Taking an Axe to the Tree of Life?

Is the tree of life a hindrance to good science? That's the opinion of Dr. Ford Doolittle of Dalhousie University whose views are discussed here. Quoting from the link (in red):

"What’s the danger in believing that all beings of the same class, living and extinct, derive from a single figurative “tree” and its branches?

“It’s not true, that would be the main danger. It misleads us,” says Ford Doolittle, Dalhousie’s Canada Research Chair in Comparative Microbial Genomics."

He does not mean it is not true because he does not want to believe it but rather that it does not accord with the evidence. More from the link:

"Current research is finding a far more complex scenario than Darwin could have imagined, particularly in relation to bacteria, archaea and one-celled organisms. These simple life forms represent most of the earth’s biomass and diversity, not to mention the first two-thirds of the planet’s history. Many of their species swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers from multiple sources."

Horizontal gene transfer has been discussed at Telic Thoughts. Joy has weighed in on this repeatedly in comment sections.