Publication date of Bulletin de la Société Philomathique

I should say up front, this is going to be a pretty esoteric one. It's just that this is something I spent a fair chunk of a morning trying to work out, and I may as well put what I found up here in case someone else finds it useful.

A few weeks back I found myself, as one does, trying to sort out the exact publication date of early numbers of the Bulletin des Sciences, par la Societé Philomathique de Paris, which has been archived online at the Biodiversity Heritage Library. The Société Philomathique was an association of French scientists and polymaths from a wide range of disciplines founded in 1788. You can find the webpage for the current iteration of the Société here. In 1791, the Societé decided to circulate a bulletin of abstracts of their meetings, including summaries of papers and letters presented there.

The title page of the volume of the Bulletin available at the Biodiversity Heritage Library gives the dates of "Juillet 1791, a Ventôse, An 7", or July 1791 to February–March 1799, which is the dates of the meetings presented therein ("Ventôse, An 7" is a date in the Republican Calendar that was introduced for a period following the establishment of the French Republic in 1792). Citations I could initially find for individual notices in the Bulletin were all attributed to dates of the separate meetings that they were presented at (e.g. something presented at the May 1794 meeting would be cited as "1794"). But it was immediately obvious to me that the notices could not have been published at the times of the original meetings, at least not as they appeared in the volume reproduced, because abstracts from separate meetings would appear on the same page! Hence my search for information on the Bulletin's actual publication date: were notices for individual meetings issued separately at the time, or did they not actually appear in print until the subsequent publication (presumably in 1799 or even later) of the collected volume? I should note that some of the abstracts in the Bulletin included descriptions of new species, so the question of publication date could have further taxonomic implications.

A page from the collated Bulletin, showing how the last entry for the December 1792 meeting is followed immediately by the section for January 1793, without a page-break for originally separate issues to have been collected together.

Eventually, I was able to establish that separate Bulletin issues had indeed been released for each meeting (you can see reproductions of the uncollated originals at Gallica). However, there is a complication. Early issues of the Bulletin were written by hand, and distributed only to the members of the Société (about 18 people at the time). It was not until November 1792 that a printed version of the Bulletin began to be disseminated more widely. Now, the International Code of Zoological Nomenclature requires that any publication for taxonomic purposes produced before 1986 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 handwritten manuscript would not meet that requirement, so any zoological name appearing in those early bulletins would not count as published. They would not become established until the subsequent publication of the collated volume, which according to an introduction written by Jonathan Mandelbaum in 1977 for a bound collection of the original Bulletin issues (reproduced at Gallica here) happened in 1802.

Original first page of the Bulletin for January 1793. As well as the separation from the December entries, note that the first entry of the original version has been omitted from the collated version, and that the title's original spelling said 'Philomatique' rather than 'Philomathique'.

As an example of the sort of consequences that might arise from this, consider Odiellus spinosus, a widespread harvestman species found in western Europe. This species was very briefly described, as Phalangium spinosum, by Bosc in 1792 in one of the manuscript issues of the Bulletin de la Societé Philomatique (the February 1792 one, to be exact). This has uniformly been accepted as the publication date, but Bosc's species was not properly published until 1802. This might be a simple question of book-keeping, were it not that, in the meantime, Latreille (1798) had used the name 'Phalangium spinosum' for a quite different harvestman species, and described what is now known as 'Odiellus spinosus' under the name of 'Phalangium histrix'. So strict application of the law of priority means that the species in question should be known as Odiellus histrix.

Fortunately, in this case there may be some loopholes available to us. Latreille's names both have strict priority over Bosc's, but they may each count as nomina oblita ('forgotten names'). This is a provision in the ICZN that a name that has not been used as valid since before 1899 can be set aside in favour of a more widely recognised junior synonym if "the junior synonym or homonym has been used for a particular taxon, as its presumed valid name, in at least 25 works, published by at least 10 authors in the immediately preceding 50 years and encompassing a span of not less than 10 years" (ICZN Art. 23.9.1.2). Latreille's Phalangium spinosum was soon recognised as a synonym of an earlier name, and was last used as valid in 1802. Phalangium histrix (or derived combinations thereof) persisted in the literature for longer, but I haven't come across it being used as a separate species after 1876. The open question is whether Bosc's name has been used often enough to warrant automatic conservation. I suspect it would have (I haven't done a proper tally myself, but a search for 'Odiellus spinosus' on Google Scholar brings up about 130 results) but, if not, then an appeal to the ICZN would be required if we wanted to keep using the current name for the species.

