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.

Malevolent Designer - How a Hostile Planet Can Kill With Deadly Toxins

Satellite image of Lake Erie.

Image credit: NOAA Great Lakes CoastWatch MODIS Satellite Image
July 6, 2020

Satellite image of Lake Erie.

Image credit: NOAA Great Lakes CoastWatch MODIS Satellite Image – July 6, 2020

Bacterial villain behind Lake Erie’s ‘potent toxin’ unveiled by U-M study | University of Michigan News

You would think that a planet designed specifically for humans would be safe—one with an abundant supply of clean water to drink and wholesome food to eat.

Sadly, that is far from the case. As recent research has shown, on top of the pathogens and parasites that abound in nature—and which seem almost purpose-built to cause suffering, not just to humans but to virtually every other life form—there now exists yet another threat. Wherever you look in the natural world, every species has one or more parasites adapted to live in or on it, and even parasites themselves often fall prey to their own parasites. To this long list we can now add a group of cyanobacteria capable of turning fresh water into a deadly neurotoxin during warm weather. It is almost as though Earth wasn’t designed by an intelligent, benevolent creator after all.

In science, this is what’s known as a falsified hypothesis. You begin with an idea—in this case, that Earth was designed for humans by an omnibenevolent, omniscient deity—then you consider what predictions would logically follow. One such prediction might be that a planet designed for human well-being would contain no natural hazards or harmful organisms that routinely inflict suffering. Then you examine the evidence. If the facts contradict the prediction, the hypothesis is falsified.

And that is precisely what the existence of harmful organisms does. The evidence directly contradicts the creationist claim of an intelligently designed planet optimally crafted for humans. This does not, in itself, disprove the existence of such a deity; rather, it falsifies the specific claim that the deity is all-loving and all-knowing, or that it intentionally designed Earth and its myriad pathogens and parasites. The alternative is that the god described in the Bible and Qur’an is not as advertised—or does not exist and played no role in designing the world. The pathogens and parasites appear to have arisen from entirely different processes while this supposed designer either looked away or was not involved at all. Such outcomes are not the work of a benevolent creator.

In fact, the deity’s reputation would fare better if it didn’t exist, because then it could not be held responsible.

Malevolent Design - How Breast Cancer is 'Designed' to Survive

Cell culture plates in the Roeder lab where scientists recently studied gene expression in breast cancer.

Credit: Lori Chertoff.

The Rockefeller University » This molecular switch helps cancer cells survive harsh conditions

Researchers at The Rockefeller University's Laboratory of Biochemistry and Molecular Biology have uncovered the mechanism that enables breast cancer cells not only to withstand environmental stress, but to turn it to their advantage. They have just published their findings in Nature Chemical Biology.

For ID creationists, these findings pose yet another challenge—one typically ignored or waved away as the consequence of ‘sin’, neatly exposing the Discovery Institute’s attempt to persuade US legislators and educators that ID is a genuine scientific alternative. No real science explains inconvenient evidence by invoking fundamentalist doctrine or unevidenced forces inherited from ancient superstition.

The Rockefeller University team has shown that breast cancer cells can override a regulatory factor that normally controls gene expression. The transcription of DNA into mature messenger RNA involves the enzyme RNA polymerase II (POL II), whose activity depends on around 30 subunits. One of these, MED1, normally carries acetyl groups. Without those acetyl groups, MED1 loses its ability to regulate POL II, allowing the enzyme to transcribe genes that help cancer cells survive. Environmental stress deacetylates MED1. In essence, conditions such as low oxygen or elevated temperature—deadly to normal cells—can instead make cancer cells more resilient.

Malevolent Designer News - Stunning 3D Images of the Yellow Fever Virus Reveal It's Irreducible Complexity - Malevolent Design or Evolution

High-resolution imaging of yellow fever virus reveals structural secrets that could power next-generation vaccines.

UQ scientists uncover secrets of yellow fever - News - The University of Queensland
Scientists at the University of Queensland, Australia, have produced near atomic-level 3D images of the yellow fever virus. These reveal the remarkable complexity that Michael J. Behe and William A. Dembski of the Discovery Institute insist constitutes evidence of intelligent design – a theme almost universally endorsed by creationists and forming the central plank of their advocacy for creationism.

