Field of Science

A New Stem-Bird and Publication in the Digital Age


Scansoriopteryx heilmanni, as reconstructed by Stacey Burgess.


First off, notification of the focus of this post came via the Dinosaur Mailing List.

It is almost a truism that the internet has changed the face of scientific publishing. Online versions of journals have become the first port of call for many, if not most, researchers. The paper reprint has become an endangered species, and articles are exchanged via e-mail as pdfs. Online-based journals such as BMC Biology and the PLoS collection have abandoned the standard journal format with articles collected into issues, and release articles as and when they become available. Even among those journals that still release regular issues, many have begun offering advance online releases of upcoming articles. For most branches of science, these advances are mostly all for the good. Good science, after all, is largely dependent on access to information, and there is much to be said for allowing the dissemination of new information as quickly and easily as possible. However, at least one branch of science, taxonomy, remains firmly attached to the printed page, and has good reasons for doing so.

As alluded to here before, taxonomy differs from other sciences in that it provides the means for communication between biologists working in other disciplines as well as being a target of investigation in its own right. In order to facilitate communication, it makes sense that (a) the taxonomic system should be as stable as possible*, and (b) when conflicting taxonomies do arise, then the means for determining the correct nomenclature to use should be as simple and automatic as possible. It is to satisfy this second requirement that taxonomic systems employ the principle of priority - if two separate names exist for the same taxon, then the correct name to use is the one that was published first.

*Though, as with governments, "stable" in this context does not necessarily mean "unchanging". Rather, it means "not prone to change without proper cause".


Scansoriopteryx again, this time by Matthew Martyniuk.


Of course, saying that the first name to be published is correct immediately raises the question of what counts as publication. The International Code of Zoological Nomenclature (Article 8) requires that a published work must be issued in a permanent format, and must be generally made available upon publication. These are pretty broad criteria, but any work (and any new names within) cannot be considered published until they are met. The date at which these criteria are met becomes the official date of publication. Release of an article online (such as in a pre-print) does not count as publication in this sense because a webpage is not permanent. While a book requires little or no attention once it has been accessed in a library and can sit there more or less indefinitely*, a webpage requires continual upkeep to remain available. The ICZN does allow a name to be published online if some form of permanent copy (such as a print-out or CD) of the webpage is deposited in a number of major public libraries (such as the American Library of Congress). As far as I know, the Botanical Code still insists on printed publication.

*Okay, theoretically a book may be at risk of decaying after a few hundred years, but that's still pretty permanent compared to a website.

In June last year, the Nature group launched Nature Precedings, an online repository for preliminary findings and manuscripts, allowing researchers to share data of interest that might or might not be sufficient for an eventual completed paper, obtain feedback on said preliminaries that might improve the final manuscript, and just generally keep other researchers informed on what was going on. Entries on Nature Precedings are not peer-reviewed before becoming available, and are generally not regarded as completed publications. A few days ago, a new entry was loaded on Nature Precedings by Zhang et al. describing a decidedly interesting new dinosaur species, complete with attached name. Officially, this taxon is not yet published. Because of the interest that surrounds any new dinosaur discovery, you can bet your ass that that won't stand in the way of its becoming widely known.


The new scansoriopterygid, which I'm calling Les. Figure from Zhang et al.


As I said, there's a name attached to the new taxon. It's a very nice name, too - kind of rolls off the tongue. But because I'd rather avoid using an unpublished taxon name, I'm keeping shtum (of course, click on the link and you'll find the name right away, so my protest is really pretty pointless). Because the new species is a member of the family Scansoriopterygidae, I'm going to call it LES (standing for "Looks like Epidendrosaurus or Scansoriopteryx"). Les was a small bird-like theropod about the size of a pigeon, and represented by a very nice nearly-complete skeleton, complete with preserved feathers including a tail of four long ribbon-like feathers that were about as long as the rest of the animal. Phylogenetically, Zhang et al. position Les as more closely related to modern birds than the dromaeosaurs (Velociraptor et al.) but less closely related than Archaeopteryx. Les is exactly the sort of thing that might eventually be published in Nature, and its appearance in Nature Precedings gives the impression of leading into doing so.

