Wednesday, March 08, 2006

Generic hostility, Part 5

My turn again.

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Subject: RE: Piss and piss

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

Fair enough. Do you mind if I post it all on the blog? :-) Seriously.

Also, thanks for taking my rant with the large grain of salt that it called for.

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.

Okay, so maybe that was a bit sweeping. But wouldn't it be interesting if there was even a single category of data that even for some vertebrates picked out what we normally label genera? I went a bit overboard last time. I don't think genera are based on nothing. At least with fossil vertebrates, I think genera are more solid than species. People have argued for decades about how many species of Apatosaurus and Diplodocus there are, but no-one argues about whether a particular specimen belongs to Apatosaurus or Diplodocus. For what it's worth, fossil genera seem to correlate with recognizable chunks of morphospace, better than species anyway. I've talked to some mammalian paleontologists about this and gotten a similar response.

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).

Sorry, I'm not on board. I don't see why a method that is useful for identifying monophyletic groups in one clade shouldn't be used just because it doesn't pick them up in all clades. mtDNA is pretty good at picking out low-level vertebrate clades, but eubacteria don't have mitochondria. That doesn't mean that we can't use mtDNA where it's useful. Similarly, if these proteins give us monophyletic supraspecific groups in bony vertebrates, I don't see why we shouldn't use them. And if the things they pick out correspond to our usual notions of genera, I don't see why we can't call them that. I know, I know, we should all renounce ranks of all kinds. Believe me, I know those arguments forward and backward. But I don't think genera are going away, at least not anytime soon, and I'd rather have objectively delineated genera, even in one little corner of the tree of life, than nothing.

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.

Ha. Now you're onto something. Yeah, we could choose just about anything to delineate genera, if we thought that was a worthwhile exercise. Here's my position:

(1) Many workers think that there is "something to" osteologically-identified genera of vertebrates. They seem to cohere better than either species or suprageneric taxa.
(2) What if we're not just whistling Dixie; what if there is a sound genetic and/or developmental basis to the chunks of morphospace we designate as genera?
(3) And what if osteocalcin picks out those chunks?

If you disagree with any link of the chain, you're not going to like what I'm saying. I can live with that. It is just a chain of not-rigorously-supported inferences and what ifs. But I am excited about the potential. And sure, we might be kidding ourselves about genera. For half a century, people peered through telescopes and drew detailed maps of nonexistent Martian canals, too. And osteocalcin might not work as advertised, or maybe it only appears to work because it ticks over every 2 million years and just by chance all of the genera on which it's been tested so far are more than 2 million years old. There are a jillion things that could derail this. But IF it works, it will be interesting, and useful, and cool.

Then how can one claim that it is genus-specific if not very many things have been tested!

Grrr. Seriously, all that anyone has said is that SO FAR it APPEARS to pick out generic differences in things THAT HAVE BEEN TESTED. That's at least three conditionals. What more do you want? Is there some better way to say it?

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.

Beats me. Darren forgot to include the relevant papers in his bibliography, and I haven't bothered to look them up yet. But Google is just a click away...here we go.

Nielsen-Marsh et al. 2002. Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Geology 30(12):1099-1102.

Nielsen-Marsh et al. 2005. Osteocalcin protein sequences of Neanderthals and modern primates. PNAS 102(12):4409-4413.

Okay, those are just the refs. I will attach the papers, and read them myself, and get back to you on how this works. And you get back to me with a further smackdown, and I will exercise more restraint in my future responses.

All the best,

Matt

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