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More Fishy Tales Afoot from Neil Shubin

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Photo: Display of Tiktaalik, Wyoming Dinosaur Center in Thermopolis, by Evolution News.

Neil Shubin at the University of Chicago wants you to appreciate your inner fish. That was the title of his award-winning 2008 book, Your Inner Fish, that launched his career as a popularizer of evolution. It celebrated his discovery of Tiktaalik, which he told the receptive media was the long-sought missing link between fish and tetrapods. His notoriety went far beyond that fossil. In the book, he purported to portray the human body as the heir of numerous evolutionary innovations that began with the first “fish-a-pod” that made the transition to land. (Correction: it was not the first.) The media gave Tiktaalik iconic status.

Shubin Is Still at It

Now he claims genetic missing links have been found. With colleagues from Spain, Chile, and his own university, Shubin has a new paper out in PNAS1 that purports to demonstrate “shared evolutionary history” between the genes and molecules involved with making fish fins and vertebrate limbs, according to news from the University of Chicago. This news release has a very similar title to a release three years ago written by the same reporter, Matt Wood, except that the new genetic analysis claims to have uncovered not just the “origins” of vertebrate limbs but also the “shared genetic history of fish fins and vertebrate limbs.” 

All vertebrates have the same basic body plan: head, spine, four appendages. Those appendages vary greatly in size, shape, and function, of course — from fins to wings, arms, and legs — but a new genetic analysis shows that genes that control development at the ends of the appendages share a deep evolutionary history. [Emphasis added.]

The issue to focus on is not similarities, since we obviously share some traits with fish (we are made of cells and are vertebrates). Can Shubin and his team demonstrate that the genes that control the development of fish fins switched overby a Darwinian mechanism before Tiktaalik to start creating digits on limbs? Finding genes that make different structures is not enough to win an evolution debate because a designer could reuse code for different purposes. For instance, the Sonic hedgehog gene (Shh) is widely used in vertebrates. Shubin needs to demonstrate an ancestral evolutionaryconnection between fish and people at the location of fish fins. Otherwise, he could illogically say about any similarity, “Fish have heads and people have heads. That proves that people evolved from fish.”

The basic argument is summarized in the PNAS paper’s “Significance” statement:

In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the size of fish fins is controlled by an ancient mechanism mediated by SHH-GLI signaling that appeared prior to the evolutionary appearance of paired fins. We also show that the key regulatory networks that mediate the expansion of digit progenitor cells in tetrapods were already in place in the fins of the last common ancestor between ray and lobe-finned fishes, suggestingan ancient similarity between distal fins and digits.

An Intuitive Guess 

Do they identify that last common ancestor? No. They assume that since fish and tetrapods have the genes and regulatory networks, the ancestor must have had them too. It’s an intuitive guess, but in other anomalous situations, evolutionists have felt free to posit independent origins of complex systems. (One example is wings in different lineages of stick insects.)

The press release states the evidence in simpler terms, “a gene that controls the growth of bones at the terminal end of fish fins play [sicthe same role in forming fingers and toes in four-legged creatures.” Shubin steps in:

The same gene also controls this process both in paired fins, which are the progenitors to limbs, and the single, unpaired dorsal fin common to all fish that evolved before paired fins. This suggests that the last common ancestor between ray- and lobe-finned fish nearly 500 million years ago already had the genetic toolkit to shape their appendages, shared to this day by fish and four-legged vertebrates.

“There’s this deep homology or similarity between fins and limbs, something ancient in structures that really don’t look alike,” said Neil Shubin, PhD, the Robert R. Bensley Distinguished Service Professor of Anatomy at UChicago and co-author of the new study. “We’re showing a deeply conserved, deeply ancient and preserved gene function that’s been around for hundreds of millions of years in vastly different structures. So, the molecular toolkit is ancient, and it does the same thing in different kinds of animals.”

Has Shubin demonstrated an evolutionary connection? No; one could use the same argument with mitosis. That too is a “deeply conserved, deeply ancient and preserved gene function that’s been around for hundreds of millions of years in vastly different structures.” The similarity argument could be used to argue anything shared between any organisms indicates relatedness.

