Of New Zoos and Old Libraries

In May 2009, a small fossil mammal was announced to the world as Darwinius masillae. Despite looking (let's be honest) like some sort of road-killed rat, Darwinius attracted a lot of interest due to its being a well-preserved early primate. Around the globe, news reports, blog posts, and strongly-worded letters to the Times were composed on the subject of wee Darwinius. You can get some idea of this attention from the links provided here. But with a publicity machine as large as the one surrounding Darwinius, one should always expect there to be spanners nearby.

As reported at The Loom, it was soon pointed out that there were problems with the name 'Darwinius massilae'. Darwinius had been published in an online-only venue, the web-journal PLoS One. At the time, the International Code of Zoological Nomenclature still did not allow for online-only publications, and a lively debate was going on as to whether provisions for such things should be made (eventually, they were). It looked like the name 'Darwinius' might have to suffer the fate of Akhenaten, erased from the public record and forbidden to be spoken aloud. In the end, a paper edition of the description of Darwinius was deposited in a number of institute libraries, which was believe to satisfy the letter of the ICZN. Peace was restored to the empire, and Darwinius was confirmed as an acceptable name.

For many who had been clinging to the fence on the acceptability of online-only publication, Darwinius massilae represented a bit of a water-shed moment. Online-only publication was here, it was happening, and it couldn't be ignored. Resistance was rapidly becoming futile. Or at least, that was the conclusion I personally felt compelled to draw from the event. The problem wasn't just the sideshow that had arisen around the christening of Darwinius. For me, the real poster-child for this mess was Aerosteon riocoloradensis, a theropod dinosaur that PLoS One had announced some eight months earlier than Darwinius. Like Darwinius, Aerosteon was subject to a fair whack of media coverage, despite the fact that, like Darwinius, its name wasn't acceptable in the eyes of the ICZN. The difference between Darwinius and Aerosteon, though, was that until the problem with Darwinius was realised, no-one had even noticed any issue with Aerosteon.

This, for me, was the very heart of the problem. In the days before electronic documents, the question of whether a given work was 'published' was largely an academic one. For most printed works, the evidence that it was 'published' was simply that it existed. Works that were regarded as 'unpublished', such as hand-written manuscripts and doctoral theses, probably only existed as one or two copies. The chance of your seeing them, except as an archivist, was fairly minute. Online publication changed all that. By the time it was realised that the name 'Aerosteon' might not be valid, its original description had been viewed by hundreds, if not thousands, of people (at the time of writing, PLoS One claims 22,417 views for this paper). The idea that all these readers should be commanded never to speak of what they saw, because they had not seen it in the required medium, seemed frankly ludicrous.

In this light, the amendment of the ICZN to allow for online-only publication (under certain conditions) was something I welcomed. As I noted at the time, it was possible (certain, in fact) that the rules would have to be further manipulated as we saw how they worked out in practice. Recently, a review in Zootaxa by Dubois et al. has purported to look at some of the issues that have arisen as a result of electronic publication. This review has itself received a brief, but snarky, commentary in the editorial section of this week's Nature. The Nature reviewer accuses Dubois et al. of having 'axes to grind'. This is probably true, but the reviewer may be sharpening an axe of their own: among the practices castigated by Dubois et al. are some, such as the publication of important taxonomic information in 'online supplements', that Nature has often been guilty of itself.

That said, I can't help but feel sympathy for the Nature reviewer's comments. I have become increasingly disenchanted over the years with any nomenclatural argument that strays too far towards the purely legalistic. For instance, Dubois et al. argue that the validation of Darwinius by the deposition in libraries of paper copies was itself invalid under current rules, as these prohibit validation through the production of 'facsimiles or reproductions as paper-printed copies of unavailable electronic publications' of the original online publication. They were also invalid under the rules current at the time, which required that a published work 'must be obtainable, when first issued'. Because the paper issues were only deposited in libraries, and were not obtainable by anyone from that first print-run, they didn't count. If PLoS One offered to print out a copy for anyone who demanded a paper issue, that didn't count either because the rules exclude 'print-on-demand' documents. If PLoS One pointed out that the paper was freely available at any time simply by going to their website and downloading a copy, that didn't count because electronic documents were not acceptable! In the meantime, their supposed 'unavailability' has been no barrier to use: Google Scholar returns 56 results on a search for 'Aerosteon', and 258 results on a search for 'Darwinius'! Dubois et al. complain that nomenclature doesn't get no respect, and call stridently for higher standards, stating positions such as that, "Publishers who since 2000 have published works containing nomenclatural novelties that do not comply with the Rules of the Code for publication availability...have betrayed the confidence of the authors who had entrusted their works to them for publication". I would counter that it is exactly this sort of legalistic bun-fighting and contrarianism that has caused many researchers (including many taxonomists) to lose respect for the nomenclatural process in the first place. We are not and we should not be here for the purpose of chanting shibboleths!

Dubois et al. complain that, "the recent decision [of the ICZN] to allow the publication of nomenclatural novelties in electronic form, was strongly influenced, if not “imposed”, by pressure from both the international biological community of non-taxonomists, and of non-scientists, e.g. Internet and Google “candid users”. Well, yes, this is exactly the point that I was making above. The users of taxonomy are not just taxonomists. They are researchers in other fields, they are policy-makers, they are farmers, they are fishermen, in fact they are absolutely everyone who has any interest, whether professional or amateur, in the world's biodiversity. The needs of these end-users cannot be simply ignored. And first and foremost among those needs is the need to not have to spend inordinate amounts of time contemplating nomenclatural angels on the heads of systematic pins before they know whether a name is usable. In the past we could be reasonably confident that if we were reading a publication, it was available. That is the ideal that we should be striving towards again.

"Anatomy of Mollusca": A Case of Plagiarism

Whilst researching material for an upcoming post, I came across this book on Google Books, published in 2010 by the International Scientific Publishing Agency, New Delhi:

Anatomy of Mollusca, by Rita Rawat

Looking at the section previewed through Google Books, I couldn't help feeling that it seemed a little... familiar. Take a look at this screenshot from Google Books:

Now take a look at this screenshot, taking from a page written by my erstwhile associates at Palaeos.com, last modified in 2006:

I can only go by what was available in the Google Books preview, of course, without direct access to the actual book, but I can confirm that most if not all of the material in pages 15 to 72 at least of the "Anatomy of Mollusca" appears to have been copied directly from Palaeos.com (unfortunately, a large part of Palaeos.com is currently offline as the site gets revamped). A quick Google search failed to uncover anything indicating whether the International Scientific Publishing Agency has a reputation for publishing lifted material, so I can't say if this is part of a broader issue.

Amazon currently has the "Anatomy of Mollusca" on sale for just over $75. Not that expensive by the standards of technical publications, but a fair chunk of change by the standards of books in general. Certainly a lot more than the cost of reading the same stuff on Palaeos.com, which carries no extra cost beyond that of the ISP charges.

Obama's Lizard? Not So Fast

Left dentary of a currently unnamed lizard from the latest Cretaceous, from Longrich et al. (2012).

Yeah, this is a pretty petty point, but what would this site be if it didn't pertain to pedantry?

In the last week of last year, a paper was published in the Proceedings of the National Academy of Sciences of the USA on lizards in the latest Cretaceous and Palaeocene of North America (Longrich et al. 2012). The paper garnered itself a certain degree of media coverage because the authors chose to name a new genus after the current president of the United States, Barack Obama: see here and here, for instance. Because I was away for Christmas at the time, I've only just gotten the opportunity to look at the actual paper.

One thing immediately sprung out at me (and those of you familiar with my dribblings have probably already guessed what I'm about to say): this genus has not been validly published. The description is not in the body of the paper itself, it is in the online supplementary info. The printed section of the paper does include very brief diagnostic comments, but does not include an explicit designation of type material. Despite the recent decision by the ICZN allowing electronic-only publication, the supplementary info in Longrich et al. (2012) does not meet the requirements for valid electronic publication. It has not been registered with ZooBank, and it does not contain any indication of having been registered.'Obamadon gracilis' is hence an unavailable name, as are the other described taxa 'Pariguana lancensis' and 'Socognathus brachyodon'. Sorry. Once again, the space-saving requirements of a 'high-tier' science publication has shafted nomenclature.

