The debate offered a great illustration of the intellectual vacuity that characterises creationism (aka intelligent design). Paul Nelson offers up an article by Doolittle and Bapteste as proof that Darwinism is unravelling. I suspect he hopes no one will read past the abstract to discover the reasonable debate scientists are having about the universality of a single tree of life. He certainly doesn’t want you to notice that the entire article is couched within evolutionary theory and not once does it claim that Darwinism has been falsified.
Here’s the hypothesis that Doolittle and Bapteste are evaluating:
“that there should be a universal TOL [tree of life], dichotomously branching all of the way down to a single root.” p2045
They then establish that gene transfer often occurs between lineages, particularly among prokaryotes, and consequently this universal tree of life does not exist. Certainly this complicates the construction of molecular trees and shows the importance for pluralism of mechanism in biology. But they write much more about the overall significance of this work.
“To be sure, much of evolution has been tree-like and is captured in hierarchical classifications.” p2048
“…it would be perverse to claim that Darwin’s TOL hypothesis has been falsified for animals (the taxon to which he primarily addressed himself) or that it is not an appropriate model for many taxa at many levels of analysis” p2048
And the crucial quote in this context:
“Holding onto this ladder of pattern […] should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import.” p2048