Although the author's opinion appears to be intelligent design:
"As a consequence, all purported evolutionary trees and sequences become highly suspect, including such icons as the whale and human series. For they are based on similarities of traits between species, and similarities are an unreliable indicator of common ancestry as implied by the trees’ typically low adjusted consistency indices. Instead, similarities appear to be the result of a designer reusing design modules in different species to meet common goals.
Ewert’s article represents only the first step in evaluating and developing his framework. Still, the significance of this research cannot be overstated. The dependency graph model explains why subsets of the biological data crudely fit a tree pattern and why so much of the data is incongruent. It also makes clear predictions on the results of future studies on the distribution across species of both physical traits and similarities in molecular data. Finally, it should lead to a robust and innovative research program based on the intelligent design framework. "
> These disappointing results have required evolutionists to devise several ad hoc mechanisms to explain the ubiquitous inconsistencies. Examples include lateral gene transfer (LGT), differential gene loss, and convergent evolution. Yet, the widescale appeal to LGT has been seriously questioned.
LGT is a synonym for HGT. I'm not sure why the article brings this up, since the model (DAG vs tree) and the mechanical implementation (LGT, etc.) are different things. The need for a mechanical explanation (defined by observation) does not change with a new model (also defined by observation). That said, new models can provide the right mental states to speed up discovery of correct mechanisms, so this work may have some significance, but it will be impossible to tell a priori.
"As a consequence, all purported evolutionary trees and sequences become highly suspect, including such icons as the whale and human series. For they are based on similarities of traits between species, and similarities are an unreliable indicator of common ancestry as implied by the trees’ typically low adjusted consistency indices. Instead, similarities appear to be the result of a designer reusing design modules in different species to meet common goals.
Ewert’s article represents only the first step in evaluating and developing his framework. Still, the significance of this research cannot be overstated. The dependency graph model explains why subsets of the biological data crudely fit a tree pattern and why so much of the data is incongruent. It also makes clear predictions on the results of future studies on the distribution across species of both physical traits and similarities in molecular data. Finally, it should lead to a robust and innovative research program based on the intelligent design framework. "