As the Worm Turns, Evolution Leaps

Researchers don’t see gradualism
in earthworm evolution, so they
propose evolutionary leaps instead.

 

by John Wise, PhD

Earthworms Uncover Evolutionary Mechanism Defying Darwin, Mirage News, 18 June 2025. I will also refer to the study on which this article is reporting, “An episodic burst of massive genomic rearrangements and the origin of non-marine annelids,”[1] in Nature Ecology and Evolution, 18 June 2025.

The article begins:

A comparative genome study of earthworms and their marine relatives … shows that marine worms shattered their genome and rebuilt it in a radically different form when they first emerged from the sea 200 million years ago. The study, published in Nature Ecology and Evolution, could challenge Darwin’s theory of evolution by showing that worms colonized land in evolutionary jumps.

Setting the Stage: The Fossil Record and Serious Saltations

My radical conversion to Young Earth Creationism in 2024, based as it was on recent discoveries in genomics and cell biology, and now writing for Creation Evolution Headlines has at times set my head spinning and my mind racing. Reviewing article after article on ‘rapid’ evolution since my first CREV article on Burmese pythons, I have been thinking of my response as a school student in the late 70s and early 80s to Gould and Eldredge’s theory of punctuated equilibrium. I cannot tell you why, but I was excited when I learned of it (yes … I was a nerd).

[A quick but important aside. Evolutionary “leaps,” such as those in the fossil record that punctuated equilibrium is designed to explain, are called saltations, from the Latin saltus, or leap. Interestingly, in logic a saltus is a gap in the logical progression of an argument. I would say evolutionary theory has more than its share of these, too.]

If I were forced to express the cause I would say that it seemed to fit the facts better than the slow and steady Darwinian theory I’d been taught. However, I was at that time too ignorant of the fossil record to have been able to explain that to anyone, even myself.

In 1859, Darwin imagined evolution as a slow, gradual progress, with species accumulating small changes over time. But even he was surprised to find the fossil record offered no missing links: the intermediate forms which should have told this story step by step. In 1972, the scarcity of intermediate forms led the palaeontologists Stephen Jay Gould and Niles Eldredge to propose the idea of the punctuated equilibrium. According to this theory, rather than changing slowly, species remain stable for millions of years and then suddenly make rapid, radical evolutionary jumps.  These large changes would happen suddenly and in small, isolated populations, well off the palaeontological radar. Although some fossils support this pattern, the scientific community remains divided: is this a rule of evolution, or an eye-catching exception?

Given the fossil record, the slow and gradual accumulation of mutations of Neo Darwinism does seem implausible, as effectively no transitional forms exist. Gould and Eldridge offered a compelling alternative evolutionary explanation. I think that my 2024 conversion to YEC was driven by a similar affinity for a reasonable explanation of the facts – recent scientific data falsified the evolutionary explanation I’d been led to believe.[2]

Science’s Paradigms: Narratives, Maps, and Assumptions

As a philosopher I was not trained to interpret empirical data (I am deliberately avoiding the term “evidence,” as it is a profoundly loaded term; more on this another time) so much as to follow the logic of claims and arguments. I trained, that is, primarily to evaluate narratives, and only secondarily to articulate them.[3] It is what I do best, I think. The articulation of a narrative is the primary role of Kuhn’s “normal science.” For me, the grand narrative of evolution fell apart in confrontation with the data.

Scientists are trained into a narrative. Their everyday job is to articulate that narrative (in the sense of articulating a skeleton) – to make the data fit (or explain how it does), and sometimes in that process the reverse is also true, to modify/articulate the narrative to better fit the data, as in this article. This explanation is not meant as a criticism of scientists, evolutionary or otherwise.

It is what scientists do:

Here’s the map of reality (the present paradigm). We need to show how all these seemingly disconnected data points (towns, cities, etc.) come together on this map. This is the puzzle-solving role of science. It also explains why there is a certain legitimacy to the claim that anyone operating outside the specific map on which “scientists” are working is not doing science. This is what we might call a self-referential definition,[4] creating the bitter battles over what is meant by “science.”  We Creationists make a similar claim concerning Christians who believe Genesis creation is myth. They’ve set aside the map that reads God’s word as perspicuous, authoritative and true. We say they interpret Scripture from a false map.

