[Taxacom] are early online publications code-compliant?
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Mon Apr 13 18:28:28 CDT 2015
2015
PS: We also have the problem (which we have always had) of new species group names being based on fictional type specimens. Such names are presumably unavailable, but their availability cannot be determined from the work itself. Therefore, availability will always depend on some external considerations. I'm not sure if fictional types can be distinguished from lost types, so things get complicated ...
Stephen
--------------------------------------------
On Tue, 14/4/15, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:
Subject: RE: [Taxacom] are early online publications code-compliant?
To: "'Neal Evenhuis'" <neale at bishopmuseum.org>, "'Frank T. Krell'" <Frank.Krell at dmns.org>, "'Sue Gardner'" <sgardner2 at unl.edu>, "'John Noyes'" <j.noyes at nhm.ac.uk>, deepreef at bishopmuseum.org
Cc: taxacom at mailman.nhm.ku.edu, gread at actrix.gen.nz
Received: Tuesday, 14 April, 2015, 12:24 PM
For "Registered Available" to work, either (1) the description would
need to be given on the registration form itself, or, (2) if
a citation to a published description is given, then the
existence of such would need to be verified. The problem
with (1) is that taxonomists would gain no vitation credit
for describing new taxa (unless the registrations themselves
were somehow included in the citation system). The problem
with (2) is that it might take too much work, particularly
for publications in obscure places.
Stephen
--------------------------------------------
On Tue, 14/4/15, Richard Pyle <deepreef at bishopmuseum.org>
wrote:
Subject: RE: [Taxacom] are
early online publications code-compliant?
To: "'Neal Evenhuis'" <neale at bishopmuseum.org>,
"'Frank T. Krell'" <Frank.Krell at dmns.org>,
"'Sue Gardner'" <sgardner2 at unl.edu>,
"'John Noyes'" <j.noyes at nhm.ac.uk>,
"'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>
Cc: taxacom at mailman.nhm.ku.edu,
gread at actrix.gen.nz
Received: Tuesday, 14 April, 2015, 12:14 PM
Thanks Neal; all
excellent points (as usual)!
> Registration in and of itself has
been
touted previously on this list (and
the iczn-
> list) as the simplest way to
deal with
when a name becomes available
(much
>
like what the
bacteriologists do).
One
point of clarification: what the
bacteriologists actually do is very different from what
Doug
and I (and others) have been
advocating. The
bacteriological registry
is a paper-based journal. The
actual
bacteriological names are published in whatever
publication they're published in,
according to rules
analogous to those of
Zoology. The Registration system is
simply publishing the name and link to the published
article
within the official journal
(IJSEM). Brian Tindall can speak
much more
definitively than I can, but I believe that the
availability of the name includes elements
within the source
publication and the
registry publication (analogous to the
current system for required registration of electronic
works
in Zoology).
The current
ZooBank model can
be described as "Registered +
Published = Available" (much like the
bacteriological
system). What Doug and I
advocate is best described as
either
"Registered = Available" (my flavor), or
"Registered = Published = Available"
(Doug's
flavor). There is actually a
continuum of millions of
possible
implementations between these two flavors,
depending mostly on the amount of required information
implied by the "Registered" part,
and the amount
of review implied by the
"Published" part.
More complete discussions of
these different models are available here:
Polaszek, A., M.
Alonso-Zarazaga, P. Bouchet, D.J. Brothers, N. Evenhuis,
F.-T. Krell, C.H.C. Lyal, A. Minelli, R.L.
Pyle, N.J.
Robinson, F.C. Thompson, &
J. van Tol. 2005. ZooBank:
the open-access
register for zoological taxonomy: Technical
Discussion Paper. Bulletin of Zoological Nomenclature.
62(4):210–220.
(http://www.biodiversitylibrary.org/part/42897)
Polaszek,
A., R. Pyle
& D. Yanega. 2008. Animal
names for all: ICZN, ZooBank,
and the New
Taxonomy. pp. 129–142. In: Wheeler, Q.D.
(Ed.). The New Taxonomy. CRC Press, Boca Raton. 237 pp.
(http://iczn.org/sites/iczn.org/files/Animal_names_for_all.pdf)
Pyle, R.L.
& E.
Michel. 2008. ZooBank: Developing
a nomenclatural tool for
unifying 250 years
of biological information. Pp. 39–50.
