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Faced with Uncooperative Data, Evolutionary Icthyologists Reverse the Predictions of Common Descent (UPDATED)

[UPDATE, 1-12-15: After posting the original draft of this article, I realized that, according to the standard phylogeny, tetrapods are not nested within teleosts (an infraclass within class Actinopterygii), but are rather nested within class Sarcopterygii. This of course would mean tetrapods are phylogenetically equidistant from any member of Actinopterygii, including teleosts or gar (gar are members of Holostei, also an infraclass of Actinopterygii). Thus, common descent wouldn’t necessarily “predict” that teleosts are closer to tetrapods than gar, but it also would not predict what the biologists found in the study discussed below — that gar Hox genes are MUCH more genetically similar to those of tetrapods than are those of teleosts.

Indeed, given their experimental results, it wouldn’t be at all surprising if the gar Hox gene they studied is more genetically similar to its orthologue in tetrapods than its counterpart in teleosts. That’s not what common descent would predict, and since the standard phylogeny holds that the gar is much phylogenetically closer to teleosts than to tetrapods, these results probably still do represent a reversal of the expectations of common descent. Thus, the criticisms I make below still hold valid: evolutionary biologists treat common descent as if it predicts whatever we find, and whatever we find is what common descent predicts.

All this makes it quite amusing that the study concludes: “Our data point to a generally conserved regulatory network governing Hox genes in fins, emphasizing the need to study subtle modifications to Hox regulation as well as additional genomic regions that may influence fin morphology and that emerged during the fin to limb transition.” Why is this an odd statement? Because teleosts — which are supposed have an equal phylogenetic distance from tetrapods as the gar — don’t show the kind of “conservation” they were hoping to find (i.e., teleost Hox genes governing fin growth aren’t similar to the Hox genes in mouse that govern limb growth). Instead, teleost Hox genes appear significantly different from our own, especially compared those of the gar. There’s no reason that common descent should predict this finding. The post below has been updated to reflect this.]

Here’s another case of common descent predicting whatever we find, even when it’s in fact not what evolutionary scientists predicted. Neil Shubin (pictured above) and his team are at it again, suggesting that Tiktaalik was a fish with a “wrist.” A Science Daily article reports:

“Fossils show that the wrist and digits clearly have an aquatic origin,” said Neil Shubin, PhD, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago and a leader of the team that discovered Tiktaalik in 2004.

In saying that wrists and digits have an “aquatic origin,” perhaps Shubin is only alluding to amphibian-like creatures like the tetrapod Acanthostega, which had true limbs with wrists and digits. But it was never established that fish with wrists or fish with digits existed in the first place. In fact, the Science Daily article acknowledges that living fish have no analogues to the bones of tetrapod limbs:

Initial attempts to confirm the link based on shape comparisons of fin and limb bones were unsuccessful. The autopod differs from most fins. The wrist is composed of a series of small nodular bones, followed by longer thin bones that make up the digits. The bones of living fish fins look much different, with a set of longer bones ending in small circular bones called radials.

Ironically, the description of bones in living fish is also a very good description of the fin of Tiktaalik. See my post from 2008, “An ‘Ulnare’ and an ‘Intermedium’ a Wrist Do Not Make: A Response to Carl Zimmer.”

Tiktaalik had no wrist, and in fact, there are no known living or fossil fish that have anything like a wrist or digits. Shubin and his team now want to use genetics to strengthen the evolutionary connection between fish and tetrapods. However, when Shubin’s new study tried to insert Hox genes from living teleost fish into mice, they couldn’t initiate growth in the autopod (the foot/hand structure). The ScienceDaily article puts it this way:

The primary genes that shape the bones, known as the HoxD and HoxA clusters, also differ. The researchers first tested the ability of genetic “switches” that control HoxD and HoxA genes from teleosts — bony, ray-finned fish — to shape the limbs of developing transgenic mice. The fish control switches, however, did not trigger any activity in the autopod.

Teleost fish — a vast group that includes almost all of the world’s important sport and commercial fish — are widely studied. But the researchers began to realize they were not the ideal comparison for studies of how ancient genes were regulated. When they searched for wrist and digit-building genetic switches, they found “a lack of sequence conservation” in teleost species.

So does the fact that the Hox genes from these teleost species didn’t work in mice count against homology of limbs and fins? Not in their view. According to these evolutionary scientists, this evidence just shows that the genomes of those teleosts got scrambled over eons of evolution such that their Hox genes were no longer compatible to work in other vertebrates, like mice. As the Science Daily article puts it: “the genetic switches that control autopod-building genes were able to drift and shuffle, allowing them to change some of their function, as well as making them harder to identify in comparisons to other animals, such as mice.”

Undeterred, they looked for sequence conservation in other fish species that are supposedly no more or less distant from tetrapods as teleosts. As the technical paper in PNAS explains, “We reasoned that the unduplicated nature of the gar genome makes its Hox clusters a better representative of the common ancestor of bony fish (Osteichthyes), revealing sequences that have diverged beyond recognition in derived, duplicated teleost genomes.” But why should we expect the gar’s Hox genes to therefore function in mice, but not those of teleosts? According to normal evolutionary reasoning, we shouldn’t: phylogenetically speaking, gar’s aren’t any closer to tetrapods than teleosts. The authors propose that the lack of a genome duplication in the gar lineage made it more likely that its Hox gene would work in mice, but there’s no reason why that should be the case. I think they really didn’t know what to expect, and it just happens that the gar’s Hox genes worked in mice whereas those of other teleosts didn’t. And why don’t the teleosts, which are the same phylogenetic distance from tetrapods as the gar, have a Hox gene that functions in mice? The paper suggests: “Teleosts, perhaps owing to genome duplication followed by subfunctionalization, represent a derived state that has lost the ability in some taxa to respond to a distal program in the developing limb.”

Isn’t that convenient. Had they found the opposite results — that the gar’s Hox genes didn’t work in mice and those of teleosts did — they would have again said this is exactly what evolution predicts. But the teleost’s Hox genes didn’t work. Instead, what they found was that fish are more genetically similar to tetrapods than other fish which are the same phylogenetic distance from tetrapods (according to the standard phylogeny). Is that what common descent predicts? Contrary to what logic would suggest, apparently we’re supposed to accept that it is.

So the expected prediction of common descent failed. But should it be so surprising that a Hox gene in a fish worked in a tetrapod (a mouse)? Even under a non-evolutionary view, this isn’t surprising. Hox genes are just regulatory switches that turn other genes on and off. They can turn on (or off) sets of genes that control the development of a variety of different features. As I have observed in the past, “Hox genes are known to be widely conserved among vertebrates, so the fact that homology was found between Hox-gene-associated DNA across these organisms isn’t very surprising.”

The notion that similar Hox genes are re-used in different organisms isn’t surprising and could just as easily point to common design as to common descent. Indeed, another study found that some of the same Hoxa genes that govern fin development in fishes also control the growth of barbels (whisker-like sensory organs on the mouths of fish, like catfish), as well as the vent (a urethra-like structure in ray-finned fishes). So the Hoxa genes that control fin development in fish or limb development in tetrapods also control barbell and vent development in fish. But no one is saying that barbels or vents are homologous to tetrapod limbs. These are just more examples of numerous features that are built using similar Hox genes. Common descent might explain some of these patterns, but they’re not exactly surprising evidence since, as I said, the same data can just as easily be explained by common design.

Image: Caleb Long [CC BY-SA 2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons

Casey Luskin

Associate Director and Senior Fellow, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.

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