Malevolent Design - How Our Cells Cooperate With Viruses to Become Infected

Cells actively help to capture and incorporate influenza viruses. Here, a cell is shown, with a virus in the centre of the image.

Illustration: Emma Hyde / ETH Zürich

How influenza viruses enter our cell s | ETH Zurich

Researchers from Switzerland and Japan, led by Professor Yohei Yamauchi of Eidgenössische Technische Hochschule Zürich (ETH Zürich), have developed a microscopy technique that enables real-time, high-resolution observation of how a virus gains entry to a cell. Their findings are described in the Proceedings of the National Academy of Sciences of the USA (PNAS).

The process, in which a virus exploits the pathways cells normally use to take in larger molecules such as hormones, cholesterol, or iron, involves the active cooperation of the cell as it reaches out to engulf the viral particle. This mechanism is triggered by receptors on the cell surface, to which viruses bind while ‘surfing’ along the membrane, seeking regions rich in receptors to form a stable attachment.

In other words, creationists often portray this as an “irreducibly complex” system, supposedly dependent on all components being present from the outset, requiring what they call “complex specified information” in both virus and cell to produce the receptors and binding proteins. Discovery Institute fellows Michael J. Behe and William A. Dembski present this as evidence of intelligent design.

Their argument depends on a statistical sleight of hand: they treat the entire process as though it originated in a single event involving one cell and one virus, then calculate improbabilities for each step and multiply them together, producing a vanishingly small likelihood of the whole mechanism arising spontaneously. This ignores the fact that evolution operates in populations — often large ones — across long periods, where components accumulate gradually over generations, dramatically increasing the probability of multiple features emerging together in the same lineage.

It also overlooks the billions of years during which viruses and cells have co-evolved. As multicellular organisms evolved ever more sophisticated ways of receiving and responding to external signals and substances, viruses simultaneously improved their ability to exploit those mechanisms.

But to the scientifically illiterate target audience of the ID-creationism industry, evolution is imagined as a single event rather than a continuous process, leaving them oblivious to the misuse of probability and the underlying mathematical errors.

Creationists trying to use this argument for intelligent design usually respond to biologists pointing out the obvious fact that they just presented their putative god as some sort of celestial malevolence, by retreating into Bible literalism and religious fundamentalism and invoking mythical 'Fall', so betraying the claims of the Discovery Institute and its fellows that ID is real science, not bible-literalist creationism dressed in a lab coat, as a lie.

The ETH Zürich-led team’s research is summarised in an ETH Zürich news item by Fabio Bergamin.

How influenza viruses enter our cells

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For the first time, researchers have observed live and in high resolution how influenza viruses infect living cells. This was possible thanks to a new microscopy technique, which could now help to develop antiviral therapies in a more targeted manner.

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In brief

• For the first time, a new high-resolution microscopy technique has allowed researchers to watch live as influenza viruses infect cells.
• The international team led by ETH Zurich found that the cells actively promote virus uptake.
• This technique could now help to develop antiviral therapies in a more targeted manner.

Fever, aching limbs and a runny nose – as winter returns, so too does the flu. The disease is triggered by influenza viruses, which enter our body through droplets and then infect cells.

Researchers from Switzerland and Japan have now investigated this virus in minute detail. Using a microscopy technique that they developed themselves, the scientists can zoom in on the surface of human cells in a Petri dish. For the first time, this has allowed them to observe live and in high resolution how influenza viruses enter a living cell.

Led by Yohei Yamauchi, Professor of Molecular Medicine at ETH Zurich, the researchers were surprised by one thing in particular: the cells are not passive, simply allowing themselves to be invaded by the influenza virus. Rather, they actively attempt to capture it.

“The infection of our body cells is like a dance between virus and cell.

Professor Yohei Yamauchi, corresponding author.
Molecular Medicine Laboratory
Institute of Pharmaceutical Sciences
Department of Chemistry and Applied Biosciences
Eidgenössische Technische Hochschule Zürich
Zürich, Switzerland.

Viruses surf on the cell surface

Of course, our cells gain no advantage from a viral infection or from actively participating in the process. The dynamic interplay takes place because the viruses commandeer an everyday cellular uptake mechanism that is essential for the cells. Specifically, this mechanism serves to channel vital substances, such as hormones, cholesterol or iron, into the cells.

Like these substances, influenza viruses must also attach to molecules on the cell surface. The dynamics are like surfing on the surface of the cell: the virus scans the surface, attaching to a molecule here or there, until it has found an ideal entry point – one where there are many such receptor molecules located close to one another, enabling efficient uptake into the cell.

Once the cell’s receptors detect that a virus has attached itself to the membrane, a depression or pocket forms at the location in question. This depression is shaped and stabilised by a special structural protein known as clathrin. As the pocket grows, it encloses the virus, leading to the formation of a vesicle. The cell transports this vesicle into its interior, where the vesicle coating dissolves and releases the virus.

Previous studies investigating this key process used other microscopy techniques, including electron microscopy. As these techniques entailed the destruction of the cells, they could only ever provide a snapshot. Another technique that is used – known as fluorescence microscopy – only allows low spatial resolution.

Combined techniques, including for other viruses

The new technique, which combines atomic force microscopy (AFM) and fluorescence microscopy, is known as virus-view dual confocal and AFM (ViViD-AFM). Thanks to this method, it is now possible to follow the detailed dynamics of the virus’s entry into the cell.

Video: Nicole Davidson / ETH Zurich.

