I have to agree with his assessment. Here is the article in question, which is, if somewhat sensationalized, fairly tame. It focuses on the concept of Horizontal Gene Transfer and the idea that Darwin's original "Tree of Life" idea does not fit modern evolutionary thought:
As more and more genes were sequenced, it became clear that the patterns of relatedness could only be explained if bacteria and archaea were routinely swapping genetic material with other species - often across huge taxonomic distances - in a process called horizontal gene transfer (HGT).
A bit later:
As it became clear that HGT was a major factor, biologists started to realise the implications for the tree concept. As early as 1993, some were proposing that for bacteria and archaea the tree of life was more like a web. In 1999, Doolittle made the provocative claim that "the history of life cannot properly be represented as a tree" (Science, vol 284, p 2124). "The tree of life is not something that exists in nature, it's a way that humans classify nature," he says.
Thus began the final battle over the tree. Many researchers stuck resolutely to their guns, creating ever more sophisticated computer programs to cut through the noise and recover the One True Tree. Others argued just as forcefully that the quest was quixotic and should be abandoned.
Of course, this discussion in no way impugns evolutionary theory. It is roughly analogous to the revelation that evolution does not always proceed slowly beneficial gene by beneficial gene, but sometimes through developmental leaps by way of hox genes. Hence the study of evo-devo.
It has become clear that evolution proceeds much more in the form of a bush rather than a tree and that is how most palaeontologists view things. The problem is that this is the cover of the newsstand copy and people that look at it will think that Darwin was wrong, therefore evolution was wrong. This is a colossal blunder. A statement should be released immediately explaining what the cover means, not that anybody will read it. The creationists will have a field day.