They have recently published their findings, open access, in the journal Nature Communications.

So, the obvious question for intelligent design advocates is this: is the irreducible complexity and complex specificity of the yellow fever virus evidence that it was intelligently designed to kill people? Or, when complex specified information and irreducible complexity do harm to humans, do these supposed ‘evidences’ for the existence of an intelligent designer (i.e. a god) somehow cease to apply, even though they benefit the virus? If so, how can a supposedly scientific definition change its meaning depending on the subjective judgement of what is being specified and how much or how little it benefits humans?

Unintelligent Design - The Design Blunder That Causes Many Diseases - Malevolence or Incompetence?

Glutathionylated mtDNA

AI-generated image (ChatGPT 5.1)

New type of DNA damage found in our cells’ powerhouses | UCR News | UC Riverside

Scientists led by the University of California, Riverside (UC Riverside) have identified a previously unknown form of DNA damage in mitochondria that may underlie a wide range of disorders linked to mitochondrial dysfunction. Their findings have just been published in the Proceedings of the National Academy of Sciences (PNAS).

Mitochondria contain their own DNA (mtDNA), which is essential for the proper functioning of these organelles that convert glucose into ATP, supplying cells with the energy needed to power metabolic processes.

The culprit is a large molecule, glutathionylate, which attaches to DNA and, if left unrepaired, can cause mutations. Researchers at UC Riverside, working with colleagues at the University of Texas MD Anderson Cancer Center, found that glutathionylated mtDNA accumulates in mitochondria at levels up to 80 times higher than in the cell nucleus. In short, the nuclear DNA repair system is vastly more efficient than its mitochondrial counterpart.

For advocates of Intelligent Design (ID), this discovery—if they understood it rather than dismissing it as part of an imagined conspiracy to undermine their faith—creates an acute theological problem. If we temporarily grant the core assumption of ID creationism, that a supernatural designer indistinguishable from the allegedly omniscient, omnipotent, and omnibenevolent god of the Bible and Qur’an is responsible for the design of mitochondrial DNA and its replication machinery, then only two coherent conclusions follow:

• the designer is incompetent, having failed to produce fault-free mtDNA and an adequate repair mechanism, despite supposedly managing this for nuclear DNA; or
• the designer could have produced fault-free mtDNA but chose instead to create error-prone mtDNA and a weak repair process, thereby intentionally designing disease and suffering—in other words, malevolence.

Moreover, the very need for a repair system betrays the absence of omnipotent, intelligent engineering. It is characteristic instead of the layered complexity produced by cumulative, unplanned evolutionary processes, which inevitably yield sub-optimal compromises.

The notion of an omniscient designer also rules out the excuse that the harmful consequences were unforeseeable. An all-knowing creator would have foreseen them; yet, according to ID logic, the designer implemented them regardless—designing mitochondrial DNA to fail and cause disease.

Thus, a biological phenomenon that fits seamlessly within the framework of evolutionary theory becomes an insurmountable theological obstacle for ID advocates, who must contort the evidence to suit a predetermined conclusion while catering to a scientifically illiterate and credulous audience.

Malevolent Design - How Some Cancers Are Designed to Win - Incompetence or Malevolence?

Cancer cells dividing

Shapeshifting cancers’ masters, unmasked | Cold Spring Harbor Laboratory

Scientists led by Cold Spring Harbor Laboratory (CSHL) Professor Christopher Vakoc have uncovered a mechanism by which certain cancers manage to evade modern medical treatments: they can disguise themselves as ordinary cells from entirely different tissues, such as those of the skin. In two recent papers — one in Nature Communications and another in Cell Reports — Vakoc’s team identify the proteins that determine whether pancreatic cancer cells retain their pancreatic identity or slip into a skin-cell-like state. They also highlight a different set of proteins with a pivotal role in tuft-cell lung cancer.

Proteins, of course, are specified by genetic information, and if that information is altered, so too is the protein’s function. In the language of ID creationists, proteins are products of “complex, specified genetic information”.

This presents intelligent design creationists with a familiar problem — one they usually address, as with parasites and pathogens, by ignoring it and relying on the scientific illiteracy of their followers. If complex, specified information were genuinely evidence of an intelligent designer, then that same designer would be implicated in the origin of the proteins that maintain and diversify cancers. Their “specified information” is neither less complex nor less specific than the proteins involved in cognition, immunity, or embryonic development.

