September 30, 2012
Having taken time to discuss at length why we posted our neck-anatomy paper on arXiv, let’s now return to the actual content of the paper. You may remember from the initial post, or indeed from the paper itself, that Table 3 of the paper summarises its conclusions:
Needless to say, we puny humans lack all seven of the features that were discussed as contributing to long necks, while sauropods have them all. But it’s interesting to look at the giraffe and Paraceratherium, the two longest-necked mammals, and see what they have in common. They share quadrupedal stance; the giraffe has elongated cervical vertebrae; and Paraceratherium has absolutely large body size. But they both lack all four of the other features:
- Small, light head
- Numerous cervical vertebrae
- Air-sac system
- Vertebral pneumaticity
And they lack them for the same reason: because they are mammals. The same is true of all mammals, and the individual reasons for those four missing long-neck features are all the same: because mammals have hit local maxima, and can’t evolve away from them.
Mammals’ heads, for example, are all set up for extensive oral processing of food — certainly among large herbivores. (I think pretty much all the toothless mammals are insectivores.) They’ve got very good at it, and there’s no evolutionary pathway that can take a giraffe from its current lifestyle to a sauropod-like crop-and-swallow strategy without passing through an adaptive valley on the way. That means they are stuck with big, solid teeth and heavily engineered jaws, which means they can’t have light heads.
In the same way, mammals have much more efficient lungs than those of their reptile-like forebears, the common ancestors that they share with birds. They have evolved to a point where their lungs are too complex and effective to easily evolve into a different shape — yet by doing so, they have cut themselves off from the yet more efficient avian lung (shared by sauropods) that is capable of extracting twice as much oxygen as our lungs.
And of course in the absence of an avian-style lung, there can be no soft-tissue diverticula or air-sacs, and so no pneumatic invasion of the vertebrae.
A final nail in the coffin of mammal neck length is that we seem to be strongly wired to have exactly seven cervical vertebrae — no more, no less. The exceptions are very few and far between: sloths and sirenians, and even then they don’t vary from the seven-cervical pattern by more than one or two vertebrae.
As for why we can’t get past seven, or at most nine, cervicals — that’s harder to answer. There’s no reason why seven should be an adaptive maximum, so it seems that the reason is genetic: the instructions to produce seven cervicals are part of the same gene complex that gives us an advantage in some other way. I have vague memories of an excellent talk at the Bristol SVP suggesting that cervical-count is linked to cancer resistance, but I can’t remember any of the details.
Anyone able to elaborate?
Anyway: this is how evolution works, and why it doesn’t make organisms (including us) as perfect as we might wish. It has no goal in mind — such as a long neck — and blindly follows the path that at that moment gives the organism the best chance of reproducing successfully. That means an animal like a giraffe, even though it is clearly selecting for neck length, is trapped on an adaptive hill and can’t get down across the valley to a higher peak.
September 28, 2012
Over on Facebook, where Darren posted a note about our new paper, most of the discussion has not been about its content but about where it was published. We’re not too surprised by that, even though we’d love to be talking about the science. We did choose arXiv with our eyes open, knowing that there’s no tradition of palaeontology being published there, and wanting to start a new tradition of palaeontology being routinely published there. Having now made the step for the first time, I see no reason ever to not post a paper on arXiv, as soon as it’s ready, before — or maybe even instead of — submitting it to a journal.
(Instead of? Maybe. We’ll discuss that below.)
The key issue is this: science isn’t really science until it’s out there where it can be used. We wrote the bulk of the neck-anatomy paper back in 2008 — the year that we first submitted it to a journal. In the four years since then, all the observations and deductions that it contains have been unavailable to the world. And that is stupid. The work might just as well never have been done. Now that it’s on arXiv, that’s over. I was delighted to get an email less than 24 hours after the paper was published, from an author working on a related issue, thanking us for posting the paper, saying that he will now revise his own in-prep manucript in light of its findings, and cite our paper. Which of course is the whole point: to get our science out there where it can do some damage.