Accordingly, the researchers have been able to show that the cell actively promotes virus uptake on various levels. In this way, the cell actively recruits the functionally important clathrin proteins to the point where the virus is located. The cell surface also actively captures the virus by bulging up at the point in question. These wavelike membrane movements become stronger if the virus moves away from the cell surface again.

The new technique therefore provides key insights when it comes to the development of antiviral drugs. For example, it is suitable for testing the efficacy of potential drugs in a cell culture in real time. The study authors emphasise that the technique could also be used to investigate the behaviour of other viruses or even vaccines.

Publication:

A. Yoshida, Y. Uekusa, T. Suzuki, M. Bauer, N. Sakai, & Y. Yamauchi
Enhanced visualization of influenza A virus entry into living cells using virus-view atomic force microscopy
Proc. Natl. Acad. Sci. U.S.A. 122 (38) e2500660122, https://doi.org/10.1073/pnas.2500660122 (2025).

Significance
Influenza A viruses (IAVs) continue to cause epidemics worldwide due to their high mutability. Nevertheless, the initial step of infection, viral uptake into cells, has been challenging to observe directly with conventional microscopy techniques. Here, we developed a hybrid imaging system combining atomic force microscopy and confocal microscopy with enhanced mechanical functionality and minimal invasiveness to directly visualize nanoscale dynamics of IAV and cell membranes during viral uptake into living cells. This system enables the analysis of IAV lateral diffusion resulting from IAV–membrane interactions and characteristic membrane morphological changes induced by IAV during endocytosis. Our approach offers a method to rapidly assess the impact of viral mutations on host cell entry, which is critical for understanding emerging IAV variants.

Abstract
Influenza A virus (IAV) entry into host cells begins with interactions between the viral envelope proteins hemagglutinin (HA)/neuraminidase (NA) and sialic acid moieties on the cell plasma membrane. These interactions drive IAV’s lateral diffusion along the cell membrane and trigger membrane morphological changes required for endocytosis. However, directly visualizing these dynamic processes, which are crucial for IAV entry, has been challenging using conventional microscopy techniques. In this study, we enabled live-cell observation of nanoscale morphological dynamics of IAV and the cell membrane by reducing the mechanical invasiveness of atomic force microscopy (AFM). A customised cantilever with less than half the spring constant of conventional cantilevers enabled virus-view AFM imaging that preserved IAV–membrane interactions. By combining virus-view AFM with confocal microscopy, we performed correlative morphological and fluorescence observations of IAV lateral diffusion and endocytosis in living cells. Variations in diffusion coefficients of single virions suggested heterogeneity in sialic acid density on the cell membrane. NA inhibition decreased diffusion coefficients, while reduced sialic acid density increased them. The timing of clathrin accumulation at virion binding sites coincided with a decrease in diffusion coefficients, a relationship that was maintained independent of NA activity or sialic acid density. As clathrin assembly progressed, ~100-nm-high membrane bulges emerged adjacent to the virus, culminating in the complete membrane envelopment of the virus at peak clathrin accumulation. Our virus-view AFM will deepen our understanding of various virus–cell interactions, facilitate the evaluation of drug effects and promote future translational research.

Influenza A virus (IAV) is an enveloped RNA virus with two key surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA). The virus surface contains 300 to 400 HA and 40 to 50 NA molecules (1). IAV envelope proteins comprise at least 18 HA and 11 NA subtypes (2), which enable IAV to infect various host species including humans, birds, pigs, bats, and other animals (3). These envelope proteins play crucial roles in IAV infection of host cells. They interact with sialic acids on cell surface glycolipids and glycoproteins (4) or with major histocompatibility complex class II (MHC class II) molecules (5–7). HA binds to sialic acids at the terminal ends of glycan chains on the cell surface. The HA–sialic acid interactions are inherently weak, with dissociation constants typically in the millimolar range (0.9 to 68.4 × 10−3 M) (8–10). However, multivalent binding of multiple HAs to sialic acids enables IAV to stably adhere to the cell membrane (11, 12). Meanwhile, NA catalyzes the cleavage of sialic acids (13), inhibiting stable adhesion of IAV to the cell membrane. Through these mechanisms, HA and NA effectively regulate the attachment and detachment of IAV to the cell membrane.

The competitive action between HA and NA allows IAV to diffuse laterally along the cell membrane surface topology (). This lateral diffusion represents a critical dynamic macroscopic phenomenon reflecting virus–membrane interactions. However, conventional microscopy techniques have struggled to detect IAV movement on the 10-nm-thick cell membrane, resulting in limited visualization success (15–18).

HA-NA-sialic acid interactions also trigger endocytosis involving morphological changes of the cell membrane. When diffusing IAV binds to functional receptors such as EGFR (19) and Cav1.2 (20) through sialic acids, it initiates the recruitment and assembly of the endocytic machinery including clathrin, actin, and dynamin. IAV utilizes multiple entry pathways including clathrin-mediated endocytosis (CME), macropinocytosis, and both clathrin-independent and dynamin-independent mechanisms (16, 21–23). IAV primarily utilizes CME for cellular entry (16, 21). Previous imaging of membrane dynamics using atomic force microscopy (AFM) has revealed that in IAV-free CME, clathrin-coated membrane invaginations (pits) larger than 100 nm in diameter form (24, 25). This is accompanied by the emergence of actin-dependent membrane bulges that develop on one side of the pit and eventually lead to its closure. Although electron microscopy has provided morphological snapshots of pits during IAV internalization (26), the membrane dynamics during IAV internalization via CME have yet to be successfully visualized.

