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A Primer on the Tree of Life (Part 3): Extreme Convergence - Common Descent or Common Design?

Note: This is Part 3 in a 5-part series titled "A Primer on the Tree of Life." Read Part 1 here, Part 2 here, Part 4 here, and Part 5 here. The full article can be found, here.

Extreme Genetic Convergent Similarity: Common Design or Common Descent?
If common descent is leading to so many bad predictions, why not consider the possibility that biological similarity is instead the result of common design? After all, designers regularly re-use parts, programs, or components that work in different designs (such as using wheels on both cars and airplanes, or keyboards on both computers and cell-phones).

One data-point that might suggest common design rather than common descent is the gene "pax-6." Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes. Because their eye-types are so different, it previously hadn't been thought that these organisms even shared a common ancestor with an eye. Evolutionary biologist Ernst Mayr explains the havoc wreaked within the standard evolutionary phylogeny when it was discovered that the same gene controlled eye-development in many organisms with very different types of eyes:

It had been shown that by morphological-phylogenetic research that photoreceptor organs (eyes) had developed at least 40 times independently during the evolution of animal diversity. A developmental geneticist, however, showed that all animals with eyes have the same regulator gene, Pax 6, which organizes the construction of the eye. It was therefore at first concluded that all eyes were derived from a single ancestral eye with the Pax 6 gene. But then the geneticist also found Pax 6 in species without eyes, and proposed that they must have descended from ancestors with eyes. However, this scenario turned out to be quite improbable and the wide distribution of Pax 6 required a different explanation. It is now believed that Pax 6, even before the origin of eyes, had an unknown function in eyeless organisms, and was subsequently recruited for its role as an eye organizer.12
Typically, extreme genetic similarity is thought to mandate inheritance from a common ancestor, because the odds of different species independently arriving at the same genetic solution are exceedingly small. But if we require a Darwinian evolutionary scheme, such an improbable event is exactly what must have occurred. The observed distribution of genes like pax-6 demand extreme "convergent evolution" at the genetic level. Mayr tries to argue that such improbable examples of extreme genetic convergent evolution are not only acceptable, but common:
That a structure like the eye could originate numerous times independently in very different kinds of organisms is not unique in the living world. After photoreceptors had evolved in animals, bioluminescence originated at least 30 times independently among various kinds of organisms. In most cases, essentially similar biochemical mechanisms were used. Virtually scores of similar cases have been discovered in recent years, and they often make use of hidden potentials of the genotype inherited from early ancestors.13
Mayr tries to explain away this extreme genetic convergent similarity by appealing to "hidden potentials of the genotype." Does this sound compatible with the kind of blind, unguided, and even random processes inherent in neo-Darwinian evolution? No. This sounds like a goal-directed process -- intelligent design.

References Cited:
[12.] Ernst Mayr, What Evolution Is?, pg. 113 (Basic Books, 2001).

[13.] Id. at 205-207.