Because the alternative is horrible, really. Horribly wasteful, horribly dispiriting, horribly retarding for science. For example, a couple of weeks ago in his SVPCA talk, David Norman was lamenting again that he never got around to publishing the iguanodont systematic work that was in his dissertation, I-don’t-know-how-many-years-ago. The result of that interminable delay is that others have done other, conflicting iguanodont systematic work, and Norman is now trying belatedly to undo that and bring his own perspective. A terrible an unnecessary slowing of ornithopod science, and a waste of duplicated effort. (Thankfully it’s only ornithopods.)
And of course David Norman is very far from being alone. Pretty much any palaeontologist you talk to will tell you of a handful of papers — many more in some cases — that were finished many years previously but have never seen the light of day. (I still have a couple myself, but there is no point in resurrecting them now because progress has overtaken them.) I wonder what proportion of all Ph.D work ever sees the light of day? Half? Less? It’s crazy.
Publish now, publish later
So, please folks: we all need to be posting our work on preprint servers as soon as we consider it finished. It doesn’t mean that the posted versions can’t subsequently be obsoleted by improved versions that have gone through peer-review and been published in conventional journals. But it does mean that the world can know about the work, and build on it, and get the benefit of it, as soon as it’s done.
You see, we have a very fundamental problem in academia: publishing fulfils two completely separate roles. Its primary role (or at least the role that should be primary) is to make work available to the community; the secondary role is to provide a means of keeping score — something that can be used when making decisions about who to appoint to jobs, when to promote, who gets grants, who gets tenure and so on. I am not going to argue that the latter shouldn’t happen at all — clearly a functioning community needs some way to infer the standing of its participants. But I do think it’s ridiculous when the bean-counting function of publication trumps the actual publication role of publication. Yet we’ve all been in a position where we have essentially complete work that could easily go on a blog, or in the PalAss newsletter, or in a minor journal, or somewhere — but we hang onto it because we want to get it into a Big Journal.
Let me say again that I do realise how unusual and privileged my own position is: that a lot of my colleagues do need to play the Publication Prestige game for career reasons (though it terrifies my how much time some colleagues waste squeezing their papers into two-and-a-half-page format in the futile hope of rolling three sixes on the Science ‘n’ Nature 3D6). Let’s admit right now that most palaeontologists do need to try to get their work into Proc B, or Paleobiology, or what have you. Fair enough. They should feel free. But the crucial point is this: that is no reason not to post pre-prints so we can all get on with actually benefitting from your work in the mean time.
Actually, I feel pretty stupid that it’s taken me this long to realise that all my work should go up on arXiv.
So are there any special cases? Any kinds of papers that we should keep dry until they make it into actual journals? I can think of two classes that you could argue for — one of them convincingly, the other not.
First, the unconvincing one. When I discussed this with Matt (and half the fun of doing that is that usually neither of us really knows what we think about this stuff until we’re done arguing it through), he suggested to me that we couldn’t have put the Brontomerus paper on arXiv, because that would have leaked the name, creating a nomen nudum. My initial reaction was to agree with him that this is an exception. But when I thought about it a bit more, I realised there’s actually no compelling reason not to post such a paper on arXiv. So you create a nomen nudum? So what? Really: what is the negative consequence of that? I can’t think of one. OK, the name will appear on Wikipedia and mailing lists before the ICZN recognises it — but who does that hurt? No-one that I can think of. The only real argument against posting is that it could invite scooping. But is that a real threat? I doubt it. I can’t think of anyone who would be barefaced enough to scoop a taxon that had already been published on arXiv — and if they did, the whole world would know unambiguously exactly what had happened.
So what is the one real reason not to post a preprint? I think that might be a legitimate choice when publicity needs to be co-ordinated. So while nomenclatural issues should not have stopped us from arXiving the Brontomerus paper, publicity should. In preparation for that paper’s publication day, we did a lot of careful work with the UCL publicity team: writing non-specialist summaries, press-releases and FAQs, soliciting and preparing illustrations and videos, circulating materials under embargo, and so on. In general, mainsteam media are only interested in a story if it’s news, and that means you need to make sure it’s new when they first hear about it. Posting the article in advance on a publicly accessible archive would mess that up, and probably damage the work’s coverage in the press, TV and radio.