I'd also be interested if anyone has comments on another potential problem. The supplementary info for Longrich et al. (2012) has been presented as a Microsoft Word document. I've no wish to argue the merits or otherwise of Microsoft Word per se—it's the word processing programme I generally use myself—but the ICZN requires that electronic publications be produced using a method that ensures 'widely accessible electronic copies with fixed content and layout'. PDF is not actually required, but is mentioned as an example of a format fulfilling this requirement. What about Word, though? Do you think a Word document can be regarded as 'fixed', or do you think that it is too easily altered after the fact?

REFERENCE

Longrich, N. R., B.-A. S. Bhullar & J. A. Gauthier. 2012. Mass extinction of lizards and snakes at the Cretaceous–Paleogene boundary. Proceedings of the National Academy of Sciences of the USA 109 (52): 21396-21401.

O Zoobank, Where Art Thou?

Does anyone reading this have experience with registering publications, etc. on ZooBank? Can you clarify how the process works?

In the comments for yesterday's post, two readers brought up a potential issue with ZooBank's records. A number of taxa published recently in PLoS One that were supposed to have been registered with ZooBank, such as Mochlodon vorosi, are not coming up in searches there. However, the original publications for these taxa cite LSIDs, the unique identifier assigned to any ZooBank registration, for them. If these taxa were never registered with ZooBank, how could there have been an LSID to cite? I ran a search of my own for two taxa recently published in a different journal, ZooKeys: Calliostoma tupinamba and Angelopteromyia korneyevi. Same result: cited LSIDs, but no results in a ZooBank search.

So what's happening here? If a paper is registered prior to being published (as must have been the case here, for the LSID to be cited in the published papers), does the registrant have to confirm publication later for that record to be visible to the public? Could these records have simply not yet been made public? Or is there a bigger problem here?

The ICZN and Electronic Publication: Where Did It Go Wrong?

Reconstruction of the dinosaur Aerosteon riocoloradensis, from here. This species was published in electronic-only format in September 2008; it was nearly six months before anyone noticed that this was a problem.

Since the ICZN approved electronic publication, we've had a few weeks to get over the initial heady rush of excitement and further assess the situation. Which means that we have to ask the question: what is wrong with the new rules?

There is no question that some of the new rules on electronic publication will need to be adjusted. This, I hasten to point out, is not an indictment. The International Code of Zoological Nomenclature for dealing with paper publications first appeared over fifty years ago, in 1961, and the earliest attempt at a formal code of nomenclature had been proposed by Hugh Edwin Strickland another 120 years before that. Despite all this time, the Code as it pertains to paper publications has still not been perfected, and revisions continue to be proposed and published. Indeed, some of the issues the code grapples with (such as what does or does not constitute 'publication') are, in the end, probably not universally soluble, because they deal with factors such as judging ethical behaviour that cannot be expressed in simple formulae applicable to every situation. So it should hardly be expected that rules for electronic publication should have immediately attained perfection when not even those for paper publication, with 170 years or more of a head start, have not yet done so. What is more, some of the failings in the current rules will not become apparent until they are able to be tested. Loopholes will have to be closed, terms will have to be clarified. And as I airily critique issues with the current rules in this post, I am well aware that the rules' composers will have probably already discussed them to death, and any suggestions I make may have their own problems that I have overlooked.

What, exactly, is an electronic publication?

As I noted in the earlier post linked to above, the ICZN effectively requires that any electronic publication has an associated ISBN or ISSN (this does not have to appear in the publication itself, but it is required for the registration of the publication on ZooBank). To a certain extent, this makes sense: it means, for instance, that taxonomists do not have to worry about taxa being 'accidentally' published in mailing groups, blogs, etc. that may not be reliably archived. But it does raise the question: in the electronic age, why should a publication necessarily be a 'book' or a 'serial'?

The ICN (International Code for Nomenclature of plants, algae and fungi; what we used to call the ICBN) apparently requires that electronic publications be in pdf format. The ICZN does not make this an actual requirement, though pdf is cited as an example of a format that meets the requirement of 'widely accessible electronic copies with fixed content and layout'. I think that the ICZN is in the right here; while it is difficult to see pdf being superseded at the present point in time, it is perhaps hazardous to assume that this will never happen. I suggest that the requirements of an electronic publication should be that, (A) at least the content (if not the format) should be intended to be immutable*, and (B) it should be somehow 'stand-alone', not requiring a larger context other than the standard requirements for reading electronic files (so, for instance, a database entry that can only be accessed as part of that database may not be acceptable).

*It is worth noting at this point that even a paper publication is, in a sense, not 'immutable' if its publishers do not behave ethically. If a publisher produces a second, altered print run without explicitly marking it as a revised edition or changing the reported publication date, there may be no indication that it represents a distinct publication from the original run. Most people will not read through two separate copies of a publication just on the off-chance that they may differ.

Do pre-releases count?

There is one clause in the new rules that I expect will be guaranteed to cause immediate problems. This is the new Article 21.8.3: "Some works are accessible online in preliminary versions before the publication date of the final version. Such advance electronic access does not advance the date of publication of a work, as preliminary versions are not published (Article 9.9)."

Remember old Scansoriepidendrosauropteryx? This was an animal that first debuted in an electronic online-early form in a well-known journal, but before the print edition of that paper was finally published the animal was described under a different name in a paper-only publication. The resulting confusion, when the earliest name publicised was not the one with technical priority, was one reason why at least some people were calling for electronic publication to be recognised. Well, guess what? Under the current rules, this case would have played out no differently. Some would look askance at accepting pre-releases as validly published because of the possibility of alteration between the pre-release and the final edition, but as I said above, perhaps this is something that requires us to discuss what exactly we regard as a 'publication'.

There is also the new Article 21.9 to consider: 'A name or nomenclatural act published in a work issued in both print and electronic editions takes its date of publication from the edition that first fulfilled the criteria of publication of Article 8 and is not excluded by Article 9.' Some may read this as saying that an electronic pre-release counts as a valid publication if, in itself, it meets the requirements of electronic publication. Some may read this as being trumped by 21.8.3.

And what about electronic versions of paper publications?

To be validly published, an electronic publication has to be registered with ZooBank and include evidence of its registration. Paper publications, on the other hand, do not yet have to be registered. The problem is, many researchers are now more likely to access electronic copies of paper publications than the original paper edition itself. And if I do so, how can I be sure that the paper edition actually exists? Even for some of my own publications in recent years, I've never actually laid eyes on the original journals. I've only seen the pdfs, and I've trusted in the publisher that the paper edition exists and that taxa I've erected are indeed validly published. Similarly, if I come across a publication from an unfamiliar journal (and with hundreds if not thousands of journals publishing in biology worldwide, I will not be familiar with them all) when searching online, would I necessarily know whether that represents an electronic-only publication or an electronic copy of a paper one?

When the question of electronic publication was still being debated, I stated more than once that the biggest problem with not accepting it was that, for many readers, it was all too difficult to distinguish valid publications from invalid. I have my doubts whether this problem has yet been solved.

It's the End of the World as We Know It...

...maybe.

For lo, it did come upon this day that the ICZN did look upon electronic-only publication, and say that it was good. Provided that it met the following requirements:

(1) the published work must be registered with ZooBank prior to publication, with provision in the ZooBank record of a permanent archive in which the the published work will be held,

(2) the published work must include evidence of registration, such as the ZooBank registration number, and

(3) the published work must be associated with either an ISSN or ISBN number, so it must be a formal 'book' or 'journal'.

You can read further details here. As is standard for new ICZN requirements, they are not intended to be retroactive, and online-only names from before the new rules were introduced are still invalid.

