Academics on archosaurs: Tom Holtz
May 16, 2012
Here’s where I thought Dave Hone’s Academics on Archosaurs series was going:
Be honest: aren’t you just a little disappointed that it’s not?
[The actual Tom Holtz article is here. The images that I used to build this one were stolen from here (by Nima), here (uncredited) and here (also uncredited).]
Plateosaurus engelhardti (originally P. trossingensis) SMNS 13200 cervical vertebrae 3-8 in left lateral view. C8 is roughly 15 cm long.
In the recent post on serial variation in sauropod cervicals, I wrote:
Even in ‘adult’ sauropods like the big mounted Apatosaurus and Diplodocus skeletons, the anterior cervicals are less complex than the posterior ones. Compared to posterior cervicals, anterior cervicals tend to have simpler pneumatic fossae and foramina, fewer laminae, and unsplit rather than bifid spines. In all of these things the anterior cervicals are similar to those of juveniles of the same taxa, and to those of adults of more basal taxa. This is also true in prosauropods–in Plateosaurus, the full complement of vertebral laminae is not present until about halfway down the neck.
I was working from memory there and actually understated things a bit. Plateosaurus presacral vertebrae don’t have well-developed spinal laminae, but they do eventually get the four major diapophyseal laminae–the anterior centrodiapophyseal lamina (ACDL), posterior centrodiapophyseal lamina (PCDL), prezygodiapophyseal lamina (PRDL), and postzygodiapophyseal lamina (PODL–please see the lamina tutorial if you need a refresher on these and the other 15 commonly identified laminae). But they aren’t all present halfway down the neck–the ACDL doesn’t really show up until the cervicodorsal transition. The other three kick in sequentially down the neck, as shown in the above image. I think that’s pretty cool, that you get different character states expressed at different points along the neck, in one individual organism, at one time. And possibly also at different times–in sauropods, the anterior cervicals tend to look more ‘juvenile’ or ‘primitive’, even in adult animals, so all of the cervicals go through a juvenile stage, but not all of them grow out of it. I don’t know if there’s a word for that–some kind of serial heterochronotopomorphy or the like–but hopefully someone will enlighten me.
I took the original photo in the collections at the Staatliches Museum für Naturkunde Stuttgart in the spring of 2004. Markus Moser and Rainer Schoch were wonderful hosts during my visit. Mike did all the work of turning the raw photo into a figure, so thanks to him for getting this off my hard drive and out into the world.
The sacrum of Brachiosaurus
May 12, 2012
In my 2009 brachiosaur paper, I gave rather short shrift to the sacrum of Brachiosaurus — in part because there is no really good sacrum of Giraffatitan to compare it to. Also my own photos of the sacrum, taken back before I figured out how to photograph big bones, are all pretty terrible.
Happily, Phil Mannion took some much better photos and gave us permission to use them. So I prepared this multi-view figure, which we plan to use in a forthcoming paper about another sacrum:
At the bottom, we have the sacrum in left lateral view; above it, in dorsal view. To the left is the anterior view (with dorsal to the right) and the right is the posterior view (with dorsal to the left). The idea of this composition is that you could print the image out, and cut and fold it into a cuboid. (In fact I might just do that.)
As usual with these things, click through for the much more impressive full-resolution version (3809 x 3157 pixels).
Filter-then-publish vs. publish-then-filter
May 10, 2012
How things have always been
Traditional scientific journals ask peer-reviewers to do two things: assess whether a manuscript is scientifically sound, and judge whether it’s sufficiently important to appear in the particular journal it’s been submitted to.
So I could have sent my 2009 paper on Brachiosaurus to Nature, and the reviewers would (presumably) have said “this is good science, but not exciting or sexy enough for Nature“. My article would have been filtered out of Nature, which after all is very limited for space. Instead, I sent it to the Journal of Vertebrate Paleontology, where the exciting-and-sexy bar is calibrated differently, and it passed both halves of the peer-review test.
