[Taxacom] human involvement (was Re: BioNames)

Scott Thomson scott.thomson321 at gmail.com
Tue Jun 4 17:25:05 CDT 2013

Just a quick thought on this thread.

I feel that what you should look at is a software package. In my view it
should not be a free ware, this is because the maintenance of freeware is
generally poor and reactionary. I think if its scope was limited to
nomenclature only it would be a more sound package. In other words it
should not be of any real use to the taxonomy, but just be a package
designed to assist in the appropriate usage of names. I would suggest
database driven by access to an online database. It can then be maintained
by appropriately identified users and anyone who has it can make updates
for new species they may describe. Checks can be in place to ensure a name
only becomes available and valid as per the accepted ICZN rules etc. Part
of me would recommend a Java based package linked to some sort of SQL
database. This allows for maximum compatibility to different users systems.
But there is also a downside to that. So a robust front end using a more
commercial language may be more appropriate.

Such a package could also have incorporated into it the means for effective
communication and even expedited mediation and "voting" on names by the
larger taxonomic community if that idea takes off, as has been suggested by
some in the past.

In some ways this is similar to what ZooBank is trying to do. But I do feel
that a distributed package that is maintained by an online connection would
be more powerful. If you forgive the analogy it is somewhat similar to the
way Online Games are maintained. All the players have a distributed product
that gives them access to an online database. But in reality the
distributable software is only a front end to the main database.

Just a thought I had on a way forward. I have not put any design thoughts
into it but I could and then make a more genuine proposal on what I think
could be useful.

Cheers, Scott

On Tue, Jun 4, 2013 at 1:22 PM, Doug Yanega <dyanega at ucr.edu> wrote:

> On 6/4/13 12:49 AM, Roderic Page wrote:
> >
> > On 3 Jun 2013, at 23:13, Doug Yanega wrote:
> >
> >>
> >> Realistically, one either needs to improve the incentive for
> >> participation in the system (such as making participation effectively
> >> mandatory, as happens with GenBank),
> >
> > Why must the incentive be making it mandatory? Ultimately this seems
> > lazy  "you must do this because we can't think of a way to make it
> > worth your while." It also requires that people can be bullied into
> > compliance.
> >
> First, note that I said "such as" - for the reason you yourself point
> out; there are certainly other ways to accomplish this.
> Second, what is intrinsically wrong with mandatory? Does the scientific
> community truly feel that being told "everyone needs to submit their
> gene sequences to GenBank in order to publish" is a form of "bullying"?
> Part of the scientific method is giving others the data to see how you
> arrived at a given conclusion, and that's what access to sequence data
> affords, in addition to vital descriptive functionality. I gave the
> GenBank example because that is the exact same context I envision,
> except that instead of gene sequences, what is required is links/cites
> to fully-resolved ZooBank records for every scientific name one uses in
> a publication. For authors working on popular taxa, the odds are that
> any taxon name they intend to publish will already be recorded, and all
> they need is to look it up and link/cite it. For authors working on more
> obscure taxa, they will often need to personally enter the information
> into ZooBank as part of their authorship responsibilities - just as
> authors need to register their gene sequences in GenBank now. Given that
> no one should be doing taxonomy without access to the original
> literature, requiring that an author transcribe the pertinent data into
> ZooBank is not adding very much to their overall effort.
> Third, I'm sure that you, Rod, of all people, can imagine ways to not
> only link to the ZooBank record, but simultaneously link to the original
> description, such that every time someone uses a scientific name, the
> work in which that name was coined gets cited in a manner that counts
> towards academic citation metrics. This would give some added incentive
> for people doing alpha taxonomy, if any time someone publishes one of
> your taxon names you get cited in the process. Right now, it is
> essentially unheard-of for any biologist to cite the works in which
> his/her study organism(s) were described, which - arguably - makes alpha
> taxonomy seem less academic than other disciplines. Heck, maybe this
> could be extended to give credit to the person who identified one's
> study organism(s), as well. Both these measures would improve things for
> both the readers of biological works AND the taxonomists - whose efforts
> are presently going unrecognized outside of the "Acknowledgments"
> sections (if that).
> Fourth, having links/cites to ZooBank records would also allow for
> backwards propagation of new information. Consider what happens if
> someone in 1950 published on, say, the gray hairstreak butterfly
> Ministrymon azia in Texas. Given that just this month a new sympatric
> cryptic species has been split off, then that 1950 paper would not
> necessarily be about the species that the author in 1950 thought it was
> about, and people (other than butterfly specialists) who read that paper
> might never know that there was any question about the actual species
> identity. Now imagine if a present-day author published a paper like
> that but with a ZooBank link, and 10 years down the road, the species
> they studied is split. If that ZooBank record is (upon publication of
> the split) converted into a disambiguation link that shows the records
> for both the original taxon and the new taxon, then *anyone* who reads
> that outdated paper will know that the species was split without ever
> themselves having to do any literature searches to track down the
> changed status.
> Again, requiring the registration of names one is using is a small
> imposition on authors, with a very large potential for benefit (for both
> authors and readers), and it distributes the labor of populating the
> registry to those who are actively using the names (and motivated to do
> it correctly).
> > What if we had a tool that offered enough value to individuals that
> > they wanted to participate? That solved a problem that users had, and
> > as a by product built something of broader value? This, to me, is the
> > lesson of Mendeley. You tackle the individual point of pain, and
> > incidentally get people to build what you wanted them to build for
> > you. Alternatively, you make an experience so compelling that you have
> > to join ("wadda you mean you're not on Facebook?").
> >
> I agree that such an approach is desirable, and apologize if you
> gathered otherwise from my comments. Folks like Rich Pyle and myself are
> all ears if you have specific ideas along these lines!
> 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
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Scott Thomson
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