Public Service Announcement: Page priority is Not A Thing

I'll admit it, the rules governing taxonomy and nomenclature can seem horribly complicated when you don't spend a lot of time dealing with them directly. This isn't because taxonomy itself is inherently complicated: in fact, the underlying principles are really quite simple. The primary rationale behind each of the various codes of nomenclature can be distilled down to two points: (a) each single taxon should have a single name that differs from that of any other taxon, and (b) if more than two possible names can be assigned to a single taxon then the name given to that taxon first should be the one used (this latter point is called the principle of priority). Where things get complicated is that taxonomy is a process run by and for human investigators. And if there's one thing that can be said about all human endeavours, from science to politics to the selection of sports teams, it's that any application of simple principles is going to run afoul of complex practicalities. So questions arise that any code of nomenclature has to deal with: is it always ideal to simply use the oldest name? How do we determine which name is 'oldest', and what do we do if it's not clear? Each of the codes has developed its own methods of dealing with these questions and others, but it is not uncommon for these methods to be overlooked or misunderstood, sometimes even by people who might be expected to know better. One particularly pernicious misunderstanding that I've often come across (and which I was reminded of recently by one paper in particular that will go unnamed) is 'page priority'.

As mentioned above, it is not uncommon for two or more names to turn out to be synonymous without one particular name being obviously 'older'. Perhaps the papers naming each species were published at the same time, or they were named within a single paper. In these situations, many authors will invoke the principle of page priority in determining which name should be used: the name which appeared in an earlier place in the publication (say, on p. 23 rather than p. 25) should be the one used. The problem is that, in the case of the International Code of Zoological Nomenclature at least, no such principle is mandated (I'm not so familiar with the other codes, but I don't think they have page priority either). Instead, the code resolves indeterminate priority through the principle of the 'first reviser'. In the code's own words:

24.2.1. When the precedence between names or nomenclatural acts cannot be objectively determined, the precedence is fixed by the action of the first author citing in a published work those names or acts and selecting from them; this author is termed the "First Reviser".

In other words, the question of which name takes priority is determined by the choice of the first person who treats them as synonyms. Any subsequent authors are required to abide by the decision made by the first reviser. There is no restriction placed on how the first reviser should make their decision; if they want to follow page priority, they're perfectly free to do so. The problem comes when a first reviser doesn't follow page priority, only to have later authors claim they made the "wrong" decision. Maybe the name that appeared on a later page in the original publication was better described, or had been more commonly referred to by later authors. Whatever the situation, the decision of the first reviser is final. No correspondence shall be entered into.

"Page priority" is a bit of a case of what's been called a hypercorrection, when someone 'corrects' something that was already right. Someone who's familiar with a principle (in this case the principle of priority) but doesn't fully understand the reasons for the principle may try to apply it more widely than they should. So, for instance, someone who knows the plural of 'hippopotamus' is 'hippopotami' may assume that the plural of 'octopus' is 'octopi'. Hypercorrections persist because, on a superficial level, they 'make sense'. Sadly, being sensible is no barrier to being wrong.

Interestingly enough, there was a brief time in zoological nomenclature when page priority was a mandated rule (Dubois 2010). Between 1948 and 1953, a page priority clause was inserted into the Règles Internationales de la Nomenclature Zoologique, the earlier code of zoological nomenclature that was used before 1961. In 1953, this clause was suppressed and invalidated, and the first reviser principle now applies almost universally. Anyone who argues that a taxonomic decision violates 'page priority' can be safely ignored.

REFERENCES

Dubois, A. 2010. Retroactive changes should be introduced in the Code only with great care: problems related to the spellings of nomina. Zootaxa 2426: 1–42.

Does A High Population Guard Against Extinction?

Rocky Mountain locusts Melanoplus spretus, from the Minnesota Historical Society.

The Cloud was hailing grasshoppers. The cloud was grasshoppers. Their bodies hid the sun and made darkness. Their thin, large wings gleamed and glittered. The rasping whirring of their wings filled the whole air and they hit the ground and the house with the noise of a hailstorm.

