[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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