I don't think that many people will be surprised by this (while you complain about the cost of prescriptions... Mike Taylor is looking very smug). As I've discussed before, I reluctantly came to accept that electronic publication would have to be allowed after I realised that most non-taxonomists (and many actual taxonomists) were finding it increasingly difficult to distinguish what was 'published' from what was not. So what does this mean in practice?

It became clear at an early date that successful management of electronic publication was going to require registration. In the past, most people were talking about registration of names, but the ICZN has decided to go with registration of the actual publication. This avoids any hiccups such as human error leading to some of the names in a publication being 'published' while others are 'unpublished'. I can see potential complications arising with the requirement that registration happen before publication, but ZooKeys has been publishing articles with ZooBank registration numbers for taxa included for a while now, so it would seem that the requirement is not insurmountable. Of course, there would have been potential problems had the requirement been registration after publication. It should be noted that, even though the published work has to include evidence of registration, there is a certain allowance for error, so long as it is clear that the work has indeed been registered (so, for instance, if a transcript error meant that the wrong registration number was included in the publication, that does not automatically invalidate the publication).

The requirement that the publication has either an ISSN or ISBN number means that names cannot be just published carelessly. If I refer to the features of an unpublished species in a blog post, I will not be accidentally 'publishing' that species and potentially confusing the paper trail (electronic trail, in this case). Note also that, while the ZooBank record of a published work must include the ISSN or ISBN, the work itself doesn't directly have to. So, for instance, the ISSN of a journal does not have to be included in every individual article.

One of the biggest concerns raised about allowing electronic publication is that it will make it even easier for would-be taxonomic 'vandals' to ply their irritating trade. The registration and ISSN/ISBN requirements, as well as making it clear what is intended for publication and what is meant to be just an online communication, are intended to impede such behaviour. They won't stop it entirely (as I've noted a few times before, that would be effectively impossible) but they do provide a couple of hoops that must be jumped through.

So all that remains to be said is: Let the games commence!

Thoughts Inspired by a Private Publication

A number of sources, including this message on the DML archive, drew my attention yesterday to the existence of a recent online publication proposing a new North American sauropod species 'Amphicoelias brontodiplodocus', as well as synonymising a whole slew of other familiar dinosaur taxa (such as Apatosaurus and Diplodocus) under the relatively unfamiliar name Amphicoelias. Quite apart from 'Amphicoelias brontodiplodocus' perhaps being the most intensely unaesthetic name ever proposed for a dinosaur (and this in a field including such wince-inducing monikers as Raptorex and Tyrannotitan!), the pdf has once again lifted the lid on a number of arguments that have been simmering away for some time now. I recommend reading the responses to the DML message linked to above, as well as Mike Taylor's discussion at SV-POW. I'm not in a position to discuss the technical details of the 'brontodiplodocus' pdf itself but I would like to discuss some of the broader issues raised by it, the questions of regulating publication and of publications based on privately owned specimens.

It should be noted that the 'brontodiplodocus' pdf currently appears to be an online document only and hence not validly published in the view of the ICZN (and whatever its publication status, there is no obligation on anyone else to accept the proposed synonymies). However, Mike Taylor has pointed out that it would be a simple matter for the publishers of the document to produce it in printed form and thereby validate it. Also, it would be easy for a non-expert in taxonomic procedure (and even a few supposed experts in taxonomic procedure) to mistake the current pdf for a valid publication as it is. As I've noted before, end-users of taxonomy should not be required to consider ICZN esoterica every time they are presented with a new name, just as non-specialist computer users should not always have to familiarise themselves with thousands of lines of computer code before using a new word-processing programme.

While self-publication of poor-quality works has always been a potential issue for taxonomy and the ICZN, modern technology has made self-publication much easier than before. It can now pontentially be done by anyone with access to a word processor of some form: i.e. pretty much everyone in the developed world and a large number of people in the developing world. Some have suggested that, to counteract this issue, only names published in peer-reviewed journals should be accepted as valid (I've pointed out why I disagree with this proposal in an earlier post). Others have suggested taking this even further and establishing a single journal for the publication of all zoological taxonomy. This is already the method used by the Prokaryote Code of Nomenclature, which requires that all new bacterial taxa be published or validated in the International Journal of Systematic and Evolutionary Microbiology. However, it is debatable whether such a model could be applied to the ICZN. Firstly, the sheer number of new zoological names published each year is much higher than the number of bacterial names, perhaps by a few orders of magnitude. A single zoological taxonomic journal would be a major undertaking, especially for an organisation such as the ICZN which lacks any major sources of funding on which to draw. Secondly, the Prokaryote Code of Nomenclature has very high basic requirements for a taxon to be considered published (such as deposition of cultures of the type strain in two separate collections in separate countries). It is unlikely that the ICZN would be able to implement such across-the-board requirements because it deals with a much broader range of organism types (such as fossils and protozoans) than the bacterial code, each of which may have their own specialised requirements for appropriate typification.

In addition, one of the reasons that prokaryote nomenclature functions so well under these restrictions is the usage of a wide range of what might be called 'grey taxa', taxa widely regarded as recognisable but which, for various reasons (most commonly their inability to date to be cultured in the laboratory), cannot be 'validly' published (one such taxon that I've previously discussed is the minute 'Nanoarchaeum equitans'). Bacterial nomenclature therefore has two distinct nomenclatural classes of taxa. This is not necessarily a problem: 'grey taxa' cannot compete for priority with 'valid taxa', for instance, which reduces the chance of an old poorly-characterised name supplanting a newer familiar one.

The current version of the ICZN does allow in Article 79 for the potential publication of Lists of Available Names for selected taxa. Under this article, a list could be published of (for instance) all published bird names that would become the definitive listing for that group. Any names published prior to the list's end-date that were not included are regarded as unavailable (and hence not competing for priority with names included in the list), even if they normally would be under the general rules of the code (the Prokaryote Code followed this path with the publication of the Approved Lists that were the foundation of current bacterial nomenclature). To date, I am not aware of any such list being successfully ratified by the ICZN (it would not be a simple process), but the facility is potentially there. At present, the Lists of Available Names are only intended to clarify the status of previously published names rather than regulate any published subsequent to the relevant list. However, even if it is not currently feasible to introduce a single journal model for all zoological nomenclature, perhaps it could be done for specific groups? Imagine if a List of Available Names could be published for (say) dinosaurs, with a requirement that all subsequent names be validated by a prominent journal such as the Journal of Vertebrate Paleontology? (On the flipside, there would have to be a requirement that the journal must validate all names that meet certain pre-existing requirements [as currently exists for the IJSEM] in order to prevent names being refused for reasons unrelated to the diagnosability of the taxa concerned, such as personal disputes between taxonomists.) If done on a group-by-group basis, such a process might also allow for workers in each group to determine the appropriate requirements for that group.

The second major issue raised by the 'Amphicoelias brontodiplodocus' pdf is that its publishers are commercial fossil dealers and at some point the brontodiplocus 'holotype' may (probably will) be privately sold. The ICZN currently recommends, but does not require, that the type material for new taxa be deposited in publicly accessible collections. If a specimen is privately held, it is less likely to be available for study by future researchers (however, it is worth noting that a privately held specimen is not always unavailable, nor is a specimen in a public collection necessarily available). In the case of fossils, some people are of the opinion that their commercial sale should be banned completely in order to prevent scientifically significant material from entering private hands. However, not all fossil material is scientifically significant—some fossils are extremely abundant (to the extent that some localities have profitable fossil mines) and there would seem to be little sense in banning the sale of a fossil species for which thousands are already held in public collections. If the possibility is floated of only banning the sale of 'scientifically significant' specimens, we run afoul of the problem of specifying how to determine which specimens are scientifically significant. For instance, articulated Tyrannosaurus skeletons are very rare and of great scientific interest, but isolated Tyrannosaurus teeth are very common (or so I've heard) and of little scientific interest. Where exactly does one draw the line?

