Ford has lots of things to say about the origin of introns, the tree of life, transpsosons, ENCODE, and the meaning of "function." Here's the bit about the tree of life.
Doolittle:I’m drifting off into philosophy in my old age. People have gotten quite heated over whether or not there is a tree of life. And really the question is what do you mean by the “tree of life?” And clearly—this is sort of Eugene Koonin’s position, which he calls the “forest of life”—there is a consensus signal.
If you make trees of all genes, it’s not completely random. Patterns emerge. And then you think, “Well duh, what the hell else do you expect?” Nobody would expect that lateral gene transfer wouldn’t respect geography or biochemistry or ecology or whatever.
There is no fact of the matter there: it’s just a question of what you want to believe. There is a consensus tree, there is a majority tree, there is some kind of central tendency of the data, but whether that central tendency reflects historical branching or instead reflects ecology is another question.
Imagine you started out with three separate populations of things, and they just started exchanging genes with each other, and population A changed genes with B more frequently than they do with C. Eventually, then, most of the genes that you might make a tree of would show A and B as being sister with each other and imply that there was a common A-B ancestor, but there need never have been a common A-B ancestor. It is possible that you could get quite a robust tree of life, but it doesn’t necessarily mean that the nodes in that tree correspond to ancestors in the history of life.
Gitschier: Now with all the many genome sequences available, what does Doolittle posit about the relationship between Bacteria, Archaea, and eukaryotes?
Doolittle: I think there are two groups of prokaryotes: Bacteria and Archaea. They are not well defined, and there are many genes that are derived from lateral gene transfer from bacteria into archaea, somewhat fewer in the other direction. So to really say that “this bug is an archaeon” when the majority of its genes are actually bacterial, what you really mean is that you are privileging the ribosomal RNA as the definer. And that is what people do, so I will let them do that.
And then what people would believe, and I guess what I would believe, is that the eukaryotic transcriptional/translational machinery—the informational machinery in the eukaryotic cell—arose within the Archaea, more recently than the Bacteria and the Archaea diverged from each other. That would be the standard view.
But we think that a tremendous number of genes have been exchanged back and forth between bacteria and between bacteria and archaea, and also between bacteria and eukaryotes after eukaryotes arose from within the Archaea—so much transfer that it is really rather arbitrary to define these lineages by virtue of their transcriptional and translational machinery any more. Had Woese started looking at glycolysis enzymes, rather than ribosomal RNA, we might not even be talking this way.
There is a nice paper coming out in Nature by Bill Martin [Heidelberg] and others claiming that the various different archael groups arose by the importation of different bacterial genes at different times in the past; so in a sense, the Archaea are the universal acceptors.
One of the poster children of the Archaea has been the halobacteria; they live in the salt and they are pink. They are aerobes—they have to be because they are sitting there on the top of water—and we’ve known for a very long time that the cytochromes and other aerobic things are bacterial in nature in those archaea. Martin and his colleagues show that they have accepted a bunch of bacterial genes for aerobic capacity. The nice thing about that view is that it makes eukaryotes just another group of Archaea that accepted a bunch of bacterial genes.
The photo is from Christina Behme at a workshop in Halifax in July 2009 on "Questioning the Tree of Life." That's me having dinner on the first evening with Ford Doolittle (left), John Dupré (standing), and Andrew Roger (right)