[Taxacom] Important note Re: two names online published - one new species

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Thu Jan 28 15:49:12 CST 2016

Yeah, but Donat, we all know that literature accessibility is your particular focus. Such a focus may prevent you from seeing the bigger picture. There is not much point having accessible taxonomic literature if there is a lack of proper regulation on what names are being used for which taxa.


On Fri, 29/1/16, Donat Agosti <agosti at amnh.org> wrote:

 Subject: RE: [Taxacom] Important note Re: two names online published -	one	new species
 To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Friday, 29 January, 2016, 10:42 AM
 What I am saying is that
 the house never collapses because of this kind of missing
 bricks, Rather the opposite, if a publication is open
 accessible and registered in Zoobank then we don't have
 your bricks anymore.
 The problem of names
 is, that the original literature is not accessible and has
 never been compiled. A problem of the past and anyways, the
 system you defend is so broken anyways and rather becoming
 obsolete rapidly, especially with this sort of
 -----Original Message-----
 From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
 Sent: Thursday, January 28, 2016 10:15
 To: taxacom at mailman.nhm.ku.edu;
 Donat Agosti <agosti at amnh.org>
 Subject: Re: [Taxacom] Important note Re: two
 names online published - one new species
 While I
 agree that nomenclatural priority is not "a
 priority" in the wider scheme of things, buildings are
 made out of individual bricks, and a crumbly brick in the
 wrong place can bring down the whole building. We need to
 get nomenclatural priority sorted out so to minimise the
 instability of different people using different names for
 the same taxon, thereby causing confusion that could hinder
 wider issues. Do you think that biosecurity or conservation
 managers want to have to keep track of who is using what
 name for which taxa? Besides, there is a whole industry
 nowadays of "aggregators" who rely on fixed names
 for taxa, or else their websites and databases become too
 complex to be of any practical use.
 On Fri, 29/1/16, Donat Agosti <agosti at amnh.org>
  Subject: Re:
 [Taxacom] Important note Re: two names online published
 -    one    new species
  To: "taxacom at mailman.nhm.ku.edu"
 <taxacom at mailman.nhm.ku.edu>
  Received: Friday, 29 January, 2016, 9:56 AM
  The issue is, that we
  neither now nor have access to the
 publications and the  names therein. If all articles would
 have to be registered  at Zoobank, irrespective if they ore
 e-only or not and a pdf  copy is available, and the names
 are registered at zoobank,  then we do not have this
 problem solved at once.
 We have all this in place, no
 needs be developed, but we keep bridling at this  option
 and keep discussing things that we will not and  cannot
 control with our system.
 Furthermore, if we want taxonomy to play a role  in life
 sciences we need to convert to such as system. A  system,
 that also allows mining content, or even better  provide
 the content in a form that third parties can use,  link and
 thus make our data part of big data.
  Only this openness will raise
 the value of new research, new data, the creation of 
 specialists who can make sound taxonomic (scientific 
  discussion on this list serve is a
 great disservice to the  community, not least because
 priority is such as minuscule  problem in understanding the
 diversity of life. It just  gives the wrong impression
 where the priorities of our  community is. The problem, the
 huge murderous problem is,  that we even today do not know
 what we describe as new  species, how they look like, can
 provide a link from GenBank  or BOLD to the respective
 taxonomic treatment that everybody  can consult, finds link
 to external resources, and  ultimately can use the data for
 their purpose - one of the  most important is to save
 diversity of life.
 -----Original Message-----
  From: Taxacom
 [mailto:taxacom-bounces at mailman.nhm.ku.edu]
  On Behalf Of Richard Pyle
 Sent: Thursday,
  January 28, 2016 7:58 PM
  To: 'Laurent
 <l.raty at skynet.be>;
  taxacom at mailman.nhm.ku.edu
  Subject: Re: [Taxacom] Important note Re:
 two  names online published - one new species
  I agree
 with everything
  Laurent says below, but I
 don't see that as the real  problem.
  I believe the
 scenario is not as rare as some people would  believe; and
