[tdwg-content] Taxon and Name
Richard Pyle
deepreef at bishopmuseum.org
Wed Nov 3 03:36:04 CET 2010
That task falls upon my shoulders, I think (as convener of the TDWG TNC
working group). I'm actually working on documentation for GNUB now, and I
hope to summarize a bunch of these ideas in there (at least the ones I'm
professing). But in my copious free time, I'll review the taxon-related
threads on this list and try to summarize the alternate perspectives, then
format something on the TDWG TNC wiki.
For now, though, I thing email technology is still the best way to engage
the broadest set of perspectives.
Rich
> -----Original Message-----
> From: Kevin Richards [mailto:RichardsK at landcareresearch.co.nz]
> Sent: Tuesday, November 02, 2010 3:35 PM
> To: Nico Franz; Richard Pyle
> Cc: tdwg-content at lists.tdwg.org
> Subject: RE: [tdwg-content] Taxon and Name
>
> 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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