Laura tried to beat them off. Their claws clung to her skin and her dress. They looked at her with bulging eyes, turning their heads this way and that. Mary ran screaming into the house. Grasshoppers covered the ground, there was not one bare bit to step on. Laura had to step on grasshoppers and they smashed squirming and slimy under her feet.

--Laura Ingalls Wilder, On the Banks of Plum Creek

In 1875, the American Midwest experienced the largest single locust swarm ever recorded. It covered an estimated area of 198,000 square miles, considerably larger than the state of California, and the person who estimated its size recorded that it took five days to pass by. The species composing this gigantic swarm was the Rocky Mountain locust Melanoplus spretus, and at the time it was America's scourge. Locust swarms in 1874, following a dry summer, had devastated Midwestern agriculture: crops were destroyed, livestock and people starved to death. After the 1874 swarms, it was estimated that only one family in ten had stored enough food to last the winter. The entire future of the region became uncertain: one homesteader observed that, "Wheat and grasshoppers could not grow on the same land, and the grasshoppers already had the first claim".

But then something extraordinary happened. After 1875, grasshopper numbers began declining. Before thirty years had passed, the Rocky Mountain locust was not merely no longer a significant pest, it had become completely extinct. No individuals of the species have been seen alive since 1902. The reasons for this precipitous decline have been much debated, but a prominent suspect has been the conversion of large areas of prairie into managed farmland.

I was reminded of the locusts by Alex Wild's recent comments on the decline of the monarch butterfly, a species that, while not yet extinct, has had a precipitous decline in recent years in North America. Alex notes that:

I don’t have many photographs of monarchs. A few bland shots of larvae, a handful of adults on flowers. I never felt any urgency. They were as common as dirt. I just sort of assumed monarchs would always be around to photograph later.

Silly me.

The Rocky Mountain locust, of course, is not the only example of a once-abundant species becoming extinct in historic times. The passenger pigeon Ectopistes migratorius and the Carolina parakeet Conuropsis carolinensis are two other well-known examples. September 1st this year will mark the hundredth anniversary of the death of Martha, the last known surviving passenger pigeon, in Cincinnati Zoo.

Population numbers are often used as a heuristic for estimating extinction threat, at least in the popular media, and often influences priorities for conservation efforts. A species with a surviving population of 1000 individuals is considered more endangered than one with 100,000 individuals. But examples such as the Rocky Mountain locust show us that even the most unimaginably abundant of animals may not be immune from sudden population crashes. Conversely, some animals persist despite very low population sizes. The black robin Petroica traversii has survived its population being reduced to only five individuals, including only a single breeding female (granted, its survival has received more than a bit of a helping hand from some very intensive conservation efforts, and is by no means typical).

So my question is this: what is the correlation between population size and extinction risk? How much does a smaller population size increase the risk of extinction, or is it secondary to factors such as habitat disturbance? I'm not implying that I think these questions haven't been asked before (I'm sure that they have), they're just something I've been wondering recently myself.

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.

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!

The Overwhelming Diversity of Life

A post yesterday at Pharyngula has referred to a series of dinosaur parks in the United States that put up an information page on their website revealing a creationist agenda. As I've noted before, I tend not to concern myself with the activities of creationists because I generally find them exceedingly dull (I'm often tempted to repurpose a line spoken by Julian Rhind-Tutt in an episode of Green Wing: "You know what? The rest of us have moved on."). However, my eye was caught by one line that reflects on one of the major misunderstandings involved. In the process of postulating how dinosaurs became extinct subsequent to the Flood:

It is not just dinosaurs that have become extinct. In the last 350 years alone, almost 400 species have disappeared.

For various numbers, the total of '400 species' is probably severely underestimated, but that's not what I want to focus on. Instead, I want to look at the number itself. If there is one thing that most people fail to grasp about biodiversity, it would be that there's just so much of it. It's an understandable failing: I work with biodiversity on a daily basis, and even I find myself constantly startled and awed by this point. So huge are the numbers involved that it's almost counter-productive to simply report them. Humans seem to have a tendency to effectively just lump any number over a hundred or so as simply 'a lot'.

