[Taxacom] BioNames and others names

Roderic Page r.page at bio.gla.ac.uk
Mon Jun 3 07:23:49 CDT 2013


Care to elaborate what you mean by circumscription?

Once reason I have used GBIF and NCBI classifications in BioNames is that they are explicitly defined as sets. Higher taxa are sets of lower taxa, terminal taxa are either sets of specimens/observations (GBIF) or sequences (NCBI). This makes them computable. Furthermore with NCBI taxa we can compute probabilities that sequences belong to a taxon based on tools like BLAST. 

Most of the rest is simply too vague to make much sense of, unless for example, people have clearly defined membership of a taxon, such as listing material examined (if those specimens have some sort of identifier we can trace then we could look at the fate of taxa via the changes in the history of those specimens).

In general I avoid discussions of taxon concepts because it seems to me there's a mismatch between the amount of effort expended of trying to reason about them, versus the payoff for doing, you known, actual science.

Regards

Rod

On 3 Jun 2013, at 10:20, Paul Kirk wrote:

> I have recently argued that a 'return' to the circumscription method - in ICNafp 'space' - might be warranted in the largely molecular/'omics digital environment we now live in ... coupled with abandoning the type method.
> 
> Paul
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Paul van Rijckevorsel [dipteryx at freeler.nl]
> Sent: 03 June 2013 09:24
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] BioNames and others names
> 
> From: "Richard Pyle" <deepreef at bishopmuseum.org>
> Sent: Monday, June 03, 2013 10:03 AM
> 
>>> The broader taxonomic/biological community is very clear in what it
>>> regards as a taxon name: generic names, binomials / binomens, and
>>> trinomials / trinomens (plus some stuff at other ranks). As the Codes
>>> are geared towards providing just these, there should not have been
>>> all that much of a problem
> 
>> This is only true with a sufficiently vague definition of "taxon name".
>> Get any two random taxonomist together in a room and ask them to
>> define it precisely, and I'd bet you have better than even odds that
>> they will have some difference of opinion as to where to "draw the
>> line".  It may be subtle, but it will be there.
> 
>> The reason I am confident in asserting this, is that I have MANY times
>> been in the room with taxonomists, and in an effort to come up with
>> precise definitions, we always start out in full agreement, but as the
>> layers are peeled off towards ever greater precision, the subtle
>> differences start to reveal themselves.
> 
> ***
> You specified the"broader taxonomic/biological community ", and
> that means a dipterist talking about plants, and a plant taxonomist
> talking about flies, in which case there will be clarity. The problems
> will start only when the dipterist starts talking about flies ...
> 
> The real challenge for bioinformatics is to track circumscriptions
> (different circumscriptions indicated by the same name), but
> apparently nobody has given this any thought.
> 
> Paul
> Paul
> 
> 
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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

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