I spent this morning reading Jonathan Badger’s T. taxus blog (“Reflections on science, literature, and history by an American Badger”) and web site. Jonathan is a microbial genomicist at the J. Craig Venter Institute (JCVI) in La Jolla, California. Taxidea taxus is the systematic name for the American badger.
In May, 2007, Jonathan provoked a long and fascinating discussion of a paper by Liu and Ochman on the formation of the flagellar system. The consensus was that the paper was irretrievably flawed because of the incorrect use of and incorrect interpretation of BLAST results.
However, Jonathan made a surprising point that many disagreed with.
Personally, I’ve never been convinced that protein structure is of much use in inferring homology or the lack of it; systematists have been burned so many times by incorrectly assumed (non)homology of gross morphological traits in light of convergent and divergent evolution; why should morphology at the protein level be any different? The beauty of molecular systematics is that it’s freed us from having to deal with morphology at all.
Others in the discussion argued forcefully and convincingly that folds are more highly conserved than sequence, and that similar folds provide strong evidence for homology (descent from a common ancestor). I learned a lot from this discussion that will be useful to me.
As I continued my reading, I discovered from Jonathan’s publications page that Jonathan was a coauther on the paper describing the genome sequence of Synechococcus CC9311. The first author was Brian Palenik, a friend of mine who was doing his postdoc in Bob Haselkorn’s lab at the same time I was doing mine. Brian is a much better scientist than I am and deserves his success.
Jonathan’s review of J. Craig Venter’s book, A Life Decoded: My Genome: My Life, piqued my interest, so now I will have to track down a copy.
This was time well spent for me, and I derived great enjoyment in reading Jonathan’s blog. Jonathan hasn’t posted since December, 2007; I am looking forward to new contributions.