The family Les belongs to, Scansoriopterygidae, has become something of a poster child for the issues surrounding online publication. Two genera have previously been named for scansoriopterygids, Scansoriopteryx and Epidendrosaurus, but most researchers suspect that these two names refer to the same animal. Unfortunately, determining which of the two names has priority is not a straightforward question, as discussed by Harris (2004). Both names were published in 2002, but the book naming Scansoriopteryx was probably less widely read than the journal naming Epidendrosaurus. Epidendrosaurus appeared in an online preprint on the 21 August, but the printed version didn't appear until 30 September. The exact date of publication of Scansoriopteryx is a little debatable, but it seems to have become available by 2 September - after the name Epidendrosaurus became widely publicised online, but before the official publication of Epidendrosaurus. Technically, Scansoriopteryx has priority, even though Epidendrosaurus was the name that became known to the public first.

The lesson from cases such as Scansoriopteryx is that the time has well and truly arrived for us to re-evaluate what it means for a name to be "published" in the digital age. In the past, the first a public would generally hear of a manuscript and its contents was when the finished publication arrived in all its official glory. Now, as demonstrated by Les, it may be possible for a manuscript to appear online as a rough draft, as a polished pre-print, as the final official product. Should these early appearances be regarded as valid publications? When the manuscript first appears, or only as it approaches its final form? The initial format for publication of Epidendrosaurus may not have been permanent, but should we regard the later appearance of a permanent printed edition as having validated that initial appearance? The rules of the game are changing. It is time to decide whether we should keep playing.

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.

12 comments:

  1. Hi Christopher
    I have posted links to your story and the "Zhang et al" article on the forums of the Canberra Ornitholgists Group, and the Aus Museum bird forum.
    Very interesting stuff.
    I had heard of this, on the ABC News a few days back, but it is good to see it written up.
    i find the spelling of the "Nature Precedings" journal cute, but annoying. But it matches precisely the dilemma you have described for digital "publication", for formal naming purposes.
    Thanks for that article.
    Denis

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  2. Now, as demonstrated by Les, it may be possible for a manuscript to appear online as a rough draft, as a polished pre-print, as the final official product. Should these early appearances be regarded as valid publications? When the manuscript first appears, or only as it approaches its final form?

    My two cents: if I submit a manuscript to a dead-trees journal, it also comes in several forms: initial submission, revised version(s), uncorrected page proof, corrected page proof, final printed version. The only one of these that 'counts' is the final version. I see no reason not to treat online publications the same way. Just because those earlier versions _can_ be made available early doesn't mean that they should have the same status as the final version. Nothing stops me from sending copies of my revised draft around to all my colleagues, but I don't, and for good reasons.

    Of course, the problem then becomes determining what is the final version. For journals with no paper version at all, I guess whatever they make available as the official final version is it. In which case, we penalize paper journals if we don't allow them to do the same. So the case of Epidendrosaurus is still a hot mess.

    However, there is a big difference between a finished paper released early online, and a pre-review draft as in the case of LES (great nickname, by the way). IMHO, it was extremely unwise for Zhang et al. to put the name in a draft that they knew would become publicly available, and even more unwise for Nature to let them. Is it really that hard to replace the name with [name embargoed until final publication] in any pre-review manuscript (paper or digital), to keep the taxonomic waters from getting muddier than they already are?

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  3. Would it be possible to kick out both Scanosoriopteryx and Epidendosaurus considering the confusion surrounding priority and just come up with a third name, different from the others, to replace both?

    Also, from this paper's format, I'm guessing it's just a draft. I wait to see the final paper. It's a wonderful specimen.

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  4. Barring formal recognition of Les, Scansoriopterygidae remains an invalid taxon as well right?

    So, technically, all the authors would have had to do was put a statement that they would print off five copies and list the names of the libraries they would reposit them in and the name would be valid?

    Not that mob-rule constitutes taxonomic validity, but Epidendrosaurus seems to hold favor in casual usage with most of the folks I've talked to about it...although I'll admit I like Scansoriopteryx better...

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  5. Matt:

    The only one of these that 'counts' is the final version.

    But even if only the final version counts as the official publication in terms of description and such, should the name priority date from the appearance of the final version only?

    One other thing that I didn't mention in the post that is relevant here is that once a printed version appears, it is more or less fixed for all eternity. An electronic publication may be changed at a later date without necessarily leaving any trace of its being changed.

    Is it really that hard to replace the name with [name embargoed until final publication] in any pre-review manuscript (paper or digital), to keep the taxonomic waters from getting muddier than they already are?

