[tdwg-content] Dlarification of taxon concept uses in biologicalpapers (from Rich's statement)

[Richard Pyle]

Hi Nicolas -

I like your suggestion!  I've always tried to document whose concepts I am
using in a paper; but I think going forward I will be more explicit about it
in the M&M, as you suggest.

Aloha,
Rich

> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org 
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of 
> Bailly, Nicolas (WorldFish)
> Sent: Sunday, October 17, 2010 4:23 PM
> To: tdwg-content at lists.tdwg.org; tdwg-bioblitz at googlegroups.com
> Subject: [tdwg-content] Dlarification of taxon concept uses 
> in biologicalpapers (from Rich's statement)
> 
> Dear All,
> 
> Again I support Rich's analysis:
> 
> " Yes, exactly!  The *SINGLE* most important thing we can do 
> to reduce the taxonomic ambiguity in our databases is to get 
> people in the habit of recording what field 
> guide/monograph/key/whatever was used in making the 
> determination of the specimen's taxonomic identity.  Even if 
> an expert pulled the identification out of his/her head, s/he 
> should document the best published representation of the 
> taxon concept that matches what the identifier (person, not 
> GUID) had in mind when making the determination."
> 
> 
> I would go even further.
> 
> As taxa are only hypotheses, their use must be clarified in 
> Material and Methods in any publication (I mean in biology, 
> ecology and others in
> general): a number of citations must be made:
> - the one that establishes the circumscription used in the 
> publication.
> - the one with identification key or diagnostic character 
> used to identify specimens or individuals in the work.
> - the one that gives the phylogeny.
> - the one that gives the classification (as far as we 
> recognized that the classification is a simplification of the 
> phylogeny, but it is not the point of discussion here).
> - and any other citations on topics, e.g., distribution, used 
> in the paper.
> 
> Hopefully, a taxonomic revision encompasses all of them, but 
> when the last revision is old, then additional citations must be made.
> 
> In chemical papers for instance, there is always the 
> description of methods, sometimes even including the brand of 
> the chemicals ... so why not precising concepts in biological 
> publications.
> 
> If these citations were done properly, there would be no 
> problem to use impact factors as well for taxonomy, and 
> databases today would be terrific. Doing the work back looks 
> overwhelming but CLEMAM on European marine Mollusks is an 
> example it is doable, although it does include few 
> publications outside taxonomy.
> 
> I feel that the taxonomic community should have been more 
> aggressive to journal editors and other colleagues to move 
> that way, a role for systematics societies all around the 
> world I suggest.
> 
> BW
> Nicolas.
> 
> 
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
> Sent: Monday 18 October 2010 04:18
> To: 'Peter DeVries'
> Cc: tdwg-content at lists.tdwg.org; tdwg-bioblitz at googlegroups.com
> Subject: Re: [tdwg-content] What is an Occurrence? [what 
> about the "token"]
> 
> > This was a bit of a "straw man" but I think what we would 
> both agree 
> > that annotating the identification to the "concept"
> > "as described by the key" would more accurately represent the 
> > assertion that was made. It is as if there is pressure to make 
> > documenting the identification process more "code compliant" than 
> > making it accurately reflect what happened.
> 
> Yes, exactly!  The *SINGLE* most important thing we can do to 
> reduce the taxonomic ambiguity in our databases is to get 
> people in the habit of recording what field 
> guide/monograph/key/whatever was used in making the 
> determination of the specimen's taxonomic identity.  Even if 
> an expert pulled the identification out of his/her head, s/he 
> should document the best published representation of the 
> taxon concept that matches what the identifier (person, not 
> GUID) had in mind when making the determination.
> 
> Jim Croft once told me that he tried to get his users to do 
> this many years ago, but he simply couldn't persuade them to 
> do this. (I think it was Jim who told me this.)
> 
> There's such a huge difference in informatic value between 
> "This specimen is Aus bus", vs. "This specimen falls within 
> the species concept of Aus bus as circumscribed by Jones, 
> 1950".  The latter sounds like a lot of extra work, but in 
> fact, all you need is one field labelled "sec", or "in the 
> sense of", with a drop-down list of publications that treated 
> "Aus bus".  For most field surveys & collections, you can 
> probably find a single default reference that would apply in 
> 90% of the cases, and then tag only the remaining 10% with a 
> different reference, as needed.
> 
> The biggest problem I have with dwc:identificationReferences 
> (http://rs.tdwg.org/dwc/terms/index.htm#identificationReferenc
> es), is that it allows many.  What to do, then, if two listed 
> references present two different concept circumscriptions 
> (e.g., one sensu lato, and one sensu stricto)?  Always fall 
> to the strictest sense?
> 
> Personally, I think a "best practices" approach to this term 
> would be "list only the best Reference, unless it's 
> absolutely necessary to indicate more than one reference, 
> from which a composite concept can be established".
> 
> > In my experience with my bugs and and some of the mammals, the 
> > original descriptions and subsequent revisions are not as 
> informative 
> > as some in the community portray them. They often do not 
> serve as good 
> > guides as to what specimens are instances of that concept and what 
> > specimens are not.
> 
> ....so what, then, are the guides following?  Or are they 
> presenting original taxonomy within the guide itself?  If you 
> can anchor the identification to the field guide, that's 90% 
> of the battle right there.
> Later we can map the field guide to a mopnograph, or some 
> other source for the full concept definition.
> 
> > Also, that perhaps the Code should be revised to fit the biology, 
> > rather than trying to get the biology and related databases 
> to fit the 
> > Code.
> 
> I don't follow.  Can you give me an example of what you mean?
> 
> Are you saying that the Code(s) should make rules for 
> defining taxon concepts, rather than just rules for 
> establishing names?  I hope not!
> But if
> so, then you might want to check out the Phylocode, which 
> basically does exactly that (to the extent that a clade is 
> also a form of defining a taxon cocnept).
> 
> Aloha,
> Rich
> 
> 
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