Type specimens, however, are by definition of scientific interest, and it is usually clear whether a specimen is a type. So while it would be somewhat ridiculous to ban the commercial sale of all fossils, perhaps it would be reasonable to preclude the commercial sale of type material? Note that I am not suggesting banning the use of privately held material in describing taxa, only that such material could not be subsequently traded*. I can think of two potential issues that might have to be considered in such a scenario. One is that commercial collectors may refuse to allow any examination of material that they hold by researchers to prevent its effective devaluation (of course, some may not see this as a problem). Another potential problem would be if a privately owned specimen is made part of the type material of a new species without the informed consent and/or involvement of the specimen's owner.

*The distinction between privately and publicly owned specimens is a lot fuzzier than those working outside the taxonomic field might expect. Many new species are described by authors on the basis of specimens they have themselves collected; while the authors may intend on eventually depositing the specimens in a public collection, this may not have yet happened at the time of publication. Depending on circumstances, it may be some time before the specimen(s) are finally passed on to the collection**.

**To give an example from my own experience, two years ago I published the new harvestman species Templar incongruens based on two specimens previously held at the Western Australian Museum that had been collected in Canterbury, New Zealand. It was decided that the new types should be transferred to the Canterbury Museum as it seemed more appropriate for them to be held in a collection in their home country, and this was the depository recorded in the publication. However, because T. incongruens has also formed part of my phylogenetic analysis of Monoscutidae currently in preparation, the specimens have not yet actually made it to Canterbury: they're still sitting in my lab here in Perth.

The Problem of Publication Again

I haven't been a member of the DML for a while so I missed the controversy of the last few days over the publication (or not) of a book called Notes on Early Mesozoic Theropods. Mike Taylor has written about the situation at SV-POW! and I recommend reading his post. Basically, the question of whether or not this book (and the new theropod taxon described within) counts as 'published' circles around the fact that the book is distributed as "print on demand". In other words, copies of the book are printed as they are ordered rather than being printed in a single run of multiple copies and some people have questioned whether this satisfies the ICZN requirement of "simultaneously obtainable copies [produced] by a method that assures numerous identical and durable copies" (Art. 8.1.3)*. Print-on-demand has been rare in the past because the cost of preparing templates made printing single copies uneconomical; as printing has become cheaper, it may be expected to become more standard. Indeed, one could argue that it should be so, being potentially less wasteful than producing large runs of potentially unwanted copies.

*In the comments for the SV-POW article, I indicated that the electronic publication procedure proposals being considered by the ICZN (ICZN, 2008) included disqualification of print-on-demand publications from availability. I was wrong about this; the proposal merely includes a discussion of issues potentially connected with print-on-demand (specifically, the possibility of alterations between printings).

In previous posts, I've discussed the availability of electronic publication, rare publications and self-published works. One issue I haven't discussed in detail, but which is perhaps the most important of all, is that it is becoming increasingly difficult for the non-specialist to decide what is 'published' and what isn't. In the past, media such as private letters, theses and conference handouts have been disqualified as valid 'publications' because they were of ephemeral nature and/or limited distribution. Conversely, anything that was widely available could usually be safely assumed to be published because there really was little way for it to be otherwise. Electronic publication has changed all that; supposedly 'unpublished' works may have audiences running into the thousands.

Even most printed journals are now more widely read as electronic versions. The largest zoological taxonomic journal currently operating is Zootaxa which now publishes issues on more or less a daily basis (twenty issues in a single day on 14 May earlier this year). The vast majority of Zootaxa's articles are distributed electronically; printed copies are effectively only produced to confirm availability. But most of us have only the word of the Zootaxa editors that these printed copies exist; we're not tracking them down ourselves because the electronic version meets our needs. For all most of us know, Zootaxa may have halted printed production some time ago (or be printing on demand). The same goes for a great many other major taxonomic journals.

The minutiae of determining whether or not a taxonomic work has been validly 'published' can be daunting enough for experienced workers; for non-specialists, they may seem impossible to follow. Nor, in an ideal world, should a non-specialist ever have to make such a decision, no more than someone should be expected to assemble the motor themselves before taking their new car for a drive. Like it or not, I'm afraid there is no escaping the conclusion that electronic publication of nomenclatural acts is inevitable and will be accepted by the taxonomic community with or without the endorsement of the Code (Taylor, 2009). It's simply too confusing otherwise.

So what, practically speaking, should we actually be doing about it? To begin with, I agree with Mike Taylor's statement in the SV-POW post that we need to make registration of new nomenclatural acts (as currently beeing developed for ZooBank) compulsory. There are potential objections that could be made to compulsory registration (I've made some in the past myself) but I think that, overall, the advantages outweigh the disadvantages. Registration will not solve the problems surrounding marginal publications but it will make it easier to manage them (especially if specialists are able to upload comments on the availability of registered names). And at least non-specialists would be able to feel secure that names not properly registered can be safely ignored.

REFERENCES

International Commission on Zoological Nomenclature. 2008. Proposed amendment of the International Code of Zoological Nomenclature to expand and refine methods of publication. Zootaxa 1908: 57-67.

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).

Taylor, M. P. 2009. Electronic publication of nomenclatural acts is inevitable, and will be accepted by the taxonomic community with or without the endorsement of the Code. Bulletin of Zoological Nomenclature 66 (3): 205-214.

"Electronic Publication of Nomenclatural Acts is Inevitable"

The Jurassic mecopteran Lichnomesopsyche gloriae, one of six new fossil species not published today. The black line is highlighting the long proboscis; the scale bar represents 10 mm. Image from Ren et al. (2009).

So sayeth Mike Taylor (for my own confused ramblings through the quagmire of electronic publication, read my earlier posts on the subject). And this day presents us with a spectacular demonstration of that point.

In a paper in today's issue of Science, Ren et al. (2009) have presented an analysis of Jurassic to early Cretaceous long-proboscid scorpionflies and their role as probable pollinators of nectar-producing gymnosperms (as has also been suggested for kalligrammatid lacewings). As part of this study, Ren et al. present descriptions of six new species and two new genera of fossil scorpionflies. Nothing out of the ordinary here, except that (Science being Science, with its notorious restrictions on article length) the species descriptions are published in the Supporting Online Material.

From the point of view of the ICZN, Science is a perfectly valid forum for publication - thousands of copies are printed every week. But these printed editions don't include the online supplements, so the online-only component of the journal is currently not a valid publication. Technically speaking, the new species of Ren et al. (which are referred to and illustrated but not described in the print version) are nomina nuda. They are not valid names. But these online-only names have not appeared in some far-flung unfrequented corner of the internet, they have appeared in one of the world's most prominent science journals (like it says on the label). Their validity is going to be pretty much taken for granted.

REFERENCES

Ren, D., C. C. Labandeira, J. A. Santiago-Blay, A. Rasnitsyn, C.-K. Shih, A. Bashkuev, M. A. V. Logan, C. L. Hotton & D. Dilcher. 2009. A probable pollination mode before angiosperms: Eurasian, long-proboscid scorpionflies. Science 326: 840-847.

Some Thoughts on How to Make Electronic Publication Work

"There is a cube of crystal here - though I can no longer tell you where -no larger than the ball of your thumb that contains more books than the library itself does. Though a harlot might dangle it from one ear for an ornament, there are not volumes enough in the world to counterweight the other."
--Gene Wolfe, The Shadow of the Torturer.

The ICZN is currently debating amendments to the Zoological Code that will formally accept the validity of names published in electronic publications (ICZN, 2008; if you're not familiar with the subject, I'd recommend reading the post just linked to before this one). Electronic publication raises a host of issues related to such matters as long-term availability and accessibility, but even an old curmudgeon like myself has to admit that it's gonna happen, whether we like it or not - in fact, it's already happening - and the question of whether or not to accept it has become more or less moot. The question, rather, is how to best respond to it.