AFM enables mechanical imaging of sample morphology with nanometer-scale resolution (27, 28). Since the development of high-speed AFM in 2001 (29), this technique has contributed significantly to molecular dynamics analysis (30–36). Additionally, the advent of cell-imaging AFM in 2013 has enabled advances in membrane dynamics analysis (37, 38). The integration of cell-imaging AFM combined with confocal microscopy has provided unique capabilities for observing nanoscale membrane morphological changes in living cells (24, 25). Despite these advances, a major challenge persists: the mechanical interference of the cantilever with biological samples. Visualizing the dynamic processes of IAV lateral diffusion and internalization requires an innovative technology capable of simultaneously observing the nanoscale morphology of the 10-nm-thick cell membrane and the 100-nm spherical IAV interacting with cell surface sialic acid-bearing glycolipids and proteins. Given that multivalent IAV–membrane interaction forces are relatively weak, ranging from 10 to 25 pN (39), achieving low-invasive imaging capabilities is critical.

In this study, we address and overcome the challenge of mechanical interference by enhancing the low invasiveness of AFM through the use of a customised soft cantilever. In combination with confocal microscopy, low-invasive AFM enables simultaneous live-cell imaging of both morphology and fluorescence. The redesigned cantilever minimizes disruption of IAV–membrane interactions, allowing accurate observation of viral dynamics. Using this system, we investigated the lateral diffusion of single IAV particles under various conditions, including NA inhibition, reduced cell surface sialic acid density, and different viral subtypes. We also analyzed membrane morphological changes before and during IAV endocytosis. While fluorescently labeled IAV was primarily used, we also demonstrate our AFM’s capability to track unlabeled viruses. This virus-view dual confocal and AFM, called ViViD-AFM, enables correlative morphological and fluorescence imaging of IAV–membrane dynamics, providing nanoscopic insights into HA-NA-sialic acid interactions.

A. Yoshida, Y. Uekusa, T. Suzuki, M. Bauer, N. Sakai, & Y. Yamauchi
Enhanced visualization of influenza A virus entry into living cells using virus-view atomic force microscopy
Proc. Natl. Acad. Sci. U.S.A. 122 (38) e2500660122, https://doi.org/10.1073/pnas.2500660122 (2025).

Copyright: © [year] The authors.
Published by [publisher]. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What ID advocates never seem to notice is that, in arguing that such mechanisms must have been deliberately engineered, they are attributing to their designer a system in which viruses are given exquisitely tailored tools for invading the very cells it supposedly created. If one insists that this is intentional design, then one must also accept that the designer crafted the molecular equivalent of lockpicks and battering rams, optimised for breaching living tissue. It is difficult to reconcile this with any notion of benevolence.

Indeed, by rejecting evolution as the explanation for viral entry, ID proponents corner themselves into an uncomfortable theological stance: their designer not only equipped viruses with the machinery to exploit cellular signalling, but also ensured that cells remained vulnerable to such exploitation. The result is an ecosystem in which suffering, disease, and death are not unfortunate consequences of natural processes but deliberate design choices.

This is, of course, why mainstream biology requires no such designer. Co-evolution naturally explains why cells have receptors essential for communication and nutrient uptake, while viruses have, over immense timescales, adapted to hijack those same pathways. No malevolent architect is required—only the simple, iterative logic of variation, selection, and replication.

Yet the ID movement persistently overlooks this simpler, evidence-based account, preferring instead an argument that—if taken seriously—presents their putative creator as either unable to prevent viral parasitism or fully complicit in engineering it. Neither option supports the benevolent, omnipotent designer they hope to defend.

Refuting Creationism - Microbes That Create Life From Non-Life

Mud volcano

Fig. 9: Schematic of microbial succession and biogeochemical processes in serpentinite mud at the Mariana forearc.
This schematic depicts lipid biomarker transitions from pelagic sediment communities to extremophiles adapted to high pH and redox conditions in serpentinite mud. The Mariana forearc biosphere is fueled by alkaline serpentinization fluids enriched in H₂, CH₄, DIC, and organic acids, sustaining specialized microbial communities. Lipid and stable carbon isotope data reveal a shift from relict methanogenic archaea, likely engaged in hydrogenotrophic methanogenesis, to a later ANME-SRB community mediating anaerobic oxidation of methane (AOM). Changes in substrate availability likely drove this transition. Distinct lipid signatures, including unsaturated diethers, acyclic GDGTs, and ether-based glycolipids, highlight adaptations to pH stress, phosphate limitation, and fluctuating redox conditions. The presence of in-situ branched GDGTs suggests previously uncharacterized bacterial communities persisting in these ultra-oligotrophic conditions. The Mariana forearc serpentinite biosphere, shaped by episodic fluid flow and substrate shifts, provides insights into deep-sea subsurface habitability. DIC = dissolved inorganic carbon, ANME anaerobic methanotrophic archaea, SRB sulfate-reducing bacteria, AOM anaerobic oxidation of methane, GDGT glycerol dialkyl glycerol tetraether.

Kumawat, P., Albers, E., Bach, W. et al. (2025).

Fats provide clues to life at its limits in the deep sea

Researchers at MARUM – Bremen University’s Centre for Marine Environmental Sciences – have made a discovery, just published open access in the journal Communications Earth & Environment, which, properly understood, should make depressing reading for creationists.

They have found living organisms both on and within the ocean floor, surviving in conditions where normal life would be impossible. These microorganisms inhabit mud volcanoes with a pH of 14, metabolising hydrogen and carbon to form methane by drawing energy from minerals in the surrounding rock. In other words, they live entirely without oxygen and with almost no organic matter, synthesising all they need from inorganic sources.