Only by refusing to define “complex specificity” in scientific terms — or to explain how it might be distinguished from information that is supposedly non-complex or non-specified — do ID advocates manage to maintain the fiction that all beneficial traits are the work of their designer, while harmful traits must arise from some other agency. This selective attribution, based entirely on subjective human preference, underscores the religious foundations of intelligent design creationism and its distance from genuine science.

The team’s findings are summarised in a Cold Spring Harbor Laboratory news release by Jen A. Miller.

Malevolent Design - How Creationism's 'Designer' Favoured The Naked Mole Rat

DNA repair mechanisms help explain why naked mole-rats live a long life

News that scientists have discovered what enables the naked mole-rat to live for up to 37 years — around ten times longer than relatives of a similar size — raises a troublesome question for creationists. The findings were reported recently in Science by a team of researchers from the Shanghai Key Laboratory of Maternal Fetal Medicine.

Creationists like to flatter themselves with the notion that they are the favoured creation of their putative designer god and the ultimate expression of design perfection. So, when evidence emerges of other species surpassing humans in some way — bats with more robust immune systems, elephants and sharks being almost completely immune to cancers, peregrine falcons with far superior vision — it is typically ignored, met with incredulity, or dismissed as an ineffable mystery and part of some divine plan which in no way diminished the unique position of humans in the grand scheme.

Now, to add to their woes, comes the discovery that the secret of the naked mole-rat’s extraordinary longevity may be traced to changes in just four amino acids. This alone undermines creationist claims that mutations are always harmful and incapable of generating new genetic information.

Malevolent Designer News - A Newly-Designed Way To Increase Suffering Is Having Major Success in Southern China

Chikungunya Virus Replication Cycle

BioRender Science Templates

Guangdong faces largest chikungunya outbreak on record | EurekAlert!

An open-access report in the journal Biocontaminant [PDF] describes a sudden, large increase in the number of infections with the chikungunya virus in southern China, with more than 4,000 cases in Foshan City, Guangdong Province, and over 3,600 cases in Shunde District. The initial spread of the outbreak was observed in this region and quickly escalated into a major public health concern. These cases have not only been documented in Guangzhou, Shenzhen, Yangjiang, and Zhanjiang within Guangdong Province but have also emerged in Macao and Hong Kong.

Let’s pretend for a moment that Intelligent Design Creationism accurately describes reality — that a supernatural entity, indistinguishable from the supposedly omnibenevolent god of the Bible, is continually intervening in living organisms to ensure they conform to a divine plan for the world, particularly for human life.

Let’s also assume that William A. Dembski, Michael J. Behe, and other “CDesign proponentsists” are correct in asserting that the presence of “irreducible complexity” and particularly “complex specified genetic information” is evidence of the work of this putative designer.

How, then, does this announcement about the increase in cases of chikungunya in southern China fit into that worldview?

Chikungunya is a virus transmitted to humans only through the bite of a female Aedes mosquito when she takes a blood meal — in much the same way that Zika, yellow fever, and malaria are transmitted. Once infected, a person develops a sudden-onset fever with painful joints and acts as a reservoir for the virus, enabling the next mosquito to pick it up and continue the chain of infection.

The recent increase in cases is believed to be due to two main factors:

• More viruses circulating in the population
• More Aedes mosquitoes, with a northward spread driven by global warming

The genetic information in the chikungunya virus genome is clearly enabling the virus population to increase in response to environmental change. If this doesn’t qualify as “complex specified information”, it’s difficult to imagine what would.

Furthermore, the feeding strategy of the Aedes mosquito is a striking example of a finely tuned process: if any part of it fails, the entire transmission cycle collapses. By Michael J. Behe’s own definition, this appears to meet the criteria for “irreducible complexity” and, within that framework, would be touted as conclusive evidence of “intelligent design”.

The inescapable conclusion, then — if we accept the Intelligent Design worldview, in which a divine intelligence is the only possible explanation for such genetic information and irreducibly complex systems — is that both the virus and the mosquito have been intelligently designed to cause human suffering. They seem to have no other purpose than to reproduce themselves and increase infection levels within the population. In other words, according to the logic of ID creationism, this virus was designed with malevolent intent.

