[Taxacom] FW: ICZN & Bacteriological Code

Fri Nov 12 17:18:32 CST 2010

On the subject of LSIDs, Rich et al. shout the benefits from the rooftops, but 
there are also problems, and it isn't clear to me if there is a net benefit. We 
are now adding considerable additional complexity to an already highly complex 
and messy system (i.e., zoological nomenlature) by assigning multiple numeric 
codes to stand in for names which are often not even available names, and in 
some cases even entirely fictitious (i.e. based on radical misnterpretations by 
man and/or machine). One example is an alleged coccinellid beetle name (a 
between Code homonym with a fungus):
http://www.organismnames.com/details.htm?lsid=812100
it is assigned LSID: urn:lsid:organismnames.com:name:812100
as far as I can tell, it is entirely fictitious, probably as a result of 
confusion due the between Code generic homonym Poria!
When ION, as in this case, doesn't cite the original authority/date for a name, 
that means that they got the name from a subsequent publication(s), which they 
cite on the page. The only publication they cite for this name is one written in 
Korean about the fungus. The PDF is available online and there does not appear 
to be any reference to anything other than the fungus...

Stephen

________________________________
From: Richard Pyle <deepreef at bishopmuseum.org>
To: Chris Thompson <xelaalex at cox.net>; mivie at montana.edu; Frank.Krell at dmns.org
Cc: taxacom at mailman.nhm.ku.edu
Sent: Sat, 13 November, 2010 11:58:38 AM
Subject: Re: [Taxacom] FW: ICZN & Bacteriological Code

Thanks, Chris -- this is very helpful historical context. Obviously, the
world of electronic information storage and dissemination has changed
somewhat in the past 15 years; and it continues to change (and will continue
to change) in time.

I am less pessimistic than you concerning the future of ZooBank.  The
prototype has been in continuous operation since 1 January 2008, with only a
few temporary periods of inaccessibility.  It contains 73,296 registered
names, 29,411 Published Works, and 11,828 Authors, and it grows by an
average of about 50 new names/month over 2010. I agree with you that the
ITZN does not have any financial resources to develop ZooBank, and it's top
priority should be focused on securing funding for the Secretariat.  ZooBank
development has already been funded by a number of small grants from GBIF,
plus substantial support from NBII/PBIN, and is currently supported
indirectly and in part by a larger collaborative NSF grant that began 1
October of this year.  Another large-scale proposal for further development
(in the context of the Global Names Architecture) is currently pending at
NSF, and will most likely be re-submitted if declined on its first pass.
Indeed; there are ongoing discussions between the ICZN Secretariat and ZR
for defining the best ways for collaboration on ZooBank.

Your last point reminds me that there remains tremendous levels of
misunderstanding about LSIDs (and persistent identifiers in general), and
how these serve a completely different function from the text-string
scientific names we all know and love. The notion that there is some sort of
"agenda" to "replace" text-string scientific names with such persistent
identifiers can only be described as ludicrous.