Informed creationists will recognise that these organisms directly refute their frequent assertion that life cannot arise from non-life — because producing life from non-life is precisely what these microorganisms are doing.

This also contradicts the biblical claim that all living things were created for the benefit of humans, since there is no conceivable way these organisms could serve any human purpose. Of course, to be fair, the authors of the Bible were completely ignorant of microorganisms, deep-ocean mud volcanoes, and chemosynthetic metabolism. They could only attempt to explain the larger creatures that lived in the limited region around their homes in the Canaanite hills.

And, as any informed creationist should also understand, these are exactly the sort of extreme conditions that biologists believe may have fostered the emergence of the earliest living organisms during the origin of life on Earth — once again undermining any claim that abiogenesis is impossible.

Creationism Refuted - How Co-Evolution Gave Us Sleep - Courtesy of Our Gut Microbiome

Key to the riddle of sleep may be linked to bacteria | WSU Insider | Washington State University

For an astonishing example of co-evolution — not just involving two organisms but a whole host that have co-evolved over millions of years — you need look no further than your own body, as a paper in *Frontiers in Neuroscience* by Erika L. English and James M. Krueger of Washington State University (WSU) shows. It reports the finding that sleep may be a co-evolved condition in which gut micro-organisms play a central role.

The researchers showed that, in mice, there is a close relationship between sleep patterns and the cyclical presence in the brain of a substance known as peptidoglycan (PG), normally found in the mesh-like walls of gut bacteria. Although co-evolutionary relationships are a well-established concept in evolutionary biology, this example illustrates just how intimate such relationships can become — to the point where it is difficult to say, in biological terms, which organism is the “product” of the other. To what extent are we the product of our gut bacteria, and to what extent are they the product of us?

Of course, creationism has nothing to say about this kind of co-evolution because the Bible is silent on the matter of micro-organisms or evolution. It contains nothing that wasn’t visible to its Bronze Age authors with the naked eye, or that lived outside the narrow confines of their limited experience. It was written by people with no appreciation of the history of life on Earth or of how it has been shaped by environmental change and ecological balances over deep time.

Malevolent Design - How Our Gut Microbiome is 'Designed' to Destroy Our Kidneys - Malevolence or Evolution?

Kidney fibrosis linked to molecule made by gut bacteria – News Bureau

Mostly, our gut microbes are beneficial or at least neutral because we have co-evolved and reached an accommodation. One benefit we derive from their presence is that they make life difficult for potentially harmful organisms, if only by monopolising the available resources and occupying the niches in our gut.

There is a downside, of course, as in any evolved system, which is inevitably a compromise and can tip over into pathology under certain circumstances. But overall, because the disadvantages are more than compensated for by the benefits, the system has evolved and been maintained.

However, a newly discovered downside is that a Staphylococcus species may be implicated in one of the serious complications of diabetes mellitus (DM) — kidney fibrosis and ultimately kidney failure. The discovery was made by researchers at the University of Illinois Urbana-Champaign and Mie University in Japan, co-led by Professor Isaac Cann of Illinois and Professor Esteban Gabazza of Mie University. The bacterium is believed to produce corisin — a small peptide — which is found at high levels in patients with diabetic kidney fibrosis. The researchers have just published their findings, open access, in Nature Communications.

For creationists, this sort of discovery is always a problem, one they normally ignore or blame on “Eve’s sin,” revealing ID creationism for what it is — Bible literalism in a lab coat — which must retreat into mystical theology when faced with problems ID cannot address. Yet creationists also claim that their omniscient creator god is personally responsible for the design of organisms such as Staphylococcus. That would mean it knowingly endowed Staphylococcus with the genes to make corisin, along with all the harmful consequences.

Taking William A. Dembski’s “complex specified genetic information,” which supposedly produces a specific outcome, at face value, the staphylococcal genes are equally “proof” of intelligent design. And so we end up with an unresolved paradox for ID creationism: “complex specified” genes that do us harm, standing as evidence of malevolent design.

Refuting Creationism - Scientists Recover Ancient Bacterial DNA - On Million-Year-Old Mammoth Teeth

Steppe Mammoths

AI-generated image (ChatGPT 5)

Ancient mammoth remains yield the world's oldest host-associated bacterial DNA - Stockholm University

Parasite–host relationships are a nightmare for creationists. Their usual escape hatch is “The Fall”, but that undermines the Discovery Institute’s claim that intelligent design is science rather than Bible-literalist dogma in a lab coat. It also raises the obvious question: if parasites only appeared 6,000–10,000 years ago, how did they spread so quickly—and why do we find fossil evidence of parasitism millions of years old?

Creationists cope by dismissing science as a conspiracy, waving away radiometric dating, or pushing myths such as dinosaur fossils being “carbon-dated” [sic] to a few thousand years old. So creationism persists, despite the vast amount of evidence against it, by a combination of wilful ignorance, disinformation and a lack of critical thinking skills.

Now creationists must also ignore new research from Stockholm University, where scientists isolated bacterial DNA from the teeth of woolly and steppe mammoths. They showed these bacteria evolved into the ancestors of those infecting modern elephants—evidence of parasites a million years before “Creation Week”, and of co-evolution continuing right up to today’s elephants, the descendants of those mammoths.

Incidentally, neither mammoths nor modern elephants are mentioned in the Bible, reflecting the parochial ignorance of its authors - a fact often overlooked in depictions of animals boarding Noah's Ark, which usually includes a pair of elephants!