Enter PLoS
The great insight of PLoS ONE was to recognise the two-pronged nature of peer-review, and to tease them apart by discarding the second prong completely. Its guidelines for reviewers are clear:
Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of ‘importance’ required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. Once the work is published in PLoS ONE, the broader community is then able to discuss and evaluate the significance of the article (through the number of citations it attracts; the downloads it achieves; the media and blog coverage it receives; and the post-publication Notes, Comments and Ratings that it receives on PLoS ONE etc).
I like to think of this as “kill ’em all and let God sort it out”, but a less colourful description that has caught on is “publish then filter“. This name contrasts nicely with the traditional model, which can be called “filter then publish“.
The models compared
On the whole, traditionalists prefer the older model, because when filtering is done in advance by professionals it saves them from having to do their own filtering.
Or does it?
No.
There was a time when it probably did: when to keep up with a field, it would be sufficient to read (or at least scan) the articles in a handful of the discipline’s top journals. But those days are long gone. I took a random selection of ten PDFs from my own library, and checked what journals they were in. In that sample, only a single journal came up more than once: there were two papers from Acta Paleontologica Polonica. The others were from Acta Geologica Sinica, the Anatomical Record, Animal Behaviour, Comparative Biochemistry and Physiology, Herpetological Conservation and Biology, the Journal of Vertebrate Paleontology and the Quarterly Journal of the Geological Society, plus a dissertation from the University of Flensburg. (And I am one of the most narrowly focussed researchers you could meet.)
In the face of such a flood of information, no-one can read everything that’s made it through the filters into all their favourite journals. So in practice what actually happens is that each of us filters again — finding relevant publications in a huge range of journals by the social web we’re in: mailing lists, blogs, Twitter, and so on. I believe some people even use FaceBook.
A tentative conclusion
So the real choice is between publish-then-filter or filter-then-publish-then-filter.
Put that way, I’m not sure I see very much value in that first filtering phase. I know it’s going to let through a ton of stuff that I don’t care about — all the palaeobotany papers in Palaeontologia Electronica, for example. But that pre-filter is also bound to stop a lot of stuff that I would care about if it were published. If JVP rejects someone’s unexciting paper on a partial Brachiosaurus specimen because it’s not sufficiently exciting, that may be good for the journal’s “prestige” (whatever that means) but it certainly doesn’t serve me as a researcher: I want all known specimens to be published.
So I am coming round to thinking that the PLoS way is best: if a paper is good science, then why even bother thinking about its likely impact? It’s not like that’s something we can expect to guess accurately, anyway. Just publish it and let the ashes fall where they may. The world will figure out for itself whether it’s worth reading and citing.
Don’t write “exhibit” when you mean “have”
May 8, 2012
Question. I am supposed to be meeting up with Mike Taylor at the conference, but we’ve not met before and I won’t recognise him. Do you know what he looks like?
Candidate Answer #1. He’s a bit overweight and has white hair.
Candidate Answer #2. He exhibits mild to moderate abdominal hypertrophy and accelerated ontogenetic degradation in the pigmentation of the cranial integument.
You wouldn’t use answer #2 in Real Life, so don’t use it in your papers. It’s not big, and it’s not clever.
Dimensions of the mounted Rapetosaurus skeleton
May 5, 2012
Thanks to the kind offices of the folks at the Field Museum, especially Fossil Vertebrates collection manager Bill Simpson, on Wednesday I got to hop the fence and spend some quality time with FMNH PR 2209, the mounted holotype specimen of Rapetosaurus krausei. I took a tape measure with me, to get some dimensions from the mounted skeleton. Of course I have the detailed descriptive paper (Curry-Rogers 2009), but mounted skeletons are three-dimensional objects and it is often surprisingly difficult to get a sense of a how a skeleton goes together in three dimensions from pictures and measurements of the individual elements. And if these dimensions are not precisely those of the animal in life, because of assumptions made during mounting–concerning, say, cartilage thickness between bones, or the angles of the ribs–at least they’re a starting point for understanding the whole-body proportions of Rapetosaurus.
