February 14, 2011
Sorry to bump Matt’s awesome Rhea-neck post off the top of the SV-POW! home page, but I have news of the rapidly developing checklist for new zoological names. As well as many, many minor and not-so-minor edits — and thanks to everyone who’s participated in this process — I have made a major structural change.
The list has been broken into two, first enumerating Requirements and then describing Best Practice. I have also reordered some of the points within lists. As a result, ALL NUMBERING HAS CHANGED; also some points have been split and others merged.
Please be sure to comment only on the most recent version.
I am worried that the Checklist is getting too big. I just copied and pasted the substance of it — the introductory paragraph and the two lists — into a new OpenOffice in 12-point Times, and found that it runs to a page and a quarter. Reduced to 10.5-point type it fits on a page, but that’s the way I want to go. So suggestions for reducing the length without losing content will be particularly welcome.
(As before, comments are closed on this post, because I don’t want to split discussion between here and the checklist itself.)
February 10, 2011
As we all know, the International Code of Zoological Nomenclature is a large and intimidating document. As a result, zoologists naming new animals often do not read it in its entirety (I know I haven’t). It’s probably because of this that many of the more avoidable nomenclatural mistakes occur.
Whatever might or might not eventually be possible in terms of simplifying the Code, everyone recognises that that would be a huge job, and something that would take years to do. So let’s ignore that possibility for now.
In the short term, what would be much more useful would be if someone could work up a very short document — no more than a single page of A4 and hopefully much shorter — that states in simple bullet-points what MUST be done to ensure that a new name is valid. Then there would be no excuse for zoologists venturing into nomenclature for the first time not to read such a document — let’s call it the ICZN Cheat Sheet.
Because it’s easier to steer a moving ship, I wrote to the ICZN email list this morning proposing an initial set of bullet points. I did not for a moment expect that they were complete, consistent or even necessarily correct; but I hoped that they could at least serve as a starting point for a very quick process of putting such a list together.
I am pleased to say that response on the list was fairly positive, and at the suggestion of one of the list members I have now posted the in-progress checklist as a page on this site, having revised it in accordance with several suggestions.
If you’re interested in contributing to this effort — helping us to derive a clear, concise and correct one-page guide to naming new zoological genera and species — please head over to the page and comment there. (Comments on this post are closed, to avoid splitting discussion across two places.)
October 9, 2010
I wasn’t going to write about this, partly because it’s so darn depressing, but mostly because in the wake of this comment it seemed like the “Amphicoelias brontodiplodocus” paper was being withdrawn, and to quote something Mike said off-list, I was happier about the retraction than I was sad about the implied revisionism. But then Henry Galliano wrote:
Although the paper has still not been completed, no changes have been made altering it conclusions. Interestingly, despite the 4000 recent hits and downloads from our website, it is surprising no evidence has been submitted challenging our claims.
If it’s really supposed to be an internal manuscript/press release type thing, why brag about the lack of criticism? Did it ever occur to you that we might be holding off out of respect, to give you an avenue of retreat where you could perhaps salvage a few scraps of dignity? But if you’re going to call us out for not tearing apart this joke of a paper, then stand by.
In the previous post, Mike wrote:
In other words, we’re being asked to believe that the new specimens are more different from all other Morrison diplodocids than any of them are from each other. And yet we’re brought to this conclusion by the very animals that are apparently not as similar. It’s as though I discovered dogs, and thereby concluded that lions, cheetahs and house-cats are are all the same species.
No, it’s way, way worse. Because, claims of the authors to the contrary, “Amphicoelias brontodiplodocus” is not some kind of morphological outlier among Morrison diplodocids. From where I stand, it looks like it’s right in the middle. So it’s as though I discovered ocelots and thereby concluded that lions, cheetahs, and housecats were all the same thing.
If no apatosaurs had ever been found, and they got the first one, and then concluded that all the apatosaurines were one taxon and all the diplodocines were another, that would at least make some kind of sense, in that they’d be drawing their taxonomic distinctions along actual phylogenetic lines. Then it would be a fairly straightforward lumper/splitter fight. In the actual event, I’m sad to say that it’s the “A. brontodiplodocus” proponents against the reality-based community.
