Taxacom: A moment for reflection [was: Dates of e-pubs ahead of print?]

Sun Sep 4 18:33:49 CDT 2022

Many thanks for the kind words, Adam.  To be fair, I live in a part of the world where the time zone is UTC-10, which means when the clock struck midnight UTC on September 4, I was banging on my keyboard at 2pm (14:00) in the comfortable afternoon of September 3rd. As I write this now, September 4 has now caught up to my part of the planet.

Regarding the issue of the need for evidence of registration to be overtly visible within electronic documents, I think you make a fair point.  The reason it was worded that way (not actually part of the legislative text of the Code, but rather in an Example) is because of the nature of electronic documents containing information *useful* to readers, even if not visible to the eyes of readers.  It was an acknowledgement of direction electronic publication was heading.

In the ten years since the de-facto start of Code-compliant electronic publication, we've learned a lot about what works reasonably well, and what doesn't work reasonably well.  Some of the latter have been addressed by many individuals (including extensively by several lengthy publications by Dubois and co-authors, including one recently published item linked by Dubois earlier in this thread). A few of the issues have not been discussed as much, in part because they are not as obvious or visible.  I mention this, because I think it's helpful to take a moment to review the broader context of all of this stuff. And as today marks the tenth anniversary, it seems like a good opportunity to capture this moment.  I can think of no better use of my leisurely Sunday than to wax on about this noteworthy moment in nomenclatural history. Fair Warning: If you’re not interested in the history of scientific nomenclature or the evolving nature of Codes governing nomenclature, NOW is the time to stop reading.  But if you are interested in these matters, I offer my take on them as follows:

Over the centuries prior to Linnaeus, there was no universal standard for applying text-string labels to defined sets of organisms (i.e., inferred taxa). By the early 18th century, the general practice of binominal nomenclature was codified in various editions of Linnaeus' Index Plantarum and Systema Naturae, after which there was much greater (though not perfect) consistency in the practice of assigning text labels to taxa.  Things got a bit confused a little over a century later with the ideas of Wallace and Darwin beginning to gain widespread acceptance in academic circles, but somehow the nomenclatural system developed by the Creationist Linnaeus managed to survive this philosophical and scientific transition regarding the relationships of living things to each other and the nature of the origins of biodiversity. This was probably largely due to the way in which Linnaeus’ hierarchical classification system and associated nomenclature was more or less applicable to representing patterns of evolutionary relationships.

Towards the latter part of the 19th Century, many practitioners of taxonomy recognized problems in nomenclatural stability.  Though the system championed by Linnaeus brought a large degree of universal practice in biological nomenclature, it included insufficient detail to address all aspects of scientific nomenclature.  Thus, Codes of nomenclature for both Plants (inclusive of algae and fungi) and Animals were created to provide more guidance and promote universal practice, with the hope of stabilizing biological nomenclature.  The early editions of these Codes were a step in the right direction, but unsurprisingly were imperfect.  Over time, shortcomings and imperfections of the rules established in these Codes were recognized, and so they needed to be updated.  For Zoology, this led to the second, third, and fourth Editions of the ICZN Code (with various Amendments), and in Botany the practice of revising the Code every six years (in association with meetings of the International Botanical Congress).  Similarly, the International Code of Nomenclature of Bacteria (now the International Code of Nomenclature of Prokaryotes) underwent multiple versions and revisions.  

All three of these major nomenclatural Codes acknowledge the need to change over time, for two main reasons.  First, the rules of each version/edition essentially represent reactions to problems or imperfections that were either not addressed by earlier versions, or in some cases were created by modifications made in earlier versions.  In each case, the community of taxonomic practitioners who follow these Codes would come to encounter problems that threatened nomenclatural stability, so solutions were proposed to address those problems. Each proposed solution and modification was something of a prediction or hypothesis along the lines of “With this change to the rules, there will be an increase in nomenclatural stability.”  Only in the years following the implementation of those changes would the “evidence” be accumulated to test this hypothesis.  In some cases, nomenclatural stability is increased (i.e., successful rule change).  In other cases, there was no net effect on stability (i.e., increased bureaucracy without benefit).  In a few cases, rule changes may have actually lead to a decrease in overall nomenclatural stability. But the point is, one of the reasons why the rules of the Code need to evolve over time is that they are not perfect, and an iterative approach of “try a different rule and see if it works” is a necessary model for progress.