Publication venues are a continuum
It’s become apparent to us only gradually that there’s really no clear cut-off where a paper becomes “properly published”. There’s a continuum that runs from least to most formal and exclusive:
SV-POW! — arXiv — PLOS ONE — JVP — Nature
1. On SV-POW!, we write what we want and publish it when we want. We can promise you that it won’t go away, but you only have our word for it. But some of what we write here is still science, and has been cited in papers published in more formal venues — though, as far as I know, only by Matt and me so far.
2. On arXiv, there is a bit more of a barrier to clear: you have to get an existing arXiv user to endorse your membership application, and each article you submit is given a cursory check by staff to ensure that it really is a piece of scientific research rather than a diary entry, movie review or spam. Once it’s posted, the paper is guaranteed to remain at the same URL, unchanged, so long as arXiv endures (and it’s supported by Cornell). Crucially, the maths, physics and computer science communities that use arXiv uncontroversially consider this degree of filtering and permanence sufficient to constitute a published, citeable source.
3. At PLOS ONE, your paper only gets published if it’s been through peer-review — but the reviewing criteria pertain only to scientific soundness and do not attempt to evaluate likely impact or importance.
4. At JVP and other conventional journals, your paper has to make it through a two-pronged peer-review process: it has to be judged both sound scientifically (as at PLOS ONE) and also sufficiently on-topic and important to merit appearing in the journal.
5. Finally, at Nature and Science, your paper has to be sound and be judged sexy — someone has to guess that it’s going to prove important and popular.
Where along this continuum does the formal scientific record begin? We could make a case that all of it counts, provided that measures are taken to make the SV-POW! posts permanent and immutable. (This can be done submitting them to WebCite or to a service such as Nature Precedings used to provide.) But whether or not you accept that, it seems clear that arXiv and upwards is permanent, scientific and citeable.
This raises an interesting question: do we actually need to go ahead and publish our neck-anatomy paper in a more conventional venue? I’m honestly not sure at the moment, and I’d be interested to hear arguments in either direction. In terms of the progress of science, probably not: our actual work is out there, now, for the world to use as it sees fit. But from a career perspective, it’s probably still worth our while to get it into a journal, just so it can sit more neatly on our publication lists and help Matt’s tenure case more. And yet I don’t honestly expect any eventual journal-published version to be better in any meaningful way than the one on arXiv. After all, it’s already benefitted from two rounds of peer-review, three if you count the comments of my dissertation examiners. More likely, a journal will be less useful, as we have to cut length, eliminate illustrations, and so on.
So it seems to me that we have a hard choice ahead of us now. Call that paper done and more onto making more science? Or spend more time and effort on re-publishing it in exchange for prestige? I really don’t know.
For what it’s worth, it seems that standard practice in maths, physics and computer science is to republish arXiv articles in journals. But there are some scientists who routinely do not do this, instead allowing the arXiv version to stand as the only version of record. Perhaps that is a route best left to tenured greybeards rather than bright young things like Matt.
Citing papers in arXiv
Finally, a practicality: since it’ll likely be a year or more before any journal-published version of our neck-anatomy paper comes out, people wanting to use it in their own work will need to know how to cite a paper in arXiv. Standard procedure seems to be just to use authors, year, title and arXiv ID. But in a conventional-journal citation, I like the way that the page-range gives you a sense of how long the paper is. So I think it’s worth appending page-count to the citations. And while you’re at it, you may as well throw in the figure and table counts, too, yielding the version that we’ve been using:
- Taylor, Michael P., and Mathew J. Wedel. 2012. Why sauropods had long necks; and why giraffes have short necks. arXiv:1209.5439. 39 pages, 11 figures, 3 tables.
