Computer methods of analyzing mutations are widely used because they are generally accurate. They do not suddenly lose their accuracy when I cite them.
What is it, metaphysically one might say, that distinguishes design in the ID sense from ubiquitous teleological design, in a Thomistic sense?
Explaining this sort of phenomenon by slight, successive modification, as Darwin envisaged, seems problematic.
It is a difficult question because, setting aside many other problems, the very starting point — the protein-coding gene — is highly complex.
In a previous article I described the evidence that cooption faces insurmountable mathematical challenges in explaining the origins of such complex molecular machines as the bacterial flagellum.