Imagine you were an avid twitcher (one with an enthusiasm for seeing new bird species) who, through a preternatural combination of flawless logistics, limitless funding and exceptional luck, was able to observe one new bird every day. At that rate, how long would it take you see every species of bird in the world? Wikipedia gives a figure of about 10,000 species of bird, which would mean that you would need 27 years, four months and 25 days. If you started at the age of 18, you would not finish until after your 45th birthday. If you moved on to mammals, you would need another fifteen and a half years. Lizards would account for another ten years; snakes another eight. Turtles you would be able to get through in just under a year, but then frogs would require thirteen and a half. Fish, on the other hand, would require the investment of some seventy years. Or, to sum up, observing every known living species of vertebrate at the rate of one a day would require nearly twice as much time as most of us are allotted in a single lifespan.

Outside vertebrates, the numbers just keep adding up. Earthworms may not seem like a hugely diverse group, but would still require an investment of more than sixteen years. You'd need more than 126 years to get through the staphylinid beetles alone. Perhaps plants are more your thing? You'd better have dedication, then: it's going to take you nearly 700 years if you want to see every variety of flower in the world. After that, the mere 33 years required to deal with the ferns will just go by in a flash.

No-one has yet tallied up exactly how many species of organism have been described to date, but using a conservative (very conservative) estimate of 1.5 million, observing every one at the rate of one species a day would take you more than 4100 years. Or 45 somewhat generous life spans (assuming, of course, that you were able to get things started from the day of your birth). Compared to this, 400 species is but a drop.

It was no accident that the concept of evolution achieved its majority in the nineteenth century. Naturalists at that time were required more and more to come to terms with just how diverse the world's organisms were, and how inadequate the popular explanations were in accounting for such diversity. What is one supposed to make of a god who would apparently bless to the world with over a thousand species of tapeworm? Or over 100 species of scabies mite? Unless, of course, we should simply take it as evidence that God has an inordinate fondness for scabies.

The Claim-Jumpers and Grave-Robbers of Taxonomy

In a recent paper in Zootaxa (openly accessible), O'Hara (2011) has become the most recent of a number of authors to discuss one of the more irritating taxonomic developments of recent years: the rise of the serial homonym replacer. A taxonomic homonym, in case you aren't already familiar with the term, is when a new taxon is given a name previously assigned to a distinct taxon (usually because the later author is unaware of the earlier usage's existence). Because the various nomenclatural codes require that any name can refer to only a single taxon, the more recently named taxon would generally need to be re-christened if it is to be accepted into polite society. However, in many cases homonymous names can lurk undetected in the literature for a great many years. After all, there is a heck of a lot of taxonomic literature out there, and it may only be a matter of luck if the existence of a homonymy is even noticed.

In recent years, this has changed somewhat. The appearance of easily searchable taxonomic databases such as Nomenclator Zoologicus have made it much easier for authors to detect if a given name has been used previously. Unfortunately, as well as making it much easier to allow authors of new taxa to avoid creating homonymies, such databases have allowed the rise of the serial homonym replacer. Serial homonym replacers scour databases on the hunt for unreformed homonyms. Having collected a bundle of them together, they then publish short papers in which they publish replacement names for said homonyms, generally in obscure little journals probably published by the authors themselves.

Most working taxonomists regard such behaviour as unlaudable at best, and as downright unethical and injurious at worst. It is felt that the publication of replacement names is best done within the context of a larger-scale review of the taxonomic group to with a homonymous name belongs. From a practical viewpoint, the publication of replacement names without putting them into a larger perspective may reduce the chance of them coming to the attention of the appropriate workers (a worker on Braconidae, for instance, will almost certainly read a paper entitled 'Taxonomic Review of the Braconidae', but may not notice potential significance in 'Five new replacement names for homonymous insect genera'), increasing the chance that they will themselves publish further, unnecessary replacement names. From an ethical viewpoint, the serial homonym replacer is, through the required practice of author citation, inflating the apparent significance of their own work and diminishing that of more exacting researchers who are forced to work more slowly.