Refuting Creationism - How Autism May Be The Result Of Compromise In The Evolution Of Human Intelligence

Trump 'fact checking' his autism claim

How evolution explains autism rates in humans | EurekAlert!

If the human genome had been intelligently designed by an omniscient, omnibenevolent, omnipotent supernatural deity, as creationists insist, it should be perfect and free from defects of any sort. In fact, it is difficult to see why there would be any variance in such an intelligently designed genome, let alone variance that causes genetic defects—unless those were intentionally included by the designer, who then cannot reasonably be described as omnibenevolent or omniscient.

If, however, the human genome is the product of hundreds of millions of years of gradual evolutionary processes — processes that prioritise survival and reproduction, with all the sub-optimal compromises that a utilitarian form of ‘design’ entails — then variance and defects are exactly what we would expect.

Creationists traditionally ignore questions about the origin of variance in a supposedly ‘perfect’ intelligently designed genome. The existence of genetic defects is usually explained away by resorting to Bible-literalist mythology about ‘The Fall’ — an abandonment of the Discovery Institute’s Wedge Strategy, which seeks to present creationism as real science rather than a fundamentalist religion dressed in a lab coat. News that autism may in fact be a by-product of the evolution of intelligence in humans will therefore be an even greater problem for creationists, who insist that our high intelligence sets us apart as the special creation of a perfect god.

Ironically, as well as possessing high intelligence, humans — unlike any other primates — also have autism and schizophrenia. It is this correlation that provides a clue to their shared evolutionary origins.

My book, The Body of Evidence: How the Human Body Refutes Intelligent Design, lists lots of examples of how the human body is the result of these sub-optimal evolutionary compromises with all the problems that has produced. This example is just another instance and more evidence of the lack of intelligence in the process.

Malevolent Designer News - How Candida Albicans (Thrush) Is Cleverly Designed to Infect Your Mouth - Evolution Or Malevolent Design?

The yeast fungus Candida albicans (blue) breaks out of human immune cells (red) by forming long thread-like cells called hyphae. The part of the hypha that has already left the immune cells is coloured yellow.

© Erik Böhm, Leibniz-HKI

The dose makes the difference - Leibniz-HKI

As has often been pointed out in these blog posts, the "evidence" offered by Discovery Institute fellows William A. Dembski and Michael J. Behe for an intelligent designer can, by the same logic and using the same evidence, be interpreted as pointing to a theologically awkward malevolent designer. This is a line of reasoning routinely ignored by the "Cdesign proponentcists", who prefer to overlook the many examples of parasites and pathogens—and the evolutionary traits that make them so successful at invading and surviving within their hosts.

A fresh example that creationists will either have to ignore or blame on "The Fall" comes from researchers at the Leibniz Institute for Natural Product Research and Infection Biology. They have shown that the fungus Candida albicans, which causes thrush, has evolved a highly sophisticated and "finely tuned" mechanism for infecting the human mouth while evading the immune system.

The stock creationist response is to shift responsibility onto the biblical myth of "The Fall," retreating into Bible literalism. Yet this is precisely the kind of literalism the Discovery Institute has been at pains to insist is not essential to the notion of intelligent design, which it markets as a scientific alternative to evolutionary theory—or "Darwinism," as they prefer to call it. This rhetorical sleight of hand was central to the Institute’s "Wedge Strategy," devised after the 1987 US Supreme Court ruling in Edwards v. Aguillard, which confirmed that teaching creationism in public schools violated the Establishment Clause of the First Amendment.

The new research reveals that C. albicans produces a toxin called candidalysin in carefully regulated doses that allow it to infiltrate the mucous lining of the mouth. Too little candidalysin, and the fungus would fail to establish itself; too much, and it would trigger an immune response strong enough to destroy it. Normally, C. albicans exists in a round, yeast-like form, but under the "right" conditions it can switch into the filamentous hyphal form typical of fungi. This transformation allows it to penetrate host tissues and, in immune-compromised patients, become life-threatening. It is in this invasive hyphal state that C. albicans produces candidalysin.

The production of hyphae, and therefore candidalysin, is controlled by the gene EED1. By any definition, EED1 would qualify as an example of "complex specified information" according to Dembski’s own formulation — evidence, according to the Discovery Institute, of supernatural intelligent design.