Back to Henry’s statement about the “surprising” lack of evidence to the contrary: dude, don’t do this to yourself. We thought you were on the right track with the implied retraction from your earlier comment. You’ve been one of the white hats, but if you go down this dark path, forever will it dominate your destiny. Consume you it will!
It’s not at all “surprising” that no one has submitted evidence to the contrary. The evidence is in the 133 years’ worth of careful morphological and phylogenetic work that you blew right past on the way to nominating your new animal, at least implicitly, as TEH MOSTEST IMPORTANT DIPLODOCID EVAR!!11eleventy! Your material is awesome, and I don’t doubt that you’ve got a new animal on your hands, but the idea that it is one of only two diplodocids in the Morrison–or worldwide–and all the others are morphs of the same thing, is both suspiciously convenient for you, and so outrageously extreme that it would take a mountain of work (that is not presented in the paper) to demonstrate. In addition to the gross, obvious morphological differences, it would be really nice to know why there are geographic, stratigraphic, and paleoecological differences among the other Morrison diplodocids. Doesn’t the work of Dodson et al. (1980), Turner & Peterson (1999), and Foster (2003, 2007), just for starters, count for anything? Instead of boasting about the uncontested status of your claims, how about doing enough work to convince us to take them seriously in the first place? People who take the time to do reasonable morphological comparisons and phylogenetic work that doesn’t hail from an opium den have better things to do than exhaustively smack down every act of Hoser taxonomy that leaks onto teh intarwebz in the first two days. Give us a minute to get over our collective shock, and in the meantime, make up your mind about what the document is. Is it supposed to be considered published, or not? If so, it’s fair game for criticism, but don’t deny that you’re at least attempting acts of taxonomy. If not, don’t beg us to criticize it. You may get a lot more than you wished for.
Sadly, this will probably go down in popular opinion as a clash between academic and commercial paleontologists, or between credentialed paleontologists and hobbyists. It shouldn’t. I don’t care if someone is employed by a university or a rock shop, or whether they have any degrees in the field. All I care about is the quality of the work. (Repeatability, which necessitates that specimens be properly curated in accredited museums to ensure perpetual access to future researchers, is an inherent component of that quality.) Jack McIntosh is a physicist, and as far as I know never got any formal training in paleontology. But that’s irrelevant, because he taught himself by looking at literally thousands of specimens and reading everything he could get his hands on, and because his papers are as exhaustively researched as one could hope for. As Robert McKee wrote of Steven Pressfield, you can’t read Jack’s papers without being overwhelmed by “the work, the work, all the work” behind them. In contrast, I couldn’t read the “A. brontodiplodocus” paper without be overwhelmed by the complete disregard–and indeed implicit contempt–for all of the work that people from Cope and Marsh to Jerry Harris and David Lovelace have done on the admittedly knotty problem of Morrison sauropod diversity.
Taxonomy is facing a crisis, brought on by two things: at least for some charismatic clades, Hoser taxonomists potentially outnumber actual taxonomists (although even one is bad enough, as herpetologists have found); and there is essentially no filtering on what counts. Anyone in the world can whip up whatever uninformed BS they want and send a certain number of hardcopies off to libraries, and according to the ICZN their crappy work counts and the rest of us just have to deal with it. And the problem is only going to get worse in the shiny digital future as electronic publication removes the already minor inconvenience associated with “publishing” acts of taxonomy. I can think of a handful of possible outcomes:
- Working scientists are going to bog down in endlessly putting out the fires of Hoser taxonomy.
- We’ll install some kind of de jure filter to deal with Hoser taxonomy.
- We’ll collectively decide to ignore acts of Hoser taxonomy, which will constitute a de facto filter.