Perhaps even more problematic, the publication of replacement names outside the context of a proper review often leads to mere compounded errors. In practice, not every junior homonym needs a replacement, because sometimes any replacement would not actually be used, and would simply clutter up the literature. If the homonym is synonymous with another previously proposed name, then that name is already available for use. For instance, the name Platypus published by Shaw in 1799 for (naturally) the platypus is a junior homonym of a genus of beetles named by Herbst in 1793. However, no replacement name is required because Blumenbach had also described the platypus in 1800 under the name Ornithorhynchus. Authors have also refrained from publishing replacement names in cases where the identity of an original homonymous name is uncertain (for instance, if the type specimens are lost): any replacement would be equally mysterious and practically unusable. In one case described by O'Hara (2011), the replacement name proposed for a genus of fly was unnecessary because the supposed 'senior homonym' had not actually met the requirements for valid publication.

In addition to the examples discussed by O'Hara (2011), let me direct your attention to one particularly horrid little paper that manages to cover many of the errors perpetrated by database scourers. Özdikmen (2009) proposed replacement names for 48 homonymous genera of unicellular eukaryotes. Let me just start by noting that Özdikmen seemed unaware that by 2009 the taxonomic concept of 'Phytomastigophorea' was more anachronistic than the ruffed collar and velvet doublet. Twelve of the supposed homonyms treated are dinoflagellates, a silicoflagellate and a chlorophyte(!), and hence members of groups whose researchers have long since generally agreed to follow the Botanical Code rather than the Zoological. Under the Botanical Code, these names are not preoccupied (because botanical names do not conflict with zoological names) and replacement is unnecessary. Even if the names were somehow problematic, I would not be surprised if the different publication requirements of the Botanical Code meant that Özdikmen's replacements were somehow not valid.

Özdikmen's (2009) proposal of a replacement name for amoeboid-endosymbiont Perkinsiella Hollande 1981 is unnecessary because a replacement name had already been published by Dyková et al. (2008), in the context of a broader molecular analysis. His proposal of a new name for the dinoflagellate family Goniodomataceae because its type genus was preoccupied is unnecessary, not only because Goniodoma is not preoccupied (see above), as family names had already been based on other genera within the Goniodomataceae and would then take precedence. Ethically speaking, many of the homonyms replaced by Özdikmen (2009) were originally published in the 1980s and 1990s and their authors are probably still alive and working today.

So what are the practical effects of this homonym harvesting? It can cause confusion and extra work for researchers, if it leads to the introduction of superfluous replacement names. It can lead to general ill will, if workers on larger projects feel that they are being unfairly pre-empted. And they can have something of a cooling effect on the very process of nomenclatural clean-up they purport to effect. Since the work of Özdikmen and his ilk became publicised, I've personally become apprehensive about the possibility of publicising, however casually, any unresolved homonyms of which I am aware.

One such homonymy I discovered nearly ten years ago, when I was fresh out of university and did not yet have any publications to my name. As the animal in question was in a group which did not then have anyone actively working on it, the idea did cross my mind that I could perhaps publish a note on it myself. My first publication! But, even at that early stage in my career, and without the benefit of mentor advice, I was able to work out that, in the end, it would be a publication of little, if any, virtue. And I hoped that I was more mature than that.

REFERENCES

Dyková, I., I. Fiala & H. Pecková. 2008. Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): coevolution demonstrated by SSU rRNA gene phylogenies. European Journal of Protistology 44 (4): 269-277.

O'Hara, J. E. 2011. Cyber nomenclaturalists and the “CESA itch”. Zootaxa 2933: 57-64.

Özdikmen, H. 2009. Substitute names for some unicellular animal taxa (Protozoa). Munis Entomology & Zoology 4 (1): 233-256.

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.

Alexandre Girault: A Man Against the World

Alexandre Girault at age 20, as he appeared in Gordh et al. (1979).

Having recently discussed the availability of privately published taxonomic works, it is appropriate that I recently received a copy of Gordh et al.'s (1979) reprinting of the privately published pamphlets of Alexandre Arsene Girault. A. A. Girault (1884-1941) is one of entomology's most controversial figures, an incredibly prolific worker possessed of a character that could charitably be described as difficult, uncharitably as barking mad. Girault named more than 3000 taxa over the course of his career (possibly more than any other taxonomist*), often under extremely difficult circumstances. As well as his monographic publications through more traditional venues, about 1000 of these taxa were published in privately produced pamphlets between 1917 and 1937.

*Update: Gunnar has reminded me in the comments of an even more prolific taxonomist, the crane-fly researcher Charles P. Alexander who published more than 11000 taxa. That represents a little less than one new species for every day of his working life.