    The Canadian Journal series (or what was the Canadian Journal series - some of them have changed names in the past few months) do exactly that. I can sympathise with your complaint in your post, Matt - I named a new genus in my MSc thesis that still hasn't officially appeared in publication. I still cringe whenever I see a museum specimen labelled with that name. Of course, harvestmen nomina vetita don't risk quite the publicity that dinosaurs do.

    Zach:

    Would it be possible to kick out both Scanosoriopteryx and Epidendosaurus considering the confusion surrounding priority and just come up with a third name, different from the others, to replace both?

    No.

    The ICZN could always make a statement one way or another, but in terms of strict application of the rules, Scansoriopteryx is actually the clear winner.

    Also, from this paper's format, I'm guessing it's just a draft.

    Yep, it quite clearly is. Especially as it refers to supplementary info sections and such that aren't available as yet.

    In fact, one can't help wondering if this was actually supposed to appear at Precedings at all, or if it somehow ended up being loaded there by mistake...

    Neil:

    Barring formal recognition of Les, Scansoriopterygidae remains an invalid taxon as well right?

    The original description of Scansoriopteryx is available here. It's awful. Truly, truly awful. Nevertheless, it's valid. Whether or not Epidendrosaurus is synonymous with Scansoriopteryx is irrelevant to the validity of Scansoriopterygidae. The name Scansoriopterygidae is somewhat redundant if there is only one species in it, but that's a different issue from validity.

    Technically, the publication of the names Scansoriopterygidae and Scansoriopteryx is fudged a little according to the strict letter of the ICZN (Scansoriopterygidae should probably be followed by an explicit statement that the type genus is Scansoriopteryx, for instance), but if one was to declare them invalid on the basis of the fudge-points one would also be required to declare a heck of a lot of other published names that make the same technical mistakes invalid. This would include about 70% of the names that have been published in Nature and Science, for instance. This is not the time to be bureaucratic.

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  6. IMHO, it was extremely unwise for Zhang et al. to put the name in a draft that they knew would become publicly available, and even more unwise for Nature to let them.

    Also, there's no guarantee that the final version of this draft will actually get into print. What if it gets knocked down in review? Some commentators on the DML have wondered if Les could be a more mature specimen of Scansoriopteryx, previously known only from juveniles, rather than a whole new taxon. While I wouldn't know one way or another, this is just one example of the sort of thing that would have to be considered in the review process. What becomes of the name if Les never gets published, or if it's described as a specimen of a pre-existing taxon?

    There is also the possibility of the name changing before the final, official publication. Nanotyrannus, Albertaceratops, Guanlong... all rumoured to have had different names in early drafts from the name that finally appeared in print. One hopes that the authors of Les won't make a change now that their chosen name has become public, but the risk is there.

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  7. I hope that taxonomists aren't uploading pre-peer reviewed manuscripts to Nature Preceedings or the like in the hopes to establish priority. One can be amazed at the number of taxonomists who feel rules of the ICZN do not apply to them or that they can be bended.

    But you and some of the commenters here raise excellent points. Stuff I've been thinking about for a while too. Regardless of being published online only, advanced online, or print only. There has to be a final product. A stopping point in the writing and editting process where editors, authors and reviewers agree this is the product that is ready to go. That is the point where standardization needs to take place. Nature Preceedings is really meaningless for taxonomy. In fact potentially damaging if people are appending names. I always use Genus sp. nov. (Zelnio in press/review) in conference abstracts, presentations, blog posts etc. I agree with Dr. Vector that it was unwise to publish a name somewhere first before the final publication. I think it is also unprofessional and a blatant disregard to the ICZN.

    Digital publication is really the wave of the future and the sooner the ICZN gets on it the better. There are plenty of workers who are tech and web savvy who can draft up meaningful amendments to the Code that will satisfy online publishing models. The current rule of depositing 5 print copies in international repositories is actually a good compromise and is easy to do. A hard copy back up is never a bad thing. PLoS servers are backed up in 3 countries I believe. That is pretty good, but anything is possible. The more copies (electronic or paper) the better right?

    Neil said "Not that mob-rule constitutes taxonomic validity"

    Ha! Its not too far off, is it?

    Christopher said "An electronic publication may be changed at a later date without necessarily leaving any trace of its being changed."

    I'm not sure what you mean here. Do mean someone can change something just because digital files are easy to manipulate (i.e. maliciously?) Do you not regards a PLoS or BMC article as a final product equivalent to any print article from a journal such as Systematic Biology or PNAS? I guess I am just confused by this statement.

