[Taxacom] are early online publications code-compliant?

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Mon Apr 13 18:28:28 CDT 2015


PS: We also have the problem (which we have always had) of new species group names being based on fictional type specimens. Such names are presumably unavailable, but their availability cannot be determined from the work itself. Therefore, availability will always depend on some external considerations. I'm not sure if fictional types can be distinguished from lost types, so things get complicated ...

Stephen

--------------------------------------------
On Tue, 14/4/15, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 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>, deepreef at bishopmuseum.org
 Cc: taxacom at mailman.nhm.ku.edu, gread at actrix.gen.nz
 Received: Tuesday, 14 April, 2015, 12:24 PM
 
 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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