Another issue, still quite unresolved, is how body forms arise from the genes. There is a lot known about structure and patterning in say Drosophila or nematodes, but the general principles behind the specific - and very complex - details are still not clear. I think this problem will be solved over the next decade or two though, and should shed a lot of light how genetic changes lead to the formation of new species. There is already good mounting evidence that speciation too is an abrupt process, like a bifurcation, and not a gradual processes with a continuum of transitional forms
As things stand I think the Intelligent Design crowd have a really strong case (athough I don't see Yaweh as a super nerdy biochemist!) because the minimal amount of mechanism needed for life to exist, is obviously quite large - even if we try to imagine a pre-DNA, pre-RNA biochemistry, and there doesn't seem to be any physical law that would create it.
An abrupt change resulting from a shuffling of exons can only produce something viable if the structure of those exons actually anticipated a future shuffle - which really means it must have been designed - like the air bag mechanism in a car is designed to come into use only in specific circumstances.
However if the physical world really is inside our mind, isn't it extremely likely that intelligence has been involved in the creation of the structure we encounter as 'reality'?
Again, I know there may be political reasons why you would not want to explore those ideas in public.