For my part, I think the ICZN’s policy of noninterference in cases like this is taking a sound principle to the point of lunacy. It’s like I walked up to a policeman, punched him in the nose, and told him he couldn’t arrest me because my assault counted as protected speech (on reflection, I’ll bet this actually happens in Berkeley). Of the options above, I suspect that we’ll end up with the third, and I won’t be entirely happy about that, because I also suspect that some credentialed academics will want to ignore the work of commercial paleontologists and hobbyists just because they’re not credentialed academics. Which would be wrong. We want to sort the work based on its quality, not who produced it.
Which is an interesting position for me to come to, given what I’ve said here in the past about filters. It was easier to deal with the thought of completely open publication when the waste products weren’t landing on my lawn. But I still think that this is the way things are going. In which case, post-hoc criticism of self-published works is often going to be the only filter we get. The comment thread is open. Filter away!
- Dodson, P., Behrensmeyer, A.K., Bakker, R.T., and McIntosh, J.S. 1980. Taphonomy and paleoecology of the dinosaur beds of the Jurassic Morrison Formation. Paleobiology 6:208-232.
- Foster, J.R. 2003. Paleoecological analysis of the vertebrate fauna of the Morrison Formation (Upper Jurassic), Rocky Mountain Region, U.S.A. New Mexico Museum of Natural History and Science. Bulletin 23.
- Foster, J.R. 2007. Jurassic West: The Dinosaurs of the Morrison Formation and Their World. Indiana University Press. 389pp.
- Turner, C.E., Peterson, F., 1999. Biostratigraphy of dinosaurs in the Upper Jurassic Morrison Formation of the Western Interior, U.S.A. Pp. 77–114 in Gillette, D.D. (Ed.), Vertebrate Paleontology in Utah. Utah Geological Survey Miscellaneous Publication 99-1.
October 7, 2010
Well, this is frustrating. Over on the VRTPALEO mailing list, all the talk at the moment is of the new paper by Henry Galiano and Raimund Albersdörfer (2010), describing their rather comically named new species Amphicoelias brontodiplodocus. And to be fair, the material they’re describing is sensational, and the photographs in the paper are pretty good.
But I don’t want to talk about that.
There are other things I do want to talk about, but I can’t help feeling that whatever else we cover here at the moment, everyone is going to be thinking “Yes, but what about Amphicoelias brontodiplodocus?” So I don’t think I can go on to write about the things I want to before we’ve at least acknowledged the existence of this paper.
And yet, and yet … I have so many problems with this paper, even before we get to the controversial part, namely the conclusion that Diplodocus, Barosaurus, Apatosaurus, Supersaurus, Suuwassea, Tornieria and Eobrontosaurus are all congeneric with Amphicoelias — more precisely, conspecific with the single species Amphicoelias altus.
Aside from the a priori unlikelihood of that, we have these problems:
- First, and maybe most important, the specimens described in this paper are all privately owned, so whatever conclusions might be gleaned from examining them are not replicable by other scientists. For the Society of Vertebrate Paleontology, that’s a deal-breaker right there (and I am in full agreement).
- Second, the new paper doesn’t seem to be published: at least, no-one’s yet claimed that it exists in numerous identical hardcopies, so for ICZN purposes the new name is a nomen nudum. (That will surely change, though: I am confident that Dinosauria International, LLC are perfectly capable of printing off a hundred copies and sending them out to libraries.)
- Third, the paper doesn’t seem to have been peer-reviewed: at least, there’s nothing in the acknowledgements that indicates that it was. It doesn’t seem to have been edited in anything like the usual sense either.
- Fourth, there is mechanical evidence of enormous sloppiness in the composition of the paper. For example, many cited papers are not included in the REFERENCES CITED section, and most of the references that are included are not in fact cited in the paper. As an example, my own Taylor et al. (2009) is cited but not referenced, while Taylor and Naish (2005) is referenced but not cited. Lots of Upchurch papers in the bibliography are never cited. That doesn’t give me confidence about the rest of the work.
- Likewise, the paper is rife with typos and grammar errors, such as this from page 28: “A. louisae is by far the most widely acclaimed example, and B. excelsus skeleton mounted and exhibited in the Peabody museum. Despite the familiarity of these Apatosaurus specimens various aspects of it [sic] skeleton remain poorly known.” Not a killer, but again it doesn’t give me confidence.
