Wednesday, March 08, 2006

Generic hostility, Part 4

Both of the previous messages were sent around to everyone who had gotten the first one, and some observers got the impression that Randy and I had our hate on. Actually, as this response by Randy shows, we were just engaged in a frank discussion of ideas.


Subject: RE: Piss & Vinegar

BTW, I'm not copying this to everyone because I don't want to clutter their inbox.

I wasn't attacking the validity of the method to provide new, important phylogenetic data at high resolution. To this extent, I think it is really exciting and has great potential. Rightly or wrongly, your email came off as a statement about taxonomy, not phylogeny. I was objecting to the statement that "we might finally have an objective basis for recognizing genera". If you are going to make this claim, then I think you need to address the body of systematic literature that has argued over this for the past 50-100 years as well as have good evidence that the method reveals some emergent property at a particular level.

My personal opinion (and one reflected in the phylogenetic nomenclature literature) is that nomenclature and taxonomy should reflect relationship (no problem with the new method), and that it should be consistent through the tree of life, because life is monophyletic, so the same rules apply (here we have a problem).

But if it works for vertebrates, if it gives us something beyond
morphology to help figure out how fossil taxa are related, then
I say it's a good thing. How could it possibly be any worse than
our current ideas of what constitutes a genus, which are based's right, NOTHING.

Well, I agree with your first sentence (phylogeny). But regarding the second sentence, why should we be looking for what constitutes a "genus" if there's no evidence that such a rank actually exists in the hierarchy of life (taxonomy)! Actually, I would say traditionally genera are based on some criteria, but these criteria are unique to each clade (and the workers working on that clade). Using this method to evaluate vertebrates is no different, it is unique to Vertebrata. When doing taxonomy (not phylogeny), I want something that has continuity across clades. Why should I pick osteocalcin markers as my "genus" separator over another character? Why don't I just pick the 1028 base pair of the cytB gene, or something else? As long as it gives me the resolution I want, I can pick anything; hence why genera will always be to some extent subjective.

No, it hasn't been tested in every genus of everything that ever
lived. The method was just invented last year.

Than how can one claim that it is genus-specific if not very many things have been tested! Again, I'm not denying its value as a phylogenetic tool and possible major source of info in the fossil record.

OK, and now for a constructive question: What exactly is the method looking at? Are they looking at the sequence of amino acids, or the folding of the protein? I would expect the former to be easier to get at than the latter in the fossil record.



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