Namely, there is a "system-level" aspect to the problem that is hard to address by appealing to individual mutations that may or may not be advantageous.
Likely you've both heard of Richard Sternberg, the evolutionary biologist involved in the Smithsonian flap. I suspect his "process structuralist" school of biology might attempt to address this lacuna, but I can't find much more on it. I came across a talk of his(my sketchy notes are here) where he, like you, notes Darwinism's blindness to the organism as a whole.
Recovering a scientific concept of the organism seems incredibly important, especially since so much is now being dismissed as epiphenomena to be ignored without consequence.
Can't say I know of Sternberg. I did, however, also notice that E. Gilson wrote on this topic toward the end of his writing career. Several articles. The odd thing is that the mistakes that are made are philosophical and logical, not scientific. But, I regret to say, I haven't done any reading in this area. I shouldn't even be posting.
You have a colorful web log!