Enter the gli3 Gene

Next, Shubin and the team mention a gene that works with Shh, called gli3. The gli3 gene is known to be involved in patterning fingers in vertebrates. When knocked out, vertebrates grow extra fingers (polydactyly). The team found that it also controls the number of rays in fish fins; when knocked out, fins have more rays. Is this his ace in the hole? No; it has the same fallacious reasoning.

The speculation is that you have a primitive function of gli3 present in all vertebrate appendages ever since about 500 million years ago, and that was to promote proliferation, or the number of cells and hence the number of bones in the terminal end,” Shubin said. “When paired fins arose it was already there, so gli3 was co-opted and gained a new role, which is anterior/posterior patterning.”

How this helps the evolutionary view is not clear. A complex patterning gene was present before fish and mammals needed it. It sounds like intelligent design, not Darwinism.

“We all share a certain genetic toolkit, even though the anatomy may look very different in adult stages. We’re finding these hidden, but very important, mechanistic similarities,” he said. “It’s really only with the benefit of the ability to do CRISPR for knockouts and the ability to do sequencing that we can really see these things at all. It’s showing an underlying architectural and genetic ground plan for a diverse set of appendages in all vertebrates.

Let’s Assess the Argument

All vertebrates use Shh, partly to form limbs. All vertebrates use gli3 to pattern digits or fin rays. Like mitosis and hundreds of other similarities, these complex functions were already present, and are present today, in fish and in tetrapods. Where is the evolution? The argument that gli3 “was co-opted and gained a new role” makes no sense unless you already believe in evolution. Can the PNAS paper help get Shubin out of his circular reasoning?

Altogether, our results show that the presence of the shh/gli3 regulatory network in fish fins, so vital for limb formation and digit patterning, is primitive to limbs. Moreover, its functions in unpaired dorsal fins, widely recognized precursors of paired appendages, suggest that the recruitment of this network may have preceded the origin of paired fins themselves.

Widely recognized? By whom? Evolutionists! It’s circularity all the way down. The only way to accept this explanation is to begin by pledging allegiance to the origin of specious reasoning. Then you are free to “speculate” that pre-existing genes and a complex regulatory network “may have preceded the origin” of fins and limbs. 

It’s like the hobo argument, “Assume a can opener; it can open a soup can and a stew can.” But the can opener is the issue! One cannot assume the existence of what needs to be proved. Assuming the chance emergence of a complex gene regulatory network might shed light on fin formation and limb formation, but where did that come from? Much less does it prove that the stew can have evolved from the soup can. Interestingly, they fail to identify a single spontaneous mutation that was naturally “selected” to originate the genes, the regulatory network, the fins, or the limbs. Those are assumed, too.

Flawed Reasoning Is the Common Ancestor of Bad Arguments

How does Shubin know that limbs evolved from fins? Answer: similarities. But what about the differences? Oh, well, those evolved. Talk about having your cake and eating it too! You could play this game with anything, like digestive enzymes or the genetic code itself. Ah, but if the similarities are not on the previously assumed ancestral tree, then those are false similarities.

This scheme is guaranteed to support Darwinism against all possible scientific criticisms. And that’s why they can brazenly tell the public in museum displays that evolution is a fact, only questioned by the “ignorant, stupid, or insane (or wicked).”

Design advocates need to understand the rhetorical and logical schemes they are up against with Darwinians. It’s not enough to present better empirical evidence that challenges their evidence. It is also necessary to shine a light on the fallacious reasoning behind the claims, including circular arguments like this one. In fact, that is best done first before evidence is brought to bear in a debate. The details of their claims don’t matter if their reasoning is flawed.

See our Long Story Short video on homology for other flaws in arguments from similarity.


  1. Letelier et al., “The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits.” PNAS November 16, 2021, 118 (46), e2100575118; https://doi.org/10.1073/pnas.2100575118.