False maps lead us astray, no matter how well they are articulated.

Sometimes, however, there are disagreements among map-articulators on how to make the pieces fit. This is the level at which this article/research is written. The large-scale evolutionary map is not challenged, despite the article’s sensational title, but a significant mechanism for drawing it is. Does evolution occur in a uniformly slow and gradual way, as Darwin thought, accumulating one small change at a time, or does it act in sudden leaps, or saltation events? The authors say,

Now a study points for the first time to a mechanism of rapid, massive genomic reorganisation which could have played a part in the transition of marine to land animals 200 million years ago.

The case made in this article is that the gradualism of Darwinian evolution requires supplementation by some form of punctuated equilibrium – sudden and drastic change – if it is to make sense of the data. They continue,

“Both visions, Darwin’s and Gould’s, are compatible and complementary. While Neo-Darwinism can explain the evolution of populations perfectly, it has not yet been able to explain some exceptional and crucial episodes in the history of life on Earth, such as the initial explosion of animal life in the oceans over 500 million years ago, or the transition from the sea to land 200 million years ago in the case of earthworms,” Fernández notes. “This is where the punctuated equilibrium theory could offer some answers.”

The high quality genomic study here represented (I have great admiration for the scientific work done in this study) claims evidence of just such radical change in the genomes of worms.

The research team has shown that marine annelids (worms) reorganised their genome from top to bottom, leaving it unrecognisable, when they left the oceans. Their observations are consistent with a punctuated equilibrium model, and could indicate that not only gradual but sudden changes in the genome could have occurred as these animals adapted to terrestrial settings. The genetic mechanism identified could transform our concept of animal evolution and revolutionise the established laws of genome evolution.

Genomic Chaos: A Miracle in the Making?

So far, so good. Marine worms changed into terrestrial worms (earthworms) through a process of adaptation. We should note, however, that the “change” expressed here is not an observed change. Such observation is on principle impossible, as Homo sapiens will not “emerge” onto the scene for another 199.8 Ma. Today, we have a variety of annelids, terrestrial and marine. That terrestrial annelids descended from marine annelids is not observational science, but paradigm driven speculation.

Or is it?

After putting together each of the genomic jigsaw puzzles, the team was able to travel back in time with great precision more than 200 million years, to when the ancestors of the sequenced species were alive. “This is an essential episode in the evolution of life on our planet, given that many species, such as worms and vertebrates, which had been living in the ocean, now ventured onto land for the first time,” comments Rosa Fernández, lead researcher of the IBE’s Metazoa Phylogenomics and Genome Evolution Lab.

So … these scientists are Time Lords like Doctor Who, doing observational science “with great precision” 200 Ma in the past! Is this a joke? Hubris? A rhetorical device? Or is it a retreat into the false certainty of one’s paradigm-commitment, of claiming to know what one does not know, as Socrates said? At the very least it is an attempt to ape (irony intended) the prestige of observational science. (See David Coppedge’s article on Physics Envy)

Is there evidence that marine annelids are the ancestors of terrestrial annelids? Sure, if you start with the assumption of evolutionary descent the data can act that part in this play. But what sort of plot twists and turns will it take to move you from marine worms to earthworms in the time allowed? And how plausible will the resulting story be?

The analysis of these genomes has revealed an unexpected result: the annelids’ genomes were not transformed gradually, as Neo-Darwinian theory would predict, but in isolated explosions of deep genetic remodelling. “The enormous reorganisation of the genomes we observed in the worms as they moved from the ocean to land cannot be explained with the parsimonious mechanism Darwin proposed; our observations chime much more with Gould and Eldredge’s theory of punctuated equilibrium,” Fernández adds.