In:
Minelli, A., Bonato, L. & Fusco, G. (eds.) Updating
the Linnaean Heritage: Names as Tools for
Thinking about
Animals and Plants. Zootaxa,
1950, 1–163. (http://www.mapress.com/zootaxa/2008/f/zt01950p050.pdf)
> But
we must look at
names as more than just
"names" and their date
of
> availability. In effect, names are
the same as patents. They each purport to
be
> something novel and the author(s)
of each
want(s) to ensure s/he is the first
to
>
propose that novel
entity so registers it: patents with a
patent office and, in our
> case,
names
of animals with ZooBank (Priority is
a major factor in
registering
> patents the same or more
than it is with names -- at least monetarily!). But as
> of now (with ZooBank), no
"evidence" [= criteria of
availability] of a
proposed
> name needs to be included in
registration - only the citation of the work
in
> which it appears.
The Code requires what the Code requires,
and
obviously any model that eliminates
traditional publication
from nomenclatural
availability would have to include ALL
non-publication-relevant Code-governed elements. For
example, the registration system would need to
include
required fields to fulfill Art.
13.1. (which the current
version of ZooBank
lacks). The way I like to describe it
is,
if you take any traditionally published description of a
new species (or genus, or whatever), and you
went through it
with a highlighter pen to
mark all the bits and pieces that
are
necessary to confer nomenclatural availability in the
sense of the ICZN Code (e.g., the name itself,
being
binomial for species-group names,
spelled according to Code
rules; the
designation of a type specimen; a description or
definition that states in words characters
that are
purported to differentiate the
taxon; etc.; etc.), then all
the
highlighted bits collectively constitute the totality of
what is required to confer nomenclatural
availability.
Everything else in the
publication (all the non-highlighted
text)
is about the science of taxonomy.
The point of what I have been advocating
all
these years is that we follow the
intent of the Code to
separate the
legalistic aspects of nomenclatural
availability from the scholarly aspects of taxonomy and
related science. All of this discussion on
early online
electronic publications, not
to mention the VAST MAJORITY of
other
contentious issues related to zoological nomenclature
(issue of determining priority, issues about
prevailing
usage, issues about availability
of a published work, etc.)
all relate to
the traditional "publication"
process. These would mostly disappear in a universe
where
the act of registration is what
confers availability, as
separate and
distinct from the process of publishing science
in the traditional model of publication.
> If registration were to
replace
"publication" as the
determinant of
availability
> of a proposed name, then
it would need to be much more than what ZooBank is
> now.
YES! Absolutely! No one that I know would
argue otherwise.
> It
would need to be what
Doug Yanega has been advocating for
years:
a
> central "journal"
for all names so that all the other criteria
of availability
of a
>
proposed name meet with compliance
of the
required Articles of the ICZN
>
Code.
Well... not
exactly. The Code does not
currently require peer review
(which is the
key difference between Doug's model and
mine). Also, I think Doug imagines more of a single
Journal in which the full/traditional
description is
published as part of the
registration process (i.e., all the
highlighted bits, and all the un-highlighted bits as
well). In my view, the registration system
would ONLY
include the highlighted bits as
required items, and would
also have some
optional bits as well (e.g., upload a photo
or illustration of the type; create a link to a companion
scientific article published in a traditional
way outside
the registration itself, but
which includes all the
peer-reviewed
non-highlighted stuff).
> But then, let's not call it a
"journal" anymore because it really is not
> [remember, we are trying to do away
with
"publication" as the medium
of
> verification of a new name].
Agreed - I wouldn't
call
it a Journal. I would call it a
Registry.
> ZooBank
would have to
then be a
"repository" of all associated data of a
name -
> - the same as a
patent office is
with patents. Every patent
has documentation
> included with it.
...More specifically,
all associated data of a
name AS REQUIRED
BY THE CODE. What I think you mean by the
patent analogy includes a lot of the non-highlighted
stuff
as well. In my view, that would all
be published in the
same way we currently
publish all of our species
descriptions
now. In fact, there would be only two changes
in my proposed scenario:
1)
ZooBank would include a
few more fields and stuff (to cover
all
requirements the Code; including e.g., Art. 13.1)
2) The traditional
publication
would not carry any relevance
to availability of the name --
it would
exist as a purely scientific document, not a
quasi-legal, quasi-scientific document. All
legalistic
aspects of nomenclatural
availability would exist within the
Registration system.
>
ZooBank, then, should also have all
the documentation
> associated with
every proposed name.
Merely pointing to a
"supposed"
> publication
outside of the registration
system can and
will be filled with abuse,
> problems,
and maybe even non-compliance
(as we
already see happening). No,
> in
order for the system to work perfectly, ALL
compliance for
the availability of
> the name MUST be
met and
deposited in the registration "repository"
upon
> registration.
I'm not completely sure
I understand what
you are saying here. It
sounds to me like you want to
maintain the
existing conflation of nomenclatural
availability and scientific taxonomy, despite the fact
that
the Code itself explicitly seeks to
avoid this conflation. I
agree with the
last part of what you said -- the
Registration system I have in mind includes much more
than
the current ZooBank does, including
required information for
ALL provisions of
the Code. But the vast majority of the
content of traditionally published new species names
include
much, much more (i.e., the
highlighted bits are usually much
less than
the non-highlighted bits).