September 26, 2012
Today sees the publication, on arXiv (more on that choice in a separate post), of Mike and Matt’s new paper on sauropod neck anatomy. In this paper, we try to figure out why it is that sauropods evolved necks six times longer than that of the world-record giraffe — as shown in Figure 3 from the paper (with a small version of Figure 1 included as a cameo to the same scale):
This paper started life as a late-night discussion over a couple of beers, while Matt was over in England for SVPCA back in (I think) 2008. It was originally going to be a short note in PaleoBios, just noting some of the oddities of sauropod cervical architecture — such as the way that cervical ribs, ventral to the centra, elongate posteriorly but their dorsal counterparts the epipophyses do not.
As so often, the tale grew in the telling, so that a paper we’d initially imagined as a two-or-three-page note became Chapter 5 of my dissertation under the sober title of “Vertebral morphology and the evolution of long necks in sauropod dinosaurs”, weighing in at 41 1.5-spaced pages. By now the manuscript had metastatised into a comparison between the necks of sauropods and other animals and an analysis of the factors that enabled sauropods to achieve so much more than mammals, birds, other theropods and pterosaurs.
(At this point we had one of our less satisfactory reviewing experiences. We sent the manuscript to a respected journal, where it wasn’t even sent out to reviewers until more than a month had passed. We then had to repeatedly prod the editor before anything else happened. Eventually, two reviews came back: one of them careful and detailed; but the other, which we’d waited five months for, dismissed our 53-page manuscript in 108 words. So two words per page, or about 2/3 of a word per day of review time. But let’s not dwell on that.)
This work made its next appearance as my talk at SVPCA 2010 in Cambridge, under the title Why giraffes have such short necks. For the talk, I radically restructured the material into a form that had a stronger narrative — a process that involved a lot of back and forth with Matt, dry-running the talk, and workshopping the order in which ideas were presented. The talk seemed to go down well, and we liked the new structure so much more than the old that we reworked the manuscript into a form that more closely resembled the talk.
That’s the version of the manuscript that we perfected in New York when we should have been at all-you-can-eat sushi places. It’s the version that we submitted on the train from New York to New Haven as we went to visit the collections of the Yale Peabody Museum. And it’s the version that was cursorily rejected from mid-to-low ranked palaeo journal because a reviewer said “The manuscript reads as a long “story” instead of a scientific manuscript” — which was of course precisely what we’d intended.
Needless to say, it was deeply disheartening to have had what we were convinced was a good paper rejected twice from journals, at a cost of three years’ delay, on the basis of these reviews. One option would have been to put the manuscript back into the conventional “scientific paper” straitjacket for the second journal’s benefit. But no. We were not going to invest more work to make the paper less good. We decided to keep it in its current, more readable, form and to find a journal that likes it on that basis.
At the moment, the plan is to send it to PeerJ when that opens to submissions. (Both Matt and I are already members.) But that three-years-and-rolling delay really rankles, and we both felt that it wasn’t serving science to keep the paper locked up until it finally makes it into a journal — hence the deposition in arXiv which we plan to talk about more next time.
In the paper, we review seven characteristics of sauropod anatomy that facilitated the evolution of long necks: absolutely large body size; quadrupedal stance; proportionally small, light head; large number of cervical vertebrae; elongation of cervical vertebrae; air-sac system; and vertebral pneumaticity. And we show that giraffes have only two of these seven features. (Ostriches do the next best, with five, but they are defeated by their feeble absolute size.)
The paper incorporates some material from SV-POW! posts, including Sauropods were corn-on-the-cob, not shish kebabs. In fact, come to think of it, we should have cited that post as a source. Oh well. We do cite one SV-POW! post: Darren’s Invading the postzyg, which at the time of writing is the only published-in-any-sense source for pneumaticity invading cervical postzygapogyses from the medial surface.
As for the non-extended epipophyses that kicked the whole project off: we did illustrate how they could look, and discussed why they would seem to make mechanical sense:
But we found and explained some good reasons why this apparently appealing arrangement would not work. You’ll need to read the paper for details.