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  8. Kevin:

    Do mean someone can change something just because digital files are easy to manipulate (i.e. maliciously?) Do you not regards a PLoS or BMC article as a final product equivalent to any print article from a journal such as Systematic Biology or PNAS?

    It need not even be malicious. Some of the promoters of web-based taxonomy have actually claimed one of the advantages of web-based monographs to be that they can be updated wikipedia-style as further data becomes available. Problem being, it may not be immediately obvious to the user that different parts of the webpage (maybe even different parts of paragraphs or even sentences) were composed at different dates. If part of a printed page is crossed out and new text written in, one can see at a glance that an alteration has been made*. This does not necessarily apply to an electronic document.

    *Of course, there could be exceptions. It might be possible for an author to publish an altered version of a paper, but leave the printing dates, etc., unchanged so that a casual reader wouldn't realise they were looking at a new edition. This is probably still a much more complicated process than an electronic alteration.

    So in that light, no I suppose I wouldn't automatically accord online-only papers the same level of trust as a printed paper. Online publishers need to develop a policy that once published, the central manuscript would remain unchanged. Publishers such as PLoS and BMC may have earned their trust in such regards, but this trust should not automatically be extended to other online sources.

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  9. It Seems To Me that as long as a peer-reviewed paper eventually gets published properly, the date an on-line draft appeared (with the exact name used in the paper) could reasonably be used establish priority. Nature Precedings, then, along with other respected venues, could log receipt and not allow (untracked) changes.

    Really, the "permanence" of print is illusory. Paper can be burnt, it can be stolen, it can be forged, and anyway, as we have seen, unscrupulous (not to say dishonest, or crooked) colleagues can rush another paper into print ahead of you. What is needed is not physical permanence, but institutional permanence, and structurally enforced scruples. For the latter, Nature serves. Submitting simultaneously to Nature Precedings and other venues keeps them all honest, and the papers safe.

    Consider where risk truly lies. Priority should be painfully easy to resolve, not fraught with ambiguities and easy to game.

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  10. In fact, one can't help wondering if this was actually supposed to appear at Precedings at all, or if it somehow ended up being loaded there by mistake...

    Oooh, it was "accidentally" leaked onto the internet. Happens all the time in film, gaming, etc. :-) It's all about drumming up enthusiasm. Just think, we'll all be standing in line for the midnight release of that issue of Nature.

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  11. It Seems To Me that as long as a peer-reviewed paper eventually gets published properly, the date an on-line draft appeared (with the exact name used in the paper) could reasonably be used establish priority.

    The proposal of Harris (2004) which is being considered by the ICZN would allow the date of registration of a DOI for an online source to count as the priority date. I think that one of the conditions of a DOI-linked item is that it can't change, too, which answers one of the main complaints I've referred to.

    Paper can be burnt, it can be stolen...

    This is why the Codes require multiple copies in multiple depositories, to reduce the risk of all copies disappearing.

    ...and anyway, as we have seen, unscrupulous (not to say dishonest, or crooked) colleagues can rush another paper into print ahead of you.

    An issue that applies whether we're talking online or print, so not really relevant to this discussion.

    What is needed is not physical permanence, but institutional permanence, and structurally enforced scruples. For the latter, Nature serves.

    I'm afraid I don't quite get your point here. For taxonomy, though, physical permanence is exactly what we need. Sources of new taxa do not just need to be available five years in the future, they don't just need to be available fifty years in the future, they need to be available one hundred and fifty years and more into the future (two hundred and fifty-five so far, and still counting...) Because electronic publications are still so new, we're still trying to work out what they offer us in the way of permanence.

    When it comes to taxonomic matters, actually, Nature and Science are often great rotting piles of foetid elephant faeces, but that's another issue...

    Priority should be painfully easy to resolve, not fraught with ambiguities and easy to game.

    That's the ideal, yes. The question is the best means to make it so.

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  12. ... applies whether we're talking online or print...

    Sorry, I don't get this. How could a corrupt referee rush something online ahead of you, if you had posted your draft yourself before they even saw it?

    For taxonomy, though, physical permanence is exactly what we need.

    For taxonomy, permanence may be important, but not for priority. Priority issues are always settled in (geologically speaking) no time. The online registration has to last only long enough for the supporting paper(s) to appear in print.

    (Really, if you want a system designed that works, ask an engineer. Scientists aren't, as a rule, temperamentally suited to it. )

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