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.

Malevolent Design - How The Poxvirus is 'Intelligently Designed' To Rapidly Multiply

A Survival Kit for Smallpox Viruses - Universität Würzburg

The tRNA ensures the cohesion of the polymerase and the associated factors; without it, they would not arrange themselves in this way.

Image: Clemens Grimm.

Researchers at Julius Maximilian University of Würzburg (JMU) have discovered that poxviruses have developed a unique strategy to multiply rapidly after infecting a host cell. They achieve this by assembling a large protein complex with the help of a transfer RNA (tRNA) molecule. Remarkably, this is the first known example of a ‘chaperone’ function being carried out by a tRNA rather than a protein. Each component of the assembly plays a specific role in the production of new poxviruses. Crucially, the complex only functions when all parts are correctly assembled, and the tRNA is indispensable for this construction.

In other words, the tRNA provides the essential element of the complex, which some might describe—using the Discovery Institute’s own terms—as containing “complex specified information” and forming an “irreducibly complex” system essential to the virus’s success.

By that same logic, it follows that the viruses responsible for smallpox and mpox (monkeypox) must have been intelligently designed. This leaves creationists with an unenviable dilemma:

• Accept the Discovery Institute’s definitions and admit their designer created deadly viruses — theologically awkward.
• Claim another intelligence designs life, beyond their god’s control — even more awkward.
• Abandon the Institute’s “evidence” for intelligent design — politically awkward.

Malevolent Design - A Paradox Creationists Pretend Not to See

The ancient city of Jerash, Jordan, epicentre of the Justinian Plague

Progress of the Black Death in Europe

By Flappiefh - Own work from:Natural Earth  Cesana, D.; Benedictow O.J., Bianucci R. (2017). "The origin and early spread of the Black Death in Italy: first evidence of plague victims from 14th-century Liguria (northern Italy)". Anthropological Science 125 (1): 15–24. DOI:10.1537/ase.161011. ISSN: 0918-7960. (page 17),
CC BY-SA 4.0, Link

USF, FAU researchers solve 1,500-year-old mystery: The bacterium behind the first pandemic

The notion of intelligent design — the current flagship of creationism’s attempt to replace scientific realism with magical superstitions and Bible literalism dressed up as “alternative science” — contains a blatant paradox its advocates must ignore: the very same “logic” used to argue that the God of the Bible created living organisms can just as easily be used to argue that any such designer is a malevolent sadist who deliberately increases suffering in the world while ignoring countless ways to reduce it.

The theological problems this raises are never discussed in polite creationist circles, except for the lazy fallback of blaming everything on “The Fall.” But this move exposes intelligent design for what it really is — Bible-literalist religion in disguise. And that sits awkwardly against over half a century of insistence by the Discovery Institute that ID is not a religious idea, but rather a scientific one that should be taught in American public schools at taxpayer expense — a direct violation of the Establishment Clause and the U.S. Supreme Court’s ruling in Edwards v. Aguillard (1987).

The paradox lies in the fact that the very same so-called evidence — Michael J. Behe’s “irreducible complexity” and William A. Dembski’s “complex specified genetic information” — can be found in the genomes, structures, and processes of parasites and pathogens, making them devastatingly effective at exploiting and destroying their hosts. In fact, Behe himself has, probably without realising it, used precisely such examples. The bacterial flagellum he highlights enables E. coli to move efficiently through our gut, causing sometimes fatal food poisoning. And his example of resistance to anti-malarial drugs in Plasmodium parasites illustrate how evolution equips them to continue killing hundreds of thousands of children every year while condemning millions more to cycles of malarial fever.

Now, new research has highlighted another gruesome example. The bacterium Yersinia pestis — responsible for multiple waves of plague throughout the Middle Ages — has been shown to have evolved into its highly lethal form only in relatively recent human history. Beginning with the “Plague of Justinian” about 1,500 years ago, Y. pestis unleashed pandemics that killed between 30% and 50% of Europe’s population.

An interdisciplinary team at the University of South Florida (USF) and Florida Atlantic University (FAU), with collaborators in India and Australia, has now confirmed genomically that the Justinian plague was indeed caused by Y. pestis, as long assumed. Analysing DNA from plague victims buried in a mass grave at the ancient city of Jerash, Jordan — the epicentre of that pandemic — one group identified the culprit, while another team traced the bacterium’s evolutionary changes that made it one of history’s most notorious killers.