Sadly, we were not able to include this slide from the talk illustrating the consequences:
Anyway, go and read the paper! It’s freely available, of course, like all arXiv depositions, and in particular uses the permissive Creative Commons Attribution (CC BY) licence. We have assembled related information over on this page, including full-resolution versions of all the figures.
In the fields of maths, physics and computer science, where deposition in arXiv is ubiquitous, standard practice is to go right ahead and cite works in arXiv as soon as they’re available, rather than waiting for them to appear in journals. We will be happy for the same to happen with our paper: if it contains information that’s of value to you, then feel free to cite the arXiv version.
September 25, 2012
Another extraordinary specimen from the wonderful Oxford University Museum of Natural History: the skeleton of a goliath frog Conraua goliath, the largest extant anuran, which comfortably exceeds 30 cm and 3 kg in life:
As noted by sometime SV-POW!sketeer Darren Naish over on Tetrapod Zoology, frogs have stupidly weird skeletons — surely the most derived of any tetrapod, despite their lowly, early diverging “amphibian” status. Rather than describe all the oddities myself, I’ll just quote Darren’s article:
Anurans have (at most) nine presacral vertebrae, and some have as few as five; ribs are either highly reduced or absent; the radius and ulna are fused (forming the radioulna); the bones of the pectoral girdle are highly reduced and complimented by an assortment of new weird bits; the pelvis consists of a rod-like central unit (the urostyle) surrounded by two super-long, shaft-like ilia; and in their (generally) elongate hindlimbs, the tibia and fibula are fused (forming the tibiofibula) while the ankle bones are elongated to form a long ‘extra’ limb segment.
That’s a pretty astonishing list; and, sure enough, frog skeletons weird me out every time I see them. (Of all the dead animals I’d like to get hold of in decent condition, to extract the bones from, frogs miss the top of the list only to bats, crocs and turtles. And maybe raptors.)
This particular species of frog has another skeletal oddity that caught my eye:
As you can see, the humerus is perforated: there is a distinct foramen running down it just behind the anterior edge. Is the anterior bar a partially detached deltopectoral crest? Or is it a completely novel ossification that has become partially fused to the humerus?
For what it’s worth, this feature doesn’t seem to be consistently present in goliath frogs. A bit of googling shows that it’s present in this skeleton, but not in this one from Bone Clones. The humerus of the latter does have a distinctly protruding deltopectoral crest, but it lacks the perforation. So I guess that is evidence against the Novel Ossification hypothesis.
Does anyone know more about this odd feature? Does it develop through ontogeny? Is it found in other frogs? What is its mechanical significance?
September 21, 2012
In a comment on the previous post, Emily Willoughby links to an excellent post on her own blog that discusses the “necks lie” problem in herons. Most extraordinarily, here are two photos of what seems to be the same individual:
You should get over to Emily’s blog right now and read her article. (Kudos, too, for the Portal reference in the title. I’ve been playing Portal and Portal 2 obsessively for the last week. Quite brilliant, and a very rare example of true innovation in computer gaming.)
Also of interest: this composite of two shoebill (Balaeniceps rex) individuals, which I made from two of the images mentioned in a comment by AL on Emily’s post:
Oh, birds, you crazy creatures!
September 20, 2012
Back when we were at Cambridge for the 2010 SVPCA, we saw taxidermied and skeletonised hoatzins, and were struck that the cervical skeleton was so very much longer than the neck as it appears in life — because necks lie. At Oxford last week for the 2012 SVPCA, we saw a similar pair of hoatzin mounts (one adult, one juvenile) that clarified the situation:
And here is juvenile in side-view:
As you can see, it’s folding its neck way down out of the way, so that externally it appears much shorter. (And comparing with the Cambridge specimen, you can see that the neck skeleton is proportionally much longer than this in adult.)
Why does it do this? I have no idea.
