A long time ago, a young graduate student wandered into the festering cesspool of creationists and evolutionists known as talk.origins and offered to write a FAQ (Frequently Asked Questions page) on whether or not macroevolution and common descent were supported by evidence. I had previously published a philosophical treatment of Macroevolution for that site’s Archive, but this guy, Douglas Theobald, being a scientist, had to attend to actual evidence, and so he wrote the excellent “29 Evidences for Macroevolution” FAQ. It’s a pretty solid piece of work.
Now a biochemist at Brandeis University, Doug has published a full test of the hypothesis of Universal Common Ancestry (UCA) in no less than Nature. And I get thanked in the Acknowledgements. A philosopher has arrived when he gets mentioned in Nature, but for a scientist to be published there is the Holy Grail. I am glad to have had a (very) minor role in this. Nick Matzke, who also commented on the draft, has a roundup here at Panda’s Thumb.
It might be thought that the target here is creationism, and so it is taken by at least one “baraminologist” (a made-up term for creationist “taxonomy”), but actually it is a test of competing hypotheses in actual science, such as the claim made a lot lately, for example by Carl Woese and Mark Ragan among others, that the treelike structure of evolution is broken by lateral genetic transfer. I’m not competent to evaluate his method, although Mike Steel and David Penny certainly are, but I am pleased to see that he analysed his data sets without presuming genealogical relationships are implied by similarity of genetic sequences. Why?
This is a matter of epistemology. If we presume that we already know that similarity implies genealogical relationship, then we will require some foundation for that claim, and if we simply assert that it is part of evolutionary theory, then we really will have done what the creationists accuse us of, and circularly defined our evidence. Doug’s FAQ is an attempt to show the open minded this is not a matter of defining the solution into existence. This paper aims to show that UCA is attested by the data without circular arguments. I mention this because in Elliot Sober’s recent book he reprises his “modus Darwin” claim that similarity implies common ancestry; which even on orthodox evolutionary theory it does not (due to convergence). Homology implies common ancestry, not mere similarity.
Molecular sequences are especially problematic with respect to convergence because the number of states a sequence can take are much lower than the number of, say, protein states, cell states, and especially developmental states, so convergent similarity is harder to distinguish from homological similarity just on sequence alone. Terms like orthology and paralogy indicate the special difficulties in molecular sequences, let alone the host of other terms invented just for that field. You may be able to identify, say, a bone in a skull as being homologous between a bird and a human because of when and how it develops; this is not possible in molecular sequencing.
So I greatly appreciate that Doug has taken a “neutral” stance here. I think I like his likelihoodist approach, but I’m not au fait with that stuff enough to know. I do however think that he has taken the right epistemic approach.
The nice thing is that the treelikeness of phylogeny is not swamped by lateral transfer in his results. Reticulation (or networking) in the trees is not enough to show that there was no tree. In fact I think this is going to be the case almost inevitably, because if lateral transfer did swamp the trees, we would still see treelike structure at different levels, since a tree is simply a representation of data structure – if you can differentiate taxa in the data, then you automatically have a tree (and a set of nested Venn Diagrams, and a list of indented taxon names, etc.). A data set that showed almost no structure would not have a treelike representation. Moreover, in order to identify actual lateral transfer, you need first to have a tree to compare it to.
But there are presumably statistical tests that can be done with minimal assumptions, and this looks like what Doug has tried to do, to avoid begging the question. It’s a good paper. In particular it is a useful tonic to the stream of scientific claims that the tree is actually unrooted, or that lateral transfer has killed off tree thinking, etc. Darwin remains triumphal…