Creationism Refuted - How Micro-oranisms Acquire New Genetic Information - Millions of Times A Day

AI generated image

ChatGPT 5

Researchers Quantify Rate of Essential Evolutionary Process - Bigelow Laboratory for Ocean Sciences

Researchers at Bigelow Laboratory for Ocean Sciences (East Boothbay, Maine, USA) have recently quantified a remarkable evolutionary process: a typical marine microorganism acquires and retains approximately 13% of its genes per million years through horizontal (lateral) gene transfer. This rate corresponds to roughly 250 genes exchanged and retained per litre of seawater each day

These transferred genes include those that provide either a selective advantage or are sufficiently neutral to persist via genetic drift—both well-established mechanisms of evolutionary change.

Some creationist arguments misapply Shannon Information Theory, claiming that gaining new genetic information violates the laws of thermodynamics. However, such arguments disregard key biological realities: cells are open systems capable of energy and material exchange; genome duplication and horizontal transfer are well-documented evolutionary processes; and substituting one nucleic acid for another does not create matter ex nihilo - facts of which any qualified biological scientists should be aware.

Furthermore, the successful retention and spread of horizontally acquired genes within microbial genomes provide clear, empirical evidence of Darwinian evolution in action. Although Charles Darwin formulated his theory without the concept of genes — speaking instead of 'heritable traits' — his mechanism of natural selection precisely explains how heritable variations can spread through populations over time.

This study also highlights that microorganisms can evolve not only through mutation and selection but also by acquiring pre-adapted genes from their environment, often from distantly related organisms. Consequently, these newly acquired genes can propagate rapidly within the recipient lineage.

The findings further challenge traditional microbial taxonomy, blurring species boundaries at the genetic level: horizontally transferred genes may function just as effectively in their new hosts as they did in their original genomes, thanks to the universality of underlying molecular machinery (e.g., replication and translation systems).

Creationism Refuted - The Subterranean Microbes That Make Creationists Sick

Karen Lloyd

Buried Alive: The Secret Life of Deep Earth Microbes

What if we could peer back through deep time and see what single-celled organisms looked like—not just thousands, but hundreds of millions of years ago—and compare them to their living descendants? It would be a revelation for science… and a nightmare for creationists.

That’s precisely what geobiologist Karen Lloyd and her team at the University of Southern California (USC) are uncovering. They study microorganisms that have made an incredible journey: born in the depths of the ocean, slowly buried under a relentless rain of sediment, and then carried by plate tectonics into the deep Earth, where subduction dragged them beneath continental crust. There, cut off from oxygen and sunlight, they survived for millions of years in a slow-motion existence, drawing nutrients from the surrounding rock. Their metabolic rates became so low they could no longer replicate, yet they endured by “breathing”—in the biochemical sense—through redox reactions, extracting energy from electrons provided by whatever electron donors the rocks could supply. Some have even evolved the ability to “breathe” carbon dioxide, something unknown among terrestrial life.

These organisms’ existence is a direct challenge to creationist dogma—not only because they have persisted for timescales far beyond the Bible’s allowance, but because they reveal how even apparently simple single-celled organisms can diverge and adapt over geological epochs. Environmental pressures have driven them into extraordinary evolutionary niches, each defined by what they have learned to “breathe.” Moreover, they exist in environments in which life as we know it couldn't survive, yet creationists insist that Earth was intelligently created, perfect for life, which begs the question, which life? The life that breathes using arsenic, lives for millions of years deep underground with almost no metabolic activity and survive in the heat and acidity of volcanic hot springs, or life the breathes oxygen and needs a regular supply of water and a narrow range of ambient temperatures in which to survive without special equipment?

Refuting Creationism - How Living Organism's Survived - 700 Million Years Before 'Creation Week'

Researchers Ian Hawes of the University of Waikato and Marc Schallenberg of the University of Otago measure the physicochemical conditions of a meltwater pond.

Credit: Roger Summons

Pustular microbial mat section such as could have existend in small melt-water ponds.

When Earth iced over, early life may have sheltered in meltwater ponds | MIT News | Massachusetts Institute of Technology

Only by systematically ignoring geological and archaeological evidence can creationists continue to delude themselves into believing that Earth is just a few thousand years old and was perfectly created by an anthropophilic god especially for humans – its supposed “special creation.”

The evidence, however, paints a radically different picture from that childish superstition. Not only was Earth clearly not perfectly created for humans, it wasn’t perfectly created for any life form. And it is far older than creationists assert. In truth, around 600 million years ago, Earth was such a hostile place for life that it was entirely covered in ice. The polar ice sheets had extended until they met at the equator. These “Snowball Earth” conditions led to a mass extinction so severe that it remains something of a mystery how any life survived – especially complex eukaryotic cells.

Now, a multinational team of researchers led by scientists from the Massachusetts Institute of Technology (MIT) has found evidence that early life could have survived in small pools of surface meltwater. They reached this conclusion after studying similar meltwater pools on the McMurdo Ice Shelf in Antarctica. What they found not only showed that single-celled eukaryotes can survive in such conditions, but also revealed that the population of prokaryotes varies according to local environmental conditions

These meltwater pools act as microcosms of diverse environments and demonstrate how local factors shape the distribution of different species – exactly as predicted by the Theory of Evolution. Had the conditions been perfect as creationists insist, there could be no variation in the populations in these pools. Variation only arises because the species need to adapt to different conditions - something that would never be needed in perfectly designed conditions.

The team has just published their findings, open access, in the journal Nature Communications.

Refuting Creationsm - Evolution By Loss of Genes, Horizontal Gene Transfer And Gene Duplication

Nitzschia sp

By Kristian Peters - Own work,
CC BY-SA 3.0,
Wikimedia

This article is best read on a laptop, desktop, or tablet

Nitzschia sing1 lives on the alginate in the cell walls of decaying brown algae.

