[Taxacom] ITS, Species 2000,

Richard Pyle deepreef at bishopmuseum.org
Fri May 25 14:26:18 CDT 2007

Hi Mary,

Here's how I look at it: 

In reality, there are no "factually" valid species -- only different degrees
of consensus among practicing taxonomists at any point in history.  Thus,
*any* assertion about the validity of *any* name is, ultimately, opinion.

ITIS/Species200 perform a valuable service to people who need to work with
scientific names, but don't care about the quibblings of us taxonomists.
These sorts of consumers of taxonomic names want someone else to monitor the
taxonomic community and distill from the debates which set of valid names to
go with. This applies even for the most contentiously debated names.

The "facts" are what I now call the "usage instances" (I used to call them
"Assertions").  For example, we can all agree as fact that Smith, in his
2001 publication, treated the name "Aus bus" as valid, and "Aus xus" as a
junior synonym of "Aus bus".  Another fact would be that Jones 2002 treated
"Aus xus" as a valid and distinct species from "Aus bus". What is not fact,
and not universally agreed to, is which of these two authors "got it right".
I would guess that well over 90% of consumers of taxonomic names don't
really care -- they just want to know which name to use. ITIS/SPecies2000
performs that service for these 90% of consumers of taxonomic names. 

Is it perfect?  Nothing is perfect.  The Linnaean system of nomenclature
certainly isn't perfect.  But, it has served (and continues to serve) an
important role in biology -- just as ITIS/Species2000 have served (and
continue to serve) an important role to a large section of consumers of
taxonomic names.

How can the situation be improved?  Why, I'm glad you asked! :-)

One of the goals of the Encyclopedia of Life is to work with groups like
uBio, GBIF, ITIS, Species2000, IPNI, Index Fungorum, ZooBank, BHL, and a
whole host of other initiatives who deal with taxonomic names to establish
what David Remsen of GBIF calls the "BIG Index" (I'll defer to David for
elaboration of the name).  This would be a giant index of these "usage
instances", or the "facts" of taxonomy, as I defined them above (e.g.,
Smith, 2001, treated "Aus xus" as a junior synonym of "Aus bus").  Building
such a comprehensive index is a monumental task, far outside the scope of
any single initiative like ITIS or Species2000 or most of the others.  But
it's not outside the scope of the collective taxonomic community as a whole;
which is why ideas like All Species, GBIF's ECAT, and EoL (the latter being
the most robustly funded) are so fundamentally important to serve as a "flag
pole" around which we can all congregate and coordinate our efforts.

If we are successful in developing this "BIG Index" of taxonomic name
usages, it will be extraordinarily valuable to us taxonomists, but still
won't, by itself, provide the 90% of consumers of taxonomic names what it is
they are looking for:  the "correct" name to use.  Now, obviously, we as
taxonomists know there is no "correct" name, because "correctness" is
ultimately a matter of taxonomic opinion (with varying degrees of consensus
or lack thereof).  Unfortunately, to the 90% of name consumers, this will
not be a helpful revelation. They still want to know which name to use in
their government report/term paper/ecological study/newspaper

Given the existence of the "BIG Index", we can derive a "best" (if not
"correct") name in one of two ways: through a computer algorithm, or through
a taxonomically-informed human expert mediator.

The computer algorithm is pretty easy to envision -- it would more or less
resemble the PageRank system of Google.  That is, some cleverly designed
(and, unlike Google, openly visible) algorithm that looks at the history of
usages of any particular name, appropriately weighs confidence indicators
based on recency and comprehensiveness of the source of each usage instance,
on authors' historical track record (e.g., to what extent the rest of the
taxonomic community tends to follow that author's assertions), and a whole
wide suite of other variables that we human taxonomists generally use to
asses which name to go with -- and ultimately arrives at a single "best"
answer that is very-much analogous to Google's "I'm Feeling Lucky" feature.
Such an automated system would do two things: 1) arrive at the same answer
as a human arbiter would for the vast majority of names that are not
currently contentious; and 2) would provide some sort of confidence
indicator as to how stable the given treatment of that name is.  Something
like "Homo sapiens" would have a pretty high confidence index, and would
show bright green on the EoL "taxonomic confidence indicator" part of each
species page.  Something like "Centropyge flavicauda" -- which has been much
less stable in recent literature -- would show red.  Others would show
various shades of amber.

However, as we all know, we can't always rely on computer algorithms to give
us the "best" answer -- so we need the taxonomically-informed human expert
mediator to make an assertion.  This is where I see the (important) role of
ITIS and Species2000 and others to come in.  They would serve the role of
"meta authorities", canvassing the taxonomic landscape and arbitrating a
single "best" taxonomy for their constituents.  EoL is already planning on
implementing a system that would accommodate many different classification
perspectives, and allow the user to select and/or compare among them.  Just
as many of us have identified movie reviewers that we tend to trust, taxon
name consumers would be able (through what is being touted as the "myEOL"
feature) to identify and/or rank these "meta authorities" to serve up

Addressing your last paragraph -- I don't think anyone thinks of ITIS or
Species2000 as the "de facto" body making "taxonomic decisions for the
world".  Rather, they perform an important service for a certain
constituency -- a service that I see as continuing to be important well into
the future.  My institution serves that same role to a different
constituency, with a much smaller scope of names.  The Catalog of Fishes &
FishBase serves that role to another constituency; and so on.

So...I guess my overarching point is: YES! I agree with you that it would be
good to have some sort of confidence indicator attached to each "meta
authority's" declaration of the status of any given name (and EoL just might
allow that to happen) -- but that notwithstanding, the role of ITIS and
Species2000 and others is not intended to tell us taxonomists what to think;
but rather to distill the morass of our collective discourse into something
that has practical value to the majority of consumers of taxonomic names.


Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
  and Associate Zoologist in Ichthyology
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

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Mary 
> Barkworth
> Sent: Friday, May 25, 2007 6:58 AM
> To: Orrell, Thomas; taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] ITS, Species 2000,
> OK - without questioning anyone's intent:
> Yesterday I was looking for Trisetum montanum on GBIF. It was 
> listed as a synonym of T. spicatum, with ITIS as the 
> authority. This is a common treatment - and one that is 
> reflected in FNA 24 (which I edited). What bothers me is that 
> it is not an unequivocal synonym, nor even a universally 
> accepted synonym: and Victor Finot, who has revised all 
> American (North, Central, and South) members of Trisetum 
> sensu lato (see
> http://utc.usu.edu/grassbib.htm) considers that it should be 
> recognized at the species level.  IF GBIF (and ITIS) were to 
> list the name as
> *sometimes* included in T. spicatum, that would be fine but 
> it does not.
> In response to Orrell's comment, I went on the Catalogue of 
> Life Web site. Trisetum montanum is also listed there as a 
> synonym of Trisetum spicatum. There is no indication that 
> there is a current difference of opinion about its treatment. 
> Oddly enough, Trisetum montanum var.
> montanum is listed as an accepted name, T. montanum var. 
> shearii as a synonym for T. spicatum. 
> We do ourselves a disservice by presenting opinions as facts. 
> I also dislike the idea that we are, de facto, being told 
> that there is a body that will make the taxonomic decisions 
> for the world.  At least state real sources for a taxonomic 
> judgement, which I hope are published treatments, not the 
> faceless ITIS - which Outlook keeps wanting to make "IT IS" ;-). 
> Mary
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