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

Thu Jan 28 14:24:58 CST 2016

Let us briefly recap the important points: 

The Amendment was issued in order to appease an unstoppable worldwide shift to electronic publishing. The ICZN is worried that it may not survive if it doesn't change with the times and appease the majority of the taxonomic community.

So, a protocol for electronic publication of new taxon names was, rather hastily it seems, put together. Lots of authors and publishers have subsequently been diligently preregistering articles on ZooBank, etc., for the sole purpose of making the online first versions available from the date that they are published online.

Problem: The Code states that preliminary versions published online cannot be made available, but fails to define "preliminary version"! This is so despite the pleas of Commissioner Krell for clarification before the Amendment was issued! Curious ...

Several people (including John Noyes) object that unpaginated versions not yet assigned to volume/issue are preliminary versions, but many (most?) other people deny that these count as "preliminary versions". This uncertainty creates uncertainty as to the exact date that many works and new names became available (in the sense of the Code), which causes problems for citation and also determination of priority, and means that a lot of work spent on ZooBank preregistrations may in fact have been a waste of time!

The "metadata" solution represents an attempt, after the fact, to define "preliminary version" is such a way as to avoid the above problem. It does avoid the above problem, but to what extent is it actually written into the Code? Is it a plausible interpretation of the Code as written, or is it just something concocted to try to solve the problem post hoc, with no "official status"?

The upshot of all this is that despite the attempts of the ICZN to appease the wider taxonomic community, they have failed to create a workable protocol for online first publication. It only works for one very specific publishing model, and we all by now know which one!

Stephen

--------------------------------------------
On Fri, 29/1/16, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: Re: [Taxacom] Important note Re: two names online published - one    new species
 To: "'Laurent Raty'" <l.raty at skynet.be>, taxacom at mailman.nhm.ku.edu
 Received: Friday, 29 January, 2016, 7:58 AM

 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.

 This
 "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.

 I
 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
 could?)

 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.

 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

 > -----Original Message-----
 > 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
 species
 > 
 > 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. 8.1.3.2 not
 satisfied).
 > 
 >
 Cheers, Laurent -

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