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

Donat Agosti agosti at amnh.org
Thu Jan 28 15:42:18 CST 2016

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 discussions.

-----Original Message-----
From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz] 
Sent: Thursday, January 28, 2016 10:15 PM
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> wrote:

 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
 technology 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  decisions).
 Again, this
 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
 Raty' <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
 following 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 364-384.
 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 Code.
 At the time #2 was obtainable
 (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 it
 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  deposited
 - 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.
 "problem" 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 scenarios.
 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
 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
 words 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  http://hbs.bishopmuseum.org/staff/pylerichard.html
 > -----Original
 > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf Of
 > Laurent Raty
 > 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
 an "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 "copy"
 > 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 format.
 > 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"
 > means
 "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 -
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 Channeling Intellectual
 Exuberance for 29 years in 2016.
 Taxacom Mailing List
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 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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