The genome is the perfect imperfect machine

In a recent paper, Avise (1) challenges the latest incarnation of the creationists manifesto—intelligent design (ID)—by adopting the posture that the structure, expression, and control of the genome has sufficient flaws, and it seems implausible that it is the handiwork of an intelligent designer. Although I agree with Avise in most respects and applaud his courage and insights on such a controversial issue (at least in the general public domain), I would like to make a few comments concerning the structure of the genome, or at least, our current understanding of its structure and why that structure and control is the perfect imperfect machine.