 indeed may be increasingly common:
  1) Journal issues a
 provisional electronic edition online, and clearly
 indicates  it as such (no LSID)
  2) A
 revised version,
  including LSID (and
 properly registered with archive, etc.)  is posted online,
 and the correct date of publication  indicated. Pagination
 is from 1-20.
  3) An
 important error is discovered, and a revised version is 
 posted online, replacing the previous one, and the website 
 (but not the PDF) indicates that it was revised.  The PDF 
 contains the original date, and Pagination is 1-20.
  4) A paper edition is produced, which
 includes  the corrected error, and indicates the correct
 date of  publication for the paper edition. Pagination is
  Each of the
 above happens on a
  different date, in the
 chronological order indicated.
  Most of us would probably
 agree that #1 is not published in the sense of the Code, 
 based on the missing LSID.  Even if there was an LSID 
 included, we could probably all agree that Art. 9.9
 applies,  and it's not published in the sense of the
  At the time #2 was
  (on the date indicated within
 the work itself), it was  intended by the publisher as the
 "version of  record".  There is no evidence in
 the work itself, or  on the website, that it's not the
 final version. 
  So, how
 do we interpret #3?
  Is it the
 "real" version of record, retroactively  making
 #2 unavailable under Art 9.9?  Is it a distinct  published
 work, establishing a new objective synonym and  homonym
 that we must track?  Assuming both #2 and #3  include the
 same ZooBank LSID, which version is the LSID 
 "actually" associated with? Does it matter which 
 version is deposited in an archive?  What if neither 
 version is ever deposited in the intended archive?  What
 if  both are?
  Or, does
  depend on the nature of the error that
 was corrected?  Examples could include:
 Correction of the
  word "teh" to
 "the" in the abstract
  - Addition
 of an accent to a character in an  author's name
  - Revised or corrected map
 showing the distribution of the taxon
  Correct spelling of the genus name for a new
 species-group  name
  - Altered spelling of
 the new
  species-group name itself
  - Addition of the
  location of
 the collection where the type specimen is to be 
  - etc., etc.
  Some of these have relevance to
 nomenclature,  some do not.  Does that matter in our
 determination of  which edition is the "version of
 record" that  should be considered as part of the
 public and permanent  scientific record, and thereby
 represent the date of  availability for purposes of
 nomenclatural priority? Do we  need an enumeration of all
 possible changes that do result  in a changed "version
 of record"?
  And what
 about the changed
  page numbers in the paper
 edition?  For those who don't  like the
 "metadata" argument, are you suggesting  that the
 paper edition represents a new published work (with 
 objective synonyms and homonyms) simply because the paper 
 edition is not an "exact copy" of the electronic 
 edition?  Even if the page numbers were identical, how
 does  one define "exact copy" in such a way that
 one  physical object consisting of paper pages with ink on
 them  is an "exact copy" of a binary object
 stored on a  computer?
 I'm sure we
  could argue about it enough
 to come to some sort of  consensus on this specific
 example.  But there are a  near-infinite number of
 possible examples out there, and the  scope of possible
 examples will probably continue to expand  in the future.
 Why?  Because despite what some have argued,  electronic
 dissemination of scientific information is still  very much
 in its infancy. The playing field is constantly 
 evolving.  Electronic publication began as a digital 
 representation of a paper work (e.g., a scanned image of
 the  actual printed pages).  As time goes on, publishers
 are  increasingly exploiting the power of electronic
 information  and its dissemination (and rightly so). As we
 move closer to  a world that resembles the vision of a
 Semantic Web, the  parallels between the old paper-based
 publication world and  modern electronic means of
 information exchange will  evaporate to the point where
 they are essentially  unrecognizable.
 isn't going away; it's going to  get worse. Even
 God Herself would be challenged to come up  with wording in
 a revised Code that accommodated all  conceivable
  completely understand why we still cling to
 the old notions  of "publication", where the
