[tdwg-content] Taxon and Name

[Kevin Richards]

My concern is that all this hard work and great discussion is going to end up in the mailing list archives!
What we really need is someone to maintain a wiki (or something) that summarises the discussions had here - I know no-one is keen to do this really, but I wonder if this might be something TDWG needs to invest in ???

Kevin


-----Original Message-----
From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Nico Franz
Sent: Wednesday, 3 November 2010 1:09 p.m.
To: Richard Pyle
Cc: tdwg-content at lists.tdwg.org
Subject: Re: [tdwg-content] Taxon and Name

Thanks, Rich:

    This might quickly turn into a test of endurance for all involved.
Nevertheless, I think a couple of things a worth taking up specifically,
as done below.

On 11/2/2010 2:36 PM, Richard Pyle wrote:
>>      I just think that there's this other taxonomy out there
>> in the future, where we taxonomists think and act more like
>> we care for others (incl. computers) to understand our
>> classifications, where the parts come from, what's congruent
>> and what has changed, how to precisely reconcile with
>> previous views, etc. And for that future to become more real,
>> perhaps a high threshold for identifying new concepts (in the
>> sense of authoring anew [versus citing], not necessarily a
>> new meaning) is needed.
> Yes, I can see that (and we've had this conversation before).  But first we
> need to come up with a common understanding of what a "taxon concept" is,
> and how to articulate it with some precision.  One way to define a concept
> is as a clade; that is, something like "all descendents of the most recent
> common ancestor of these two organisms".  This is one of the ways that
> Phylocode establishes the definition of a clade.  It's not perfect (nothing
> is ever perfect), because with such definitions you will often have
> organisms that belong to two different taxon concepts simultaneously
> (hybridization, introgression, etc.) But that's not intrinsically a bad
> thing, as long as it's understood and accomodated.  The real problem, of
> course, is that we're still in our relative infancy in our ability to
> discirn whether or not a paricular organism is, or is not, a descendant of
> the most recent common ancestor of two other organisms.  Also, there is the
> problem of mapping to centuries of legacy information.
Disagree, on the following grounds. The basic model of reference in play
is (crudely):  uses of human language <==>  some sort of
mapping/reference <==>  entities in nature. This model allows for the
mapping of language to nature to be spot on or way off, which is
critical for proper modeling of taxonomic practice through time. Using
precise terminology, a taxonomic concept could never be a clade, that
would be nature (on the right side of the equation), but a best a
perceived clade, according to a particular perspective. In addition,
there can be valid concepts that are not clades (in the
Hennigian/phylogenetic sense), and not even intended to be clades, for
example in groups with lots of horizontal gene transfer or at and below
the species level. In short, concepts are meant to variously refer to
clades or other reference-worthy groups in nature, but they are not
fruitfully equated with clades themselves.

> So I think the most practical way to define the cirumscription boundaries of
> a taxon cocnept at this point in history (and the one that is most likely to
> leverage historical content) is via type specimens (proxied by heterotypic
> synonyms).  It's much fuzzier and less precise than the mechanism described
> in the previous paragraph, but far more practical.
>
> What you're advocating is, I think, represents a reasonable path forward
> towards more robustly defined, and objectively articulated, taxon cocnepts.
>
Many historically published published make use of a combination of
ostensive components (things being pointed to; type specimens, type
species, other members) and intensional components (properties being
referenced; diagnostic features, synapomorphies, metabolic functions,
etc.). Each component has strengths and weaknesses, but it's hard for me
to image that we can do a passable representation job focusing mainly on
one and not the other. I'll leave it at that.
>>      In other contexts, possibly including the representation
>> of identification events in museums, the bar for calling
>> something a concept need not be that high (informal names,
>> names outside of publications, local checklists, etc.). In
>> any case, it's a matter of where one puts the emphasis, and
>> hopefully I've pointed out where I would set it and why.
> I think the key distinction that should be made is the distinction between a
> "defined" concept, and an "implied" concept.  Almost every Taxon Name Usage
> (sensu lato) instance carries with it an implied taxon concept, but as I
> said, the vast, vast majority of those (especially if you include Museum
> specimen identifications) are extremely anemic on deails for understanding
> the boundaries of the implied taxon concept, and therefore it's difficult or
> impossible to reliably map the congurnecy (or not) with other implied or
> defined taxon concepts.  On the other hand, what we should be really
> striving for is recognition of taxon concepts that are well "defined". These
> are also rooted in TNU's, but carry with them robust information for
> inferring the boundaries of the circumscribed concept (full synonymy, robust
> mateial examined, robust descriptions of morphological and/or genetic
> characters, etc.)  I think this distinction is important to make ("defined",
> vs. merely "implied"), because what we'd ultimately like to do is find a way
> to map implied concepts to well-defined concepts.
Agree.
> Getting back to DwC, one area of direct relevance to this is the
> Identification class.
>
> Most datasets out there simply slap a taxon name to a specimen or
> observation.  Some of them go so far as to say who identified it to that
> name, and when.  But most do not take the final step and anchor the
> identification to a particular well-defined concept (or, indeed, any TNU).
> All specimen identifications represent an action that places the specimen
> within the boundaries of a circumscribed taxon cocnept (whether the person
> making the identification realizes this or not).  What we should be striving
> for is a mechanim to tie specimen identifications to particular TNUs that
> represent reasonably well-defined taxon cocnepts.  The statement should be:
>
> "On this date, this person asserted that this specimen falls within the
> taxon concept circumscription of Aus bus (L.) sec. Smith 1990".
>
Yes.
> If an Identification is a tuple of a Taxon instance (in the DWC sense) and
> an Occurrence instance (or an Individual instance, if that class becomes
> established), with associated metadata, then I think DwC is already primed
> to make the quoted statement above (i.e., to anchor Identifications to
> particular usage instances, because "taxonID" can represent a specific usage
> instance -- assuming the right attributes ae included).  Retsated in DwC
> terms, this would be:
>
> "On [dwc:dateIdentified], [dwc:identifiedBy] asserted that
> [dwc:occurenceID|dwc:individualID] falls within the taxon concept
> circumscription of [taxonID], which represents a taxon name usage for
> [dwc:scientificName] according to [dwc:nameAccordingToID]"
>
> In the future, if Peter DeVries is successful with his ambitions, then this
> could be simplied to:
>
> "On [dwc:dateIdentified], [dwc:identifiedBy] asserted that
> [dwc:occurenceID|dwc:individualID] falls within the taxon concept
> circumscription of [taxonID], which represents [dwc:taxonConceptID]"
>
> Or maybe even:
>
> "On [dwc:dateIdentified], [dwc:identifiedBy] asserted that
> [dwc:occurenceID|dwc:individualID] falls within the taxon concept
> circumscription of [taxonConceptID]"
>
> In the latter two examples, taxonConceptID would represent an array or set
> of TNUs with congruent taxon concept definitions.
>
> I'm still not 100% sure how best to use dwc:identificationReferences, other
> than perhaps as a method for aggregating multiple TNUs (assumed to refer to
> congruent, or at least overlapping concept circumscriptions), which were
> used by someone when making an identification.
>
> Aloha,
> Rich
>

Cheers,

Nico


Nico M. Franz
Department of Biology
University of Puerto Rico
Call Box 9000
Mayagüez, PR 00681-9000

Phone: (787) 832-4040, ext. 3005
Fax: (787) 834-3673
E-mail: nico.franz at upr.edu
Website: http://academic.uprm.edu/~franz/
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