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

[Roderic Page]

Dear Curtis,

> 
> It seems to be that any finite set with exemplars in various states of 
> identifiability will produce the same sort of curves as the ones you've 
> characterized.


Nice analogy, although I wonder if it's not so much that the books are fragmentary, but that they are written in a language that we don't understand, apart from a few phrases. It's not that the books are fragmentary (your analogy made me think of insect draws where the specimens had decayed, leaving just a few bits and pieces), it's that we can't read them.

It might be fun to try and play with your model in more detail. I guess we're assuming that we've preferentially sequenced known, identifiable taxa, and that the rate of new species description is not keeping pace with sequencing, hence the curves. I'm wondering whether it would be worth looking at when the named taxa where described, because the model would need to include the addition of new books to the pile. 

Regards

Rod

On 13 Apr 2011, at 02:16, Curtis Clark wrote:

> On 2011-04-12 06:53, Roderic Page wrote:
>> This post may be of interest to TAXACOM readers. "Dark taxa: GenBank in a post-taxonomic world"
>> 
>> http://iphylo.blogspot.com/2011/04/dark-taxa-genbank-in-post-taxonomic.html
>> 
> 
> Apologies if a commenter mentioned this and I missed it: I think what 
> you need is a null model.
> 
> Imagine a finite set of books, and a web site for cataloging them based 
> on selected passages. Early in the history of the site, contributors 
> will be working with intact books, that they can identify to title. If 
> /Dracula/ has already been investigated and the sequence between the 
> primers of "in example" and "spade of the sexton" has already been 
> characterized, I'm unlikely to contribute the same sequence from a 
> different physical book. But there are still lots of books, and I can 
> sequence another.
> 
> After time, the number of easily available intact books that have not 
> been sequenced starts to diminish. But there are book fragments, which 
> can also be sequenced. Let's say I find a fragment that I can only 
> characterize as "British English turn of the 20th C 67534567" and 
> develop sequences. A search might suggest that some of them are very 
> similar to the corresponding sequences in /Dracula/, but if I assume 
> that my fragment is part of that book, either I fail to submit the 
> sequence, and take the chance that a novel book (pun serendipitous) 
> would go uncharacterized, or else submit a new sequence for an existing 
> book, which might imply variation that doesn't exist.
> 
> Much better to submit it under its fragment identifier, and let others 
> with greater knowledge in the future sort it out.Over time, more of the 
> submitted sequences will be from book fragments that can't be easily 
> identified.
> 
> It seems to be that any finite set with exemplars in various states of 
> identifiability will produce the same sort of curves as the ones you've 
> characterized.
> 
> -- 
> --
> Curtis Clark
> Cal Poly Pomona
> 
> 
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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page at bio.gla.ac.uk
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