[Fwd: ITIS and a US Taxonomic Standard]

Stuart G. Poss sgposs at SEAHORSE.IMS.USM.EDU
Fri Sep 4 00:10:14 CDT 1998


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--
_____________________________________________________________________
Stuart G. Poss                       E-mail: sgposs at whale.st.usm.edu
Senior Research Scientist & Curator  Tel: (228)872-4238
Gulf Coast Research Laboratory       FAX: (228)872-4204
P.O. Box 7000
Ocean Springs, MS  39566-7000



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_____________________________________________________________________
Stuart G. Poss                       E-mail: sgposs at whale.st.usm.edu
Senior Research Scientist & Curator  Tel: (228)872-4238
Gulf Coast Research Laboratory       FAX: (228)872-4204
P.O. Box 7000
Ocean Springs, MS  39566-7000</PRE>
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Message-ID: <35EF7567.C4D78BF3 at seahorse.ims.usm.edu>
Date: Fri, 04 Sep 1998 00:06:47 -0500
From: "Stuart G. Poss" <sgposs at seahorse.ims.usm.edu>
Organization: Gulf Coast Research Laboratory Museum
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To: Karstad-Schueler <bckcdb at ISTAR.CA>
Subject: Re: ITIS and a US Taxonomic Standard
References: <35EF2F9A.1756 at istar.ca>
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> This way inclusion of reams of synonyms wouldn't be mandatory for any
> higher taxon: ITIS could just enter the American Fisheries Society list
> of Unionid names at first, but later and previous lists and revisions
> could be spliced into the system as they occur or time or necessity
> allows.
>
> fred schueler.
> ------------------------------------------------------------
>          Eastern    Ontario    Biodiversity    Museum
>                 Grenville Co, Ontario, Canada
> (RR#2 Oxford Station, K0G 1T0) (613)258-3107   bckcdb at istar.ca
> ----------------------------------------------

> -------------

We better hurry before there are no unionids left and the sciences of
taxonomy and systematics soon follow right behind them.

One can only hope that the currently nebuluous standard and standards
making process will be able to represent true phylogeny well enough to
accurately and quickly estimate which other taxa will disappear next.

Perhaps its a shame that some so vigorously advocate the strict requirement
of naming only holophyletic taxa, with so many different ways to generate
names, instead of being content at times to allowing paraphyletic taxa to
be named for nomenclatural simplicity, perhaps from a not necessarily
overly large but finite list.

I believe that those of us who advocate the usefulness of naming
paraphyletic taxa are more appropriatelly termed evolutionary taxonomists
or phylogenetic systematists rather than eclecticists, a term that does
sound as if I should be in the Linnean priesthood.  However, I do agree
with Kinman that the distinction is largely resonsible for uncecessary
confusion and nomenclatural instability in the recognition of taxa of
higher rank.

With a definite understanding of the mapping of the true tree partial
orders or with their consequence in terms of their evolutionary biology so
typically lacking in most efforts, we can only hope that the management
strategy implicit in our use of taxonomic names increases rather than
decreases the probability that a species survives.

Certainly, the consequence of the loss of the trees, the real rather than
the phylogenetic kind, has been having a demonstrable effect on the fishes,
particularly when the effects are direct, such as in the greater North
America basin or in Amazonia.  Let us only hope that we can leverage the
use of the names we use well, lest the entire enterprise soon end, perhaps
in as little as 250 to 300 years, (ignoring the possiblity that various
microbial and viral species and numerous other lower forms may assume this
task after our departure).  Let us futher hope that we can use the list in
a timely fashion as world populations of species diminish asymtotically
toward levels where inevitable stochastic processes take over.  That human
induced habitat fragmentation, invasions of non-indigenous species,
outright habitat destruction, and over-exploitation steepen the decent
toward such a level for most species provide grim reminders that we must
build our lists and information systems quickly, if we are to have a chance
to use them.  Fortunately for fishes, with the help of NSF Eschmeyer has
largely already provided the list for ITIS to use.  What does the
ITIS effort propose to add?

If it is to only rely on one system, I hope that my government has the wits
to develop the system carefully.  However, I grow concerned when I purchase
the ITIS CD-ROM and find antiquated thinking in terms implicit in the
information models used to organize such data.  The file format used still
reflects the need to conform to fixed format file, in some ways still
constrained by the original 80 character wide computer cards the original
NODC list was built from.  Incidently, these do include synonyms as well as
other names, but with an arcane mechanism for identifying them.  One that
has more to do with the peculiarities of the historical sources of the data
captured to date rather than with clear ideas as to how to organize its
content or address a mechanism for establishing its comprehensiveness or
assuring the quality of the data.

