[Taxacom] Nomenclatural availability of preliminary electronic versions of taxonomic papers

Scott Thomson scott.thomson321 at gmail.com
Fri Oct 16 16:01:24 CDT 2015


Heya Richard,

enjoy your <rant> ... </rant> style, must actually code that...

Anyway, heading into the future I agree, moving to a registration
acceptance of availability and away from a publication one makes sense.
Books are wonderful things, I collect them but even as a self professed
bibliophile I accept that they are outdated and do not work with our modern
system of information exchange.

We do everything with algorithms these days, we taxonomists are fine with
using algorithms to get our trees that we publish (be it PAUP, TNT,
Mesquite, whatever they are all algorithms). There comes a point where you
need to realise and accept that a method you are doing is archaic. I accept
it cannot be changed overnight, and in the meantime it will require
fiddling with the old system enroute to a better way. Also some poor group
is going to have to register and set in place every previously described
species (about 2 million I believe) in whatever is the accepted method. On
a practical side your also going to need one awesome server and guaranteed
funds to keep it running. Your not going to store the data for some 7 - 8
million species on a university server or in cloud space.

Also on this, anyone thought of putting into a future version of the code
an objective for the future? That is that as of X date (say 5 years away)
the code will move to some system, in the meantime people can use the old
way or try the new way, then with less numbers doing it we can test and
refine the problems before the system is fully realised. I say this
because, to me, the current issues with electronic publication has in part
come about because something was permitted (electronic publication) and we
are forever trying to play catch up to tweak it since. With major changes,
particularly on the internet, it is better to alpha test (in house), beta
test (selected public testing) open beta (anyone can try it) then release
and in that order. Why because in programming no matter how much you think
you "idiot proof" (yes thats the programming term for it) a software or
method someone finds a way to stuff it up. In the end its called Quality
Assuarance.

Just my thoughts on this.


 Cheers, Scott




On Fri, Oct 16, 2015 at 5:17 PM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:

