There is a growing body of experimental knowledge about the evolution of genomes, which shows that decidedly directed forces at work. The genome is best viewed, not as a happenstance gathering of parts, but as a holistic mechanism which functions as a whole. A good summary paper of these sorts of ideas is Mutation is modulated: implications for evolution. While the author does attempt to reconcile this directed view of evolution with Darwinism, ultimately it is the directed mutation, not the reconciliation with Darwinism, which is supported experimentally.
Some interesting points about the genome:
- Tandem repeats can be used as tuning knobs to quickly and reversibly adjust biological function of genes
- The vertebrate immune system has “an integrated set of mechanisms that focus mutation at the binding sites of potential antibodies and T-cell receptors” (emphasis mine)
- Mutation tends to occur at binding sites rather than structural sites, allowing a protein to diversify in a useful way (note to readers — this means the cell must contain intelligence of some sort about which sites are binding sites and which sites are structural sites)
- A global method of gene regulation exists in methylation. Methylation can be used to tag certain sequences for conservation, variation, and repair, and can also tag transposons to be mobile or non-mobile
- Bacteria can sample foreign DNA and incorporate it into its genome for adaptation, which process is regulated by stress
This is an area which is just beginning to be explored, and certainly in the coming years we will learn more and more about the way that mutation is modulated.
Where the author goes wrong is in assuming that Darwinistic evolution can account for such evolutionary strategies. The general argument is that the author confuses the difference between whether or not something is “favored by selection”, and whether or not it could be produced without following a higher-order pattern. The assumption present throughout the paper was that anything which would be favored by selection would necessary come into being. The contention of ID is that the search constraints require that a higher-order pattern exist, and cannot be derived in and of itself from a lower-order pattern (for justification, see here and here).
Anyway, it was a fascinating paper (one of several excellent papers by the author). This field is just beginning to see the fruits of the search for directed forms of mutation, and I think in the long run we will get a much, much different view of the genome than what is currently seen and taught.
Caporale, L.H. “Mutation is modulated: implications for evolution”. Bioessays 22(4):388-395.
Kashi, Y. and D.G. King. “Simple sequence repeats as advantageous mutators in evolution”. Trends in Genetics 22(5):253-259.