- “brontodiplodocus” is a stupid name.
Against that backdrop, consider the radical taxonomic hypothesis. All Morrison formation diplodocids (and some from elsewhere) are considered to belong to a single species, Amphicoelias altus … except for the new specimens, which belong to the new and separate species A. brontodiplodocus. In other words, we’re being asked to believe that the new specimens are more different from all other Morrison diplodocids than any of them are from each other. And yet we’re brought to this conclusion by the very animals that are apparently not as similar. It’s as though I discovered dogs, and thereby concluded that lions, cheetahs and house-cats are are all the same species.
So this is not just a matter of extreme taxonomic lumping: it’s weirder than that. It’s “all the other stuff is just a single species except the one we’ve discovered which is different”.
As Tom Holtz is fond of saying, extraordinary claims demand extraordinary evidence. I’m not going to come out and say it’s impossible that all Morrison diplodocids except the new specimens were conspecific. But if I were the one setting out to propose such a heterodox hypothesis, I would do myself every possible favour: I’d do it from properly accessioned specimens in public museums, I’d publish in a recognised peer-reviewed journal, I’d take care to get my nomenclature right, match up my citations and references, and generally dot the i’s and cross the t’s.
Until that’s done with this new material, I’m not sure there’s much point in investing a lot more effort in evaluating the phylogenetic/taxonomic claims.
(Henry, I know you’re an occasional reader here. Sorry to be so negative, but I’m sure you’ll understand that I have to call ‘em as I see ‘em.)
- Galiano Henry, and Raimund Albersdörfer. 2010. A new basal diplodocid species, Amphicoelias brontodiplodocus from the Morrison Formation, Big Horn Basin, Wyoming, with taxonomic reevaluation of Diplodocus, Apatosaurus and other genera. Dinosauria International, LLC, Wyoming. 50 pages.
- Taylor, Michael P. and Darren Naish. 2005. The phylogenetic taxonomy of Diplodocoidea (Dinosauria: Sauropoda). PaleoBios 25(2): 1-7.
- Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2): 213-220.
August 26, 2010
A bit frightening to realise it’s been more than a month since the last SV-POW! post. We have some excuse for that: I am just back from a fortnight’s holiday with my family, and shortly before that Matt was at a conference in Uruguay. Still, a whole month?
And this post is going to be disappointingly short and off-topic — it’s just a bit of housekeeping really.
Back at the end of June, I pointed out on this blog that the awesome new Miocene sperm whale Leviathan was a junior synonym of Koch’s name Leviathian which he introduced as a more than usually stupid synonym of Mammut, the mastodon. (See the original piece for the gory details.)
I am pleased to note that this has now been resolved: the authors of the new Leviathan paper have published a short corrigendum proposing the replacement name Livyatan, resulting in the new combination Livyatan melvillei. Since the corrigendum is so short, here it is in its entirety:
The genus name Leviathan, proposed in this Letter for a new fossil physeteroid from the Miocene of Peru, is preoccupied by Leviathan Koch, 1841 (ref. 1), a junior subjective synonym of Mammut Blumenbach, 1799 (ref. 2). We propose here a replacement name Livyatan gen. nov. The type species is placed in this genus to form the binomial Livyatan melvillei. The diagnosis and content of the new genus follow our Letter. ‘Livyatan’ is a Hebrew name applied to large marine monsters in popular and mythological stories. We thank M. P. Taylor and D. Yanega for bringing this to our attention.
It’s nice to get a mention, though a shame they weren’t able to include a link to SV-POW!. Probably Nature‘s guidelines don’t allow that — they wouldn’t be alone — and in any case we’ve hardly been a friend to the Nature Publishing Group, so maybe we’d have even less reason to expect any love from them :-)
June 30, 2010
By now most SV-POW! readers will have heard of Leviathan melvillei, the big-toothed Miocene sperm whale that was named in Nature today (Lambert et al. 2010) — if not, see for example the Discover Magazine blog article for the basics.