> <rant>
>
> The answer has always been obvious to me.  In the age of the emerging
> internet (and yes, it is very-much still emerging -- we've only just begun
> to see the changes to information exchange amongst humans), we need to
> fundamentally re-think how we establish nomenclatural availability (at
> least for as long as we continue to use Linnean nomenclature).
>
> For 250 years, the practice of taxonomy has grown in a context where the
> primary mechanism of information exchange among humans was ink symbols
> affixed to "very thin slices of wood" (as Paul Kirk likes to say). For more
> than a hundred years, the Codes of nomenclature have been framed around
> that fundamental foundation (paper-printed works).  Now, and in the
> near-term future, the primary mechanism of information exchange is to
> transmit binary data encoded in standardized formats (UTF-8, JPEG, PDF,
> etc.) via the internet.  The Commission had to scramble to accommodate this
> rapid paradigm shift in the form of an Amendment to the Code, but that was
> really just a temporary band-aid.
>
> For the next edition of the Code, I sincerely hope we can fundamentally
> change the way in which new names are established and anchored to
> biological organisms. Specifically, rather than awkwardly try to force-fit
> our legacy system (ink-on-paper) into an electronic form (e.g., PDFs, with
> arbitrary and artificial "pages"), we should re-engineer the entire process
> in such a way that we EMBRACE the potential for electronic information
> exchange and management.  The simplest step in that direction is to
> de-couple the scientific notion of "Publication" from the legal process of
> nomenclatural availability.  In other words: "registered=available".
>
> The devil is in the details, of course -- and in this case, it's about
> what "registered" actually means.  I'm not talking about what ZooBank
> currently does.  I'm talking about a brave new approach that re-crafts the
> rules for nomenclatural availability into a form that can be translated
> into pure logical rules that computer algorithms can rigorously enforce.
> If done right, Homonymy can be eliminated entirely, Synonymy can likely be
> reduced (and when it exists, much more easily managed), and we will NEVER
> AGAIN have to argue about what constitutes a "published work" in the sense
> of the Code.  This is just the tip of the iceberg for how we can
> simultaneously improve nomenclatural stability AND increase access to
> information through embracing the electronic information paradigm, rather
> than futzing around the edges of it (as we do now).
>
> </rant>
>
> Aloha,
> Rich
>
>
> > -----Original Message-----
> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> > Of Roderic Page
> > Sent: Friday, October 16, 2015 7:09 AM
> > To: taxacom at mailman.nhm.ku.edu
> > Cc: John Noyes
> > Subject: Re: [Taxacom] Nomenclatural availability of preliminary
> electronic
> > versions of taxonomic papers
> >
> > Hopefully eBooks (similar to Kindle), HTML, XML will never be accepted as
> > pubs under the Code because they are dynamic.
> >
> > And that, in a nutshell, is why some of us despair at the current state
> of
> > taxonomy. Do we really wish that some of the more innovative means of
> > publishing (never mind what will come in the future) are never accepted.
> > Never, really?
> >
> > Regards
> >
> > Rod
> >
> > ---------------------------------------------------------
> > Roderic Page
> > Professor of Taxonomy
> > Institute of Biodiversity, Animal Health and Comparative Medicine
> College of
> > Medical, Veterinary and Life Sciences Graham Kerr Building University of
> > Glasgow Glasgow G12 8QQ, UK
> >
> > Email:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
> > Tel:  +44 141 330 4778
> > Skype:  rdmpage
> > Facebook:  http://www.facebook.com/rdmpage
> > LinkedIn:  http://uk.linkedin.com/in/rdmpage
> > Twitter:  http://twitter.com/rdmpage
> > Blog:  http://iphylo.blogspot.com
> > ORCID:  http://orcid.org/0000-0002-7101-9767
> > Citations:
> > http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> > ResearchGate https://www.researchgate.net/profile/Roderic_Page
> >
> >
> > On 16 Oct 2015, at 17:48, John Noyes
> > <j.noyes at nhm.ac.uk<mailto:j.noyes at nhm.ac.uk>> wrote:
> >
> > Rod,
> >
> > What you are talking about here (E-books etc.) are not publications under
> > the ICZN so they are not really relevant. We are only talking about
> e-pubs
> > that are accepted under the current Code. Hopefully eBooks (similar to
> > Kindle), HTML, XML will never be accepted as pubs under the Code because
> > they are dynamic.
> >
> > John
> >
> > John Noyes
> > Scientific Associate
> > Department of Life Sciences
> > Natural History Museum
> > Cromwell Road
> > South Kensington
> > London SW7 5BD
> > UK
> > jsn at nhm.ac.uk<mailto:jsn at nhm.ac.uk>
> > Tel.: +44 (0) 207 942 5594
> > Fax.: +44 (0) 207 942 5229
> >
> > Universal Chalcidoidea Database (everything you wanted to know about
> > chalcidoids and more):
> > www.nhm.ac.uk/chalcidoids<http://www.nhm.ac.uk/chalcidoids>
> >
> > From: Roderic Page [mailto:Roderic.Page at glasgow.ac.uk]