> In that great pie-in-the-sky, this all
seems perfect and with oodles of Petabyte
> servers and unlimited funds supporting
such a, all-encompassing registration
>
system, it might even be
doable.
That's
hyperbolic. At most, it would
require
about 10-20% more storage space than the current
ZooBank database. The entire GNUB database
(where ZooBank
resides) is only 2.7GB; and
the ZooBank part is probably
only about
half of this. There are many orders of
magnitude between 3GB and "oodles of Petabyte
servers". My laptop has 7TB of storage
on it --
enough to hold more than 2,000
copies of the entire GNUB
database, or
about 5,000 copies of ZooBank.
Actually, now that I think
about it, most of the hard drive space is consumed by the
literature citations, not the name
registrations. So
adding support for
things like Art. 13.1 while eliminating
all
the metadata associated with the Published Work might
actually result in a net DECREASE in the
amount of disk
space required for each
registration. Hard to say for
sure.
In any case... No,
from a technological perspective, there is
no
"might" about it -- it
very-much **IS** doable.
> However, until employers
(mainly in
academia) do away with evaluating their
> employee taxonomists based on where they
publish (i.e., high ranking journals),
>
many taxonomists will
not switch over to this
zero-ranking
> registration/repository
system.
And THAT is
the
crux of it! It's not
technological, it's
social.
So, imagine two
worlds:
1)
The current
world: Taxonomists publish good
taxonomic science in high
ranking journals,
including descriptions of new species.
Separately they register those new species in ZooBank.
Nomenclatural availability requires elements
of both the
ZooBank registration and the
publication [for electronic
publications
now; probably all publications in the future].
Chaos and confusion reign.
2) The world I propose: Taxonomists
publish
good taxonomic science in high
ranking journals, including
descriptions of
new species. Separately they register those
new species in ZooBank. Nomenclatural availability is
contained entirely within the ZooBank
registration. Peace
and harmony reign.
Dude...
even most taxonomists don't fully understand the
subtleties of where the actual legal
Code-compliance happens
in publication vs.
registration. Do you sincerely believe
that their *employers* will give a rip about the
difference
between options 1 & 2 above
in terms of evaluations?
Yes, yes, I've heard (many
times) the
argument , "But...but.... taxonomists will
only do the registration of new names, and
will never bother
with publishing the
science of the taxonomy they do!"
If
that were a legitimate concern (it's not), then we
would already be dominated by taxonomists who
self-publish
their minimal descriptions of
new names with no associated
science.
Hoser wouldn't be the outlier, he would be
the norm. The reason people like Hoser are
outliers is
because scientists care about
their scientific
reputations. I'm not
worried about employers
evaluating
taxonomists based on their publication track
records -- I'm COUNTING on it! It's
what will keep
the science flowing!
What
I'm advocating is that we eliminate *entirely* the
time
we currently WASTE arguing about
availability of
"published
works", and related issues of priority
and early online publications, and electronic vs. paper,
and
prevailing usage, and blah, blah, blah,
blah. [Note:
we're talking about
prospective new names in the future
-- we
still have to deal with all that other stuff for
existing/historical names.]
> We will, IMO, for the foreseeable
future,
be "publishing"
(electronic or
> print) and having to
deal with the high
ranking journals who
tell US what to do
>
because they have many by the short-and-curlies because
those taxonomists
> need
to keep their
jobs and keep publishing in
those high ranking journals.
....
I COMPLETELY agree
(sad as it may be). However, this has no
relevance to what
I'm proposing. All
I'm saying is that we should
consolidate the legalistic aspects of nomenclatural
availability in ONE place (rather than two,
that have to be
cross-checked against each
other), and that we follow the
wisdom laid
out in the Code to SEPARATE taxonomy from
nomenclature. Taxonomists will still continue to
publish
their science in high-ranking
journals, and employers will
continue to
evaluate them based on the quality &
quantity of the science they produce (rightly or
wrongly).
Almost no one will even notice
that the burden of
nomenclatural
availability shifted subtly from being spread
across two separate events (publication and
registration) to
being consolidated in one
event (registration). What they
WILL notice
is that all these arguments about availability
(or not) of "published works", and
arguments about
the precise moment at which
a published work became
available in the
sense of the Code, will disappear. Then we
can all go back to documenting biodiversity before
it's
gone.
> And registering
names in
ZooBank that point to where they are
"published".
I
don't care if the registration points
to one (or more)
publications or not. I
do care that we avoid the current
situation
where all future taxonomists must forevermore
consult two separate sources (registration and
publication)
to determine nomenclatural
availability.
Phew....
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
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