A borrowed bacterial gene allowed some marine diatoms to live on a seaweed diet | PRESS-NEWS.org

A fundamental axiom of creationism is the claim that any loss of genetic information is invariably detrimental—so much so that any mutation resulting in such a loss would be fatal and could therefore play no role in evolution. A second axiom asserts that new genetic information cannot arise naturally and must instead be supplied by a supernatural intelligent designer.

Both of these assertions are demonstrably false. Nevertheless, they continue to feature in creationist apologetics, relying on the audience's ignorance and incredulity to pass as justification for belief in an intelligent creator.

To add further difficulty for creationist claims, scientists have now identified a marine diatom, Nitzschia sing1, that has not only lost the genes and organelles required for photosynthesis — present in its photosynthetic relatives — but has also adapted successfully without them. It achieved this by acquiring new genetic information through horizontal gene transfer from a marine bacterium. The transferred gene subsequently underwent extensive duplication and diversification into three gene families, each with complementary functions. Together, these 91 versions of the acquired gene enable N. sing1 to metabolise alginate, a carbohydrate found in the cell walls of brown algae such as kelp.

Mallevolent Design - How Salmonella Sneaks Past Our Defences To Make Us Sick

Salmonella infects the small intestine and alters the colon environment

Intestinal lumen

New study shows how salmonella tricks gut defenses to cause infection

There is a simple paradox at the heart of creationism that I have never even seen an attempt to resolve. It all comes from two beliefs: there is only one designer god capable of designing living organisms and that designer god designed us complete with our immune system with which we can attempt to resist attack by pathogens, and that pathogens are not the work of this design, but are the result of 'genetic entropy' and 'devolution' since Adam & Eve let 'sin' into the world. The fact that Michael J. Behe, who invented that excuse, has let slip that ID Creationism is Bible literalism in a lab coat seems to be lost on his followers who still dutifully insist that it is a scientific alternative to evolution and should be taught in school science class (presumably now with the tale of Adam & Eve taught as real history and 'sin' as a real force in science).

The paradox is, did the designer god give Adam & Eve an immune system, or did it design an upgrade when 'sin' allowed pathogens to exist? If the former, it was anticipating and planning for the so-called 'fall'; if the latter, it lacked foresight so is not omniscient.

But however creationists resolve this paradox they still have to explain why the 'intelligently designed' immune system doesn't work very well and why whatever is designing pathogens seems to be able to overcome it.

The nonsense about 'sin', 'the fall', etc., is trivially easy to refute because any improvement in a parasite's ability to parasitise its host can't possibly be regarded as a devolution from some assumed initial perfection because an improvement can't be worse that what it's an improvement on. The whole nonsense of 'devolution' is biological gobbledygook, intelligently designed to appeal to scientifically illiterate simpletons who want to fit the Bible superstition somewhere in the reasoning without bothering too much about the logic or the biology.

So, the paradox boils down to why an intelligent designer would be having an arms race with itself so the parasites it creates can continue to parasitise the victims it creates complete with their immune system it created to stop them. Creationists normally flee in terror at the mere mention of arms races, which is why you'll never see them discussed in the cult literature apart from where pathogens are waved aside as 'caused by sin', blah, blah, blah...
So, it would be refreshing indeed to see a genuine attempt by an intelligent design creationist try to give some rational explanation, and hopefully without giving away the fact that ID creationism is merely Christian fundamentalism in disguise, for the discovery by a new UC Davis Health study that shows how the Salmonella bacteria, a major cause of food poisoning, can invade the gut even when protective bacteria are present.

As an added embarrassment for creationists, Salmonella is closely related to Escherichia coli (E.coli) that they usually cite Michael J. Behe as 'proving' it must have been designed by their god because its flagellum is 'irreducibly complex'.

First a little AI background information about Salmonella, where it came from and what it does to us:

Common Ancestry - Ancient Choanoflagellates Genes Used To Make A Mouse

Electron micrograph of the choanoflagellate, Salpingoeca.

By Sergey Karpov - http://www.choano.org/wiki/Choanoflagellate_Gallery#Salpingoeca_sp._Gallery, CC BY-SA 3.0, Link

Choanoflagellates, singly and as a colony.

Scientists recreate mouse from gene older than animal life - Queen Mary University of London

If there is one thing designed to get creationists chanting 'Common Designer!' it's evidence of the same gene doing the same thing in lots of different organisms, no matter how distantly related they are.

But when that gene is needed because of a basic design blunder long ago in the evolution of multicellular organisms, that chant looks increasingly forlorn.

For example, scientists have just shown how SOX and POU genes isolated from a single-celled choanoflagellate can be used to convert a mouse cell to function as the stem cell to clone another mouse. The reason this works is because something needs to reset the epigenetic setting in specialised cells. In a multicellular organism like a mouse, this effectively means any cell produced after the first few cell divisions of the fertilised zygote.

But why would a single-celled organism like a choanoflagellate need to do that? The answer it that epigenetics originally evolved to make an organism more able to respond to environmental changes and stresses.

Refuting Creationism - How Eggs Evolved Hundred of Millions of Years Before Chickens

A cell of the ichthyosporean C. perkinsii showing distinct signs of polarity, with clear cortical localization of the nucleus before the first cleavage. Microtubules are shown in magenta, DNA in blue, and the nuclear envelope in yellow.

