[Taxacom] Article 8 compliance

Adam Cotton adamcot at cscoms.com
Wed Apr 12 06:50:00 CDT 2017

----- Original Message ----- 
From: "Richard Pyle" <deepreef at bishopmuseum.org>
To: "'Adam Cotton'" <adamcot at cscoms.com>; <taxacom at mailman.nhm.ku.edu>
Sent: Saturday, April 08, 2017 3:46 AM
Subject: RE: [Taxacom] Article 8 compliance

Hi Adam,

Thanks for taking the time to participate in this discussion!  I am finding 
it very thought-provoking and helpful!


Great, that's what I would like to do, provoke constructive thought.


> I really do think that John has some very valid points, particularly on 
> pdfs and his
> reservations about a number of aspects of the proposed ZooBank model.

And I likewise agree (as indicated in my reply to John just now)/

> In my opinion it would be much easier for the user, more economical  and 
> have
> other significant advantages if ZooBank changed its modus operandi from
> "registration" to "mandatory archive".
> What I am proposing is that in order to confer availability on 
> nomenclatorial acts
> all that is necessary is to upload a pdf of the paper to ZooBank. The date 
> and
> time of receipt of the pdf becomes the publication date/time and there 
> will thus
> be no future issue of argument over publication priority for e-only 
> publications.

I think this system could work as well.  For many reasons I don't believe it 
would be as good as the system I am advocating, but I do agree that such a 
system would be better than what we currently have, and may be easier to 
"sell" to the community.


What particularly appeals to me about this is the simplicity of the idea, 
upload a pdf of your nomenclatorial acts to ZooBank and they become 
"published". Even I can do that ;)


> If an author wants to replace a previous version of the publication with a
> subsequent version the old pdf is deleted from the archive and the new 
> version
> uploaded in its place, and the publication date for priority purposes 
> becomes the
> date on which the new version is uploaded. That would solve the current
> problems with versions of record and their publication dates.

This seems a bit problematic.  Would there be a time limit on when an author 
could replace an earlier version?  What happens when other works start 
citing the old version, then years later a new version is uploaded.  Would 
all the other works citing the old version be using unavailable names?  What 
if a new name is established in the interim that is considered a junior 
synonym?  Would it then take on nomenclatural priority if the author of the 
earlier name later replaced the PDF?  I think that once a PDF is submitted 
and archived in ZooBank (in your system), it would need to be permanent. 
Otherwise, I see all sorts of opportunities for tremendous nomenclatural 
instability to ensure.


The whole point of my suggestion here is that the author has to decide 
whether he feels it is necessary to substitute the version of record with a 
newer one. Currently many journals publish "early bird" versions of papers 
online maybe a year before the paper version is actually published, and 
unless registered as per the Code Amendment any nomenclatorial acts are 
unavailable until the printed version is published.

What I am saying here is that the nomenclatorial acts can become available 
from the "early bird" version, purely by uploading a pdf to ZooBank. This 
would instantly solve the current problem of unavailable nomenclatorial acts 
in unregistered "early bird" versions of publications being accepted as 
available by other authors, as sometimes happens now. This would also solve 
the issues behind e-only jpurnals that are not currently Code compliant.

However, if the author(s) of the paper decide that they want to substitute 
the original pdf they uploaded with a newer version they CAN do so, but all 
the nomenclatorial acts become available from the date the new pdf was 

Indeed, if another author publishes a junior synonym of a new taxon 
published in the "early bird" version which was originally uploaded to 
ZooBank before the final version of the first paper is uploaded to 
substitute for the "early bird" pdf, then that new taxon in the substitute 
version would become the junior synonym and the previous junior synonym 
would become the valid taxon name.

Of course this would probably not happen very often, but the consequences 
would be the responsibility of the author(s) who decide to substitute the 
original pdf with a newer version. Before deciding to change the version of 
record the authors should be aware of the possible consequences and accept 
the possibility that one or more nomenclatorial act could be affected.


> Instead of ZooBank investing huge sums in building complex software needed
> for the registration process and further sums for upgrades and 
> maintenance, I
> believe that it will be much more cost effective with much simpler 
> software if
> ZooBank becomes the ONLY MANDATORY ARCHIVE for all nomenclatorial acts.
> The publication model would thus become "PDF archived at ZooBank =
> published".