I do have to apologise in advance for a few things I'm going to quote here without attribution that I know I've heard someone say somewhere, but I can't remember where or who. This post was partially inspired by Taylor (2009; that's Mike Taylor of SV-POW! fame, not me) and its rather snotty little title, but I wouldn't call it a direct reply. I'll also note that one of the interesting side effects of the debate on how to handle electronic publication is that it provides a much-needed impetus to tackle some of the neglected questions of how we handle printed publications.

Many of the complaints about electronic publication revolve around permanence. Supporters of electronic formats point out (and correctly so) that on-line publications* are both more readily and widely distributable than printed publications. However, for the purpose of taxonomy, we need to be thinking not only about current distribution, but also future distribution. Preservation of taxonomic works, theoretically, needs to be permanent (in the long term, of course, this is a problem for both printed and electronic works). It has been claimed that the large number of electronic copies floating around on people's private computers provides a guard against loss of an electronic publication, but this is not a sufficient guard in the majority of cases, because of the simple fact that not all organisms garner the same degree of attention. Taylor (2009) refers to the public interest around the publication of Darwinius masillae Franzen et al., 2009 - I mean, come on, it's a bloody monkey with its own bloody TV documentary, of course it raises a lot of interest. But taxonomy doesn't only concern fossil monkeys or honking great lizards, which are the other cases Mike cites. Yochelson (1969), working on Palaeozoic molluscs, estimated that the species description he wrote were "read by a worldwide audience that ranges from three to seven persons"**. This is not an audience that guarantees preservation. Also, there is a potential generational issue - when a researcher passes away, her copies of printed publications may be donated to a library and archived, but her hard-drive is likely to be thrown away or wiped.

*Including on-line versions of printed publications, which in a significant proportion of cases have become the effective primary version.

**Yochelson (1969) is a rather interesting publication for the current debate because he wrote it arguing that the ICZN should accept publications on microfilm. The more things change...



However, while permanent storage may be more of an issue for electronic media than printed media, it's one that is already being addressed, with the current proposals already including requirements for archival that, while arguably not perfect, are perhaps good enough for government work. The really major problem is not long-term availability, but long-term accessibility. To read a printed publication, I have simply to use my eyes, and for most of us they come pre-installed*. Reading an electronic publication, however, requires appropriate machinery and software. Claims that there will "always be a way to read PDF" are just hopelessly naïve, as are claims that we will be able to rely on conversion of electronic publications into newer formats as they gain prominence. Media will be converted if there is an immediate demand for their conversion, and the longer a given publication goes without being converted, the lower the chance that it will ever be converted (I'm pretty sure that a significant number of movies once available on VHS have not become available on DVD and probably never will). In the quote at the top of this post from a book set in our world's far-distant future, the librarian Ultan refers to what is obviously some sort of electronic storage device. What he fails to mention is that the technology to read the material stored on it no longer exists.

*Of course, it has to be in a language I can read, but that issue applies equally to electronic and printed media.

So electronic publications are not sufficiently reliable, but electronic publications are already here and only going to become more predominant. Are we doomed to confusion then? No, because I don't think that the means of evading the issues are really that difficult. The current code allows for the effective publication of electronic media if a permanent copy is deposited in a number of libraries on CD. The proposals in front of the ICZN include phasing out CD publication, and rightly so in my opinion - CD publication carries all the issues of accessibility associated with electronic media, without any of the advantages of online publication. But why not request the deposition of print-outs? That both allows for the validity of the electronic publication (with all its advantages of disseminability), while still maintaining the printed counterpart as a back-up.

Taylor (2009) points out that the current requirements for back-up deposition are vague and difficult to comply with. I would definitely agree that, if nothing else, they lead to something of a logical paradox in their current requirement that the publication itself include details of its own depositories. A simple reprint of the current requirements with "printed copy" substituted for CD would not help matters. But what about ZooBank? ZooBank is the proposed register of zoological names currently being developed. The current code does not require registration of names, but it is being considered and the electronic publication proposals include compulsary registration for electronically-published names at least (though as pointed out in the comments to the post linked to at the top of this one, if they're going to make it compulsary for some they might as well make it compulsary for all). A separate proposal that has been made that would make registration compulsary for all new names (Polaszek et al., 2005) allows a window of two years between publication and registration for a name to be validated*. Perhaps ZooBank could be expanded to also hold listings of archives of printed copies for electronic publications with, again, a two-year window to allow the authors/publishers to arrange the depositories and submit the info. Heck, the same thing could be done for names published in rare printed publications such as the journal Lansania that I've discussed previously.

*And it was this simple point that made yours truly no longer an avid opponent of registration. In a workable system, registration would have to come after publication, because the potential consequences of a name being published but not registered afterwards are minor compared to those of a name being registered but not published.

One potential complaint is that the printed version may not be identical to the electronic version. This would be particularly unavoidable if the electronic version includes such features as video that are not reproducible on paper. But for the purposes of taxonomy, what does the permanent record actually need? Name, type material, description/diagnosis. If the entire publication cannot be stored in printed form, then maybe allowances could be made for an abridged version containing the vital points to be deposited in its stead. Cantino et al. (2007) provides something of a precedent in botanical nomenclature (which currently excludes electronic publication) - a shorter, printed version of this work on plant phylogenetic nomenclature was published containing the essentials of definitions and such, while a longer electronic version allowed for more expansive discussion. So long as the two were not in direct conflict, then the existence of two versions does not actually pose a problem for nomenclatural purposes. For those wishing to guard against potential issues, perhaps a clause could be included in the code giving one of the versions priority over the other - I'd suggest something to the effect of the electronic version having priority so long as it remains available and accessible, because that's the version people are more likely to have access to in such cases.

Discuss.

REFERENCES

Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, P. S. Soltis & M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56(3): E1-E44.

Franzen, J. L., P. D. Gingerich, J. Habersetzer, J. H. Hurum, W. von Koenigswald & B. H. Smith. 2009. Complete primate skeleton from the Middle Eocene of Messel in Germany: morphology and paleobiology. PLoS One 4 (5): e5723.

International Commission on Zoological Nomenclature. 2008. Proposed amendment of the International Code of Zoological Nomenclature to expand and refine methods of publication. Zootaxa 1908: 57-67.

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).

Taylor, M. P. 2009. Electronic publication of nomenclatural acts is inevitable, and will be accepted by the taxonomic community with or without the endorsement of the Code. Bulletin of Zoological Nomenclature 66 (3): 205-214.

Yochelson, E. Y. 1969. Publication, microfilm, microcard, microfiche, and the International Code of Zoological Nomenclature. Systematic Zoology 18 (4): 476-480.

The Perils of Peer Review

There is an awful lot of crap taxonomy out there. Incoherent ramblings, near-unidentifiable taxa, or "new" taxa of dubious distinction from their previously-published relatives are all too common. Because inadequate taxonomic works can create an enormous hurdle for subsequent workers*, many suggestions have been made on how to reduce the number of such publications. One point that I've heard raised a number of times recently is that the current ICZN places very few limits on where a new taxon can be published, and the suggestion has been made (at least informally) that only names published in peer-reviewed publications should be acceptable. While I can see the appeal in this proposal, I disagree - I don't think the ICZN should introduce such a requirement.

*As Charles Michener (1963) put it: "In other sciences the work of incompetents is merely ignored; in taxonomy, because of priority, it is preserved, and too much of the time of subsequent taxonomists is devoted to straightening out work of such people".

At the risk of stating the obvious, peer review is not a guarantee of quality. A lot of absolute dreck has survived the peer review process unscathed; a lot of excellent non-peer reviewed work has been published. Indeed, it is worth keeping in mind that formal peer review is, for the most part, a quite modern phenomenon. Until fairly recently, it simply wouldn't have been logistically feasible to send copies of a manuscript to multiple reviewers - especially for researchers in places like Australasia who were often working in isolation and for whom the only suitable reviewers would have been on the other side of the globe. A significant number of major taxonomic monographs that are still being referred to today were never peer reviewed.

