The figure below is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American
Doolittle has a new paper out in PNAS (Doolittle and Bapteste, 2007). In that paper he restates his ideas about the web of life and emphasizes the fact that most of us are making unsubstantiated assumptions about the treelike structure of life. This is not a criticism of evolution—far from it—but as you might expect it has attracted the attention of anti-science writers such as Casey Luskin.
Doolittle and Bapteste (2007) are opposed to the bifurcating tree of life such as the one shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes]. They say,
The meaning, role in biology, and support in evidence of the universal "Tree of Life" (TOL) are currently in dispute. Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life's earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse.The argument is long and complex but the essence is that we need to abandon our assumption that the tree of life can be represented by: (i) a unique hierarchical pattern, (ii) the historical record can be best represented by a branching pattern, and (iii) natural selection is the primary cause of speciation.
We've pretty much abandoned the third point ...
As to this third possibility, modern evolutionists accept the uncoupling of selection from divergence, not only at the molecular level (the neutral theory) but in certain models for speciation, without seeing the Darwinian (or at least the neo-Darwinian) theory as refuted (21, 22). We have come to appreciate the plurality of evolutionary processes of lineage diversification. But most of us hold on to the first two tenets, that there is a real and universal natural hierarchy, and that descent with modification explains it, in much the same way as Darwin did. We may be process pluralists, but we remain pattern monists.This brings us to the title of their paper Pattern Pluralism and the Tree of Life Hypothesis. Doolittle and Bapsiste want us to not only be pluralists with respect to the mechanism of evolution but also with respect to the pattern of evolution.
Doolittle maintains that lateral gene transfer (LGT) is so common that it's impossible to construct a reliable bifurcating tree to represent the actual history of life. In other words, a Tree of Life is not only technically difficult but impossible in theory as well. This problem extends to all branches of the prokaryotic tree including the major divisions. Even the existence of two prokaryotic domains is questionable. Rooting the tree of life is out of the question.
I'm a big fan of Ford Doolittle—after all, he's an honorary Canadian! I certainly agree with him about the demise of the Three Domain Hypothesis. (Most people seem to have missed the death announcement.) I also agree with him that early evolution is more like a web of life than a tree of life. Nevertheless, I think he goes too far. Lateral gene transfer is an important, and common, phenomenon but I don't think it's quite as prevalent as he makes out. I still think that a bifurcating tree can be used to represent most species evolution after about 2.5 billion years ago.
Doolittle, W.F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. (USA) 104:2043-2049. [PubMed]