[Taxacom] are early online publications code-compliant?

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Mon Apr 13 18:24:12 CDT 2015


For "Registered = Available" to work, either (1) the description would need to be given on the registration form itself, or, (2) if a citation to a published description is given, then the existence of such would need to be verified. The problem with (1) is that taxonomists would gain no vitation credit for describing new taxa (unless the registrations themselves were somehow included in the citation system). The problem with (2) is that it might take too much work, particularly for publications in obscure places.

Stephen
 
--------------------------------------------
On Tue, 14/4/15, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: RE: [Taxacom] are early online publications code-compliant?
 To: "'Neal Evenhuis'" <neale at bishopmuseum.org>, "'Frank T. Krell'" <Frank.Krell at dmns.org>, "'Sue Gardner'" <sgardner2 at unl.edu>, "'John Noyes'" <j.noyes at nhm.ac.uk>, "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>
 Cc: taxacom at mailman.nhm.ku.edu, gread at actrix.gen.nz
 Received: Tuesday, 14 April, 2015, 12:14 PM
 
 Thanks Neal;  all
 excellent points (as usual)!
 
 > Registration in and of itself has been
 touted previously on this list (and the iczn-
 > list) as the simplest way to deal with
 when a name becomes available (much
 >
 like what the bacteriologists do). 
 
 One point of clarification:  what the
 bacteriologists actually do is very different from what Doug
 and I (and others) have been advocating.  The
 bacteriological registry is a paper-based journal.  The
 actual bacteriological names are published in whatever
 publication they're published in, according to rules
 analogous to those of Zoology.  The Registration system is
 simply publishing the name and link to the published article
 within the official journal (IJSEM). Brian Tindall can speak
 much more definitively than I can, but I believe that the
 availability of the name includes elements within the source
 publication and the registry publication (analogous to the
 current system for required registration of electronic works
 in Zoology).
 
 The current
 ZooBank model can be described as "Registered +
 Published = Available" (much like the bacteriological
 system).  What Doug and I advocate is best described as
 either "Registered = Available" (my flavor), or
 "Registered = Published = Available" (Doug's
 flavor).  There is actually a continuum of millions of
 possible implementations between these two flavors,
 depending mostly on the amount of required information
 implied by the "Registered" part, and the amount
 of review implied by the "Published" part.
 
 More complete discussions of
 these different models are available here:
 
 Polaszek, A., M.
 Alonso-Zarazaga, P. Bouchet, D.J. Brothers, N. Evenhuis,
 F.-T. Krell, C.H.C. Lyal, A. Minelli, R.L. Pyle, N.J.
 Robinson, F.C. Thompson, & J. van Tol. 2005. ZooBank:
 the open-access register for zoological taxonomy: Technical
 Discussion Paper. Bulletin of Zoological Nomenclature.
 62(4):210–220.
 (http://www.biodiversitylibrary.org/part/42897)
 
 
 Polaszek, A., R. Pyle
 & D. Yanega. 2008. Animal names for all: ICZN, ZooBank,
 and the New Taxonomy. pp. 129–142. In: Wheeler, Q.D.
 (Ed.). The New Taxonomy. CRC Press, Boca Raton. 237 pp.
 (http://iczn.org/sites/iczn.org/files/Animal_names_for_all.pdf)
 
 
 Pyle, R.L. & E.
 Michel. 2008. ZooBank: Developing a nomenclatural tool for
 unifying 250 years of biological information. Pp. 39–50.
 In: Minelli, A., Bonato, L. & Fusco, G. (eds.) Updating
 the Linnaean Heritage: Names as Tools for Thinking about
 Animals and Plants. Zootaxa, 1950, 1–163. (http://www.mapress.com/zootaxa/2008/f/zt01950p050.pdf)
 
 
 > But we must look at
 names as more than just "names" and their date
 of
 > availability. In effect, names are
 the same as patents. They each purport to be
 > something novel and the author(s) of each
 want(s) to ensure s/he is the first to
 >
 propose that novel entity so registers it: patents with a
 patent office and, in our
 > case, names
 of animals with ZooBank (Priority is a major factor in
 registering
 > patents the same or more
 than it is with names -- at least monetarily!). But as
 > of now (with ZooBank), no
 "evidence" [= criteria of availability] of a
 proposed
 > name needs to be included in
 registration - only the citation of the work in
 > which it appears.
 
