The article seems to make two main points: 1) that natural selection is limited in what it can select for, because it can only select from phenotypes that are available and 2) that traits can become widespread (or ubiquitous) in a population even when they themselves are not specifically selected for.
Neither point is wrong, but then neither point is new, surprising, original or incompatible with Darwinism.
Yah, it doesn’t seem to me to be anything but a warning against overreaching when you try to logically reverse Darwinian natural selection to get to an answer of “why” a trait exists in a species.
This is what Michael Behe’s latest book, The Edge of Evolution was trying to explain.
In his observation, no new variation develops to allow natural selection to go anywhere other than within its limits. I think the author is trying to say this -— natural selection is a conservative force, not because it cannot drive novelty but because it doesn’t have the resources on which to act.
It would have been very easy for Natural selection to act as the driving force of evolution if only variations exist to drive it. The weakness of Darwinism is not natural selection but the lack of diversity in the genome to drive it anywhere.