More GBIF questions (was: ITIS)

Doug Yanega dyanega at UCR.EDU
Thu Jun 24 11:19:12 CDT 2004

Richard Pyle wrote:

>I tend to agree.  Indeed, in my grand vision of how to solve the
>informatics of nomenclature, ICZN/ICBN should play a central/leading

But - and I think Richard and I agree here - not as a static entity;
in order to best interact with the informatics people, the Codes
themselves will require some revisions to reflect the nature of the
changes in how we all do business.

>Rod Paige wrote:
>>  I suspect the way forward is to adopt the tools and mindset
>>  of the Open Source software community. Have open databases of
>>  names that people can annotate (i.e., report "bugs"). The
>>  bugs themselves can be seen by (and commented on by)
>>  everybody. Hence, the error mentioned by Richard Petit (the
>>  type species of the genus Cancellaria being attributed to
>>  Pilsbry, 1940 instead of to Linnaeus, 1767) would be visible
>>  for all to see (and comment on).
>To which I respond, Yes, YES, and YES!!!   This is *exactly* how I think
>the way forward should be.  Doug Yanega has made similar arguments on
>this and other lists, which is why I tried to bait him into this

Consider me baited, then. The context in which I present those
arguments, however, is usually regarding how to create a List of
Accepted Names (a "registry"). Specifically, that such an open system
with public comment also needs to be PRIOR to publication of any new
names, for a great many reasons, not the least of which is to prevent
(as much as possible) the creation of any new synonyms or homonyms,
which relates to the following:

>Meredith Lane wrote:
>  > At present, we
>>  estimate that *on average* for every valid, accepted
>>  scientific name, there are two synonyms. This means that
>>  there are 3 X 1.75 million species names out there that need
>>  to be listed, sorted and "cleaned up".
>Indeed; but it goes beyond this.  We also have to think about the
>estimated 10-30 million or so names that have yet to be established for
>the as-yet undescribed species of the world.  It would be a real shame
>if the historical average of 3 names per later-accepted species
>continued (do we really need 100 million names for 30 million species?)
>One way to reduce (certainly not eliminate) such over-description is to,
>as Meredith has already described, provide a service to access all
>existing names. It is this goal about which I preach.

Access to names *and opinions*, that is. The latter is a very
different issue, but an absolute necessity. Along these lines, Roger

>I believe what we need, in botany, is the equivelent of a central 'meta'
>directory of names. This directory would store all published names ( could
>be based on IPNI as a starting point ) and opinions about those names. No
>data would be discarded. Interfaces (through SOAP or simple http calls)
>would be provided for other databases to reflect their opinions on the
>names, give an indication of what other data they carry on these names and
>provide a link to the data. Anyone at any time would be able to log in and
>provide a comment on a name or submit a new one. There would be no
>moderation only abuse control. The whole dataset would be served over the
>net and would be available as a download or snail-mailed CD-ROM on a monthly
>snapshot basis. There will be news feeds and watch lists so you can be
>notified of new entries in the categories you are working on.

We need this for all taxa, not just plants, and (as above) on
*proposed* taxon names, as well as those already published. But
consider the practical consequences of trying to treat "opinions
about a name" as a simple data element linked to a name, and you'll
see one of the things that worries me about this particular approach:

Pat Curator, who has just taken a position at a small institution
whose collection hasn't been curated in 50 years, wishes to organize
the taxa (plants, animals, whatever), and submits a set of queries
designed to give a listing of taxa such that all synonyms are listed
under each species, each species is in a genus, each genus is in a
family, and each family is in an order. Not too much to ask, right?
But if the "opinions" data is not used to build a classification,
poor Pat is going to find that a substantial number of species-level
taxon names will (a) have more than one alternative opinion whether
they are synonyms or not, (b) have more than one alternative opinion
what genus they belong to, (c) have more than one alternative opinion
what family the genus belongs to, and (d) have more than one
alternative opinion what families are in each order. Pat might need
to sit down and plow through all the literature at each level of the
hierarchy, for anywhere up to thousands of taxa, in order to arrive
at a single functional classification. Let's face it: MOST users of
names aren't themselves experts, and aren't equipped to decide for
themselves whether to follow, say, Opus' 1933 standard versus
Soenso's 1996 cladistic analysis versus Whozis' 2002 molecular

I maintain that what may seem perfectly logical, objective, and ideal
to those who are designing such names databases - to wit, the
"hands-off" approach to opinions (and, effectively, all
classificatory matters) - stands to leave a LOT of nomenclatural data
almost completely worthless to a large community of potential users.
We need something more, to address this.

Part of the "sociology" of the taxonomic community that needs to be
developed alongside names databases is a working consensus
classification, and - more to the point - this needs to be an
*interactive* and *ongoing* portion of the data resource, and not
based solely on published classificatory opinions (I believe that
there is much more authoritative taxonomic opinion that resides in
the heads of living taxonomists than can ever be published, and if we
stick with the tradition that nothing is of any merit until it is
printed on paper, we are crippling ourselves). Without a resource
that puts forth a consensus opinion to all users (with appropriate
caveats, obviously), we are failing to address one of the most
serious objections that the critics of taxonomy are (and have been)
making: that you can almost never get a straight answer from a
taxonomist when you want to know what the name is for something and
where it fits in the classification. I understand why GBIF wants to
steer clear of it, and "not take sides" when compiling a list of all
taxon names, but we can't neglect the very real need to
*simultaneously* develop a single authoritative classification
framework into which those names will fit. Name compilation efforts
undertaken in a classificatory vacuum aren't going to serve the
larger user community to the degree needed, and I think a greater
effort should be made to develop a mechanism by which taxonomists can
arrive at a public consensus.

This would not require much more than what Roger mentioned above, and
what Rich and I have also proposed in the past: "news feeds and watch
lists so you can be notified of new entries in the categories you are
working on". This can be applied to classificatory matters just as
well as to purely nomenclatural ones. A single central website can
accomplish this - the software and logistics are, in fact, trivial.
Beyond funding, I see no serious obstacles other than tradition and
egotism preventing us from building a single Tree of Life - with each
taxonomist choosing the branches therein upon which they will focus
their efforts. With active, day-to-day participation by everyone in
the taxonomic community, this could easily become a reality.


Doug Yanega        Dept. of Entomology         Entomology Research Museum
Univ. of California - Riverside, Riverside, CA 92521
phone: (909) 787-4315 (standard disclaimer: opinions are mine, not UCR's)
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82

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