Evolutionists Resurrect Discarded Notions

Evolutionary theory keeps recycling ideas,
discarding them as discredited one decade,
reviving them under a new name the next

 

From Cloaca to Claws: How Evolution Recycles Its Myths

by John D. Wise, PhD

This article doesn’t mince words: Fish buttholes may be the reason we now have fingers, (ScienceAlert, 22 September 2025).

That’s right — a new Nature paper, Co-option of an ancestral cloacal regulatory landscape during digit evolution,” (Nature, 17 September 2025), claims our digits – fingers and toes – arose when evolution “co-opted” regulatory DNA originally used in the cloaca, the common outlet for waste and reproduction in many animals. If you think that sounds like evolutionary storytelling with a potty-mouth twist, you’re not wrong. But the real story here isn’t cloacas or fingers. It’s how evolutionary theory itself keeps recycling ideas — discarding them as discredited one decade, reviving them under a new name the next, and calling the process “progress” in an endless Hegelian loop.

The Study Behind the Hype

The team reporting in the Nature article, summarized in From fish cloaca to fingers: Scientists trace the origin of our digits, (Phys.org, September 17, 2025), worked with zebrafish, testing a conserved stretch of noncoding DNA near the HoxD[1] cluster, the master “architect genes” of development. When they deleted this region, gene activity faltered in the cloaca of the zebrafish, but not in the fins. From this, they concluded that the same regulatory landscape was later “co-opted” to help pattern digits in land animals.

This surprising result suggests that the cloaca—an organ where the intestinal, excretory, and reproductive systems meet at their extremities in many species—has been reused in terrestrial vertebrates to develop digits.

So instead of inventing a new system for fingers, nature allegedly “rewired” an old one.

Evo-devo: The Return of Haeckel’s Ghost

This is where evo-devo (evolutionary developmental biology) loves to flex. The field rose in the 1990s, when scientists discovered that the same Hox toolkit patterns fruit flies and humans alike. But behind the new jargon lurks an old specter: Ernst Haeckel’s infamous claim that “ontogeny recapitulates phylogeny.”

That idea was discredited a century ago — embryos don’t literally replay their evolutionary history, and Haeckel’s own embryo sketches were exposed as doctored. Yet evo-devo revives the spirit of the claim: that embryonic development reveals evolutionary origins. Yesterday’s recapitulation theory is today’s co-option model. Same story, new label — the ghost of Haeckel walks again.

Evolution’s Recycling Plant

Darwinism, it seems, runs a recycling plant for old theories:

• Lamarckism died under Weismann’s experiments and theory (late 19^th c.),[2] only to rise again in the 21st century as epigenetics and transgenerational inheritance.
• Goldschmidt’s hopeful monsters were mocked, then reborn as evo-devo’s “large-effect mutations” and sudden regulatory shifts.
• Orthogenesis (built-in direction) was dismissed as mystical,[3] yet biologists now unapologetically speak of “developmental constraints” and “biased variation.”
• Vitalism was pronounced dead, but “emergence” and “self-organization” in systems biology smell suspiciously similar.
• Group selection was written off, then revived as “multi-level selection.”

And now: Haeckel’s embryo-as-phylogeny idea, once ridiculed, returns in evo-devo guise as “co-option.”

This isn’t scientific progress — it’s reincarnation. Evolution may be the only “science” where ideas are killed, buried, dug up again, relabeled, and paraded as new “discoveries.” Each resurrection is driven not by prediction, but by stubborn facts that refuse to fit the Darwinian script.

The House of Cards Effect

Here’s the irony: every resurrection of Darwinian theory rests on discovering order where accidents were expected.

• Hox colinearity: the linear order of DNA mirrors the linear order of the body.
• Conserved enhancers: noncoding switches preserved across deep time. The evolutionary explanation? Profound change is explained by near-stasis.
• Epigenetic memory: chemical tags that lock developmental decisions into place.

None of these “look” like cobbled accidents. They “look” like design.[4] Yet each time a new layer of order appears, evolutionists rummage through the graveyard of discarded theories and recycle an explanation.

Rummage Sale

If Darwinism survives only by re-animating its dead ideas, what does that say about its theoretical power? Real science grows by prediction and confirmation. Darwin’s “science” collapses like a house of cards, only to be rebuilt each generation with the same old deck.