My first thought was “Wow, that is one awesome animal.”
My second was, “I can’t believe no-one’s used the genus name Leviathan before”.
But it’s really not clear what’s being said here: the relevant page from the printed edition says “Levathan Koch , Descr. of Missourium, 1840, 13 (as Leviathan p. 14). — Mamm”. The use of italics suggests that the NZ editors considered the name as nomenclaturally valid, but the relation between the names Levathan [sic] and Leviathan is not clear.
Looking around a bit more, I found Lindsay (1991) which happens to discuss the specimen in question, and at least some of the publications. The first page of this article is freely available and says:
The mastodon’s remains had been discovered by Albert Koch in 1840 on the Pomme de Terre River in Benton or Hickory County in Missouri, and possibly parts were from Jefferson County as well. A skeleton was assembled later that year in Koch’s St. Louis museum and went on display as the Missourium or Missouri Leviathan. Koch also referred to the specimen as Levathan [sic] Missourii (1841) and Leviathan Missouriensis (1843), by which time he had also given it the name Missourium Theristocaulodon on account of “its enormous sickle shaped tusks”.
[Update, 1st July. It’s now apparent that Lindsay (1991) overlooked a passage in the 1841 first edition of Koch’s pamphlet in which he established the name Leviathan two years before the 5th edition in which its name was included in the expanded title. Thanks to Christopher Taylor for pointing this out.]
The first thing to note is of course that Koch was a truly horrible taxonomist. He proposed three distinct genus names for a single specimen in a space of three years, and as in fact became apparent subsequently, they are all junior synonyms of Mammut, the mastodon. The second thing to note is that he was a truly horrible palaeobiologist, concluding for spurious reasons that his specimen was an aquatic animal (hence his use of the name of the biblical sea-monster).
I don’t know whether Lindsay addressed this question, as I only have the first page of his article (and if anyone who has access can send me the whole thing I’ll be grateful). But now that I knew to search for the relevant date, 1843, I was able to find Montagu and Peterson (1944), which contains the answer:
Sometime during 1843 Koch took his collections to Ireland where they, together with the Missourium, were exhibited at Dublin. Here appeared the “Fifth edition, enlarged,” of his pamphlet together with a new title-page and a completely rewritten and revised text .
And note 25 is the full reference:
Description of the Missourium Theristocaulodon (Koch) or Missouri Leviathan (Leviathan Missouriensis,) together with its supposed habits, and the Indian Traditions: also, comparison on the Whale, Crcocodile, and Missourium, with the Leviathan, as described in the 41st Chapter of the Book of Job; by Albert Koch. Printed by C. Crookes, 87 Chapel Street, Dublin: 28 pp., 8°, 1843.
It seems apparent from the typography here — with the words “Leviathan Missouriensis” being the only words of the title set in italics — that Koch was indeed publishing this as a scientific name.
Just to reiterate: if the name was validly published according to the tenets of the ICZN, then the genus name Leviathan Koch 1843 is nomenclaturally valid even though taxonomically it’s junk, being a junior objective synonym of Levathan Koch 1841 and a junior subjective synonym of Mammut Blumenbach 1799. And if it’s nomenclaturally valid, then that name is preoccupied, and Lambert et al. will need to propose a replacement name for their awesome whale.
All of this is based on glimpses of single pages and suchlike of the various relevant papers: I don’t have the full text of Lindsay (1991) or Montagu and Peterson (1944), and I have never clapped eyes on the crucial Koch (1843) at all. So it’s perfectly possible that I’ve overlooked something, and the genus Leviathan Koch 1843 was not validly published. This should definitely by confirmed or denied by someone who has a copy of that publication.
But at the moment, things aren’t looking good for Leviathan Lambert et al. 2010.
- Koch, Albert. 1843. Description of the Missourium Theristocaulodon (Koch) or Missouri Leviathan (Leviathan Missouriensis,) together with its supposed habits, and the Indian Traditions: also, comparison on the Whale, Crcocodile, and Missourium, with the Leviathan, as described in the 41st Chapter of the Book of Job. C. Crookes, Dublin. 28 pages.