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: Chris Thompson [mailto:xelaalex at cox.net] 
> Sent: Friday, November 12, 2010 12:42 PM
> To: Richard Pyle; mivie at montana.edu; Frank.Krell at dmns.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] FW: ICZN & Bacteriological Code
> 
> Richard, et alia:
> 
> Fifteen years ago we dealt with these questions.
> 
> See our draft version of the ICZN (Published online and on 
> paper in June 1995).
> 
> We, the editorial committee, proposed to follow the lead of 
> the bacteriologists and allow electronic publication so long 
> as there was "International notification," that is, the 
> publication was indexed by the Zoological Record. For the 
> draft, ZR put online a simple system to allow people to check 
> whether their publications were indexed. That simple system 
> continue to this day as ION (go to 
> http://www.organismnames.com/ ). And we got an agreement ZR 
> (then BIOSIS) that they would index all publications 
> submitted to them. Thomson-Reuters continues to do this.
> 
> At the time of the discussion of the draft there was also a 
> listserver, like Taxacom, available. The majority of the 
> people on that listserver approved of this approach to 
> solving the growing digital publication media, etc. 
> Unfortunately, many other old fashion zoologists objected and 
> our approach was abandon.
> 
> And today we struggle with ZooBank***, which probably fail as 
> the costs are too great for the ITrustZN, the idea of 
> "International Notification" should be re-considered. It cost 
> the community NOTHING. And already indexes about 90% of the 
> names published. And what it misses are the obscure private 
> paper journal that some taxonomists still publish for themselves!
> 
> We also put in provisions following the bacteriologists for 
> List of Available Names in Zoology (Art. 79) so groups could 
> clean up their taxa and abandon all the old junk that could 
> not be identified / verified. But so far no-one has taken up 
> this option.
> 
> The problem is that the majority of our community still lives 
> in the past.
> 
> ***The other thing about ZooBank, when the old timers realize 
> its agenda is to replace simply understandable names, like 
> Leptomydas notos, with lSIDs, such as 
> 26BD416E-6E07-44FB-9450-9AACE98E9021 it will be abandoned, etc.
> 
> Oh, well ...
> 
> Chris Thompson
> from home
> 
> -----Original Message-----
> From: Richard Pyle
> Sent: Friday, November 12, 2010 4:34 PM
> To: mivie at montana.edu ; Frank.Krell at dmns.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] FW: ICZN procedure question
> 
> 
> Indeed!
> 
> As was pointed out to me off-list, the bacteriological Code 
> has already
> accomodated e-only publications since 2005.  So really we're 
> talking about
> botanical and zoological communities playing catch-up.
> 
> But, of course, our communities are somewhat larger and more 
> heterogenous,
> and we have a much longer legacy of historical names to deal 
> with (unless,
> like the bacteriologists, we're comfortable with establishing 
> a definitive
> list of available names and abandaoning all previous names 
> not on the list
> -- which I don't think we'll be ready for anytime soon).
> 
> But in any case, I think Michael's point is, the reality is 
> increasingly
> clear, and we can either ignore that, or find ways to deal 
> with it as best
> we can, keeping in mind not just our needs, but the needs of 
> the generaitons
> to follow. Indeed, the issues about long-term archiving are 
> for them, not
> us.
> 
> Aloha,
> Rich
> 
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu
> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> > Michael A. Ivie
> > Sent: Friday, November 12, 2010 10:40 AM
> > To: Frank.Krell at dmns.org
> > Cc: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] FW: ICZN procedure question
> >
> > OK, it is time for a reality check. I like paper, I like
> > books. BUT, paper is GOING TO GO AWAY.  Can't change that.
> > Scientific names are going to be used, and they will
> > eventually be based on works without paper  REALITY.
> >
> > Our choice it to either manage this transition so that there
> > are some controls on the process, or lose control completely,
> > because the use of names is going to happen either within the
> > Code or the Code will be come an arcane and ignored document.
> >
> > Drop the idea of stopping change, get used to the idea that
> > even today paper publications are "the living dead," and come
> > up with a reasonable and useful way to manage what is coming.
> > It does not matter that a majority of the CURRENT taxonomic
> > community (including me) does not like this, it maters that
> > we lead in such a way that the FUTURE taxonomic community
> > considers our actions useful enough to use.
> >
> > Michael Ivie
> >
> > > Oops, I seem to have sent this to dipteryx only...
> > >
> > > -----Original Message-----
> > > From: Frank T. Krell
> > > Sent: Friday, November 12, 2010 8:23 AM
> > > To: dipteryx at freeler.nl
> > > Subject: RE: [Taxacom] ICZN procedure question
> > >
> > > Paul wrote:
> > > "I do not know if electronic publishing of scientific names
> > is going
> > > to happen (given that the Codes are retroactive, it is
> > possible that
> > > it already exists, for example if a future change of the Codes
> > > determines that all electronic publishing from
> > > 1 January 2000 onwards is accepted as effective/available.
> > > This is unlikely, but possible!), but the more 
> discussions I see on
> > > the topic, the more I get the feeling that the immediate
> > issue before
> > > us is formulating what exact conditions and requirements these
> > > Official Permanent Paper Copies will have to meet."
> > >
> > > Just to make clear: Electronic publishing of scientific
> > names has been
> > > happening for a while and continues to happen. Whether we set
> > > requirements or not for their availability, they have been and are
> > > entering the
> > > (printed) scientific record. Since most of us, I guess, 
> get most of
> > > their literature as pdfs, it is generally difficult to establish
> > > whether a print version of the document we read is in
> > existence. Most
> > > non-taxonomists don't care whether a print version exists
> > or not. So
> > > those names continue to enter the (still printed) 
> scientific record.
> > > The question is: Should the ICZN accomodate reality and set
> > rules with
> > > which the reality can work, or should we try to convince/force the
> > > e-only world to change their modus operandi? I guess this
> > would fail.
> > > I have advocated from the very beginning of ZooBank planning that
> > > ZooBank should include an archive of archival printouts (as far as
> > > xerocopy can be
> > > archival) of papers containing nomenclatural acts. 
> Limiting this to
> > > e-only publications could be a manageable start. This 
> would be only
> > > one archive
> > > (meaning: one fire = complete distruction; but it can be
> > printed again
> > > from the electronic archive).  However, better than no archive. A
> > > handfull archives around the globe would be even better,
> > but the ICZN
> > > can only suggest that. If the world doesn't want to play safe, at
> > > least the ICZN could do so and establish such an archive itself.
> > >
> > > Frank
> > >
> > > Dr Frank T. Krell
> > > Curator of Entomology
> > > Commissioner, International Commission on Zoological Nomenclature
> > > Chair, ICZN ZooBank Committee Department of Zoology Denver
> > Museum of
> > > Nature & Science
> > > 2001 Colorado Boulevard
> > > Denver, CO 80205-5798 USA
> > > Frank.Krell at dmns.org
> > > Phone: (+1) (303) 370-8244
> > > Fax: (+1) (303) 331-6492
> > > http://www.dmns.org/science/curators/frank-krell
> > >
> > > _______________________________________________
> > >
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > >
> > > The Taxacom archive going back to 1992 may be searched with
> > either of
> > > these methods:
> > >
> > > (1) http://taxacom.markmail.org
> > >
> > > Or (2) a Google search specified as:
> > > site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> > >
> > >
> >
> >
> > --
> > Michael A. Ivie, Ph.D., F.R.E.S.
> > Montana Entomology Collection
> > Marsh Labs, Room 50
> > 1901 S. 19th Ave
> > Montana State University
> > Bozeman, MT 59717-3020
> > USA
> >
> > (406) 994-4610 (voice)
> > (406) 994-6029 (FAX)
> > mivie at montana.edu
> >
> >
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The Taxacom archive going back to 1992 may be searched with
> > either of these methods:
> >
> > (1) http://taxacom.markmail.org
> >
> > Or (2) a Google search specified as:
> > site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with 
> either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as: 
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here 
> 
> 

_______________________________________________

Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

The Taxacom archive going back to 1992 may be searched with either of these 
methods:

(1) http://taxacom.markmail.org

Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  
your search terms here