Born and raised in Maryland in the United States, Girault worked for the U. S. Department of Agriculture from 1904-1911 until a request from the Queensland government for a capable entomologist sent him to Australia with glowing recommendations. Girault worked on pests in sugar plantations until 1914 when he decided to return to the States and focus entirely on purely taxonomic entomology. However, he was frustrated in that design and returned to Australia in 1917. After his return, his employment was irregular, including extended periods of unemployment and periods when he held day jobs as shopkeeper or quarry worker. His behaviour on a personal level became increasingly difficult and he was eventually admitted to a mental asylum in 1939 suffering from paraphrenia two years before his death.

Girault was obsessed with the importance of pure research for its own sake without recourse to low economic considerations ("The fear was, these things would no longer be studied was it thought they helped man's agriculture no more than the sunshine does. But who can doubt its greater use when love is the inspiration; man's soul is helped so"¹). In between the basic taxonomic descriptions, his privately published papers are littered with poetry and commentaries on this subject including numerous invections against those of his colleagues whom Girault felt had betrayed this ideal ("Are we coming to be a nation of lilliputs, the socalled entomologists reduced to farmer's clercks and others accordingly? Is there a scientist here who dares to speak out what he sees or ought or who can e'en think freely, without his thought be limited by mandate to some "problem"? Find him" ¹). Some of these inserts can be a little jarring, to say the least; one list of synonymies reads, "Hemiptarsenoideus is Hemiptarsenus. Baocharis marlatti is Aphelinus subapterus. Liberty is Soul. Rhopalicus americanus is Spintherus pulchripennis"¹. They are also often disproportionately vituperative; a particularly bitter paragraph, complaining of "An outrage, I should think, robbing the poet as Tarquineus raped Lucrece; worse insulting the heavens"², was written in response to an editor publishing a paper of Girault's as "New chalcid parasites from Malaya" when Girault had intended it to be called "New chalcid-flies from Malaya".


Girault in 1924 with his wife Elizabeth and three of their children. Elizabeth Girault (whom Girault described as a "faithful friend and true-hearted wife"⁴) became seriously ill with tuberculosis in 1923 and remained so until her death in 1931. His wife's health and the strain of raising five children on his irregular income added to Girault's difficulties. Photo from here.

It was primarily Girault's insistence on including these discourses that required him to publish privately. His acerbic nature lead a number of editors to make blanket refusals to handle any of his manuscripts. However, it is also true that research without direct economic application was not viewed favourably in a country passing through the fiscally straitened aftermath of the Great War. While he was working for the Queensland Department of Agriculture in the early 1930s, successive directors attempted to curtail his taxonomic work, presumably because the time he was devoting to it was intefering with his work on economic entomology. Also, economic restrictions after 1915 meant that Girault was no longer able to publish extensive manuscripts in the Memoirs of the Queensland Museum as he had done previously.

Setting aside their eccentric presentation, the descriptions of new taxa themselves vary in their usefulness. Some are dreadful, others were (at least by the standards of their time) very good. Often more problematic for succeeding researchers has been the exceedingly poor condition of many of Girault's type specimens. With no access to supplies other than what he could beg from more fortunate associates, Girault resorted to measures such as mounting multiple specimens under fragments of coverslip on a single slide. He also often mounted body parts such as heads on a separate slide from the remainder of the specimen. Girault also expressed disdain for such niceties as labelling ("We do not desire specimens any more per se. It is the label we want now"¹), orthography ("A crooked line, a blot causes no worry; they are bodies, not souls"¹) and detailed descriptions ("Longer descriptions are not needed, are even confusing"⁴).

The legitimacy of Girault's private publications for nomenclatural purposes was long disputed but over time a consensus has developed that they are acceptable (even if only because the usage of names from those publications by later authors has made it potentially more problematic to dismiss them than accept them). If there is one object lesson to be derived from Girault's failings, it is the value of type specimens. While there is no denying that the sheer volume of Girault's publications has represented a significant hurdle for later researchers, the continued availability of Girault's types (mostly in the Queensland Museum) has allowed progress where it would have otherwise been impossible. For instance, of the hundreds of Giraultian taxa referred to by Bouček (1988), only one was regarded as completely unidentifiable. For many others, the currently available information is inadequate but may be enough that further investigation has a reasonable chance of resolving matters.