It is interesting to read this article with an eye to its rhetorical devices. In this quote we have the dramatic phrase “explosions of deep genetic remodeling.” Scientists as a group aren’t given to the histrionic – have you read scientific literature? – but this article and the peer-reviewed study it is commenting on are filled to overflowing with dramatic language like this. How believable is the resulting theater? Witness this gem:

The international team of scientists has discovered [physics envy?] that certain marine worms shattered their genome into thousands of fragments—only to reassemble it and continue evolving on land. [Presumably this “discovery” happened with that highly advanced and sophisticated scientific instrument known as “the Tardis.”] This phenomenon challenges current models of genome evolution [though, of course, not evolution itself], which show that in most species—from sponges and corals to mammals—genomic structures remain remarkably conserved over time. “The entire genome of these marine worms was broken down and then reorganized in a completely random way, in a very short period on the evolutionary scale,” explains lead researcher Fernández. “I had my team repeat the analysis over and over because I simply couldn’t believe it.”

I understand, Dr. Fernandez. I can’t believe it either. An “entire genome” shattered into thousands of fragments, yet the annelids remained living and thriving annelids throughout the process. How exactly are we to believe that a carefully balanced and successful genome ‘shatters into thousands of fragments,’ and when it (without intelligent intervention) ‘reassembles itself,’ it is a fully functional annelid capable of thriving in a new niche-environment, rather than what we would expect, given all that we know about genetic structure and cellular biology – its extinction?

Also, what does it mean to say “that marine worms shattered their genome”? Is this a figure of speech, or are we to infer agency on the part of the worms, or perhaps the genome itself? Does this scenario fit with what we know, however provisionally, about the genetic nature of life? Do shattered genomes “reorganized in a completely random way” result in new and improved genetic blueprints? Try that with computer code. How does this happen? This is what evolutionary science asks us to believe. It is not merely biological saltation but faith saltation, a miracle!

Occam’s Razor: Simplicity, Creation, and Evolutionary Strain

Why is it not the case that no catastrophic massive tectonic rearrangements of genetic scrambling (just a few of the many superlatives invoked in this article) took place in marine annelids in order to evolve them into terrestrial annelids? Why is this not evidence that evolutionary theory itself is bankrupt, unable to construct a cohesive and believable map of reality? Why is this not evidence of intelligent design? How could such a catastrophic rearrangement of genetic material not prove fatal? Doesn’t it make more sense to say that God made annelids in marine kinds and terrestrial kinds? Another question:

Has Occam repossessed his razor from the scientific community to attend to his own toilet (in the archaic sense, of course)?

What if we do not assume that marine annelids became terrestrial annelids? What if they never moved from sea to land? What if the evidence for massive genetic explosions is a consequence of the assumption being made? Remember, all that scientists can observe (despite their comical nod to time-travel) are the genomes of marine annelids and terrestrial annelids in the present. They observe a striking dissimilarity in genomic organization. There is nothing in the comparative genomes to indicate a transition from one to the other absent this assumption. This evidence of sudden transition is only evidence of sudden transition because they first assume a transition!

It exists, so it evolved.

Do you recall from your high school studies the old Greek trick of rescuing a narrative from absurdity? It was called the deus ex machina. Our authors recognize the blind alley this research has driven them into, but they are forced to embrace it:

“You could think this kind of genomic chaos would doom a species, but it’s possible that some lineages owe their evolutionary success to exactly this kind of superpower,” Fernández concludes.

Time travel and superpowers. Slow and steady accumulation over millions of years, but blindingly fast in the present so that we can “see” it (and overcome our congenital skepticism). Catastrophic and chaotic when missing links remain, stubbornly, missing. Proterozoic life is remarkably simple (if one can utter such an oxymoronic phrase as “simple life”), and then suddenly the Cambrian explosion of variety and complexity. What can the authors of this play do?

Punctuated equilibrium is lowered onto the Darwinian(?) stage to set things right.