 economics  of  producing multiple subtly different
 versions of a work  produced as thousands of copies on
 paper effectively ensured  that problems of the sort
 described above were rare  outliers. The new electronic
 information dissemination model  completely changes the
 cost-effectiveness of producing  incrementally altered
 versions of pseudo-static works.  We  could
 "encourage" publishers to respect our 
 traditional notions of publication, but how effective will 
 that campaign be?  And do we really want to burden the 
 field of taxonomy with additional handicaps? (Even if we
 are tasked with
  finding a way to maintain
 nomenclatural stability in the  context of this rapidly
 changing playing field. I find it  helpful to step back and
 remember what, exactly,  "stability" means, and
 how, fundamentally, we  attempt to achieve it.
  - A system of latin
 universally shared and used as labels for taxa
  - A mechanism for unambiguously linking the 
 names to the biological world through type specimens
  - A mechanism for unambiguously establishing 
 priority among potentially competing names (subjective 
 synonyms; homonyms)
 That's really the essence of nomenclatural 
 stability.  We still need a complex series of rules to
 deal  with legacy names until a complete and universal
 registry  exists (i.e., the uber-LAN).  However, if we
 continue to  try to force-fit the rapidly changing modes of
 electronic  information exchange in science into a model
 that was  fundamentally designed around ink-on-paper
 documents, these  problems will continue to dominate our
 time and energy.
  We can
 probably maintain the
  status quo for a few
 more years; but if we don't get  serious about
 fundamentally adjusting (and future-proofing)  our system
 of nomenclatural availability (and, by extension, 
 stability), then the "problems" we fret about
 now  will seem trivial compared to what's ahead.
 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
  (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org 
  > -----Original
  > From:
 Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
  On Behalf Of
  > Laurent
  > Sent: Thursday, January 28, 2016
 3:30  AM  > To: taxacom at mailman.nhm.ku.edu 
 > Subject: Re: [Taxacom] Important note Re:
  two names online published -
 > one new
  > Producing
 "exact copy" (bit-for-bit) of a pdf file is, on 
 the  > contrary, one of the easiest  things to do. Just
 select the file in  >  your file manager and hit
 <Ctrl>-C, <Ctrl>-V:
  done. Of
 course, in a
  > vanishingly
  small proportion of the cases, you may get a 
 "mutation",  > and end up with  a corrupt
 file. However, this is not a real problem,  > as it is
 also extremely easy to check that  a file is an "exact
 copy" of another file, using  things like hash values
 / checksums.
  > On the other hand, checking whether
  the non-metadata portion of the
  content and layout that
 will be displayed when viewing a pdf  file is  > the
 same as that which will be  displayed when viewing another
 pdf  >  file, that otherwise differs, is a nightmare.
 (Most likely  plain impossible.) If you adopt any
  > concept that departs
 from the
  "exact", bit-for-bit
 copy, you basically  > accept, knowingly, never to be
 able to  check for the integrity of a  > work in  pdf
  > The
  problem (?) is that some publishers NEVER
 produce pdf files  that  > are "exact
 copies". If  you download twice the same work from,
 say,  > http://onlinelibrary.wiley.com/ , the 
 two files that that you get will  > be  "exact
 copies" of each other. But if you do the  same from,
 eg.,  > http://www.tandfonline.com , the
 files  will differ: each downloaded "copy"
  > is in fact a *new* pdf file, generated
 on  demand by the website, with  > each page 
 "tagged" in the margin with your IP and the time 
 of download. If "copy"
  "exact copy", this method
 does not produces  "copies" of a single  >
 work at  all, it produces a unique file at each download,
 and nothing
  > is
 published (Art. not
 Cheers, Laurent -
  Taxacom Mailing List
  Taxacom at mailman.nhm.ku.edu
  The Taxacom Archive back to 1992 may be 
 searched at: http://taxacom.markmail.org
  Channeling Intellectual
  Exuberance for 29 years in 2016.
  Taxacom Mailing List
  Taxacom at mailman.nhm.ku.edu
  The Taxacom Archive back to 1992 may be 
 searched at: http://taxacom.markmail.org
  Channeling Intellectual
  Exuberance for 29 years in 2016.

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