The second reason that the rules need to change over time is that the priorities and needs of the constituents (i.e., the community of practicing taxonomists) change.  Sometimes this is a result of the evolution of what role nomenclature plays in how taxonomists (and biologists, and other scientists and non-scientists) communicate with each other (and what factors are regarded as the highest priority for communication).  For example, in Linnaeus’ time, there was very little priority (none, really) placed on representing the evolutionary relationships of organisms through nomenclature and classification.  Since the time of Darwin (and especially over the past half-century or so), this priority has increased.  Technological advancement also plays a role.  The increasing utilization of molecular analysis (especially DNA sequencing) has changed somewhat dramatically over the past few decades, and this also has an impact on the rules of nomenclature (see multiple discussions about how to interpret Art. 13.1.1/13.1.1, for example).  And of course, the nature of “publication” has changed rather dramatically since about the turn of the most recent century… which brings me back to the topic at hand.

Speaking in terms of the Zoological Code of nomenclature (with which I am most familiar, but parallels exist in the other Codes as well), the three Editions of the ICZN Code that existed when I began my career as a taxonomist in the early 1990s had all been crafted/drafted in the context of a widely adopted mechanism for scientific communication.  That is, in the form of words and symbols printed with ink on physical pages of paper (or, as my friend Paul Kirk likes to call them, “very thin slices of wood”).  This, of course, made perfect sense: the practice of capturing and disseminating knowledge in this form had gone back many centuries, and with certain famous examples notwithstanding (e.g., Library of Alexandria), had a pretty decent track record for promulgating information from one generation to the next.  Thus, the rules of the various Editions of the Code were structured around the notion of “publication” in this context. It would have made no sense to craft them otherwise.

During the latter part of the 20th century, the advent of the internet and electronic forms of communicating information began to grow rapidly. In fact, during the 1990s the internet was by many metrics the fastest adopted new technology in all of human history (evidently since surpassed by cryptocurrency, but that’s a whole ‘nother Pandora’s can of beans I won’t dare to open here).  Also at that time, the Fourth (and still current) Edition of the ICZN Code was drafted and disseminated for public commentary, prior to going into effect on 1 January 2000.  This was the first Edition of the Code that needed to confront the evolving way in which scientists were starting to share information with each other via electronic forms of documentation.  The internet was still so new (and perhaps scary), that the Fourth Edition of the Code added a provision (originally Art. 9.8) that excluded any work consisting of “text or illustrations distributed by means of electronic signals (e.g. by means of the World Wide Web)” from being “published” in the sense of the Code. This was further indicated by adding the word “durable” to Art. 8.1.3.  However, acknowledging that electronic information technology was a “thing”, and was rapidly changing at the time the Fourth Edition of the Code went into effect, the drafters of that version of the Code did allow for works to be considered published if they were produced and disseminated on “optical disc”, provided some additional requirements were met.

This “optical disc” business is worth an additional moment of examination.  At the time the Fourth Edition was being drafted, the internet was deemed too ephemeral and “new” to be considered as a mechanism for documenting and promulgating Code-governed nomenclatural acts (inclusive of new names), so it was excluded from consideration.  But it was obvious that computer technology more generally was a real “thing”, and would continue to be so into the foreseeable future, so the Code needed to be modified to accommodate it.  Although references to “optical discs” (and earlier in the Introduction of the Code, “laser disks”) seem quaint (almost comical) to us now, at the time it was the best that the drafters of the Code could do to anticipate how to accommodate future needs of taxonomists.  In doing so, they felt the need to add extra requirements to this form of “publication” (e.g., they “must contain a statement naming at least five major publicly accessible libraries in which copies of the optical disc were to have been deposited”).  It was the best they could do to accommodate a rapidly changing landscape of information dissemination, so we should cut them some slack.  In the decade that followed the implementation of the Fourth Edition of the Code, it became clear that this approach to accommodating technological change was not quite as prescient as had been hoped, so the Code was amended to stop this practice. Of course, that wasn’t the only part of the Code that was amended…