© DudinLab

Chromosphaera perkinsii resembles the early stages of animal embryo development during its multicellular life stage

DudinLab

The egg or the chicken? An ancient unicellular says egg! - Medias - UNIGE

Scientists believe they may have cracked the chicken and egg 'problem' that creationists have been fooled into thinking is a killer problem for the Theory of Evolution. With their child-like understanding of evolution, creationists can't imagine how species emerge over time from earlier species by a process of evolution and think that their mythical magic creation without ancestors is actually what happens, or at least what evolutionary biologists think happens. So, they imagine explaining how the first chicken hatched from the first egg before there was a chicken to lay it, is an insurmountable problem.

In fact, of course there never was a first chicken just as there never was a first human, and eggs are simply a phase in the life cycle of, in this case, chickens, so hens' eggs are chickens just as much so as adult hens are. The ancestral species that the Southeast Asian jungle fowl evolved from had been laying eggs ever since they diverged from the egg-laying avian dinosaurs that had evolved from the egg-laying theropod dinosaurs, etc, etc, back to the egg-laying tunicates and chordates in the Cambrian and their egg-laying ancestors...

Malevolent Design - How Chlamydia Is 'Designed' to Cause Maximum Sufferring.

Chlamydia pneumoniae

AI-generated image (ChatGPT4o)

Schematic representation of how a C. pneumoniae cell infects a human cell. The bacterium injects the protein SemD (green) into the cell, which activates the cell protein N-WASP, which in turn initiates vesicle formation.

Credit: HHU/Fabienne Kocher.

Universität Düsseldorf: Original or copy: How Chlamydia manipulate the host cell

The problem of parasites for creationists is one that, despite the best efforts of apologists like Michael J Behe of the Deception Institute, just won't go away.

Sadly, Behe shot himself in the foot with his original claim to have proven 'intelligent [sic] design in living organisms with his choice of the bacterial flagellum in E. coli, where he persuaded his willing audience that these nasty little pathogens had been intelligently designed - and by unspoken assumption, designed by the locally-popular god.

Now creationists wave his 'proof' of design as evidence for their creator god because only their god is capable of creating living organisms.

But, with characteristic double-think, creationists also argue that their god is omnibenevolent, so something else must have created parasites like E. coli, and, courtesy again of Michael J. Behe, they cite 'Sin' causing 'genetic entropy' and the absurd idea of 'devolution' this supposedly causes, as the cause of parasites and pathogens (but not the bacterial flagellum, obviously!).

The problem with that notion is that they need to do their double-think trick one more time and believe that a trait with improves a pathogens ability to live and reproduce in its host makes it somehow less perfect that one without that trait. So, in the creationist's world, an improvement is a move away from perfection!

But, with a cult that appears to believe learning is a move away from the 'perfection' of pristine ignorance (from whence comes expertise in all aspects of science), that's probably not too difficult a feat of mental gymnastics for a creationist to perform.

Refuting Creationism - Even More Signs of The Divine Malevolence's Obsessive Compulsive Disorder?

AI-generated image (ChatGPT4o)

Over 160,000 new virus species discovered by AI - The University of Sydney

This is the second paper today to show the apparent obsession creationism's putative designer has with creating viruses, if you believe that superstition.

The first paper dealt with the discovery that there are some 600 different viruses to be found on a used toothbrush and on the shower heads in US bathrooms; this one reports on a discovery that makes that finding pale into insignificance. It is the discovery, using the machine learning of AI, of 161,979 new viruses!

This is just tip of the iceberg as the authors say the method just scratches the surface of biodiversity and opens up a world of discovery with millions more to be discovered.

Refuting Creationism - Is Creationism's Divine Malevolence Sufferring from Obsessive-Compulsive Disorder?

Northwestern microbiologists found more than 600 viruses on samples collected from used toothbrushes and shower heads.

AI-Generated graphic (ChatGPT4o)

Structural model at atomic resolution of bacteriophage T4

By Dr. Victor Padilla-Sanchez, PhD https://www.drvictorpadillasanchez.com
Own work, CC BY-SA 4.0, Link

Viruses are teeming on your toothbrush, showerhead - Northwestern Now

Creationism's putative creator is nothing if not obsessive.

One of its obsessions appears to be designing ever-more exquisite ways to kill its creation as almost nothing in nature exists that doesn't have something that lives on or in it, often killing it in the process or at least weakening it in some way.

Its most visible obsession seems to be with designing beetles of which there are some 500,000 species with more being discovered almost daily. It's highly likely that there may be as many as a million different beetles in the world, many of which catch and devour other arthropods.

But it's in the field of virology that we find another obsession with designing variations on a general theme. Not only are there literally hundreds of thousands of viruses but every species has multiple variants - look at the number of different variants of the SARS-CoV-2 virus that have emerged since the initial wave of the COVID-19 pandemic!

Refuting Creationism - Living Bacteria Sealed Inside 2 Billion-Year-Old Rock

Microbial cells stained green

© Y. Suzuki, S. J. Webb, M. Kouduka et al. 2024/ Microbial Ecology

2-billion-year-old rock home to living microbes | The University of Tokyo

The Bushveld Igneous Complex (BIC), South Africa.
This picture shows a very famous outcrop where nearly horizontal black and white layers are observed. The BIC made of layers of igneous rock in a basin shape, formed over a period of about 1 million years, after which it seems to have barely changed.

© Y. Suzuki.

In today's incidental rebuttal of creationist dogma, archaeologists have discovered living colonies of microbes sealed within cracks in 2-billion-year-old rocks from South Africa.