- Lambert, Olivier, Giovanni Bianucci, Klaas Post, Christian de Muizon, Rodolfo Salas-Gismondi, Mario Urbina and Jelle Reumer. 2010. The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru. Nature 466:105-108. doi:10.1038/nature09067
- Lindsay, William. 1991. “Mammoth” Task. Curator: The Museum Journal 34(4):261-272.
- Montagu, M. F. Ashley, and C. Bernard Peterson. 1944. The Earliest Account of the Association of Human Artifacts with Fossil Mammals in North America. Proceedings of the American Philosophical Society 87(5):407-419.
A comment by Charles Epting on the recent article about self-publication led me to check the relevant section of the draft Phylocode, which I’ve read once or twice before but not recently enough for this to have hit me with the force it ought:
From Chapter II. Publication, and specifically Article 4. Publication Requirements:
4.2. Publication, under this code, is defined as distribution of text (but not sound), with or without images. To qualify as published, works must be peer-reviewed, consist of numerous (at least 50 copies), simultaneously obtainable, identical, durable, and unalterable copies, some of which are distributed to major institutional libraries (in at least five countries on three continents) so that the work is generally accessible as a permanent public record to the scientific community, be it through sale or exchange or gift, and subject to the restrictions and qualifications in the present article.
4.3. The following do not qualify as publication: (a) dissemination of text or images solely through electronic communication networks (such as the Internet) or through storage media (such as CDs, diskettes, film, microfilm and microfiche) that require a special device to read.
I am … flabbergasted, if that’s the word I want. (I always want to spell that with an “h” after the “g”.) This language is obviously derived from what’s in the ICZN — for example, “must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies” becomes “must consist of numerous (at least 50 copies), simultaneously obtainable, identical, durable, and unalterable copies”.
And the result is that, just like the ICZN, the draft Phylocode does not recognise electronic publication.
Just think about that. It means that if you define a clade in most of the PLoS journals, it won’t count (unless the journal does one of its inkjet-and-staples special print runs for you). It also means that any clades you define in Proceedings of the Royal Society of London will not count when the initial online article is published, but only when the later printed edition comes out. In other words, it means that both the science journals that are growing most quickly in influence and prestige and the oldest science journal in the world will both be useless for phylogenetic nomenclature.
I am sure that’s not what the Phylocode authors want.
That’s particularly true in light of the code’s further requirement that in order to be valid, clade definitions need to be registered. Really, once a name is officially registered in the Phylocode database and its definition is in a paper published by a reputable publisher and existing in thousands of bit-for-bit-identicial copies in every country in the world, what else is needed for stability? Fifty stapled inkjet copies?
It seems particularly startling in light of the fact that even the notoriously slow-moving ICZN seems now to be recognising that electronic publishing is inevitable; it would be pretty horrible if by the time the Phylocode is finally implemented, the ICZN has accepted its electronic publishing amendment and the Phylocode is seen to be trailing behind the ICZN in recognising the reality of the world we live in. (For anyone who is not yet convinced of that reality, I recommend *cough* Taylor 2009, which is a pleasantly easy read.)
Is it too late? Can the Phylocode be fixed before it’s implemented? Can it just be done, or will it need lengthy discussion first? If this doesn’t get fixed, will anyone take the Phylocode seriously? Is there even a serious argument for keeping the Article 4.2 language as it is now?
I don’t know the answers to any of these questions. Does anyone else out there?
In other news …
I am astounded at the lack of response to University of California vs. Nature, which seems to me just about the most significant thing that’s happened in the world of academic literature since, well, forever. Can it really be that everyone else’s response is, and I quote, “meh”?
- Curry Rogers, K. 2009. The postcranial osteology of Rapetosaurus krausei (Sauropoda: Titanosauria) from the Late Cretaceous of Madagascar. Journal of Vertebrate Paleontology 29(4):1046-1086.
- Taylor, Michael 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.