This is valuable because AFAIK this specimen is the only mounted titanosaur in North America, and maybe the only one outside of South America and China. [UPDATE: Alert commenters pointed out that I forgot about the Opisthocoelicaudia in Warsaw, which is almost entirely real, and the Argentinosaurus in Georgia, which is almost entirely fake.] And because Rapetosaurus is far out, man. ALL of the neural arches are unfused, even in the distal caudals–even the Arundel Astrodon (formerly Pleurocoelus) material has fused arches in the distal caudals (Wedel et al. 2000: fig. 15). So it’s a very young juvenile, but the neck is already more than twice the length of the body. I say ‘already’ because there is pretty good evidence that the cervical vertebrae grew proportionally longer over the course of ontogeny in at least some sauropods (Wedel et al. 2000:368-369). The neck is 336 cm long, and the femora are 69 cm long. If we isometrically scaled this animal up to have a 2-meter femur, the neck would be 10 meters long, without any such ontogenetic telescoping of the vertebrae. The implications of this for possible neck lengths in the supergiant titanosaurs are pretty darned interesting. The vertebrae of Rapetosaurus don’t really look anything like those of Argentinosaurus. Nevertheless, a sauropod with an Argentinosaurus-sized femur (2.5 meters for the largest known) and Rapetosaurus proportions would have a 12-meter neck–again, that’s assuming this very young Rapetosaurus already has adult proportions, when in fact it may be ontogenetically short-necked (now there’s a thought). In Apatosaurus and Camarasaurus, the cervicals grew in proportional length (i.e., relative to diameter) by 30-50% over ontogeny, but that’s starting from tiny baby vertebrae. The Rapetosaurus vertebrae are already very long, proportionally, but it is interesting to consider the possibilities that they might have been even longer in adults, and that that scaling might have been shared with other titanosaurs.
The tail in this mount is oddly short. Only about every third vertebra is real, with the rest sculpted, so the tail length inevitably depends on how many intermediary vertebrae were added. But unless there are a LOT of missing vertebrae, it’s probably not far off. I can tell you that when I first saw the mount I looked at the tail and said, “No way”. But up close, seeing the real vertebrae and the interspersed intermediates, it looked pretty reasonable, in part because the individual caudal vertebrae are proportionally short. This is one of those things where we may just have to wait for more and better material–although that might be a long wait, because this skeleton is already freakin’ gorgeous. For someone who is used to dealing with hideously incomplete and groadily distorted fossils, this Rapetosaurus material is just mouth-wateringly beautiful.
There’s loads more weird stuff to talk about, like how the cervical vertebrae are taller than the dorsals, which is opposite the condition in every other sauropod I’ve gotten to look at, and the shape of the ilium, and the conformation of the rib cage, but those will all have to wait for future posts. This one is already much longer than I intended it to be (standard).
For the curious, here are all of my measurements. Neck length, dorsal length, etc. are lengths of those sections of the column as mounted–that is, including both the vertebrae and the spaces between them. I haven’t compared any of these to the published measurements, these are straight from the tape measure to my notebook to you. I’m giving them in mm, because that’s what I naturally think in, but they’re all rounded to the nearest cm because given my methods–hand-holding a physical tape measure up next to a bone while I crouch contorted under a fragile mounted skeleton–giving measurements to the nearest mm would be illusory precision.
- Skull length: 290
- Neck length: 3360
- Dorsal length: 1210
- Sacrum length: 480
- Tail length: 1720
- Total length of skeleton, snout to tip of tail (sum of above): 7060
- Glenoid height (ground to top of socket): L – 1110 (forefoot off floor by a few cm), R – 1080
- Acetabular height (ground to top of socket): 1320 on both sides
- Max height of body (ground to top of 5th sacral spine): 1630
- Gleno-acetabular distance: L – 1500, R – 1440
- Width across acetabula: 440 between weight-bearing centers, 470 to outer margins of ilia
- With across glenoids (at bottom of scap-coracoid joints): 710
- Femur length: 690 on both sides
- Tib/fib length: 470 on both sides
- Vertical height of foot: L – 90, R – 120 (different poses)
- Humerus length: L – 530, R – 500
- Radius/ulna length (between articular surfaces, not including olecranons): L – 370, R – 360
- Metacarpus length (MT3): 190 on both sides
References
- Curry Rogers, Kristina. 2009. The postcranial osteology of Rapetosaurus krausei (Sauropoda: Titanosauria) from the Late Cretaceous of Madagascar. Journal of Vertebrate Paleontology 29:1046-1086.