The microbes became sealed in the cracks by tightly-packed layers of clay so effectively creating sealed chambers from which nothing could escape and, more importantly, nothing could enter. They have survived over geological time by firstly having an extremely low metabolic rate, with a generation time measured in thousands, even millions of years, compared to surface-dwelling microbes with generation times in hours or minutes, and by utilising sulphates as their energy source.

What they demonstrate, apart from the fallacy of Earth only being made by magic 10,000 years ago, is that in a highly stable environment, a plentiful source of energy and the ability to recycle their dead with almost no loss of energy, there is no environmental pressure to evolve, so the microbes have remained virtually unchanged for hundreds of millions, even billions of years.

Malevolent Design - A Newly-Discovered Gut Bacterium That Suppresses Immunity!

Drs. Thaddeus Stappenbeck, M.D., Ph.D., (left) and Qiuhe Lu, Ph.D., in the lab.

Cleveland Clinic Discovers Bacterium Causing Gut Immunodeficiency

The human gut, like that of other mammals, birds and vertebrates in particular and the gut of many insects and worms, in fact any organism with a moth and an anus, is an ideal environment for a whole host of other organisms, most of which will have co-evolved with humans and have been with us since our ancestors were small insectivores, skulking in the dark of the night to avoid dinosaurs and predatory proto-birds.

They for a complex and dynamic ecosystem of competing and cooperating bacteria, viruses, fungi and protozoa which exists in a more or less stable balance of arms races, predation and symbiosis.

Refuting Creationism - An Improved Method For Analysing Ancient Microfossils To Discover How Life Evolved

Research News - Unveiling Ancient Life: New Method Sheds Light on Early Cellular and Metabolic Evolution | Tohoku University Global Site

One of the clutch of science publications which casually and unintentionally refute creationism to be published today, comes in the form of a paper by a team from the University of Tokyo, Tohoku University and Kochi University, Japan, which describes a new method for analysing ancient microfossils, and so discovering more about how key processes evolved in early cellular life.

The purpose of this is to discover not whether (that is never in doubt) but the precise details of how and when these key processes evolved.

Malevolent Designer News - Why Cholera is So Good at Killing Us

Vibrio cholerae

AI generated image (ChatGPT4o)

Vibrio cholerae

AI generated image (ChatGPT4o)

News - Experts discover the deadly genetics of cholera, which could be key to its prevention - University of Nottingham

Although good hygiene and safe drinking water have most brought cholera under control in developed societies, it is still a major kill, especially of children, in poor and technologically under-developed countries.

It was a cholera outbreak of 1849 in Soho, London, the John Snow famously showed was statistically linked to drinking water from a well in Broad Steet, eventually persuading the authorities to remove the pump handle from the well, so ending the epidemic, that Snow conformed the Germ Theory of disease and founded modern epidemiology.

The cause was later shown to be a leaking septic tank which was contaminating the water in the well, and more remotely to a baby which caught cholera elsewhere whose nappy (diaper) was washed into the sewer, introducing the Vibrio cholerae into the septic tank.

I was born and brought up in North Oxfordshire in a rural community where, a generation earlier, cholera had been the single most common cause of death of children. A perusal of the parish burial registers shows regular patterns of epidemics causing a sudden increase in child deaths.

Even in technologically advanced countries, natural disasters such as earthquakes and floods, and man-made conflicts such as those currently in Gaza and Ukraine can destroy the infrastructure and quickly lead to conditions in which cholera can further devastate an already weakened population.

It would be an especially despicable malevolence that designed an organism to exploit people in those situation to ensure there was even more suffering, but those subscribing to the intelligent design hoax are unwittingly attributing exactly that to their putative designer god.

Malevolent Designer News - What Was The Divine Malevolence Doing With Plague Bacteria 5000 years ago?

Spread of Yersinia pestis (Black Death)

AI generated

In the study, scientists performed a genetic analysis on the bones of 133 human individuals from late Neolithic megalithic graves near Warburg in North Rhine-Westphalia. The team discovered the genome of the bacterium Yersinia pestis in the bone samples of two independent individuals. Additionally, previously published genomic data from a bone sample of a Neolithic dog found in Ajvide (Sweden) suggested a potential infection route.

© Carsten Reckweg, CRC 1266/Uni Kiel

Neolithic plague bacterium did not cause mass mortality

What was creationism's divine malevolence up to with one of its most successful pathogens with which if killed hundreds of millions and changes society - the Yersinia pestis bacterium which caused the waves of black death and plague that regularly spread across the world?

It seems to have been experimenting, possibly trying to either perfect its virulence or work out the best delivery system to ensure it got to and killed as many people as possible. Sometimes, entire villages were wiped out. Not far from where I currently live are a couple of former villages that disappeared during the black death - the village of Woodperry near Oxford is an example, surviving now only in the name 'Woodperry Road' and a farmhouse later built on the site.

But 5000 years ago, Y. pestis doesn't seem to have been anything like a virulent as it became in the 12th Century. According to a recent discovery, it was capable of killing the occasional neolithic farmer but not of becoming a major pandemic able to kill hundreds of thousands and depopulate vast areas.

So, what changed, and more to the point, which explanation would a creationist prefer; the one which blames their god or the one which attributes it to evolution, climate change and cultural changes in human society? One thing we can be sure of though is the Michael J. Behe's biologically nonsensical religious apologetic of 'genetic entropy', causing the bacterium to 'devolve' away from an assumed created perfection (as though that were remotely possible), can be ruled out, because whatever the changes were, it led to a massive increase in the number of Y. pestis organisms, so was indisputably beneficial to it - in other words, in classical terms, it evolved.