What is hysterically funny to me is the omnipotence and conscious purpose scientists are now forced to smuggle into natural selection (Hegelian Process) in order to make the data fit the theory. Hummingbirds in California and pythons in Florida evolve in a decade, yet the emergence of the eye – imagine if you can – took a few tens of millions of years, and then suddenly it’s omnipresent in the Cambrian era, and in a cornucopia of varieties.

Perhaps this new emphasis on rapid evolution (remember, evolution is process-metaphysics) should be a welcome sign that reality (the data) is pushing evolutionary biology to recognize the complex adaptational engineering God built into His Creation. After all, ALL this diversity around us today is the result of stuff happening very quickly following the Flood. Maybe, as was the case for me, it is the evolutionary biological scientists themselves that will bring down the guillotine on the theory of evolution via this particular saltation – rapid evolution:

All in all, our study illustrates how saltational rather than gradual changes played an important role during the evolution of an animal lineage characterized by a series of morphological and ecological innovations, providing new insights into the mode and tempo of macroevolution in animals.

Stuff happened and worms became … worms? If this sort of catastrophic genome revision is a representation of what it takes to evolve from a worm into a worm, what sort of genetic violence is required to transform a dinosaur into a bird? or a chimpanzee into a human? Being aware of how ridiculous all this apocalyptic language may appear, the authors give us this little nugget:

“The 3D organization of the genome provides a structural framework that allows genes to remain functionally connected, even when their linear order is dramatically altered,” says Aurora Ruiz-Herrera. “This plasticity could be what made such extreme genome reconfiguration compatible with survival and adaptation.” Thanks to this flexibility, genes located in different parts of the genome may have been able to shift positions while still functioning together. This ability could have been essential in allowing major DNA rearrangements without compromising the organism’s viability.

Oh … it could have, could it? Did we catch that to which Dr. Ruiz-Herrera appeals here … a higher level of organization? Again with the deus ex machina. The two-dimensional genome may become catastrophically chaotic and remain viable because the three-dimensional genome remains intact. That’s a novel claim, isn’t it?[5] “O be careful little minds what you think!” (You’ll be humming the tune all day!) Small heresies often metastasize into full-blown ones. Follow that chain of logic, Dr. Ruiz-Herrera, and see where it takes you. In a year or so, you might be writing for Creation Evolution Headlines.

I have a bit of experience with such cases.

Footnotes

[1] Vargas-Chávez, C., Benítez-Álvarez, L., Martínez-Redondo, G.I. et al. An episodic burst of massive genomic rearrangements and the origin of non-marine annelids. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02728-1

[2] Like a lamb to the slaughter.

[3] For this reason I tend to dislike calling myself a philosopher in my typical vocational activities. Philosophers, on my view, articulate a philosophy of their own. Socrates was a philosopher, as were Plato, Aristotle, Kant, Hegel and Sartre. I hesitate to place myself in their ranks. As such I’ve spent a great deal of time studying philosophy, but much less time doing philosophy, or being a philosopher.

[4] This is a recurring phenomenon in the history of science and, really, in all branches of human inquiry. To take an example outside of science think of how the history of music is divided into periods. The composers in Mozart’s day might attempt to write a madrigal, but it would get them nowhere fast among the classical artists and even the public of his day. Scientists do science, so whatever scientists do as scientists defines Science. To do something else, however legitimate, is to be outside of science. In this (relative) sense, the practitioners define the practice.

[5] To say nothing of how ridiculous this becomes when we remember that “the genome” is not the chemicals that make up the DNA, but the information that those chemicals carry. Information is non-physical, and that holds at both the two-dimensional and the three-dimensional levels. How does it know to organize itself this way? I thought we were methodological materialists? Now, to rescue our theory we are willing to appeal not just to the immaterial two dimensional information in DNA, but to an even more abstract immaterial third dimension of intelligent organization. At what point does the evolutionary story become overloaded with elements that contradict its fundamental assumptions – things like non-material entities, appeals to conscious purpose, and intelligent choice? Is evolutionary biology ever subject to self-reflective criticism?

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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.