[Taxacom] are early online publications code-compliant?

Richard Pyle deepreef at bishopmuseum.org
Mon Apr 13 18:14:39 CDT 2015


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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