It is unclear if ITIS and the larger FGDC committee structure in their bid
to serve in the role of taxonomic information arbiter for the United States
has developed sufficient structure, not to mention resources, to adequtely
identify the criteria for recognition of expert opinion and how to improve
the wisdom of that opinion.

Since at times I program for the United States on contract, I sometimes
wonder if the $60 purchase price for the NODC CD bought in attempt toward
compliance with "emerging standards" might not have been saved by making
the entire list fully available for download at all times.  This would save
futher use of government funds needed to buy the list in CD format, which
though useful, rapidly becomes dated.   However, I find the CD format
acceptable as a periodic "formal" edition that could be referred to as
though it were a published work.

One can find these data on line but, the ease with which one can download
large segments using well-specified user selectable criteria is not great,
nor have suitble criteria for the creation of metadata been established,
nor do the elements provide hyperlinks to other important data sources.
Nonetheless, I believe the project to be of value so long as as a
taxonomist and systematist I am not forced to use names that are largely
useless in understaning the biology of the taxa involved in specific
studies.  There is nothing more irrelevant than a solution that doesn't
work.

Presumably ITIS is asking for a big budget, since it will take armies of
students (government workers?, contractors? philanthropists?) to manage the
data entry load necessary to keep this list current and the project
relevant to the often indirect march of biological and evolutionary
research toward a limited number of potentially true phylogenies and
towards a large, but probably fluctuating and diminshing total number of
species.

Perhaps a way can be found to permit this effort to usefully include the
expansive databases developed by the UN, since these have much better
coverage of old world taxa, so many of which are now becoming new world
taxa.  This would tie well into IKLARM, FAO Species Catalogs, and similar
databases developed by other governments.   Again, it is useful to ask what
does ITIS propose to add with respect to fishes that Eschmeyer or these
databases haven't already largely provided?  If it is it only that these
lack an official government imprimatur, let us hope that they utilize the
fruits of the wisdom NSF demonstrated in funding Eschmeyer's work and
others like it.

The ITIS and other arms of the US government effort would do well to
consider the advice of our Brazilian colleague Doug Yanega in offering its
support to distributed projects to extend the Tree of Life and similar
efforts, in which important alternate approaches, clasifications, species
lists, etc. can be developed, yet associated under a single "accepted"
standard tree/network of URLs, each with at least one summary for
particular individual species that serves as a node pointing to the
organization of all other data for a given species.  This is the approach
we are attempting to take for two websites developed for the US Gulf of
Mexico program (see http://www.ims.usm.edu/~musweb/endanger.html) dealing
with species at risk in the Gulf and an emerging website
(http://www.ims.usm.edu/~musweb/invaders.html) dealing with non-indigenous
species in the Gulf ecosystem.  Resources are certainly needed to integrate
ITIS efforts and those of others with databases such as that provided by
Kinman for mammals, Eschmeyer for fishes, numerous similar databases
already mentioned by others, and many still unknown to most of us.  Might
it not be a good idea to design into our system, as does NASA, a little
duplication to insure a fail-safe mechanism in the event that one
life-support system fails?

Such an approach could well serve to establish a commonly accepted body of
information that could form a scientifically sufficient basis for
nomenclature of species that may need to be added or deleted from the list,
without creating a separate vast government infrastructure.   The Madisons
for example have suggested a convention (NEXUS format) for such a system
that could in principle serve to coalesce and organize knowledge around
taxonomic names, although I believe that this format needs to be emended to
more appropriately focus on individual specimens or parts of specimens to
increase its usefullness in characterizing taxa, especially species and
less definite higher taxa, such as exemplied in the incipient morphological
databases found at http://www.ims.usm.edu/~musweb/laserarchive.html, not to
mention better incorporate burgeoning molecular databases whose content are
indispensible in developing reasoned phylogenies.  Other knowledgeable
citizens should encourage our government (ITIS and affiliate programs) to
include links to such alternate systems so that sufficient information
exists to provide reasonable assurance of the correctness and scientific
usefulness of a single "official taxonomic standard".

Nonetheless, such a network could contain the criteria by which informed
decisions could be identified and distinguished from less informed
decisions.  Such a network of alternate lists and listing strategies would
more likely provide the basis of a factually correct standard taxonomic
list, through the use of which informed formal governmental decisions could
be made.  I believe this approach would work better than a single
monolithic standard that would be difficult for any small group of persons,
government employees or otherwise, to manage in real time.