But I do know it’s not unique to hoatzins. Another nice illustration of how misleading birds’ necks are when viewed in a live animal is this parrot (probably Amazona ochrocephala) in the Natuurhistorisch Museum of Rotterdam (from this Love in the Time of Chasmosaurs post):
One thing that’s not clear to me is how much of the neck the bird can extend in life. If the parrot wants to uncoil all that spare cervical skeleton to reach upwards or forwards, can it? Will the soft tissue envelope allow it? My guess is not, otherwise you’d surely see them doing it. But then … why is all that neck in there at all?
September 18, 2012
Friday evening I was in a pub with Mike, Darren, John Conway, and Emma Lawlor. We were killing time waiting for the Pink Giraffe Chinese restaurant down the street to open. I was chatting with John about “All Todays”, his speculative presentation with Cevdet Kosemen (a.k.a. Nemo Ramjet) on how future sentients might reconstruct Holocene animals if they were known only from fossils. Like his “All Yesterdays” presentation last year, John’s flights of scientific fancy had fired my imagination and gotten me thinking about how paleontology forms sort of a skin or membrane between the bubble of what we know and the surrounding ocean of what we don’t. I decided that we should pass a pad around and each sketch a speculative sauropod.
My own entry is based on the holotype of Mamenchisaurus hochuanensis, which was found almost complete except for the skull (naturally) and forelimbs. I have often joked that diplodocids were basically bipeds whose forelimbs happened to reach the ground. Mamenchisaurs were probably not that back-heavy, but their presacral vertebrae were extremely pneumatic and if our hypothetical future paleontologists had no other sauropod material to work with, I think it’s possible that they would reconstruct the M. hochuanensis holotype as a biped.
I’m not sure there’s much to say about Mike’s brachiosaur, beyond the Ebert-like observation that if a brachiosaur dressed up in a coat and top hat and went cruising for dames, this, I am forced to conclude, is more or less how it would look.
John Conway also drew a mamenchisaur, this time Mamenchisaurus youngi with its bizarrely bent-back sacrum. John’s explanation for the weird sacrum brings to mind ground sloths and–for those who saw “All Yesterdays” at SVPCA 2011–a certain black-feathered therizinosaur. I’d also like to note that he knocked this out in about 5 minutes, thus demonstrating the difference between a professional artist and a mere doodler like myself.
Darren’s hindlimb-less sauropod complements my bipedal Mamenchisaurus. Here the animal, evidently known from only the front half of the skeleton, has been restored as a giant bird. Dig the giant thumb claws and spreading metapodials. Surely, you say, future paleontologists of any species or machine culture would know a pectoral girdle when they saw one. But I’ll bet a sauropod scapulocoracoid could pass for an ilium, if said future paleontologists were still in the early stages of understanding the morphology and diversity of vertebrates. Remember that Seeley described the sauropod Ornithopsis as “a gigantic animal of the pterodactyle kind” based on its pneumatic vertebrae. There is also a long and honorable (?) tradition of mistaking sauropods for hadrosaurs (Sonorasaurus), theropods (Bruhathkayosaurus), and tree trunks (Sauroposeidon), so don’t be too quick to rule this out.
What I want to see next is a skeletal reconstruction of Darren’s sauro-bird, using only elements from the front half of a sauropod skeleton. Anyone want to give it a shot?
Our penultimate entry is Emma’s rendering of an evil bastard snake devouring an innocent baby sauropod. Tragically this one is not speculative–we have very good fossil evidence that the scene shown here really happened, probably a lot. She tried to make it up to us with a smiley face on the next page, but it was too late. We were so depressed after this that we could barely choke down four courses of excellent Chinese food.
One more for the road: a totally new depiction of the enigmatic sauropod Xenoposeidon by yours truly. I expect to see this incorporated into future talks and papers dealing with European sauropod diversity in the Early Cretaceous. Just credit me as you normally would.
That’s all, folks. I hope that speculative sauropod sketches get to be a Thing, and that we see lots more of them from future conferences.