There are also limitations to peer review that are particularly applicable to taxonomy. A reviewer of a manuscript is always forced to exercise a certain degree of faith in the author(s) he/she is reviewing. They can re-run the data analyses reported in the manuscript to see if the sums add up, they can try and think of any other analyses that the author(s) should have done but didn't, but generally they must first make the assumption that the author(s) are reporting their data accurately (almost the only alternative would be to re-run the entire investigation from scratch, an investment of time that most reviewers would simply not have the freedom to make). Unless there are great glaring holes in the reported data, most reviewers may not be likely to spot cases of fabrication, omission or basic error*. This is a particular limitation in taxonomy because of its often interpretive and material-dependent nature. If you present me with a manuscript saying "Specimen group A and specimen group B have the following distinct characters, and should be regarded as separate species", then I am limited in how much I can check this assertion because most likely I do not have access to your specimens.

*To give a practical example of what I'm trying to say: imagine you said to me, "Today I saw two red cars and one blue car; therefore, red cars are more common than blue cars". I can criticise your conclusion on the basis of the data you've given me (for a start, I would hardly think that three observations is a large enough sample to be statistically significant), but I would have no way of knowing whether you actually had seen two red cars and one blue car.

Of course, while both these points are worth keeping in mind, neither one is in itself a reason not to introduce a peer review requirement into taxonomy. The recency of peer review would not be likely to be a problem because most revisions of the Code have not been retroactive. And while peer review may not ensure that only quality work is published, it usually still acts as a general filter to prevent the worst abominations. The real reason why I don't think that the Code should introduce a peer review requirement is that if you are going to require something, you must first be clear about what it is that you are requiring.

Last year one of the big news items for vertebrate palaeontology was Aetogate, in which allegations of academic misconduct were levelled against an American palaeontologist and his associates. Without wanting to comment specifically on that whole sordid affair, one of the major take-home messages that I thought came out of it was the difficulty of defining "peer review". Among the accusations being made was that the journal publishing many of the allegedly offending articles could not really claim to be "peer reviewed", because the "reviewers" were made up of people closely connected to the journal itself and so not impartial. If the reviewers of a manuscript have a vested interest in the progress of that manuscript, then obviously their suitability as reviewers is questionable.

Unfortunately, the solution to this problem is not as simple as requiring that a manuscript must be reviewed by someone other than the author's nearest and dearest. If one is working in a specialist field that encompasses only a small number of workers, then there simply may not be any qualified reviewers other than one's nearest and dearest (or furthest and most loathed, which is arguably just as bad). And because the details of the review process are not usually made public (for perfectly valid reasons) there is usually no direct way of telling after publication what level of review a manuscript has passed through. As I've discussed in a previous post, it can often be contentious enough establishing whether or not a name has been properly published. Imagine the confusion that could ensue if subsequent workers had to establish whether it had been properly reviewed.

So what is the appropriate solution to inadequate taxonomy? As it happens, the ICZN already has some powerful tools up its sleeve. It has the ability to eliminate problematic names or, if necessary, entire publications from nomenclature. It is also worth noting that many of the workers who have suggested a peer review requirement are not considering just the simple quality of taxonomic work, but more its currently dispersed nature. In that case, a central registration system (currently being proposed and developed for the ICZN) may remove a large number of the current issues. Registration is a concept that is not without its issues, but at least determining whether or not a name has been registered would be much more straightforward than determining whether or not a name has been reviewed.

REFERENCES

Michener, C. D. 1963. Some future developments in taxonomy. Systematic Zoology 12 (4): 151-172.

Define "Published"

The other day, Rob Taylor of the DML was asking about the status of electronic and Advance Online publications in the eyes of the ICZN - do they count as officially published? You can read my response to him here (unfortunately, the DML archive has borked Rob's original message, otherwise I'd link directly to that, but the greater part of the original is present in indented form through my reply). I've discussed electronic publication on this site before (see here and here). I think I've stayed fairly neutral in those posts, though my personal attitude towards electronic-only publication is roughly comparable to my attitude to such things as prostitution and recreational drug use. They're probably a bad idea, but they're going to happen anyway, so it's probably more important to structure things so that they can be properly managed than to simply hope they're going to go away.

But in all this discussion of how to establish when online references are validly published - what are the necessary archiving requirements, if a publication comes out online before it appears printed on paper should it be dated from its online or printed appearance, etc. - there is one ugly but widely-known secret that has been mentioned surprisingly little. As difficult as it may be to establish whether an online resource has been validly "published", it can be equally difficult to establish the same for a printed resource.

In the eyes of the ICZN, it is not enough for the printed resource to simply exist, and for fairly obvious reasons. If I set up a printing press in my garage (after all, seeing how I don't own a car, I'd have no shortage of space in a garage) and printed myself a copy of some pamphlet naming a new taxon, that new taxon still wouldn't be valid. Taxonomy, like all other sciences (indeed, in some respects even more than other sciences) is ultimately dependent on communication if it is going to work properly. It's no coincidence that the word "published" is so similar to the word "public". If there's only a single copy of my little pamphlet, how is it going to be communicated? How are my fellow taxonomists going to be able to critique the validity or otherwise of my new taxon? What is the likelihood of that pamphlet being available ten, twenty, two hundred years down the track after I myself am dead and buried*? There's also the credibility factor - say some amazing new taxon is published in a high-level journal (Ubertyrannosaurus ohbuggerme, or something), and I start waving around my little pamphlet, which is dated to earlier than the journal, shouting that I described this new taxon first. If nobody else has seen it before, what evidence do I have that I didn't print out the pamphlet after the journal article came out and slap a fake date on it?

*Though if I am the type of person who churns out secret pamphlets on my own printing press in the garage, that would possibly be buried within a raccoon.



So instead of letting just anything go, the ICZN has the following requirements:

8.1. Criteria to be met. A work must satisfy the following criteria:

8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,

8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and

8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies.

I can still print papers out on my private press at home (alas, some people do) but in order for anything in those papers to be valid, there has to be a decent number of copies, those copies have to be readily available after publication, and there has to be a decent chance that copies are still going to be out there and available thirty years down the track. Still, it's all just a little vague, innit? Just how many copies is a "decent number"? It's one of the great ironies of the ICZN (and it hasn't gone uncommented on) that the Code has strict guidelines for the one form of electronic publication it does currently allow (CD publications must have at least five copies deposited in separate major public libraries), but has no such baseline for the paper publications that are its supposed backbone.

It doesn't take a great deal of imagine to develop hypothetical problem cases for these rules. Say I print out a large number of copies of my private paper, more than enough to satisfy that part of the requirements. But then instead of distributing them right away, I keep them stacked in a box in my basement*. Even though the copies exist, they're still not satisfying the desired purpose of communication. They shouldn't really be counted as "published" until I actually get off my arse and start distributing them to people. The problem is, though, that the date on their cover would be the date I printed them out, not the date I made them available (this is exactly one of the issues involved in the Scansoriepidendrosauropteryx fiasco). There are a number of cases in taxonomy of synonymous names being published at very close times, and working out which of the two (or more, if your luck is really evil) names has priority can be an absolute bitch. The longer ago the papers were published, the harder it can become to establish their relative priorities. What's more, there's always a nearly comical sense of bleak futility about such investigations. In the case of the aforementioned Scansoriopteryx, it's currently widely known that its source, the Dinosaur Museum Journal (volume one, if I recall correctly) didn't become publicly available until a while after its printing, making the date on the book out by at least a month (during which time, the probable synonym Epidendrosaurus appeared in an Advance Online publication). The thing is that while that may be general knowledge now, will it necessarily still be general knowledge in twenty years' time. If the information floats around in informal communications, but no-one actually mentions in print that the date is out**, then that piece of info is going to be forgotten, and the claimed date will become treated as correct by default.

*I seem to have both a garage and a basement - I'm beginning to like this hypothetical house of mine.

