[Taxacom] Dark taxa: GenBank in a post-taxonomic world

[Richard Zander]

Okay, it's an analogy, Curtis. Take any finite set, and ergodic processes can analyze all possibilities eventually. But do we have a finite set of sequences, given that new sequences or modifications of old sequences are contributed daily by mutation AND we can never sample all of nature given extinction and limits to human endeavor. Phylogenetic analysis starts as an NP-hard problem, just with a finite data set, what do we do with a moving target? 

This is my usual devil's advocate stance, but given some attention to limitations, okay certainly some research is possible on just a raw big set of sequences. It should be grounded in expressed traits and environment, somehow, eventually, as Bob Mesibov says.

R.

 
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Richard H. Zander 
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
Web sites: http://www.mobot.org/plantscience/resbot/ and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
Sent: Wednesday, April 13, 2011 9:34 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Dark taxa: GenBank in a post-taxonomic world

On 2011-04-13 06:33, Richard Zander wrote:
> Ah, but are we sampling fragments of a book or fragments of an index to books? Are the sequences used for phylogenetic analysis more of a guide to the literature or of who borrowed the book than a sampling of the results of evolution?
>
> If sampling of results of evolution, then we must expect convergence from selectional pressure for some sequences. The only way to distinguish between neutral expressed traits (for a range of habitats) and traits under selective pressure is to analyze the sequences with respect to actual selection. If so, then this is not randomly generated data that tracks gene history but a combination of biased and unbiased data. Any analysis of this data alone is tongue-in-cheek.
>
> There is a psychological mechanism in literature called "als ob", or suspension of disbelief, substituting something known to be contrary to logic or observation with something delightful or satisfying.
Don't push the analogy too far. My point was that the curves might not represent a change in attitude, but rather the playing out of constant processes over a finite but not fully characterized set. It's an actual hypothesis: "The existing curves can be accounted for by constant processes."


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Curtis Clark