[Taxacom] taxonomic names databases

Richard Pyle deepreef at bishopmuseum.org
Wed Sep 7 13:45:39 CDT 2016


As someone who manages a database that represents the reality of current and historical taxon name usages and the links among them (as Paul alludes to below), I think there are two general classes of stakeholders in the realm of organized taxonomic information:  the producers, and the consumers.  Obviously, producers are also consumers, but there are many consumers who are not producers, so I define these two general classes accordingly.

Most of us on Taxacom are in the first of these two classes (Producer-Consumers).  We, of course, are very sensitive to the dynamic (and sometimes chaotic) nature of synonymies and classifications (and, to a lesser extent, nomenclature); and as such we want the kinds of databases Paul talks about, which capture this dynamic (and sometimes chaotic) nature, particularly with cross-links to primary literature.

There are far, far more people in the second of these two general classes (Consumers who are not also Producers).  These include most of the rest of biology, the scientific community, and the public at large.  For the most part, they really only care about a single consensus classification and synonymy so they can get the "best guess" approximation for the context of some particular organism.

Aggregators exists SPECIFICALLY to accommodate "one stop shopping" through providing an "All-Encompassing Portal", so it's a bit silly to represent this as some sort of criticism.  I see many of them as representing a window onto the taxonomic landscape for the people I have defined above as belonging to the "Consumer" class.  Personally, I think that's wonderful!  Different aggregators provide varying levels of tools that also happen to be useful (sometimes extremely useful) to us Producers, and that's great.  But I don't see the logic in criticizing the aggregators for not tailoring their activities towards those of us in the vast minority of data consumers.

The taxonomic utopia that many of us have been working towards will establish a layered data infrastructure, where the raw facts (aforementioned dynamic and chaotic nature of actual boots-on-the-ground taxonomy needed by the Producers) underpin layers of abstracted, synthesized, aggregated and (MOST importantly) interlinked summaries that serve the needs of the majority of consumers.  

Now... cue the whines and complaints for why this doesn't exist yet after decades of effort, and then after that cue the counter-whines and complaints of how there has only been scattered/sporadic funding at the scale needed to create such infrastructures.  And then follow that up with a healthy dose of whines and complaints about why more money needs to go to actual taxonomy, rather than databases about taxonomy, so we can continue our PERPETUAL cycle of whining and complaining in our field while the physicists and astronomers continue to get their multi-billion-dollar colliders, satellites and telescopes.

Ooof.... that turned into a bit of a rant, didn't it?  Not my original intention.

So, speaking of funding, I have a big grant proposal due on Friday, so ta...

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences | Associate Zoologist in Ichthyology | Dive Safety Officer
Department of Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html




> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Paul van Rijckevorsel
> Sent: Tuesday, September 6, 2016 10:00 PM
> To: taxacom
> Subject: Re: [Taxacom] taxonomic names databases
> 
> Leaving aside the question of how desirable such a One True Tree, enforced by a
> Superstate, or some other Higher Authority, may or may not be, this is not the
> reality we have now.
> 
> What we have now is a wealth of information, organized around names
> established by tradition, and governed by Codes of Nomenclature. What seems
> called for, in my view, are databases that represent that reality, making
> appropriate links, that is, links accurately reflecting the relationships (which are
> many).
> 
> Apparently, aggregators all too often succumb to the lure of the One Shop
> Stopping, All-Encompassing Portal, into which input is shoehorned any which
> way (not rarely 'creating' species which don't exist).
> 
> Paul
> 
> ----- Original Message -----
> From: "Tony Rees" <tonyrees49 at gmail.com>
> To: "Doug Yanega" <dyanega at ucr.edu>; "taxacom"
> <taxacom at mailman.nhm.ku.edu>
> Sent: Wednesday, September 07, 2016 12:44 AM
> Subject: Re: [Taxacom] taxonomic names databases
> 
> 
> >I have to say I am with Doug here, which is why I previously cited the
> > example of the APG (Angiosperm Phylogeny Group) evolving "consensus"
> > classifications of angiosperms, from 1998 to the present (now at APG IV).
> > At each point, the subtext of releasing APG I through IV is, "here is the
> > best we can do at this time; it is better than we had before, and no doubt
> > will be superseded at some point again, but we present it as a system for
> > use in a standardized manner by those who wish to do so".
> >
> > Meanwhile research goes on, new data are accumulated and pondered on
> with
> > the possibility to influence the next iteration of the system, and indeed
> > any particular release is generally accompanied by statements to the
> > effect
> > that "treatment of this group is conservative at present although there is
> > already evidence that it may need to be changed in the future..."
> >
> > I do not see the problem with this approach: taxonomic/phylogenetic
> > research in the background (engine room), iterative taxonomic treatments
> > as
> > periodic products (outputs) for museum and herbarium clients such as the
> > one described by Doug, plus other syntheses e.g. in textbooks, taxonomic
> > guides, encyclopedias including Wikipedia, Wikispecies, etc., data systems
> > such as GBIF, and more, to use as desired. If divergent view exist, then
> > the consensus classification can still be created while noting the
> > divergent views (happens all the time).
> >
> > In the APG series of treatments, the only flaw I found was that APG II
> > introduced a number of "optional" families - use if you want, or don't. A
> > terrible idea, rectified in APG III...
> >
> > Regards - Tony
> >
> > Tony Rees, New South Wales, Australia
> > https://about.me/TonyRees
> >
> > On 7 September 2016 at 07:56, Doug Yanega <dyanega at ucr.edu> wrote:
> >
> >>
> >> <snip>
> >> As a corollary, instability of classification also makes it much harder
> >> to
> >> communicate with non-taxonomists, at many levels. If we have to preface
> >> every single thing we say, or write, when communicating to
> >> non-taxonomists,
> >> with a comment like "Bear in mind that there is no consensus as to what
> >> names we really should use for the organisms I'm about to mention..."
> >> then
> >> that just makes taxonomists look like complete idiots, at a time and in a
> >> political climate where anti-science sentiment is strong and getting
> >> stronger. Nothing makes taxonomy look more *irrelevant* than being
> unable
> >> to give a straight answer. If you go to a museum or library, or read a
> >> field guide, you want clear organization, and expect answers, not a
> >> lecture
> >> in epistemology. If I can't answer a simple question regarding a
> >> butterfly
> >> someone found in their yard without expressing that there are three
> >> possible species names, two possible genus names, and three possible
> >> family
> >> names, then while my response might be a "sound reflection of our
> >> science,"
> >> it won't reflect well ON our science, in most people's minds. All a
> >> layman
> >> is going to take away from that experience is "Taxonomists don't know
> >> what
> >> the heck they're talking about," and I can't say I'd blame them.
> >>
> > </snip>
> >
> >>
> >> While it may be true that SOME people don't need a synthesis, this does
> >> not mean there is NO need for a synthesis.
> >>
> >> Sincerely,
> >>
> >>
> >>
> > _______________________________________________
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> >
> > Injecting Intellectual Liquidity for 29 years.
> >
> >
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> Injecting Intellectual Liquidity for 29 years.




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