse population.

Within such a population, variation would inevitably occur, and whatever produced the most copies of itself would come to dominate. One of the earliest characteristics to emerge would have been rapid replication, because in a vast population with generation times measured in minutes, even “million-to-one” mutations are not rare events — they occur thousands of times a day. Under such conditions, what creationists portray as wildly improbable becomes not only plausible, but effectively inevitable over time.

Several independent evolutionary pathways could also have developed in parallel: RNA molecules coding for particular enzymes, ribosomes assembling from self-catalysing RNA, and primitive membranes forming across which chemical energy gradients could arise. Only once these components were already present could they come together within an enclosing membrane to form the first true prokaryotic cells.

The research team led by Aaron Goldman has now developed a method for determining which genes were likely present in LUCA, and which must already have been available to be incorporated when LUCA first emerged. In other words, some genes appear to predate LUCA itself, pushing parts of evolutionary history even deeper into the pre-cellular past.

What Was LUCA — and What Came Before It? The Last Universal Common Ancestor (LUCA) is often misunderstood, especially by creationists who portray it as the very first living organism. In reality, LUCA was not the origin of life, nor the first cell, nor some single creature that suddenly appeared fully formed.

LUCA is simply the most recent population of organisms from which all life alive today ultimately descends — bacteria, archaea, and eukaryotes alike. Crucially, LUCA already possessed a level of biochemical sophistication. Most researchers agree it likely had:

• a genetic code based on RNA and DNA
• ribosomes capable of translating RNA into proteins
• enzymes for metabolism and replication
• membrane structures maintaining internal chemistry
• the ability to exploit chemical energy gradients

This means LUCA could not have been the beginning of life. Instead, it must have been the product of a long evolutionary history that preceded it.

Pre-LUCA Evolution: A World of Competing Proto-Life

Before LUCA, early Earth was almost certainly home to a diverse population of simpler self-replicating systems — sometimes called proto-cells or pre-cellular life. These were not fully modern organisms, but chemical systems capable of reproduction, variation, and selection.

Rather than a single miraculous event, abiogenesis is best understood as an extended evolutionary process in which:

• self-replicating molecules competed for resources
• advantageous variants spread through populations
• metabolic pathways evolved gradually
• membranes formed to enclose and stabilise reactions
• genetic and protein machinery became increasingly integrated

LUCA represents the point at which one lineage became the common ancestor of everything that survived, not the moment life began.

Genes Older Than LUCA

What makes the new research so significant is the finding that some genes associated with LUCA appear to be even older — suggesting that early evolutionary innovations were already circulating in the pre-LUCA world and later became incorporated into the first universal ancestor.

This is exactly what evolutionary theory predicts: life did not begin with a fully formed cell, but with populations of evolving systems, long before anything resembling modern biology existed.

Their methodology is explained further in a press release from Oberlin College, via EurekAlert!.

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

Gut microbiome - AI-generated image (ChatGPT 5.2)

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.

Malevolent Design - How Ovarian Cancer Looks Intelligently Designed to Spread Rapidly

Creationism's intelligent designer at work

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Cancer cells (red) stick to mesothelial cells (green) and form hybrid spheres that cut into surrounding abdominal tissue.

Credit: Uno et al., 2026

Scientists now know why ovarian cancer spreads so rapidly in the abdomen | Nagoya University

If intelligent design advocates were honest enough to follow the logic of their own arguments and apply it consistently to the real world, they ought to be acutely embarrassed by the deity they are presenting to the public. Their putative designer god, judged by the evidence they themselves cite, looks less like a benevolent engineer and more like the author of suffering, disease, and death.

That uncomfortable reality is illustrated by yet another research paper showing that pain and mortality can be the direct result of the very things ID proponents celebrate as hallmarks of design: irreducible complexity and “complex specified information”.

This latest example comes from scientists at Nagoya University, Japan, who have shown how ovarian cancer forms an alliance with healthy cells that enables it to spread rapidly to other organs in the abdomen. Their paper has just been published in Science Advances.

As regular readers will be aware, a recurring theme of this blog is that ID advocates conspicuously ignore the vast number of examples from parasitology, oncology, and genetics where the very evidence they cite for an intelligent designer applies just as readily to diseases caused by parasites, pathogens, and genetic malfunctions. Applying ID’s own logic, these are not signs of benevolent craftsmanship but evidence of something far darker — a malevolent intent behind the supposed designer.

The paper in Science Advances is yet another case in point, and doubtless there will be many more soon.

