Literature

Darwin's one illustration in "On the Origin of Species" was of a branching "Tree of Life" (TOL). This has entered the mindset of evolutionary biologists and there has been a very real danger of confusing concept with reality. The authors of a discussion paper suggest that this concept has acted like a ladder to climb over an obstacle. "The TOL was thus the ladder that helped the community to climb the wall of acceptance and understanding of evolutionary process. But now that we have climbed it, we do not need this ladder anymore." Not only do we not need it, we are better off without it! "Holding onto this ladder of pattern is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred."
How can this be? Do the authors not know how important the TOL concept is to evolutionary biologists? They do. But they also know that it cannot be justified using empirical data. "The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree."
But some argue that the nested hierarchy branching pattern is a proof of Darwinism. These people have something to learn from the authors, who write: "The notion that a tree pattern is the product of induction, obvious to any intelligent observer, is belied by most of the early history of systematics, during which quite different schemes seemed fully defensible." Also, that "hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so." For more on this, go here.
None of this, in the authors view, is to undermine evolutionary theory. The TOL concept "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 wilful misunderstanding of its import." If this is a broadside against ID, it is an unfortunate choice of words. ID advocates are fond of the phrase "follow the evidence wherever it leads" and we applaud the authors for their analysis of the TOL concept. However, we want to encourage discussion of the import of this research and reserve the right to come to a different judgment. To describe this as "wilful misunderstanding" is actually opting out of scientific discourse.

Pattern pluralism and the Tree of Life hypothesis
W. Ford Doolittle and Eric Bapteste
Proc. Natl. Acad. Sci. USA, Early Edition 29 Jan 2007 | doi 10.1073/pnas.0610699104

Abstract: Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

See also:
Cranston, M., Taking an axe to the Tree of Life, Dalhousie News, July 11 2007.