I disagree with these statements by the author:
1. The point of claims for Darwinian evolution is to explain the diversity of species. There's no claim that this won't be a complex process.
2. Saying that a scientific theory operates with "greater subtlety and complexity than previously thought" is not a polite way of saying that the theory is false. It might be a way of saying that the theory needs to be refined, or that there are other factors that should be taken into account.
I'm fine, though, with the author's belief that there is "a mind in or behind the universe".
Standard warning: The belief that "God exists if and only if biological evolution is false" is neither good science nor good theology. The author seems to want to follow this path.
The article does not use language that make it easy to discuss.
I wish that scientific articles would be better written, in this respect.
But, I took the article to be pointing at the changes that have happened
in biological life, to be much more complicated and subtle, than the
configuration of DNA. (That would be the basis of Neo-Darwinism.)
I also understood the article as pointing to the problem of trying to measure
"distance" between 2 genomes, as a sound metric of which was the most
closely associated with which other genomes, in a theoretical tree of life.
Although I would like to see better writing in scientific journals, I take this
article as admitting that the plain reading of the Neo-Darwinian model,
just doesn't get you a workable model of "evolution".
I posted the article, because this is the sort of sea change, that you will see
in scientific articles that deal specigically with epigenetics, and the role of
"culture" (aka, "nurture), in the behavior of a younger generation.