Malevolent Design - How a Spider Uses Captive Fireflies To Lure More To Their Death - Malevolence or Evolution?

Sheetweb spiders have outsourced prey attraction to their prey's own signals.

Firefly caught in a sheetweb spider's web

Spider uses trapped fireflies as glowing bait - BES

This news will thrill devotees of a creationist god of divine malevolence; but for those who prefer their deity to resemble the all-loving god of the New Testament, it will be a cause for concern. Even more worrying for the latter, the current campaign by creationist organisations such as the Discovery Institute—trying to promote the pseudoscience of Intelligent Design as a scientific alternative to evolutionary biology—unwittingly strengthens the case for a malevolent designer. After all, Michael J. Behe’s notion of irreducible complexity and William A. Dembski’s concept of complex specified genetic information apply just as well to parasites and stealth predators as they do to supposed “beneficial” features such as human intelligence or the biological systems that keep us alive.

The latest example comes from scientists at Tunghai University, Taiwan, who have shown that a sheet-web spider has evolved a particularly nasty trick for luring fireflies to their deaths. The method is brutally simple: once the spider captures a firefly, it keeps it alive, so its flashing courtship signal continues to glow. Instead of attracting a mate, the unfortunate insect draws more fireflies into the spider’s web—and to certain death.

To an evolutionary biologist, this is a fascinating demonstration of how a mindless natural process can hone behaviour in whatever direction produces more offspring, regardless of whether humans judge the outcome “good” or “evil.”

Malevolent Designer - How Creationism's Divine Malevolence Is Actively Killing Children With Malaria - If You Belive ID Creationists

Novel Maneuver Helps Malaria Parasite Dodge the Immune System | Newsroom | Weill Cornell Medicine

Here’s one of those discoveries in biological science that should have ID creationists jumping up and down yelling, "Told you so!". It’s news that the parasite that causes malaria shows both what they call 'irreducible complexity' and 'complex specified genetic information'. According to Discovery Institute fellows Michael J. Behe and William A. Dembski, that would mean it is intelligently designed and, by implication, designed to do exactly what it does — by the Christian God.

But, for reasons which can only be guessed at — and probably not a million miles from the fact that this conclusion would mean the Christian god is actively designing ways to kill people, particularly children, and especially in Africa — creationists tend to ignore it. After all, that’s the very antithesis of the compassionate, benevolent, loving god of the Bible.

Instead, they quietly sidestep the inconvenient reality that examples of their supposed 'proof of intelligent design' are found just as often in parasites and pathogens as in their hosts. This is precisely what evolutionary biology predicts: a host–parasite relationship invariably leads to an evolutionary arms race, producing sophisticated and complex systems that equip the parasite to survive in the host and to infect new victims.

And, true to form, we now have another such example in the major cause of malaria, Plasmodium falciparum, which killed some 569,000 people in Africa in 2023:

Key Facts:

• Globally in 2023, there were an estimated 263 million malaria cases and 597,000 malaria deaths in 83 countries.
• The WHO African Region carries a disproportionately high share of the global malaria burden.
• In 2023, the WHO African Region was home to 94% of malaria cases (246 million) and 95% (569,000) of malaria deaths (432,400 children under 5).
• Children under 5 accounted for about 76% of all malaria deaths in the Region.

Malevolent Design - How 'Intelligent Design' Exposes Divine Malevolence

Schistosoma mansoni

Schistosoma mansoni

Parasitic Worms Evolved to Suppress Neurons in Skin - AAI News

It gets tedious repeating this point so often, but so long as creationists keep using what they claim is irreducible complexity and/or complex specified genetic information as evidence for intelligent design, they need to be reminded that the same argument can also be used as evidence of their putative designer’s malevolence.

Creationists, of course, ignore the fact that parasites are no less “designed” than humans and have structures and processes that are “irreducibly complex” and depend on “complex specified information” in order to succeed in their environments. Yet their existence, and how they interact with and even manipulate their hosts, inevitably increases suffering in the world – a theological problem that creationist disinformation organisations such as the Discovery Institute avoid like the plague.

