[Taxacom] global species lists and taxonomy ( was Re: Draft Checklist ...)

[Doug Yanega]

On 8/28/13 9:50 PM, Tony.Rees at csiro.au wrote:
> Dear Doug, all,
>
> I for one would be (fairly) happy to defer to a single "management classification" governed by an editor for each section even if this is not strictly consensus: compare e.g. the Sybil Parker, ed., 2-vol. printed work "Synopsis and Classification of Living Organisms" (1982) or Michael Benton, ed. "The Fossil Record" (1992) for example treatments. One can then use such a system as the basis for a standardized treatment between different systems even if they then choose to deviate from it in parts for local use. If Parker's work were produced today I am sure it would be on the internet and it would not be a burden for others to say "classification follows [new]Parker, 20xx except where noted".
>
> FYI the two works cited above go down to level of family; getting in the genera and species is a different level of effort but at least partly done in such operations as Catalogue of Life and elsewhere as we know. Alternatively we could lean gently on "major players" with an interest in this area to do this work themselves since it is clearly in [some of ] their own interests anyway (hint hint...) - e.g. GBIF already have a "GBIF Nub" classification which attempts to operate in this space even if at present it has some issues as have been pointed out elsewhere; Dennis Gordon's 2009 discussion paper for Cat. of Life (available at http://www.catalogueoflife.org/col/info/hierarchy) is also a relevant pointer to a possible way forward.
>
> This to me would seem a more positive direction than that suggested by your last 2 paragraphs wherein everybody has to agree before a useable system can be produced.
>
Maybe I did not make clear the distinction between "useable" and 
"definitive" (or "authoritative", if you prefer). To return to the 
example I used, the APG system is most certainly useable, but not every 
botanist follows it, nor every publication, nor every herbarium, nor 
every plant database. The simple existence of a resource that CAN 
fulfill a certain purpose does not mean it is used TO fulfill that 
purpose, and - as such - if some layman or politician comes to you and 
asks "What family is this endangered plant in?" then you cannot, in good 
conscience, give them a single definitive answer, because the APG 
classification is not the only possible one - i.e., not everybody has 
agreed to follow it. We can also, just for now, put aside the far larger 
concern that virtually no attempts at authoritative resources deal with 
fundamental taxonomic units like species or genera.

Fred Schueler wrote:

Maybe we want to take a lesson from the physicists' ideas of infinite
parallel universes, and program systems where all published
classifications are represented, but with some sort of combined voting
or weighting by the recency of publication, and wiki-style comments and
discussion, to show users which classifications are more currently
approved and used.


This runs afoul of the exact same issue: such a system would not give a 
single answer to a simple question like "What family is this plant in?". 
It gives an enormously esoteric and complicated answer that makes sense 
only to a taxonomist who is family with plant taxonomy - "Here are the 
15 competing classifications, in which this plant is in family X in 9 of 
them, family Y in 4 of them, and family Z in 2; of the three most recent 
classifications, it was placed in X twice and Z once, with Z based on 
chloroplast DNA sequencing." That sort of answer is precisely the kind 
of thing that confirms the impression of taxonomy as hopelessly 
impractical. No one outside the taxonomic community cares how many 
competing classifications exist, who published them, or who is citing 
and/or following them. Lumpers versus splitters, molecules versus 
morphology, strict monophyly or not... the end users of taxonomy *don't 
care* about our internal arguments and controversy, and it is a mistake 
to force everyone else to accept ambiguity just because WE strive for 
objectivity.

Erik Rijkers wrote:

So databases should amass these opinions with plenty factual detail but without implicitly endowing any
classification-opinion with the distinction of being "fact".

It would seem this obvious way of doing taxonomical databases is not too hard to implement but I have never seen it done ,
or even acknowledged as necessary.

Yet again, a suggestion that would result in no single answer to even 
the simplest question. A database that amasses alternative 
classifications in a neutral and unbiased way is useless to 
non-taxonomists, and non-taxonomists are the people who pay our 
salaries, fund our grants, and support non-profit organizations that 
help preserve the organisms we study.

Karen Cranston wrote:

Both IPNI and Open
Tree of Life are currently implementing a relatively new graph database
model (database called neo4j) to load and store multiple hierarchies in the
same data structure. Then, you can traverse the graph (which contains all
of the nodes and edges, and therefore all of the conflict) in various ways
in order to summarize / resolve conflicts / find interesting patterns. You
could use algorithmic and / or human-curated approaches to annotate or
resolve parts of the hierarchy, while still keeping all of the information
from the sources.