Perhaps, but I'm pretty sure you're wrong on the costs estimates.  Initial 
setup costs for establishing an archive (instead of enriching ZooBank) MIGHT 
be less than US$1.5M (but I doubt it).  And certainly maintenance costs 
would be MUCH higher for an archive than it would be for a registration 
system.  The archive you describe would require many PETABYTES of storage 
space (instead of a few 100 GB), and as you noted, perhaps the largest cost 
for maintaining electronic information systems of this sort is repairing 
replacing hard drives, pushing content onto media, and maintaining a regular 
off-site backup system.  Establishing ZooBank as a single-point archive for 
ALL publications of Code-governed names and acts would be vastly more 
expensive in the long run than developing and maintaining the robust 
registration system that I have been advocating.  In fact, BHL tried to do 
exactly this (create a "safe harbor" for PDF deposition) a few years ago, 
and they eventually decided it would be too expensive (mostly relating to 
copyright issues).  And their budget is way more than what has been needed 
(and what would be needed) for ZooBank.


I will take your word for the potential costs of ZooBank becoming a pdf 
archive and additional maintenance etc costs, as I actually have no idea of 
the real costs.

I do think that people who are able to estimate the costs of various models 
should do so and present these estimates to the community before a decision 
is made on which model to adopt.


> There are a number of distinct advantages for users of this proposal that
> ZooBank changes from a registration facility to an archive. All an author 
> needs
> to do is upload a pdf to ZooBank, no need to fill out fields in a database 
> for
> registration of each act (even 2 extra days at the end of a long research 
> project
> is an inconvenience, never mind subsequent problems caused if the author
> enters information incorrectly when staring at a computer screen for 2 
> days).

See my reply to John on the "2 extra days" thing.  There's no reason that 
couldn't be MUCH lower overhead time cost.

> Subsequent users who want to access the nomenclatorial acts can access the 
> pdf
> files directly from the ZooBank portal, and read the necessary details of 
> the
> published acts. If there are copyright issues with the pdf publications 
> ZooBank
> could provide a "snippet view" of the paper, such that only the actual
> nomenclatorial acts are visible to the reader (similar to Google Books) 
> rather
> than the whole pdf.

OK, now you're talking about a system that would be VASTLY more expensive 
than US$1.5M to develop -- even ignoring the massive costs associated with 
the legal side of copyright. Just look at all the copyright legal battles 
that Google has had to deal with for Google Books.  They have a LOT more 
money than ICZN does (probably more than all of taxonomy worldwide); and 
even they considered it a major problem.


OK, I understand that this suggestion could be problematic, and extremely 
expensive for anyone other than an organisation with the resources of 

However, there is a practical alternative. Instead of an author uploading 
the pdf of the whole paper containing nomenclatorial acts he uploads an 
extracted pdf only containing the pages with the information relevant to 
each nomenclatorial act SEPARATELY. So the author of 10 new taxa and 3 
Lectotype designations (for example) would upload 13 separate pdfs, one for 
each nomenclatorial act. Let the author produce the effective "snippet view" 
at registration rather than ZooBank software do it on request.

This would take a little more of the author's time, but it is actually not 
really difficult to extract 1-2 pages from a pdf of the whole paper per 
nomenclatorial act and save each as a separate file then upload them to 
ZooBank. Of course it may be that more than one nomenclatorial act is on the 
same page of the paper, and in that case the same page is uploaded several 
times with a different file name.

The point I am trying to make here is that anyone can subsequently read each 
nomenclatorial act in an "open access" mode without infringing potential 
copyright if the whole paper was available as a single pdf.


> Surely this has to be a much more user-friendly, economically viable and 
> simpler
> system than the current model?

User-friendly?  That's debatable.  Economically viable?  I will have to say 
"not even close", given what you've described above.  As for "simpler", I 
refer back to my original reply to John on this thread: by what metric are 
we defining "simple" vs. "complicated"?


Perhaps my suggestions will provoke thought that eventually ends up with a 
SIMPLE user friendly system (whatever it may be) that anyone anywhere in the 
world can easily comply with.


> Did I really see a Hymenopterist agreeing with the Lepidopterists that
> gender agreement should be scrapped from the ICZN Code???

You can add an Ichthyologist to that list as well... :-)  [Sorry, 



It's amazing how many taxonomists across different animal groups actually 
want gender agreement to be removed from the Code, but that's another topic 
that should not be discussed here.



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