¹Descriptiones hymenopterorum chalcidoidicarum variorum cum observationibus. V. 1917.
²New animals of Australia and old men of the earth. 1921.
³Some gem-like or marvellous inhabitants of the woodlands heretofore unknown and by most never seen nor dreamt of. 1925.
⁴New pests from Australia, VIII. 1930.

REFERENCES (Girault's publications in the footnotes above)

Bouček, Z. 1988. Australasian Chalcidoidea (Hymenoptera): A biosystematic revision of genera of fourteen families, with a reclassification of species. CAB International: Wallingford (UK).

Gordh, G., A. S. Menke, E. C. Dahms & J. C. Hall. 1979. The privately printed papers of A. A. Girault. Memoirs of the American Entomological Institute 28: 1-400 (including biography of Girault by E. C. Dahms).

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.

A Question of Availability

About a year ago, I wrote a post discussing the potential difficulty of establishing whether a taxonomic work of restricted availability has been validly 'published'. If you head over to Mickey Mortimer's Theropod Database Blog, you'll be presented with a perfect (and perfecty 'orrible) example of just this issue, concerning the dinosaurological publications of one Stephan Pickering. Mickey has regarded the works as not validly published; Pickering himself has posted a number of comments to argue otherwise.

The arguments that have been made there about copyright (a completely separate issue from ICZN availability), private publication and peer review (in which the ICZN effectively has no interest) are irrelevant to the question of whether the works count as published for ICZN purposes. The important details in that regard are:

1. Pickering had 50 copies of each of the works professionally printed in 1995 (at least one was printed later in 1999). I have not personally seen the works in question, but the indications are that the diagnoses presented therein would satisfy ICZN requirements.

2. No printed copies of the works were deposited in institution libraries (and Pickering has objected strenuously to suggestions that he should have done so); however, copies were distributed to various recipients. At least some copies were distributed shortly after printing.

3. An excerpt or reprint of one of the works was distributed as an insert in 1996 with an issue of the popular magazine _Prehistoric Times_.

As a reminder, the ICZN requirements for a work to count as 'published' are:

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.

Do Pickering's works meet those requirements? 50 copies is low for a publication run but I don't think it can be argued to fail the requirements of 8.1.3. Publications existing in similar or lower numbers have been accepted as valid in the past. Similarly, the fact that Pickering distributed copies to various recipients suggests at least a nominal accordance with 8.1.2 (that most of these recipients, such as Michael Crichton and Stephen Spielberg, appear to have not been working palaeontologists is problematic but does not violate any explicit ICZN requirement). However, I think that a strong argument can be made that by refusing to place any copies in public depositories, Pickering has failed to meet the requirements of 8.1.1, a "public and permanent scientific record", whatever his original intentions may have been ("by their fruits you shall know them", to insert a touch of pretension). To provide a permanent scientific record, it is necessary that future researchers be able to evaluate the publication; if they are unable to gain access to a copy then they are unable to evaluate it. Unless any of the recipients of Pickering's publications take it upon themselves to secure the future availability of the works, they will end up being lost to history. As already noted by Mickey, the _Prehistoric Times_ insert, having had a much wider distribution, is a potential exception to this problem; my personal inclination would be to accept the names diagnosed therein as available though again the future availability of the work is a pending question.

Indeed, hovering over all of this is a much broader question about the publication requirements of the ICZN. Implicit in the current rules is the assumption that "once available, always available" but time, of course, is a great destroyer. In my earlier post, I discussed the rare Japanese journal Lansania, for some issues of which only a handful of (or even single) copies survive while others may have been lost entirely. There can be no doubt that the publisher of Lansania, Kyukichi Kishida, intended these issues to provide a "public and permanent scientific record"; they have evidently failed to meet that intention. What becomes of taxa whose original descriptions can no longer be evaluated?

How to Write a Key

My current job primarily involves insect identifications with any type of insect (or arachnid or terrestrial mollusc) potentially requiring an ID. Because I am not intimately familiar with every single insect species found in Australia (terribly remiss of me, I know), this means that I find myself using a lot of identification keys. The construction of an identification key can be a somewhat underrated part of the taxonomic process; a key often gets tacked on to a review without much apparent concern, but the key has the potential to be the most regularly used section of the review. Also, the skills involved in constructing a good key may not be the same as those in constructing a good taxonomy and an excellent taxonomist will not always be an excellent key-writer. As a result, the available keys out there can vary from the impressive to the appalling. So, with the typical hubris of any snotty customer, I offer a few guidelines for the construction of a successful key*. Some of these rules may clash on occasion and a little discretion may be required about whether you should follow them (except for Rule 1 which should never be broken).

