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.

Incompetent Design - How Sunlight Turns Off Cancer Protection in Skin

Schematic of the role of YTHDF2 in regulating U6 snRNA decay and interaction with TLR3 to control UVB-induced inflammation and tumorigenesis.

Seungwon Yang, Yan-Hong Cui, Haixia Li, et al.(2025), Fig.7 P

New study reveals how controlling sunburn-triggered inflammation may prevent skin cancer - UChicago Medicine

Researchers at the University of Chicago have uncovered how prolonged exposure to ultraviolet (UV) radiation can lead to skin cancer by disabling a vital protective mechanism in skin cells. They have just published their findings, open access, in Nature Communications.

This protective mechanism relies on a protein called YTHDF2, which plays a key role in regulating RNA metabolism and maintaining cellular health. Sunlight degrades this protein, removing that safeguard and allowing damage to accumulate.

For advocates of Intelligent Design (ID) creationism, this research presents several awkward questions—questions they will either ignore or attribute to ‘sin’.

First, why is this protection needed at all? If life were intentionally and intelligently designed, why would RNA metabolism require an additional, failure-prone layer of regulation to keep cells functioning? Why not design it to be robust in the first place?

Second, why create a system so fragile that sunlight—an unavoidable feature of life on Earth—can disable it? Designing a repair mechanism that breaks down precisely when it is needed most hardly inspires confidence in the designer’s competence.

And then there is the broader problem: ID creationism equates its designer with the supposedly omniscient and omnipotent god of the Bible or Qur’an. If that is true, why design a mechanism that predictably causes cancer? Was this an act of malevolence or oversight?

If YTHDF2 were flawless and impervious to degradation, Discovery Institute fellow William A. Dembski would no doubt present it as an example of “complex specified information,” a supposed indicator of intelligent purpose. But its vulnerability raises uncomfortable possibilities: Is this an unsuccessful attempt to patch over earlier design flaws in RNA metabolism? A sign of competing designers beyond the control of ID’s putative omnipotent creator? Or evidence that the designer is actively introducing harm and suffering?

The answer, of course, is that this problem arises because the human body is not the product of intelligent design at all, but of a long evolutionary process that modifies existing processes and structures to produce workable—though often imperfect—solutions. Evolution favours whatever improves short-term reproductive success, even if it introduces compromises and sub-optimal outcomes that undermine long-term survival and health. These sub-optimal systems then drive the evolution of an additional layers of complexity to minimise the results of failure.

Like other organism's the human body is full of these examples of evolutionary compromises and sub-optimal solutions that cause diseases and health problems that illustrate the difference between an intelligently designed system and an evolved system. Looked at in detail, the human body is evidence against intelligent design and strongly supports the Theory of Evolution, as I show in my book, The Body of Evidence: How the Human Body Refutes Intelligent Design.

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

Glutathionylated mtDNA

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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.

Unintelligent Design - The Defect that Causes Alzheimer's - Incompetence or Malevolence?

Exosomes

Researchers discover cell defect linked to the development of Alzheimer’s

Researchers at Aarhus University in Denmark have identified a defect in the production of exosomes within cells, linked to a mutation found in patients with dementia. Their findings are published in the journal of the Alzheimer’s Association, *Alzheimer’s & Dementia*.

Advocates of Intelligent Design argue that all genetic information must originate from an intelligent agent, claiming that anything both complex and specified cannot arise without deliberate design. Their proposed designer is invariably indistinguishable from the god of the Bible and Qur’an: an all-knowing, all-powerful and supposedly benevolent creator.

What they never address is why a system attributed to such a being should fail at all—let alone in ways that cause profound suffering. It is akin to a human engineer producing an aircraft with engines that randomly fail or wings that detach mid-flight. And because this designer is held to be omniscient, the failure cannot be inadvertent. It must have been foreseen and deliberately incorporated, making such mutations part of the intended plan rather than unfortunate accidents.

