When The Edge of Evolution The Edge of Evolution: The Search for the Limits of Darwinism was first published, some Darwinist reviewers sneered that the problem it focused on — the need for multiple mutations to form some protein features (such as binding sites), where intermediate mutations were deleterious — was a chimera. There were no such things, they essentially said. University of Wisconsin geneticist Sean Carroll, reviewing the book for Science, stressed examples where intermediate mutations were beneficial (I never said there weren’t such cases, and discussed several in the book). In the same vein, University of Chicago evolutionary biologist Jerry Coyne assured readers of The New Republic that “[i]n fact, interactions between proteins, like any complex interaction, were certainly built up step by mutational step … This process could have begun with weak protein-protein associations that were beneficial to the organism. These were then strengthened gradually…” The take-home message of the reviews for the public and for scientists in other fields was the same: Nothing to see here, folks. Move along. No problem here.
Contrast those assurances with a recent paper that addresses “the old enigma [my italics] of the evolution of complex features in proteins that require two or more mutations.” Those words (reminiscent of the title of my 2004 paper in Protein Science with David Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues,” which is cited by the recent paper) were written by the prominent bioinformatician (and no friend of ID) Eugene Koonin in his review of the paper, “The look-ahead effect of phenotypic mutations” (Whitehead, D. J., et al. 2008, Biol. Direct 3:18). (Reviews are published along with papers on the Biology Direct web site.)
Old enigma? Old enigma? Who knew that evolving just a couple of interactive amino acid residues was a long-standing mystery? Someone should tell Carroll and Coyne….
I will discuss the specifics of the paper in Part 2. But let me first drive home this point. The development of protein features, such as protein-protein binding sites, that require the participation of multiple amino acid residues is a profound, fundamental problem that has stumped the evolutionary biology community until the present day (and continues to do so, as I explain below). It is a fundamental problem because all proteins exert their effects by physically binding to something else, such as a small metabolite or DNA or other protein, and require multiple residues to do so. The problem is especially acute for protein-protein interactions, since most proteins in the cell are now known to act as teams of a half-dozen or more, rather than individually. Yet if one can’t explain how specific protein-protein interactions developed, then it is delusional to claim that we can explain how anything that depends on them developed, such as the molecular machinery of the cell. It’s like saying “we understand perfectly well how a car could evolve; we just don’t know how the pieces could get fit together.” If such a basic requirement for putting together complex systems is not understood, nothing is understood. Keep this in mind the next time you hear a blithe Darwinian tale about the undirected evolution of the cilium or bacterial flagellum.