As former evolutionary paleontologist Gunter Bechly put it:

The whole of evolutionary biology turns out to be a house of cards — wild speculations built upon further speculations with very weak and highly ambiguous circumstantial evidence. To sell any of these evolutionary speculations as scientifically established facts … is nothing but a great deception of a gullible public.

Each collapse and resurrection exposes the truth: Darwinism is not an engine of discovery, as it is so often painted in academia and popular culture, but a mask worn to hide the unmistakable architecture of design.

The Creationist Prediction That Landed

Long before ENCODE and CRISPR, creationist scientists like Jerry Bergman and A. E. Wilder-Smith argued that the 98% of DNA written off as “junk” would prove broadly functional. That design-based prediction has aged remarkably well. Study after study confirms that these so-called genetic wastelands are in fact regulatory hubs, switchboards, and control centers. Evo-devo now leans heavily on precisely the parts of the genome Darwin’s disciples mocked as useless.

So who, in the end, made the truly scientific prediction — those who expected disorder, or those who expected design?

The Elephant in the Room: Fish Butts Aren’t Blueprints

You can believe the headlines that fingers are repurposed “fish sticks,” but the real story is the one evolutionists keep dodging: the elephant in the room — information. What evo-devo papers are actually responding to is not prediction but surprise: the discovery of astonishing order, modularity, and foresight in the genome. Perhaps it isn’t Nature that’s “recycling” itself, but Darwinism recycling its excuses.

Darwin fretted about the “abominable mystery” of flowering plants. Today the mystery is deeper: why is the genome so exquisitely ordered? Why does evolutionary theory keep returning to its vomit – renaming it, and calling it “progress”?

In the end, the real question is always kicked down the road: where did the original information come from — the modules, the switchboards, the regulatory landscapes that choreograph development?

That answer is forever in the futureware.[5]

Information isn’t chemicals; it’s instructions — and no one has explained how blind chance writes code. Evolutionary theory can talk about “repurposing” or “rewiring,” but these metaphors only make sense if the information was already there to be reused.

Maybe the real recycling program isn’t in DNA, but in Darwin’s theory itself. Not the majesty of the Ouroboros, but the absurdity of the Flying Spaghetti Monster – forever swallowing its own cloaca.

Repurposing isn’t origin. A story still demands an Author.

Footnotes

[1] Hox genes are clusters of “master switches” in the genome that act like body-plan architects. Each gene produces a protein that turns other genes on or off, telling cells where they are along the head-to-tail axis. Strikingly, the order of Hox genes on the chromosome matches the order of the body parts they control — a phenomenon called colinearity. In mammals there are four clusters (Hox A–D), conserved across animals from flies to humans. Even small shifts in their regulation can make the difference between a fin, a limb, or a digit.

[2] The Weismann barrier (late 19^th century) asserts that the germ cells (eggs, sperm), which pass on genetic information to offspring, are completely separate from somatic cells, negating Lamarck’s idea that acquired traits – like a blacksmith’s muscles or a giraffe’s stretched neck – could be inherited.

[3] Analogous to Marx’s substitution of materialism for Hegel’s “mystical” Spirit.

[4] Each time I write words to this effect I am reminded of Richard Dawkins in the Blind Watchmaker, insisting that what looks like design must be treated as illusion – a logic that requires rewriting the obvious as the nearly-ridiculous.

[5] In Expelled, Dawkins floated the idea of life being seeded by an advanced civilization — an idea he calls “intriguing.” But this just pushes the question back one step. Evo-devo performs the same dodge: parade “modules” and “regulatory landscapes,” but never answer the real question — where did the information originate?

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John Wise received his PhD in philosophy from the University of CA, Irvine in 2004. His dissertation was titled Sartre’s Phenomenological Ontology and the German Idealist Tradition. His area of specialization is 19th to early 20th century continental philosophy.

He tells the story of his 25-year odyssey from atheism to Christianity in the book, Through the Looking Glass: The Imploding of an Atheist Professor’s Worldview (available on Amazon). Since his return to Christ, his research interests include developing a Christian (YEC) philosophy of science and the integration of all human knowledge with God’s word.

He has taught philosophy for the University of CA, Irvine, East Stroudsburg University of PA, Grand Canyon University, American Intercontinental University, and Ashford University. He currently teaches online for the University of Arizona, Global Campus, and is a member of the Heterodox Academy. He and his wife Jenny are known online as The Christian Atheist with a podcast of that name, in addition to a YouTube channel: John and Jenny Wise.