Such a system could be used to develop a coherent model of information
needed to associate biologial data with a unique name for a species and a
potentially large, but not fully specified number of other names currently
in use for that species or for taxa to which this species belongs,
regardless of their holophyly.   Most importantly, such a list could point
to a collection of specimens that could serve to provide definitive
standard reference as to which species are involved in the use of a
particular name, as well as to locations (URL's) at which these data can be
accessed.

That the project intends to follow International Codes of Nomenclature is
reassuring, although these too remain unclear as to how higher level names
are to be treated.  This way, others, such as myself who strive to provide
my government as an interested party to the Gulf of Mexico Program (GOMP)
and IABIN InterAmerican Biodiversity information Network (IABIN) with
useful information about species, can gain guidance on how I might best
engage my Brazilian colleague in the design and development of a network to
better manage the rapidly diminishing and more frequently interacting
species that we and others study.  I believe the way to do this most
effectively is to have numerous "standard lists", whose content can be
modified to suit specific circumstances, yet whose content attempts to
provide a measure of understanding with respect to other specific bases of
comparison.  In this sense it would be helpful each world government to
strive toward the use of an "offical taxonomic standard" which could guide
all parties toward scientific consensus.  However, we must be cognizant of
the probable inability of governments to officially list/delist species or
correct factual errors in a timely fashion.  One only need to look at a
much smaller list of species, those formally listed as threatened or
endangered to see how ineffectual the government listing process can at
times be for some species, such as the Texas pipefish (see
http://www.ims.usm.edu/~musweb/saffinis.htm)  that will probably never be
listed before it goes extinct, if it hasn't already.

Although the problem is a large one, keeping up with names in databases is
actually the easiest part of the development of a standard taxonomy.  The
larger challenge will be in repeatedly and assuredly identifying the
specimens that must necessarily be associated with these names.  This
activity will largely determine, if a list of species names, standard or
nonstandard, can be used to any practical utility, at least from the
perspective of the studies of their biology and conservation, not to
mention their nomenclature.

Hopefully, a way can be found to save the data and body of taxonomic and
nomenclatural knowledge derived from historically important efforts.  Can
we really afford to ignore the consequences of failling to include efforts
abroad toward the development of such a standard taxonomy?   Many works,
such Darwin's treatise on barnacles, remain important.  Many ongoing
projects not yet included in the ITIS list have already been cited by
others.  We must consider, for example, what the consequence will be of
loosing the observations, nomenclature, and classifications that at one
time supported legions of taxonomists, such as those in the former Soviet
Union by accepting a particular list and classification as "standard".
Such important contributions may now soon be lost to us for a variety of
miscalculations of many parties and because of a failure to develop
adequate training programs for species identification.   Admittedly, this
is an aspect of developing a "standard taxonomy" that is not well
understood by those who do not identify specimens themselves, but must
instead rely on lists developed by others to study species.

Its not surprising that the ITIS emphasizes the marine invertebrate, since
much of the funding derived form collection and archival of materials still
at CAS using NODC standards from NOAA/BLM efforts to inventory the Arctic
Alaska in consideration of utilization of its petroleum reserves.  For
several years I served as Archive Project Manager directly in charge of
these specimens, ranging from invertebrates to fish and walrus.  I remain
unsure if I learned more about these species by using the NODC list than
avoiding it, which in my mind at the time largely served to pin a binomen
to a unique NODC number rather than provide the definitive, comprehensive
list of taxa necessary to understand their biology.   Perhaps with
sufficient input, this could change.  The list as issued on CD is far more
complete now than it was when I first began to use it some 15-20 years ago.

To be convinced that the databases that presently serve as the kernel of
this effort will achieve the stated goals if expanded, I personally need to
see more concrete indications of what the new ITIS "standard taxonomy"
database will include.  I need to know how included information will be
organized, how it will be made accessible, and how the ITIS and FGDC will
formally interact with the broader collections, taxonomic, and biological
community and other governmental agencies both federal and non-federal, who
collectively contain the expertise essential to make the list meaningful
and usefully organized and integrated with other knowledge bases.

Despite my reservations, I still would like to see the construction and
development of a general system in which all can usefully contribute and
emend as the practice of good science warrants.  However, science is, at
times, a little like baseball, in that there is a limit to the number of
times each player is permited to swing and attempt to hit the ball in a
useful direction.  Hopefully we can encourage our government to keep the
diamond designed in a way that permits all to bring in a run for the team
and win the game before the end of the ninth.

Stuart Poss

--
_____________________________________________________________________
Stuart G. Poss                       E-mail: sgposs at whale.st.usm.edu
Senior Research Scientist & Curator  Tel: (228)872-4238
Gulf Coast Research Laboratory       FAX: (228)872-4204
P.O. Box 7000
Ocean Springs, MS  39566-7000



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