*These guidelines apply primarily to the writing of a linear key where the user is guided through a series of alternatives in a predetermined order. These days, an increasing number of computer-based non-linear keys are available, such as those constructed using LUCID, where the user can choose in which order they want to look at characters. Both linear and non-linear keys have their advantages and disadvantages: a non-linear key is less likely to leave the user stranded at a single indeterminable couplet but a linear key can sometimes offer more guidance as to which characters the user needs to look at.

Rule 1: A key has one purpose, and one purpose only. That purpose, of course, being to provide an identification. A key is not a classification and the characters that are useful in determining taxonomy are not necessarily the characters that you should be emphasising in a key. For instance, your insect classification may be heavily influenced by characters of the genitalia but that doesn't mean that you should be requiring users to dissect out genitalia right from the first couplet (especially if said genitalia are only found in adult males). Conversely, a note to users: just because two species sit next to each other in a key doesn't necessarily mean that they're closely related.

Rule 2: Don't assume that your users know the organism being identified as well as you do. Indeed, the fact that they need to work through a key in the first place suggests that they probably don't. This is one of the trickiest rules to follow because you tend to forget that you didn't always know everything you know now; sometimes, it seems that the more qualified someone is to write a key, the worse is the key that they end up producing. Try to avoid jargon, and be especially careful if the group you're working on has any conventions in the use of terms that differ from their 'common-sense' meanings. For instance, one key I've used regularly distinguishes fulgoroids (a group of leafhoppers) from other Auchenorrhyncha (cicadas and leafhoppers) by whether the antennae are 'in front of' or 'below' the eyes; however, this refers to their position relative to the rest of the insect's face which is not straight up and down but may be angled backwards at up to 45°. So to anyone who doesn't know this convention (e.g. me, when I first started using the key), an antenna can easily appear 'below' the eye when it is really 'in front of' it.

Rule 3: First, eliminate the obvious... If only one of the species you're providing a key for has a bright blue head when the rest are unicolor, or only one species has a large horn when the others are unarmed, then split off that species first. Don't make the user work through twenty couplets of more difficult characters when they could have spotted the ID straight off bat.

Rule 4:...but make sure the 'obvious' is actually obvious. How a specimen has been collected and preserved may affect how it appears. Colours may be bleached, soft body parts may have their shapes distorted. So try to choose characters that are as resistent to distortion as possible.

Rule 5: Start on the outside and work your way in. Again, try to start with characters the user can find easily with a minimum of specimen manipulation. Don't make them cut anything open unless they really have to.

Rule 6: Start at the middle and work your way out. This mainly applies to arthropods, but I'm sure that other organisms have analogous situations. Insect and arachnid specimens regularly lose legs, antennae, etc. Using characters on the main body when possible reduces the risk that the user may not be able to identify the required character state.

Rule 7: Offer alternatives where possible. Another way to get around the above issue is to suggest informative characters elsewhere on the organism. 'Hind tibia spinose; antennae branched' means that if the specimen's tibiae are missing, the user may still be able to antennae.

Rule 8: Illustrations are good. The best way to explain to the user just what you mean by 'spinose' or 'well-developed' is to show them.

Rule 9: Define relative characters when possible. Remember Rule 2? If you want to separate taxa depending on whether a feature is 'small' or 'large', then say exactly what you'd regard as 'small'. Something that a mite worker regards as 'large' might not seem large to someone used to working on butterflies. On the other hand, rather than using direct measurements (which can be difficult to judge, especially with small organisms), try using comparative measures - 'wings shorter than legs', for instance.

Rule 10: Don't require multiple specimens. I've had a couple of occasions when a key asks me something like whether the male has larger eyes than the female. Not very useful when I don't have both. Especially when I don't know the animal in question well enough to tell which is the female and which is the male.

Rule 34: Individual breast larger than head... Lolo Ferrari.
Individual breast smaller than head... 2.

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.