> > Sent: 16 October 2015 17:40
> > To:
> > taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>
> > Cc: Laurent Raty; John Noyes
> > Subject: Re: [Taxacom] Nomenclatural availability of preliminary
> electronic
> > versions of taxonomic papers
> >
> > Isn’t part of the issue here that we are applying one notion of locating
> text
> > (page number) to a situation where the notion of “page” may be fuzzy at
> > best?
> >
> > Documents such as web pages or eBooks either don’t have pages, or the
> > “page” may change depending on font size, device screen, etc.
> >
> > People who develop software to annotate web pages, eBook pages, etc.
> > have multiple ways of locating bits of text, such as XPaths [fragments
> of the
> > HTML or XML that may underly the document], text fragments before and
> > after, number of characters into the document, etc. These work, as anyone
> > highlighting text in the Kindle app or iBooks, or indeed Google Docs or
> Word
> > will attest.
> >
> > The nature of “publication" has changed, so we need to embrace more
> > general notions of location in documents. This is a problem others have
> > faced, and solved.
> >
> > Regards
> >
> > Rod
> >
> > ---------------------------------------------------------
> > Roderic Page
> > Professor of Taxonomy
> > Institute of Biodiversity, Animal Health and Comparative Medicine
> College of
> > Medical, Veterinary and Life Sciences Graham Kerr Building University of
> > Glasgow Glasgow G12 8QQ, UK
> >
> > Email:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
> > Tel:  +44 141 330 4778
> > Skype:  rdmpage
> > Facebook:  http://www.facebook.com/rdmpage
> > LinkedIn:  http://uk.linkedin.com/in/rdmpage
> > Twitter:  http://twitter.com/rdmpage
> > Blog:  http://iphylo.blogspot.com<http://iphylo.blogspot.com/>
> > ORCID:  http://orcid.org/0000-0002-7101-9767
> > Citations:
> > http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> > ResearchGate https://www.researchgate.net/profile/Roderic_Page
> >
> > On 16 Oct 2015, at 16:33, John Noyes
> > <j.noyes at nhm.ac.uk<mailto:j.noyes at nhm.ac.uk>> wrote:
> >
> > The page number must definitely be fixed. Otherwise it might become a
> > nightmare, or at best a confusing pain, to give a meaningful citation to
> a
> > nomenclatural act in on-line or even hard copy databases/catalogues,
> > especially where longer publications are concerned. That is the absolute
> crux
> > of the matter. If the text and other associated details remain the same
> then I
> > have absolutely no problem. It is the change in page number between early
> > pubs and final pubs that makes all the difference!
> >
> > John
> >
> > John Noyes
> > Scientific Associate
> > Department of Life Sciences
> > Natural History Museum
> > Cromwell Road
> > South Kensington
> > London SW7 5BD
> > UK
> > jsn at nhm.ac.uk<mailto:jsn at nhm.ac.uk>
> > Tel.: +44 (0) 207 942 5594
> > Fax.: +44 (0) 207 942 5229
> >
> > Universal Chalcidoidea Database (everything you wanted to know about
> > chalcidoids and more):
> > www.nhm.ac.uk/chalcidoids<http://www.nhm.ac.uk/chalcidoids>
> >
> > -----Original Message-----
> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> > Of Laurent Raty
> > Sent: 16 October 2015 16:21
> > To:
> > taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>
> > Subject: Re: [Taxacom] Nomenclatural availability of preliminary
> electronic
> > versions of taxonomic papers
> >
> > On 10/16/2015 03:47 PM, Scott Thomson wrote:
> >
> > In response to Laurent. I agree there seems to be no real and absolute
> final
> > version if you count the adding of #tags as a part of the document.
> >
> > Well, I think that, ideally, it should (have) be(en) possible for the
> user to
> > assess the integrity of a work distributed electronically. If a
> publication had
> > been defined as a given distributed file, with a fixed sequence of
> bytes, this
> > would (have) be(en) fully straightforward--all it requires is that a
> checksum
> > value be released together with the original work. This is fairly
> standard
> > practice for other types of files distributed through the Internet.
> > Assessing the integrity of a "content and layout", if the file is
> allowed to
> > change, is at best a nightmare.
> >
> > OTOH, I'm not sure there's a real, deep, qualitative difference between
> > allowing file alteration as a result of a change in a download date and
> ip
> > address added to the footer, and allowing file alteration as a result of
> a
> > change in a page number added to the header.
> > Thus if you *must* allow the file to change, is it really worth the
> effort to
> > require that the page numbers be fixed...?
> >
> > L -
> > _______________________________________________
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> >
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> >
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> >
> > Celebrating 28 years of Taxacom in 2015.
>
> _______________________________________________
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>
> Celebrating 28 years of Taxacom in 2015.
>



-- 
Scott Thomson
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