Admissions of Ignorance in Evolutionary Theory

August 11, 2008 — For a scientific idea some have proclaimed as a fact no longer in need of proof, and as well-established as gravity, Darwin’s theory of evolution still reveals surprising weaknesses when its defenders speak about the details. Detecting these weaknesses requires tuning out the media hype, and tuning into scientific papers and pro-evolution journals where evolutionary theory is debated. Elisabeth Pennisi wrote one such account in Science last week.¹ It revealed that the public is getting a very misleading view of evolution – both its operation and the strength of the evidence for it.
It would seem obvious that evolution needs a genetic basis. Darwin attempted to explain it in his day, unsuccessfully. The neo-Darwinian synthesis of the 1930s was supposed to explain it. Serious questions about how evolution works at the genetic level remain, however, to this day. This was evident in Pennisi’s use of war metaphors to describe two groups of evolutionists that are “locking horns” over a current issue: whether genes or regulatory elements (in particular, cis regulatory factors) are key to evolutionary change. The latter, a “fashionable idea,” has been growing in popularity among those in the evo-devo subculture: i.e., evolutionary biologists who focus more on developmental than genetic influences. When Jerry Coyne and Hopi Hoekstra wrote a pointed critique of the regulatory-element hypothesis in the journal Evolution last year, “Egos were bruised. Tempers flared. Journal clubs, coffee breaks at meetings, and blogs are still all abuzz,” she wrote.
None of the combatants doubt Darwin’s theory in the slightest, of course. Still, some statements in Pennisi’s account could give a Darwin-doubter cause for gloating. Consider this paragraph:

[Sean] Carroll [U of Wisconsin] argued that mutations in cis regions were a way to soft-pedal evolutionary change. Genes involved in establishing body plans and patterns have such a broad reach--affecting a variety of tissues at multiple stages of development--that mutations in their coding regions can be catastrophic. In contrast, changes in cis elements, several of which typically work in concert to control a particular gene’s activity, are likely to have a much more limited effect. Each element serves as a docking site for a particular transcription factor, some of which stimulate gene expression and others inhibit it. This modularity makes possible an infinite number of cis-element combinations that finely tune gene activity in time, space, and degree, and any one sequence change is unlikely to be broadly disruptive.

This sounds like damage control. Is the standard explanation too risky? Yet critics of the evo-devo alternative argue that every such “fine-tuning” change must be adaptive to persist through natural selection. Precious few examples, they say, can be found to illustrate a regulatory change related to a morphological change. One regulatory change in a mouse, for instance, can make its digits grow slightly longer (see 01/18/2008), but the mutant mouse is hardly ready to take off flying like a bat.

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