Which again is useless to non-taxonomists who want a single definitive 
answer - and even if we assume that you can develop an algorithm that 
can produce a fully-resolved tree, is it a tree that the taxonomic 
community would unanimously support? Everyone is talking about tools to 
allow taxonomists to evaluate classifications more objectively, but 
that's not what the end users of taxonomy want or need, and not at all 
what I was referring to.

Nicky Nicolson likewise wrote:

we are using the nomenclators (IPNI and IF) to provide the fundamental
units (names and the objective relationships between them) and then
supporting multiple overlapping - even contradictory - classifications to
be built using these same fundamental units. We are storing enough data on
the relationships which form the taxonomic classifications to do the kind
of assessments that Fred suggests - e.g. to take into account how recently
the hypothesis was published, who published it and where (e.g. was it a
regional treatment or a globally-scoped monograph).

The same thing, yet again. Just because we, as taxonomists, find 
contradictory classifications to make for rousing intellectual debate, 
does not mean we can expect any laymen to be excited by /not having any 
idea what family organism X actually belongs to/. I gave a nature hike 
this spring, and pointed out a very common local insect, and mentioned 
that not only did no one know whether it was one species or multiple 
species, but that different authorities classified it in three entirely 
different families, all within the last decade, and one hiker responded 
"Well, that's just silly". That is how the public perceives taxonomy 
when we essentially brag that we can't agree on anything. It's really 
not something to be proud of.

Donat Agosti wrote:
> Regarding linking to policy making: Hasn't ITIS  such a function as the ultimate reference system in the US and Canada administration, and if so, how has it been created? What have been the argument that made it fly on the first hand?
>
FWIW, ITIS is cobbled together piecemeal from different sources, and is 
missing lots and lots of taxa. It should not be viewed as an 
authoritative source itself.

Finally, Rich Pyle wrote:

But complaining about something that is blindingly obvious to everyone
doesn't help much.  It's not that we're not doing stuff.  Many of us are
doing stuff.  Good stuff. Often VERY good stuff.  It's just that we're not
coordinating our stuff very effectively.

The question is, even if we get our stuff coordinated, will it result in 
a resource that is only fuel for esoteric arguments among taxonomists, 
or a definitive practical resource that can be used by everyone else on 
the planet? The longer we take to do the latter, the less likely any of 
us will be employed to do the former. People expect answers, and the 
taxonomic community just gives them more questions (e.g., "Which of 
these 5 competing classifications would you like to follow?"). Fiddling 
while Rome burns, living on borrowed time, you pick the metaphor. If we 
don't find a way to give people what they want, they'll stop supporting us.

But (for those of you still reading) I'm not here just to complain about 
this, and here's why: RIGHT NOW we are experiencing (from what I can 
see) a resurgence of public interest in the environment, and especially 
in biodiversity. That means we have an *opportunity* available to us, 
and if we can seize it now, we could really give a major boost to the 
profession. I'll tell you what is NOT going to engage the public's 
awareness and support: endless bickering over which classification to 
adopt, what names to use, how to define a species, or how taxonomy 
should be done. That's not the way to attract a new generation of 
taxonomists, or a new generation of philanthropists. We all SHOULD feel 
a sense of urgency, rather than complacency. If we can't step up and 
deliver answers to an information-hungry world, then the void we leave 
will be filled with misinformation, and we'll get left behind. At least 
a few of you will understand how I can see this playing out *right now* 
in the controversy over the "Pterosaur Heresies" website. Are we 
willing, as a community, to allow taxonomy to be co-opted by whoever it 
is that can produce the flashiest web page, where every time a layman 
does a Google search, they only find one classification - and it is NOT 
the one the taxonomic community would agree upon, based upon the best 
science? This isn't hypothetical, and it isn't 10 or 20 years in the 
future. I'm here to light a fire under people, if there's anyone who can 
see the problem AND a solution. I believe that if we can't come up with 
an authoritative classification, soon, it won't be long before no one 
will listen to us.

Sincerely,

-- 
Doug Yanega      Dept. of Entomology       Entomology Research Museum
Univ. of California, Riverside, CA 92521-0314     skype: dyanega
phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
              http://cache.ucr.edu/~heraty/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82