[Taxacom] Types, circumscriptions, and Science (hypotheses)

Paul Kirk P.Kirk at kew.org
Mon Jun 3 09:20:45 CDT 2013


I am suggestion a transition from where we are now - type based method for fixing the application of names - to what you refer to in the last paragraph of your reply. Specifically, that the publication of the name of a new taxon for organisms in the remit of the ICNafp (not ICZN ... which I still do not fully understand) can be Code compliant without a physical object or image as the type.

In haste again,

Paul
________________________________________
From: Chris Thompson [xelaalex at cox.net]
Sent: 03 June 2013 14:25
To: Paul Kirk; Roderic Page
Cc: taxacom at mailman.nhm.ku.edu
Subject: Types, circumscriptions, and Science (hypotheses)

Sorry, Paul, but I am not sure I fully understand you.

Yes, circumscriptions are CRITICAL as they do represent the scientific
hypotheses that various authors are using for a name. So are types in our
current system.

In practice, given that a correct identification is made, one can always say
that a circumscription contains the type (or types if synonyms exist) of the
name (or names) used for it.

The type is the anchor point for the circumscription of the name for which
it represents, etc., as it must always be included in any subsequent CORRECT
circumscription.

The only issue for workers is whether a subsequent circumscriptions are
broader and narrower than the original one. AND for the best Science as Rod
has indicated one should ALWAYS list / identify all the specimens one
includes in their published circumscriptions, etc.

So, I do believe BOTH the type concept and circumscription are necessary to
maintain and understand our current system of names, nomenclature and
taxonomy.

Yes, there is a future computer based world which would be more accountable.
That is, one generate an unique code for each circumscription published and
links/ties all the specimens examined to that code. No need for names.

Sincerely,

Chris



-----Original Message-----
From: Paul Kirk
Sent: Monday, June 03, 2013 8:50 AM
To: Roderic Page
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] BioNames and others names

The type method requires a physical object (or an image) to define the taxon
'we' call a species - environmental sampling can reveal the existence of
taxa where this requirement in impractical. Hence the suggestion that we
abandon (the strict requirement) of a type based system.

The circumscription is all that is associated with a taxon name usage
(specimens, sequences, previously cited name usages ... so Rod, I agree with
what you say below.

In haste,

Paul

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu
[taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
[r.page at bio.gla.ac.uk]
Sent: 03 June 2013 13:23
To: Paul Kirk
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] BioNames and others names

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

Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
Skype: rdmpage
Facebook: http://www.facebook.com/rdmpage
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ORCID id: http://orcid.org/0000-0002-7101-9767

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