Parasite–host relationships also inevitably involve evolutionary arms races – the antithesis of intelligence if both “sides” are supposedly designed by the same designer.

So, to keep reminding them: if their justification for designating their god as the designer of living systems holds true, then it is also justification for designating the same god as the cause of suffering. Here is another example of a parasite that falls within their definition of an organism “designed” to do what it does and to participate in an arms race with its host in order to do so. This concerns the discovery that the parasitic worm Schistosoma mansoni, which causes schistosomiasis, is able to suppress neurons in the skin to evade detection as it burrows into its victim’s body (usually the leg).

Malevolent Design - Has Creationism's Intellgent Designer Favoured a Goulish Parasite?

The jewel wasp, Nasonia vitripennis

Nasonia vitripennis female drilling into a host pupa (Calliphora vomitoria)

Wasps may hold the secret to slowing down the ageing process | News | University of Leicester

The jewel wasp, Nasonia vitripennis, is as striking as its name suggests — a tiny, glittering insect that, at first glance, might seem like a textbook example for creationists eager to claim “intelligent design.” Their reasoning, as usual, rests on little more than ignorant incredulity, a lack of understanding of evolution over deep time, and a confusion between the appearance of design and actual evidence for it.

But that enthusiasm evaporates when the facts crawl out. This insect’s life cycle is anything but beautiful — in fact, it’s the sort of thing that would make an all-loving creator god look more like a sadistic tinkerer. The jewel wasp is a parasitoid, laying its eggs inside the pupae of parasitic carrion flies such as blowflies. When the eggs hatch, the larvae devour the pupa from within, eventually emerging as adults, leaving behind only an empty shell.

It takes a particularly selective creationist to ignore this grisly reality and still point to the wasp’s jewel-like beauty as proof of divine craftsmanship, viewed through the narrow lens of human aesthetic tastes.

Now, researchers at the University of Leicester have discovered that — if creationist claims were taken seriously — these wasps have been uniquely blessed with the power to suspend ageing during their parasitic phase, a privilege denied to other organisms.

Malevolent Design - We COULD Have Been Designed To Re-Grow Lost Or Damaged Eyes - Malevolence Or Evolution?

Golden apple snail, Pomacea canaliculata

This Snail’s Eyes Grow Back: Could They Help Humans do the Same? | UC Davis

First, we had the example of Australian lizards which, unlike humans, have been endowed with immunity to snake venom through a simple mutation — the kind of change that creationists like William A. Dembski of the Discovery Institute would insist is the result of "intelligent design" because it is both complex and specified.

Now we have the example of the aquatic golden apple snail, Pomacea canaliculata, which — again, unlike humans — can regenerate a lost or damaged eye. The snail’s eye is genetically and structurally similar to the mammalian eye, so there appears to be no reason why an omnibenevolent, omniscient intelligent designer could not have endowed humans and other animals with that ability too. And of course, according to William A. Dembski and Michael J. Behe, the irreducibly complex eye and the complex, specified genetic information are both evidence for intelligent design by the same intelligent designer that designed the mammalian eye and it genetic underpinning.

Creationists, of course, believe that humans are the pinnacle of their putative intelligent designer’s work. So, from their viewpoint, the only reasons it didn't grant us the ability to regenerate eyes — or to resist snake venom — must be that it either didn’t want to, didn’t think to, or didn’t know how to. Yet all of those options are inconsistent with the claimed attributes of being omnipotent, omniscient, and omnibenevolent.

Which leaves us with only one other explanation: that it wants us to suffer when we damage or lose an eye.

All rather strange, really — especially considering that, according to the Bible, God views blemishes such as blindness as a form of profanity:

And the Lord spake unto Moses, saying, Speak unto Aaron, saying, Whosoever he be of thy seed in their generations that hath any blemish, let him not approach to offer the bread of his God.

For whatsoever man he be that hath a blemish, he shall not approach: a blind man, or a lame, or he that hath a flat nose, or any thing superfluous, Or a man that is brokenfooted, or brokenhanded, Or crookbackt, or a dwarf, or that hath a blemish in his eye, or be scurvy, or scabbed, or hath his stones broken;

No man that hath a blemish of the seed of Aaron the priest shall come nigh to offer the offerings of the Lord made by fire: he hath a blemish; he shall not come nigh to offer the bread of his God.