**In this specific case they have (Harris, 2004), but let's make allowances for hypotheticals.


The Japanese arachnologist Kyukichi Kishida, publisher and editor of the ill-fated journal Lansania. Photo from here

As a concrete example, I'm going to present you with one of the worse cases out there. The journal Lansania was privately published in Japan by the zoologist Kyukichi Kishida from 1929 to around-about-1941, and its history was recently reviewed by Tennent et al. (2008), whose article makes recommended if somewhat disturbing reading for anyone interested in the subject of this post. For the first couple of years, Lansania seems to have a fairly normal run, with issues appearing as one might expect. After that, though, it all seems to have gone a little pear-shaped (funding for publication may have become an issue). Issues appeared erratically, and not necessarily in order. A number of scheduled issues never seem to have been printed in any form. For others, individual articles exist as offprints, but there is no sign of a complete issue. Issue 58, for instance, is represented in offprints by pages 113-115 and pages 125-128, but there is no sign of 116-127*. What happened to these intervening pages? Did they ever actually exist? It seems that what happened was that Kishida assigned individual articles to planned issues as they were submitted for publication, had them printed as offprints when they had been prepared for publication, then printed the final issue when all the articles for it were ready.

*Ironically, the article represented by pages 113-115 of this issue, which does exist, is supposedly a supplement to an "earlier" Lansania article that seemingly doesn't exist.

Things were not improved by Kishida's somewhat lax attitude towards publication and dating. There is evidence that in many (but not all) cases, the date placed on a published issue or article was the date the article was submitted for publication, not the date it appeared in print (which might not have been until some years afterwards). One publication of Kishida's bore a date of "1938", but gave his address as one which he did not reside in until 1957! When asked by a colleague to explain the discrepancy, Kishida apparently replied that he had begun composing the article in 1938. On a number of occasions, Kishida also seemingly cited as if published articles and names from articles that would have still been "in press", not all of which ever made it into actual print.

Unless they did... You see, Lansania never had a huge circulation, and copies of issues have become few and far between (Tennent et al. give a listing of all the holdings for Lansania they could find - for instance, the latest issue they could locate, no. 127, is only held by two libraries in Japan, while it is possible that only a single copy still exists of each of the issue 58 offprints). Kishida stored a number of unpublished manuscripts and published journals in a shed behind his house that were disposed of after his death in 1968 - could these have included some of the missing issues of Lansania? A lot of Kishida's material had earlier been taken for use as waste paper in times of shortage during the Second World War. Could some of the "unpublished" issues (or even extra copies of the rare published issues) still be held in private libraries? Should the taxa described in the exceedingly rare printed issues or offprints of Lansania even be treated as published at all?

Though extreme, the case of Lansania is not unique. Anyone who has had to invest a fair amount of time in obtaining copies of old publications knows that they can sometimes be exceedingly difficult to find (one of the first pieces of advice I would give to a student starting taxonomic research is to make friends with a really good interloans librarian). They may have satisfied all the requirements for valid publication when they first appeared - but over the years, copies get lost, destroyed... Are there taxa out there in current use for which copies of the original descriptions simply don't exist anywhere anymore? What is the status of these taxa under the ICZN? Can an available name become unavailable?

REFERENCES

Harris, J. D. 2004. 'Published works' in the electronic age: recommended amendments to Articles 8 and 9 of the Code. Bulletin of Zoological Nomenclature 61 (3): 138-148.

Tennent, W. J., M. Yasuda & K. Morimoto. 2008. Lansania Journal of arachnology and zoology – a rare and obscure Japanese natural history journal. Archives of Natural History 35 (2): 252-280.

Electronic Publication in the ICZN - new proposals

Hot on the heels of the Les debacle, the ICZN has released its proposed regulations allowing electronic publication. For those interested in the full legalistic details, a complete description of the proposed amendments is openly available at Zootaxa (full reference at the bottom of this post). Because this is (needless to say) A Big Thing, and the proposals affect printed as well as electronic publications, I'm going to give my own comments on a number of points.

Before I do, though, I think that it's important to stress that these proposed amendments are not yet in effect. The Zootaxa paper (and an apparently upcoming release in the Bulletin of Zoological Nomenclature) have been released to publicise the proposals and allow researchers to submit comments before they are voted on by a future meeting of the ICZN. The alterations to the Code that end up coming into force will not necessarily be exactly those proposed in the Zootaxa paper. Some or even all of them may be altered in the process.

On to the paper. Italics in sections quoted below come from the original paper. When presenting ICZN articles, the paper uses normal text to indicate regulations that are in the current Code and italics to indicate proposed text alterations.

In Paris, Commissioners voted separately in favour of three principles relating to publication. None of these passed unanimously, but all had at least a two-thirds majority among the twelve voting.

• Electronic-only publications should be allowed, if mechanisms can be found that give reasonable assurance of the long-term accessibility of the information they contain.

• Some method of registration should be part of the mechanism of allowing electronic publication of names and nomenclatural acts.

• Physical works that are not paper-based (e.g. CD-ROMs, DVDs) should be disallowed.

The primary issue with online publication has always been long-term availability. As noted before, guaranteeing the availability of publications to future researchers is a far more difficult issue for electronic rather than printed formats. The half-life of a website is far shorter than that of a book. Will the electronic publication still be available ten years in the future? Twenty years? Two-hundred years? The ICBN has, to date, avoided the question by refusing to accept electronic publication entirely. The current code of the ICZN attempted to ensure availability by requiring that copies of electronic publications be lodged as compact discs or some other permanent, unalterable electronic format in major libraries. However, this rule has caused a lot of debate. While CDs may be fairly permanent, the problem is that reading something on a CD requires that one have the appropriate equipment to do so, and the rapidly changing nature of electronic equipment could cause problems if CDs become no longer the storage format of choice in the future. When was the last time you saw an ultrafiche reader, for instance? The proposed amendments suggest that the development over the last few years of reliable electronic archiving services "such as Portico, which offers a permanent archive for electronic journals, and LOCKSS (Lots of Copies Keep Stuff Safe), an international, communal initiative based at Stanford University Libraries" may offer a more suitable alternative to CDs.

8.1. Criteria to be met. A work must satisfy the following criteria:

8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,

8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and

8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures


8.1.3.1. numerous identical and durable copies (see Article 8.4), or

8.1.3.2. widely accessible electronic copies with fixed content and format (e.g. PDF/A, ISO Standard
19005-1:2005) (see Article 8.5).

No problems here, but it's necessary background for what comes after. Note in particular the requirement that an electronic publication have "fixed content and format". One of the potential issues with electronic publication is that a document may be altered after its release, which is obviously undesirable for the purposes of a permanent archive. Should an altered edition of an electronic publication become available, then it would be required to be treated as a new publication and archived separately and in addition to the original version.

8.4.2. Works on CD-ROM or DVD. To be considered published, a work on CD-ROM or DVD

8.4.2.1. must have been issued after 1999 and before 2010, and

8.4.2.2. must contain a statement naming at least 5 major publicly accessible libraries in which copies of the CD-ROM or DVD were to have been deposited.

Because of the aforementioned potential problems with CD publication, the ICZN is proposing removing the option in favour of electronic archiving. However, the general principle in amending the ICZN is that new regulations should generally not be retrospective, because of the obvious issues that could arise if the availability or otherwise of a publication was to change many years after its publication. Therefore, anything validly published on CD during the period when that publication method was allowed will still retain its availability.

8.5. Works issued and distributed electronically. To be considered published, a work issued and distributed electronically must

8.5.1. have been issued after 2009,

8.5.2. state the date of publication in the work itself, and

8.5.3. be archived with an organization other than the publisher in a manner compliant with ISO standard 14721:2003 for an Open Archive Information System (OAIS), or the successors to that standard. (For documentation of the location of the archive, see Article 10.9.2.1.)


8.5.3.1. The archiving organization’s website must provide a means to determine which works are contained in the archive.