 The Code requires what the Code requires, and
 obviously any model that eliminates traditional publication
 from nomenclatural availability would have to include ALL
 non-publication-relevant Code-governed elements. For
 example, the registration system would need to include
 required fields to fulfill Art. 13.1. (which the current
 version of ZooBank lacks).  The way I like to describe it
 is, if you take any traditionally published description of a
 new species (or genus, or whatever), and you went through it
 with a highlighter pen to mark all the bits and pieces that
 are necessary to confer nomenclatural availability in the
 sense of the ICZN Code (e.g., the name itself, being
 binomial for species-group names, spelled according to Code
 rules; the designation of a type specimen; a description or
 definition that states in words characters that are
 purported to differentiate the taxon; etc.; etc.), then all
 the highlighted bits collectively constitute the totality of
 what is required to confer nomenclatural availability. 
 Everything else in the publication (all the non-highlighted
 text) is about the science of taxonomy.
 
 The point of what I have been advocating all
 these years is that we follow the intent of the Code to
 separate the legalistic aspects of nomenclatural
 availability from the scholarly aspects of taxonomy and
 related science.  All of this discussion on early online
 electronic publications, not to mention the VAST MAJORITY of
 other contentious issues related to zoological nomenclature
 (issue of determining priority, issues about prevailing
 usage, issues about availability of a published work, etc.)
 all relate to the traditional "publication"
 process.  These would mostly disappear in a universe where
 the act of registration is what confers availability, as
 separate and distinct from the process of publishing science
 in the traditional model of publication.
 
 > If registration were to replace
 "publication" as the determinant of
 availability
 > of a proposed name, then
 it would need to be much more than what ZooBank is
 > now. 
 
 YES!  Absolutely!  No one that I know would
 argue otherwise.
 
 > It
 would need to be what Doug Yanega has been advocating for
 years: a
 > central "journal"
 for all names so that all the other criteria of availability
 of a
 > proposed name meet with compliance
 of the required Articles of the ICZN
 >
 Code. 
 
 Well... not
 exactly.  The Code does not currently require peer review
 (which is the key difference between Doug's model and
 mine).  Also, I think Doug imagines more of a single
 Journal in which the full/traditional description is
 published as part of the registration process (i.e., all the
 highlighted bits, and all the un-highlighted bits as
 well).  In my view, the registration system would ONLY
 include the highlighted bits as required items, and would
 also have some optional bits as well (e.g., upload a photo
 or illustration of the type; create a link to a companion
 scientific article published in a traditional way outside
 the registration itself, but which includes all the
 peer-reviewed non-highlighted stuff).
 
 > But then, let's not call it a
 "journal" anymore because it really is not
 > [remember, we are trying to do away with
 "publication" as the medium of
 > verification of a new name].
 
 Agreed - I wouldn't call
 it a Journal.  I would call it a Registry.
 
 > ZooBank would have to
 then be a "repository" of all associated data of a
 name -
 > - the same as a patent office is
 with patents. Every patent has documentation
 > included with it. 
 
 ...More specifically, all associated data of a
 name AS REQUIRED BY THE CODE.  What I think you mean by the
 patent analogy includes a lot of the non-highlighted stuff
 as well.  In my view, that would all be published in the
 same way we currently publish all of our species
 descriptions now.  In fact, there would be only two changes
 in my proposed scenario:
 
 1)
 ZooBank would include a few more fields and stuff (to cover
 all requirements the Code; including e.g., Art. 13.1)
 
 2) The traditional publication
 would not carry any relevance to availability of the name --
 it would exist as a purely scientific document, not a
 quasi-legal, quasi-scientific document. All legalistic
 aspects of nomenclatural availability would exist within the
 Registration system.
 
 >
 ZooBank, then, should also have all the documentation
 > associated with every proposed name.
 Merely pointing to a "supposed"
 > publication outside of the registration
 system can and will be filled with abuse,
 > problems, and maybe even non-compliance
 (as we already see happening).  No,
 > in
 order for the system to work perfectly, ALL compliance for
 the availability of
 > the name MUST be
 met and deposited in the registration "repository"
 upon
 > registration.
 
 I'm not completely sure I understand what
 you are saying here. It sounds to me like you want to
 maintain the existing conflation of nomenclatural
 availability and scientific taxonomy, despite the fact that
 the Code itself explicitly seeks to avoid this conflation. I
 agree with the last part of what you said -- the
 Registration system I have in mind includes much more than
 the current ZooBank does, including required information for
 ALL provisions of the Code.  But the vast majority of the
 content of traditionally published new species names include
 much, much more (i.e., the highlighted bits are usually much
 less than the non-highlighted bits).
 
 > In that great pie-in-the-sky, this all
 seems perfect and with oodles of Petabyte
 > servers and unlimited funds supporting
 such a, all-encompassing registration
 >
 system, it might even be doable.
 
 That's hyperbolic.  At most, it would
 require about 10-20% more storage space than the current
 ZooBank database. The entire GNUB database (where ZooBank
 resides) is only 2.7GB; and the ZooBank part is probably
 only about half of this.  There are many orders of
 magnitude between 3GB and "oodles of Petabyte
 servers".  My laptop has 7TB of storage on it --
 enough to hold more than 2,000 copies of the entire GNUB
 database, or about 5,000 copies of ZooBank.
 
 Actually, now that I think
 about it, most of the hard drive space is consumed by the
 literature citations, not the name registrations.  So
 adding support for things like Art. 13.1 while eliminating
 all the metadata associated with the Published Work might
 actually result in a net DECREASE in the amount of disk
 space required for each registration.  Hard to say for
 sure.
 
 In any case... No,
 from a technological perspective, there is no
 "might" about it -- it very-much **IS** doable.
 
 > However, until employers
 (mainly in academia) do away with evaluating their
 > employee taxonomists based on where they
 publish (i.e., high ranking journals),
 >
 many taxonomists will not switch over to this
 zero-ranking
 > registration/repository
 system.
 
 And THAT is the
 crux of it!  It's not technological, it's
 social.
 
 So, imagine two
 worlds:
 
 1) The current
 world: Taxonomists publish good taxonomic science in high
 ranking journals, including descriptions of new species.
 Separately they register those new species in ZooBank. 
 Nomenclatural availability requires elements of both the
 ZooBank registration and the publication [for electronic
 publications now; probably all publications in the future].
 Chaos and confusion reign.
 
 2) The world I propose: Taxonomists publish
 good taxonomic science in high ranking journals, including
 descriptions of new species. Separately they register those
 new species in ZooBank.  Nomenclatural availability is
 contained entirely within the ZooBank registration.  Peace
 and harmony reign.
 
 Dude...
 even most taxonomists don't fully understand the
 subtleties of where the actual legal Code-compliance happens
 in publication vs. registration.  Do you sincerely believe
 that their *employers* will give a rip about the difference
 between options 1 & 2 above in terms of evaluations?
 
 Yes, yes, I've heard (many
 times) the argument , "But...but.... taxonomists will
 only do the registration of new names, and will never bother
 with publishing the science of the taxonomy they do!" 
 If that were a legitimate concern (it's not), then we
 would already be dominated by taxonomists who self-publish
 their minimal descriptions of new names with no associated
 science.  Hoser wouldn't be the outlier, he would be
 the norm.  The reason people like Hoser are outliers is
 because scientists care about their scientific
 reputations.  I'm not worried about employers
 evaluating taxonomists based on their publication track
 records -- I'm COUNTING on it! It's what will keep
 the science flowing!
 
 What
 I'm advocating is that we eliminate *entirely* the time
 we currently WASTE arguing about availability of
 "published works", and related issues of priority
 and early online publications, and electronic vs. paper, and
 prevailing usage, and blah, blah, blah, blah. [Note:
 we're talking about prospective new names in the future
 -- we still have to deal with all that other stuff for
 existing/historical names.]
 
 > We will, IMO, for the foreseeable future,
 be "publishing" (electronic or
 > print) and having to deal with the high
 ranking journals who tell US what to do
 >
 because they have many by the short-and-curlies because
 those taxonomists
 > need to keep their
 jobs and keep publishing in those high ranking journals.
 ....
 
 I COMPLETELY agree
 (sad as it may be).  However, this has no relevance to what
 I'm proposing.  All I'm saying is that we should
 consolidate the legalistic aspects of nomenclatural
 availability in ONE place (rather than two, that have to be
 cross-checked against each other), and that we follow the
 wisdom laid out in the Code to SEPARATE taxonomy from
 nomenclature.  Taxonomists will still continue to publish
 their science in high-ranking journals, and employers will
 continue to evaluate them based on the quality &
 quantity of the science they produce (rightly or wrongly). 
 Almost no one will even notice that the burden of
 nomenclatural availability shifted subtly from being spread
 across two separate events (publication and registration) to
 being consolidated in one event (registration). What they
 WILL notice is that all these arguments about availability
 (or not) of "published works", and arguments about
 the precise moment at which a published work became
 available in the sense of the Code, will disappear. Then we
 can all go back to documenting biodiversity before it's
 gone.
 
 > And registering
 names in ZooBank that point to where they are
 "published".
 
 I
 don't care if the registration points to one (or more)
 publications or not.  I do care that we avoid the current
 situation where all future taxonomists must forevermore
 consult two separate sources (registration and publication)
 to determine nomenclatural availability.
 
 Phew....
 
 Aloha,
 Rich
 
 Richard L. Pyle, PhD
 Database
 Coordinator for Natural Sciences | Associate Zoologist in
 Ichthyology | Dive Safety Officer
 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
 http://hbs.bishopmuseum.org/staff/pylerichard.html
 
 
 
 



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