He shall eat the bread of his God, both of the most holy, and of the holy. Only he shall not go in unto the vail, nor come nigh unto the altar, because he hath a blemish; that he profane not my sanctuaries: for I the Lord do sanctify them.

And Moses told it unto Aaron, and to his sons, and unto all the children of Israel.

Leviticus 21:16-24

Almost as an added insult to the humans it denied this regenerative ability to, while giving it to golden apple snails, the golden apple snail is a major invasive agricultural pest which causes widespread damage to rice crops, when it gets into paddy fields.

Creationism Refuted - Complex Specified Information in 'Spanish Flu' Virus Makes ID Creationists Sick

Emergency hospital in Zurich’s Tonhalle during the so-called “Spanish flu” in November 1918

Image: Schweizerisches Nationalmuseum, Inventarnummer LM-102737.46

Swiss Genome of the 1918 Influenza Virus Reconstructed | UZH

A major stumbling block that non-biologist Christian fundamentalist theologian William A. Dembski has blundered into is that his so-called ‘proof of intelligent design’ (i.e., the Christian god) also, by the same reasoning, constitutes evidence for malevolent design — something found in virtually every genome of every parasite and pathogen. This presents CDesign proponentsists with a fatal paradox: either their ‘proof of intelligent design’ also proves the existence of an evil designer, or ‘complex specified information’ is not the definitive evidence for design they like to claim it is.

A classic example — and another blow to creationist reasoning—has just been described in a study by researchers from the Swiss universities of Basel and Zurich. They have recovered and analysed the genome of the virus responsible for the 1918–1920 ‘Spanish flu’ pandemic, which killed more people than were killed in the First World War. In fact, the term ‘Spanish flu’ is a misnomer; the virus is now believed to have originated in a U.S. military base in Kansas and was brought to Europe by American soldiers.

The Swiss team discovered that from the outset, the virus appears to have been pre-adapted for infectivity and immune evasion. They identified three key mutations that remained unchanged as the virus evolved over the course of the pandemic. Two of these mutations made the virus resistant to an antiviral component of the human immune system, while the third enabled it to bind more effectively to receptors on the surface of human cells, allowing it to enter and infect them more readily. These mutations were so effective that victims frequently died within hours of the onset of symptoms.

Malevolent Designer - Does The Designer Favour Zebrafish Or Just Hate Humans?

Two zebrafish genes hold the key to regenerating inner ear cells, offering hope for future human therapies.

Stowers Institute for Medical Research

Regrowing hearing cells: New… | Stowers Institute for Medical Research

It's more bad news for Intelligent Design (ID) creationists who believe their putative designer is the anthropophilic, omnibenevolent God of the Bible. Hot on the heels of the discovery that some lemurs do not suffer from the age-related degenerative conditions that cause such misery for humans, comes the news that zebrafish can regenerate lost hair cells—cells that, in humans, enable hearing but cannot be replaced once lost.

These hair cells, located in the human inner ear, detect vibrations and are crucial for hearing. They can be destroyed through prolonged exposure to loud noise, resulting in permanent deafness. However, zebrafish possess homologous cells in their lateral lines—structures that allow them to detect vibrations in water, effectively functioning as a form of hearing. Remarkably, these cells can regenerate under the control of two specific genes.

It doesn't take a genius to realise that, if we accept the intelligent design argument that a divine designer deliberately created these genes, then the same designer could have endowed its supposed special creation—humans—with this regenerative ability too. Within the ID framework, the only possible conclusion is that the designer god chose *not* to give humans this ability, and instead preferred us to go deaf.

The problem for creationists deepens when one considers that these genes exemplify what William A. Dembski of the Discovery Institute cites as evidence of intelligent design: they are complex and specified, containing the genetic information to produce a defined result. Dembski insists that such "complex specified information" can only originate from an intelligent designer.

Creationists, of course, are compelled to reject the notion that these differences are simply the result of evolutionary processes. But if they also refuse to accept that this zebrafish trait—clearly underpinned by "complex specified genetic information"—constitutes evidence of intelligent design (and therefore points to a deliberate *absence* in humans), they are also undermining Dembski's single defining argument for intelligent design.

This striking discovery was made by researchers at the Stowers Institute for Medical Research and has just been published open access in Nature Communications.