Following the internal logic of ID creationism, Alzheimer’s dementia would therefore count as an intended outcome—meeting William Dembski’s own criteria for “complex specified genetic information”. This provides yet another instance, alongside the cancer example I discussed recently, of biological processes that appear designed to destroy. It sits comfortably among the many parasites and pathogens explored in The Malevolent Designer: Why Nature’s God is Not Good, all pointing to a distinctly malign pattern in the supposed “design”.

ID proponents typically fall back on blaming “The Fall”, implying the existence of another creative force beyond the control of their designer. This manoeuvre only further undermines their claim that ID is a scientific enterprise rather than creationism thinly disguised, since it relies on biblical literalism to rescue the argument from the conclusion of an incompetent or malevolent designer—an outcome that is theologically awkward and, for many believers, outright heretical.

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.

Unintelligent Design - Flatworms Can Regenerate Body Parts - So Why Can't Humans?

The planarian Schmidtea mediterranea

Credit: FLI / Anna Schroll

Schmidtea mediterranea

New research shows a tiny, regenerative worm could change our understanding of healing Stowers Institute for Medical Research

Researchers at the Stowers Institute for Medical Research have uncovered new details explaining how the planarian flatworm, Schmidtea mediterranea, can regenerate not just a missing body part, but an entire organism from a tiny tissue fragment. Their findings have just been published in Cell Reports and represent a major advance in our understanding of regeneration at the cellular and genetic level.

This little worm continues to surprise scientists. Remove its head? It grows a new one. Slice it into pieces? Each piece becomes a complete worm. Such astonishing powers naturally prompt two very different kinds of questions – one scientific, one theological.

If one temporarily accepts creationist premises for the sake of argument, we are forced into a series of uncomfortable and contradictory conclusions.

Why would a supposedly omniscient, omnipotent, and omnibenevolent designer grant a humble flatworm the ability to regenerate an entire body, yet deny this life-saving ability to humans and virtually all other organisms? If this designer could abolish suffering, disease, and limb loss – and knowingly chose not to – what does that imply about its nature?

Creationists are left defending a worldview in which their designer appears either: unwilling to prevent suffering; unable to create beneficial traits consistently; or deliberately designing suffering into its creation. None of these options are theologically tidy – and they certainly do not align with the claim of a universally benevolent designer. The creationist framework produces contradictions, apologetics acrobatics, and moral dilemmas rather than answers.

By contrast, when we ask the evolutionary question – “How did this ability evolve?” – the picture becomes coherent.

Planarians have followed a unique evolutionary trajectory in which extreme regeneration conferred a significant survival advantage. Natural selection acted on stem-cell behaviour, gene regulation, and patterning networks over deep time, refining a mechanism that happens to be far beyond the needs of most other species.

Other organisms have regenerative abilities too – salamanders, zebrafish, sea stars, even humans to a limited extent – but the selective pressures and biological constraints differed. Regeneration is complex, energetically costly, and evolution works from what already exists. Most lineages simply did not follow that path. To borrow Michael Behe’s favourite term, planarian regeneration may appear “irreducibly complex” – and yet, as usual, complexity proves to be a testament to gradual evolutionary refinement, not evidence for supernatural assembly.

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

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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).

Refuting Creationism - LECA Was An Asgard Archaea

An artist’s depiction of an Asgard archaeon, based on cryo-electron tomography data: the cell body and appendages feature thread-like skeletal structures, similar to those found in complex cells with nuclei.

Graphic: Margot Riggi,
Max Planck Institute of Biochemistry

Asgard tubulin.

Origin of Life: How microbes laid the foundation for complex cells | ETH Zurich

Recent research indicates that the last universal common ancestor of complex (eukaryotic) cells, which encompass all multicellular plant and animal life, likely originated from the Asgard group of archaea. This ancestor is believed to have formed a symbiotic relationship with an alphaproteobacterium, which eventually evolved into the mitochondrion.

The initial nature of this symbiotic relationship—whether parasitic or predatory—remains uncertain. However, its establishment was pivotal in setting the evolutionary course that led to the diversity of life on Earth. Compelling evidence supporting the Asgard archaea hypothesis has been uncovered by Professor Martin Pilhofer and his team at the Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland. Their findings have been published in the journal Cell and is explained in an ETH news item by Peter Rüegg: