As so often when we are faced with the riddle of how complex and improbable things can arise in evolution, it is a fallacy to assume that the final perfection that we see today is the way it always was.
He's talking here about enzyme molecules, not animals, but nevertheless it has been my understanding (from reading the work of Richard Dawkins, among others) that it is a fallacy to assume that anything that evolves ever reaches a point of "final perfection"--with the possible exception of Ben Affleck's crapitude.