This now brings us to the year 2008.  The Fourth Edition of the Code had been in effect for nearly a decade, and a couple of things had become clear at that point. First, as already alluded to, the laser disk/optical disc thing was not panning out, so it needed to be changed in the Code (preventing the practice from continuing further). This is an example of the iterative trial-and-error nature of changing the Code, and fixing the bits that turn out to have not contributed to increasing nomenclatural stability. Second, and more acutely (and more directly relevant to the topic at hand), the internet was very rapidly taking over as THE mechanism by which taxonomists (and biologists, and other scientists and non-scientists) communicate with each other.  The practice of mailing out physical copies of reprints to colleagues via the post was giving way to e-mailing electronic documents (especially PDFs) to colleagues and others.  

The ICZN met in Paris that year to discuss a variety of issues that were occupying the time and thoughts of the Commission, and the need to deal with “electronic publication” was high on the list of topics to discuss and debate. At the time, it was clear that PDFs were not only beginning to dominate the publication world in terms of replacing reprints, but in some cases it was starting to look like they were replacing paper-printed editions of scientific publications.  Several examples of electronic-only works introducing new names and/or other nomenclatural acts had been identified, and the Commissioners realized the trend was only going to increase, so urgent action (via an Amendment to the Code) was needed.  After much discussion, a draft Amendment was hammered out and debated within the Commission. The two biggest issues of those debates were: 1) how to address the obvious disparity between the centuries-old proven method of ink-on-paper publication and the decades-old and very-much-Unproven method of electronic documents – especially in terms of ensuring perpetuation of original works?; and 2) what role should the then-new ZooBank play?

The first issue is pretty self-evident:  The reason the Code forbade works “distributed by means of electronic signals” was because there was only a short history of electronic means for storing information long-term.  Moreover, that short history had not inspired a lot of confidence (I recall a lot of references to 8-track audio tapes, lost or corrupted floppy discs, crashed hard drives, etc.).  Several ideas to address this issue were proposed and debated, with a wide range of practical and philosophical implications. None of these satisfied everyone and, indeed, I seriously doubt that there is such a universally satisfactory solution – at least not with existing available technology. In the end, the cracks in the damn holding back the deluge of electronic publications were ominous enough that the need to accommodate electronic publication within the Code exceeded the fear of losing all copies of electronic documents due to insufficient long-term electronic storage technology, so we ended up with an extremely feeble (in my opinion, anyway) compromise.

As for ZooBank, at the time it was relatively new, and very-much “unofficial” from the perspective of the Code and Commission. It existed as a website and associated database, and had been launched publicly on 1 January of that same year (2008) to coincide with the 250th anniversary of the official start of modern zoological nomenclature (see Art. 3.1 of the ICZN Code), and also to coincide with the publication of the first prospectively registered scientific names (five new species in the genus Chromis; DOI: 10.11646/ZOOTAXA.1671.1.2); but it was not yet in any way associated with the Code of Nomenclature. It had even less of a track record than electronic publication, and therefore an even more uncertain future, so there was a wide range of opinion for how much it should be incorporated into the Amendment to the Code.  For the record:  I was NOT one of the people arguing for its inclusion in the Amendment as a requirement.  As the person who primarily developed and maintained it, I had wanted to allow it more time to evolve as an online service before bearing any form of role  for Code-compliance. I was eventually persuaded that the Amendment to accommodate electronic publication was the obvious golden opportunity to introduce ZooBank to Code regulations in a limited way, so I acquiesced.  However, I did successfully persuade the majority of Commissioners that its role should be limited to ONLY electronic publications, and ONLY require registration of works (not of names or acts).  My key rationale was that we were going to amend the part of the Code that dealt with published works, so we should confine any registration requirements accordingly.

