[Taxacom] Important note Re: two names online published - one new species
Donat Agosti
agosti at amnh.org
Thu Jan 28 16:01:28 CST 2016
No, my main focus is this http://www.nature.com/nature/journal/v416/n6877/full/416115b.html (but unfortunately you can't read it) out of which open access followed. I guess, we are rather 14 years ahead
d
-----Original Message-----
From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
Sent: Thursday, January 28, 2016 10:49 PM
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; 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
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.
Stephen
--------------------------------------------
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 discussions.
d
-----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
Donat,
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.
Stephen
--------------------------------------------
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.
Donat
-----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.
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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