The authors discovered that ovarian cancer cells gather clusters of mesothelial cells from the peritoneum and form hybrid spheres. These protect the cancer cells, help them invade other organs, and create a pathway for metastasis throughout the abdomen. Worse still, these hybrid spheres resist chemotherapy more effectively than cancer cells alone.

If something this complex resulted in something beneficial for humans, Discovery Institute fellows Michael J. Behe and William A. Dembski would doubtless have produced one or more books about it, written magazine articles, and embarked on television tours explaining how the finding devastates “Darwinism” and constitutes scientific proof of an intelligent designer — leaving their audiences in no doubt that the locally favoured god is the only entity capable of producing such complexity.

As it is, we can expect only a deafening silence from the Discovery Institute, while their hapless supporters cast about for a fundamentalist religious excuse such as “the Fall”, or perhaps invoke some other evil agent — anything, in fact, except the god of the Bible, who is apparently only credited with designing good things.

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.

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.

Refuting Creationism - How A Chance Mutation Allowed The Evolutionary Transition From Invertebrates To Vertebrates

Sea squirt, Ciona intestinalis

Credit: Shunsuke Sogabe

New discovery sheds light on evolutionary crossroads of vertebrates | University of St Andrews news

Researchers from the University of St Andrews, working with colleagues from the University of Aberdeen and the University of Oxford, have identified a pattern of gene evolution that appears to have been crucial to the origin and subsequent diversification of vertebrates from their common ancestry with invertebrates. They have just published their findings in BMC Biology.

This discovery will be a major disappointment for creationists who cling to the notion that there is no evidence for what they call “macroevolution” — a term so ill-defined that it can be stretched to mean whatever a creationist happens to need at the time. Sometimes it is invoked to mean the origin of a new species, at other times a new genus, an entire new order, or even the biologically absurd idea of one species giving birth to an individual belonging to a completely different order. More often, though, “macroevolution” is said to mean the origin of entirely new anatomical structures.

Even that definition collapses immediately under scrutiny. Asked what novel structure humans possess that chimpanzees lack, “macroevolution” abruptly becomes the evolution of anything creationists choose to label a “kind” — another conveniently nebulous term, defined precisely nowhere and flexibly everywhere.

Yet if the origin and diversification of vertebrates does not qualify as “macroevolution”, it is difficult to imagine what possibly could. The St Andrews–led team has shown that this transition was enabled by gene evolution — that is, mutation acted upon by natural selection — affecting the genetic control of cell signalling during embryonic development. These changes influence when and where new cell types arise as a developing embryo progresses from a single-celled zygote to a complex multicellular organism, complete with differentiated tissues and specialised organs.

As this gene regulatory system evolved, it allowed the vertebrate phylum to diversify into the many classes and orders that now dominate marine and terrestrial ecosystems. No doubt this will require yet another round of misrepresentation by creationists, along with further blurring of the already elastic definitions of “macroevolution” and “kinds”.

Creationism Refuted - How The Fossil Record Tracks Climate Change

Tata Aka (CC BY 2.0)
via Wikimedia Commons

The climate in Catalonia was much rainier 10 million years ago - Universitat Autònoma de Barcelona - UAB Barcelona

A paper published a few days ago in the Journal of Mammalian Evolution describes how the climate in Catalonia was much wetter 10 million years ago than it is today, with rainfall roughly twice the present rate, and how this was reflected in the evolution of mammals in the region. The study was conducted by palaeontologists at the Institut Català de Paleontologia Miquel Crusafont (ICP-CERCA), in association with colleagues from the Universitat Autònoma de Barcelona (UAB).

This must be deeply frustrating for creationists because, no matter how much they ignore the evidence, misrepresent it, or shout abuse at scientists, the evidence stubbornly refuses to support creationism and invariably supports evolution over deep time on an ancient Earth. The findings presented in this paper are, of course, no exception.

Scientists have previously established a close link between rainfall and the composition of mammalian communities, with wetter conditions favouring insectivores. Increased rainfall promotes the development of forests, which in turn provide abundant niches for insects and other invertebrates—the primary food source of insectivorous mammals. This relationship between small mammals and climate was first studied in detail by Jan van Dam, an associate researcher at the ICP. Van Dam developed equations that allow both average annual rainfall and its seasonal distribution to be estimated from fossil assemblages of small mammals.

Building on that earlier work, the present study analyses the abundant fossil record of small mammals to reconstruct populations that changed dynamically through time in response to shifting climatic conditions—exactly as predicted by the Theory of Evolution. There is, unsurprisingly, no evidence of spontaneous creation of species, nor of a global biological reset caused by a genocidal flood a few thousand years ago.

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.

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.

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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.