At the time, my perspective was that a centralized online/electronic registration system would eventually serve the goal of nomenclatural stability very effectively (this is still is my perspective).  However, the key word there is “eventually”.  Major changes to international standards like the ICZN Code are most effective when they are evolutionary (as opposed to revolutionary).  The thing that most persuaded me to get on board the “require ZooBank registration for electronic publications” was the opportunity to embark on a “test” period for registration as a concept in this space.  I was very nervous because I knew how rapidly the technology was changing, and I was wary of creating another “laser disk/optical disc” situation for the Code. But real progress often requires real risk, so I looked upon the Amendment for electronic publication as an opportunity to kick off a grand experiment that would allow us to test (and more importantly, refine) our “hypotheses” about how best to shape the Code of nomenclature to accommodate the rapidly evolving landscape of scientific norms and practices.

So… was the Amendment to allow electronic publication (and introduce ZooBank registration) successful?  In one sense, clearly not.  There are many issues that have come to light during these past ten years that highlight the imperfections of the how the rules were modified. This includes a wide variety of issues, most of which are in the realm of what the Commission refers to as “limbo names” (i.e., names published in electronic works that meet all of the “spirit” of the Code rules, but fail on the basis of one or mor specific technicalities).  On the other hand, in a much broader (and more important) sense, the Amendment was a nearly-unqualified and monumental success.  Why?  Well… consider how many “limbo” names we’d have if NONE of the electronic works of the past decade would be published in the sense of the Code?  Sure, a some journals that now publish only in electronic form might have taken the Code seriously enough to have continued the practice of producing an issue containing “numerous” “durable” ink-on-paper copies, but many (most?) would not have done so.  And even the ones that did continue with paper copies, would likely have done so with minimal compliance in mind.  Technically, only two paper copies that are made simultaneously obtainable would fulfill the “numerous” requirement, which very-much would NOT be keeping with the spirit/intention of the Code.  Obviously, many journals do continue to produce paper versions of their publications, so the old-school practice does continue. But there is still a great deal of confusion with respect to the date of publication, especially when PDF versions are often obtainable months before the paper editions are.  Moreover, I’m pretty sure that the majority of new names and nomenclatural acts today are published only in electronic form, without paper versions.

Keeping in mind that it’s nearly impossible to predict the future (especially in the dynamic way in which “publication” continues to change), I’d say that the Amendment was crafted the best way it could have been, at the time.  Some might suggest that they could have foreseen the problems at the time, and would have argued for a different approach to how to accommodate electronic publication.  That may well be true, but if so, then I wonder why they didn’t contribute to the public discussion that spanned several years (2008-2012) on multiple platforms (including this list, Taxacom).  And if they did contribute, then their suggestions certainly were considered at the time, but ultimately were offset by alternate considerations.

As Adam noted, we are now in the midst of a wonderful opportunity to capitalize on ten years of real-world experience with both electronic publication and online registration via ZooBank.  We have learned a LOT over those years, and unsurprisingly there are a LOT of good ideas on how to improve things.  The Commission is carefully (and somewhat painstakingly, but with good reason) going through the text of the Fourth Edition of the Code, scrutinizing every word (sometimes ad-nauseum) to generate the first draft of the Fifth Edition.  Francisco Welter-Schultes has done a MASTERFUL job leading this effort on behalf of the Code editorial committee.  The Fifth Edition of the Code will most likely be the most substantive change (and improvement) in the Code’s history.  It will be open to public commentary for at least a year (I suspect longer), and I consider this to be the most important part of the process.  The Code, and the Commission, exist to serve the needs of the taxonomic community, so the highest priority should be on understanding and accommodating those needs as effectively as possible. The experience we’ve had this past decade (and by “we”, I include myself, the Commission, and the entire taxonomic community) has proven to be immeasurably valuable for shaping the Fifth Edition of the Code – not just for things like ZooBank and electronic publication, but for almost all aspects of the Code.  An enormous amount of work has already been done, and perhaps even more work remains.  But overall, I’m increasingly excited about the future of the Code, and of nomenclature and taxonomy in general.