8.5.3.2. The archiving organization must have permanent or irrevocable license to make the work accessible should the publisher no longer do so.

8.5.3.3. If it is found that the work was not deposited in an archive within one year after the work’s stated date of publication, or that after the publisher or its successor no longer supports distribution of a work it cannot be recovered from an archive, the case must be referred to the Commission for a ruling on the availability of any names and nomenclatural acts contained in the work.

You got all that? This is the real meat of the discussion, and there are a number of really interesting provisions to try to ensure availability as much as possible. Take note of the proposed Articles 8.5.3.2 and 8.5.3.3. According to the Zootaxa article, "Both [Portico and LOCKSS] are curated, dark archives; “dark” in that a work will be released by the archive only if the publisher no longer supports distribution; “curated” in that the archive takes responsibility for migrating the content to new formats as needed to address changes in technology" (note that the article states that there is no intention to mandate the use specifically of those two archives, simply that they are used of examples of what a suitable archive service might be like). The archive services will not release copies of publications so long as they are available from the publisher - this is comparable to current "fair use" copyright regulations for in-print vs. out-of-print publications. The ICZN requires a guarantee that, should the publisher make a work unavailable direct from them, they will not be able to also prevent the archive from distributing the publication. I can see potential issues with determining exactly when the publisher "no longer supports distribution" (just as, with a printed work, it might be debatable whether a publisher "supports distribution" if one print run has been sold out but the next print run has not yet been started), but this is more a matter for copyright law than the ICZN.

Article 8.5.3.3 is particularly significant. I think that it is quite appropriate that, in the case a supposed "permanent" electronic publication proves to not be so, that the question of how this affects any names published therein should be decided on a case-by-case basis rather than by a blanket rule. For instance, if the validating information (type data, etc.) has been republished in a later source, such as a redescription, it may be possible to conserve the taxon as described in the later publication with priority retained from the original publication, and potentially maintain greater nomenclatural stability than if the name should become unavailable. In a way, this would be comparable to the current procedure of designating neotypes for species whose type specimens are no longer available. What is surprisingly not mentioned in the Zootaxa article is that this could have implications for more than just electronic publications. While I am not aware of any printed publications actually having become permanently unavailable, some very old publications have become exceedingly difficult to obtain. the day may yet come when all available copies of a printed publication have fallen to the ravages of time, and it may be useful for the ICZN to have procedures in place for dealing with such situations.

8.6. New methods of publication and archiving. The Commission may issue Declarations to clarify whether new or unconventional methods of production, distribution, formatting, or archiving can produce works that are published in the meaning of the Code.

This proposed regulation would mean that if further new non-paper methods of disseminating information are developed (say, direct brain-to-brain data downloads), the ICZN would potentially be able to decide whether or not such methods produce nomenclaturally valid results without having to publish a whole new edition of the Code.

Recommendation 8B. Minimum edition of printed works. A work on paper should be issued in a minimum edition of 25 copies, printed before any are distributed.

Can I just say that this is absolutely fantastic? One funny thing about the ICZN to date is that while the current edition laid down very strict guidelines on what constituted a valid electronic publication, the only requirement for a printed publication (except for various formats specifically excluded by Article 9) was that "it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies" (Article 8.1.3), a sufficiently vague phrasing to have caused much debate in the past as to whether or not a given publication counts as taxonomically valid. For instance, Rafinesque's (1815) Analyse de la nature, ou tableau de l'univers et des corps organise's was a privately-published pamplet distributed to only a small number of friends and leading zoologists (Bock, 1994). Or try running an internet search for "Avgodectes". In my opinion, it is long since time for the ICZN to be more explicit on what are the basic requirements for a printed publication.

According to the Zootaxa article, this has become more of an issue in recent years with computer technology leading to the increasing availability of "print-on-demand" publications, where rather than a number of copies being produced in a single print-run, only a small number or even single copies of issues are printed off as ordered. Such "publications" are particularly difficult to assess as regards their availability under the ICZN, especially if the possibility exists for corrections and alterations to be made to the source document between successive printings.

10.8. Availability of names and nomenclatural acts in electronic works. New names and nomenclatural acts cannot be made available in electronic works issued before 2010 (Article 8.5.1; see Article 10.9 for other requirements).

10.8.1. Where stability of nomenclature would be promoted thereby, a name or nomenclatural act appearing in such a work may be referred to the Commission for a ruling under the plenary power on its availability, if the work otherwise fulfils the requirements of Article 8.5.

This follows on from the principle described earlier that changes in regulations should not be retrospective. So Scansoriopteryx is still Scansoriopteryx, unless someone successfully petitions the ICZN otherwise.

10.9. Registration of names and nomenclatural acts. Registration in the OFFICIAL REGISTER OF ZOOLOGICAL NOMENCLATURE (Article 78.2.4) is required for a new scientific name published in an electronic work (Article 8.5) to be available. Additional requirements for availability of such names are:

10.9.1. the registration number assigned in the OFFICIAL REGISTER must be cited in the work itself, and

10.9.2. at least the following information must be recorded in the OFFICIAL REGISTER:


10.9.2.1. for the name of a taxon at any rank, sufficient bibliographic information to identify the work in which the name is proposed, and the name and Internet address of the archiving organization, and

10.9.2.2. for a species-group name, the depository for the name-bearing type and the location of that depository;

10.9.2.3. for a genus-group name, the type species;

10.9.2.4. for a family-group name, the type genus.


10.9.3. Registration of nomenclatural acts other than the proposal of new names in an electronic work is voluntary.

10.9.4. Names and nomenclatural acts published on paper may be registered voluntarily and retrospectively; such registration does not affect their availability.

10.9.5. Registration without publication in conformity with Articles 8 and 9 does not confer availability.

One of the biggest changes that is being proposed for the new edition of the ICZN is the introduction of ZooBank, an online register of all zoological names. While it appears that mandatory registration may not be introduced for new names in printed publications, it is being suggested for electronic publications. I suspect one major reason for this is to facilitate proceedings if situations arise as covered in Article 8.5.3.3 above.

Even though the proposed article explicitly states that a name is not available if it is registered but not published, I can see definite confusion arising in such situations. An alternative is the previous proposal (Polaszek et al., 2005) that had authors releasing publications prior to registration, then having two years to register the name on ZooBank.

21.8.3. Some works are accessible online in preliminary versions before their final publication date. Advance electronic access does not advance the date of publication of a work.

Again, Scansoriopteryx is still Scansoriopteryx. However, as the Scansoriopteryx example shows, this could still lead to problems if the early online version is widely publicised, and personally I think this is one of the more problematic proposals. Harris' (2004) proposal that would allow the date of DOI registration to count as the date of publication might have been preferable.

And finally:

21.9. Works issued on paper and electronically. A name or nomenclatural act published in a work issued in both print and electronic editions is available from the one that first fulfils the relevant criteria of availability.

This seems fairly obvious - however, I'm wondering if researchers could be confused as to how this article interacts with Article 21.8.3 given just above. So online early editions do not count as proper publications, except for cases where they do? Scansoriopteryx might not be Scansoriopteryx after all? Mind you, as pointed out in the Zootaxa article, this issue is not actually unique to electronic publications - "The same situation already exists with repaginated reprints, or second printings that still state “new species”". The Zootaxa article suggests that the new Code will make explicit what sensible researchers have generally been doing all along - when the same content is published twice, it should be counted as a single publication dating from the first valid appearance.

REFERENCES

Bock, W. J. 1994. History and nomenclature of avian family-group names. Bulletin of the American Museum of Natural History 222: 1-281.

Harris, J. D. 2004. 'Published works' in the electronic age: recommended amendments to Articles 8 and 9 of the Code. Bulletin of Zoological Nomenclature 61 (3): 138-148.

International Commission on Zoological Nomenclature. 2008. Proposed amendment of the International Code of Zoological Nomenclature to expand and refine methods of publication. Zootaxa 1908: 57-67.

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).