As a closing thought, I wanted to point to what I think are the most prescient words in the entire Fourth Edition of the ICZN Code, located in the Introduction section, as the last sentence of the second paragraph under the heading, “Development of underlying principles”:

“But it seems likely, in the longer term, and with the development of new information systems, that the solution will not lie in patching up a definition of publication but, rather, in scrapping it and finding a means of replacing "publication" as a primary determinant of availability.”

These words capture my own perspective very eloquently – something I’ve articulated many times on this and other public forums.  There is no doubt in my mind that this is where zoological nomenclature is heading.  The only real questions are how long it will take to get there, and how best to navigate the transition.

If you made it this far, then you’ve earned your title as “nomenclatural nerd”. Welcome to the club! 

And again, happy 10th Anniversary to the era of Code-compliant electronic publication!

Aloha,

Rich

P.S. I realize this post is extraordinarily long, but after having spent the first part of my day digesting the even lengthier electronic publication posted earlier in this thread (and alluded to earlier), I was feeling somewhat logorrheic myself.

Richard L. Pyle, PhD

Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail: deepreef at bishopmuseum.org

BishopMuseum.org

Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

> -----Original Message-----

> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Adam Cotton via

> Taxacom

> Sent: Saturday, September 3, 2022 10:46 PM

> To: taxacom at lists.ku.edu

> Subject: Re: Taxacom: Dates of e-pubs ahead of print?

> 

> On 04/09/2022 07:34, Richard Pyle via Taxacom wrote:

> > <snip>

> > 3) Any name or nomenclatural act appearing in an electronic document can

> only be made available if the requirements of Art. 8 are fulfilled, and none of the

> provisions of Art. 9 apply.  The requirements specific to electronic works

> include:

> >         <snip>

> >         c) The work itself must contain evidence of registration. Examples of

> > evidence include the registration number of the work, or the exact

> > date of registration of the work, the registration number of a name

> > within the registered work, and perhaps other things as well. The

> > registration of an Author of the work does not count as evidence.  The

> > evidence may be formatted in a way that is visible to humans in the

> > electronic document, or it may be embedded in some non-visible way

> > (e.g., in the electronic document metadata, or as an embedded

> > hyperlink within the electronic document). (Art. 8.5.3)

>  >

>  >

>  >

> 

> 

> Firstly I would like to say thank you to Richard for putting all of this down for

> everyone to read instead of sleeping (mind you Richard may be a late sleeper

> like me).

> 

> One point that I think needs to be addressed in the 5th edition of the Code is

> that brought up in 3c) above:

> >   The evidence may be formatted in a way that is visible to humans in

> > the electronic document, or it may be embedded in some non-visible way

> In my opinion the evidence should HAVE TO be 'formatted in a way that is visible

> to humans in the electronic document' otherwise it is very difficult for a real

> person to look at a pdf and be confident that it conforms to the Code

> requirements of e-publication.

> 

> It is not difficult for a Zoobank registration 'string' to be included in the text of

> the publication, and indeed most publications do include this now. If this is not

> included most readers conversant with the Code (mainly taxonomists, I guess)

> will conclude that either it is a pdf copy of a paper originally published on paper

> or it is not validly published according to the Code.

> 

> I suspect that registration on Zoobank will be included as a publication

> requirement in the 5th edition, as has been hinted at previously. If so it would be

> helpful to humans if the evidence of registration is visible to humans too. That

> would remove any question of Code compliance and save the time needed to

> check in Zoobank whether registration had taken place in order to confirm the

> availability of a name or names in the publication.

> 

> Adam.

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