- Wedel, Mathew J., Richard L. Cifelli and R. Kent Sanders. 2000. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4): 343-388.
The speed that things are happening at the moment is astonishing.
Whenever we talk about the economics of open access — when I argue that it costs the community eight times as much to publish a paywalled article with Elsevier as it does to publish it as open access with PLoS ONE — I always hear the same argument in response. And it’s a good argument. It goes like this:
Yes, the total cost to libraries around the world of an Elsevier article may be eight times the cost to the author of publishing an open-access article that is free to read. But you can only expect to save that money if libraries cancel their Elsevier subscriptions and plough that money into funding open-access publications instead. And no library will ever do that, because the researchers that they serve need the subscriptions.
Well, it turns out — somewhat to my own surprise, I’ll admit — that libraries will cancel their Elsevier subscriptions. The Department of Mathematics at the Technical University of Munich has just voted to do exactly that:
Because of unsustainable subscription prices and conditions, the board of directors of the mathematics department has voted to cancel all of its subscriptions to Elsevier journals by 2013.
So what does this mean? A lot of things.
1. This is no idle far-in-the-future threat: 2013 is only one year away! So this is an actual policy. Something that they’re going to do.
2. Universities are not messing about. When Harvard say they can’t afford subscriptions, they probably mean it — it’s not just a negotiating tactic.
3. Where one university department leads, others will probably follow. Maybe initially it will be mostly maths departments in other universities; maybe it will be other departments of the Technical University of Munich; maybe it will be all of Harvard.
4. So far, this announcement is only about cancelling subscriptions and says nothing about open access. If that’s all they do, it will be a mere cost-saving exercise and a missed opportunity. To be truly transformational, the department needs to channel a significant chunk of its subscription savings into funding Gold OA publications.
5. Publishers who are paying attention will surely start to realise that they have pushed their exploitative prices too far, and that they don’t hold libraries in a steely grip any more. I wonder how this will play into investment advice regarding Elsevier?
This isn’t the kind of problem that can be fixed by hiring a PR person. I’ve argued this before, but if Elsevier are going to survive, they’ll need to be much clearer in the their communications, eliminate practices that alienate authors, and ultimately change their business model entirely.
For more on the Munich development (interesting more for the comments they may generate than for carrying much additional information):
Yesterday, David Willetts, the UK government’s Minister for Universities and Science, gave a speech at the annual general meeting of the Publisher’s Association. The full text of the speech is online and very well worth reading, though it’s long. He Gets It.
Also well worth reading (instead of the speech if you’re pushed for time) is Stephen Curry’s excellent analysis of the key points, which is almost word-for-word the post I would have had to write here if Stephen hadn’t already done such a fine job.
And for those who don’t have the time or inclination even to read that, the TL;DR is that Willetts understands the scientific publishing process, has been an author himself, recognises the value of publishers and their economic contribution to the UK, and generally has a good grasp of all sides of the issue; and that, from that perspective, he is absolutely clear that open access will happen in Britain, and that the goal is for that to be part of a collaborative international transition.
Some highlights from the speech, without further comment:
“Our starting point is very simple. The Coalition is committed to the principle of public access to publicly-funded research results. That is where both technology and contemporary culture are taking us. It is how we can maximise the value and impact generated by our excellent research base.”
“A pay wall … creates a barrier between the academic community and the rest of us, which is deeply unhealthy.”
“[The subscription] funding model is surely going to have to change even beyond the positive transition to open access and hybrid journals that’s already underway. To try to preserve the old model is the wrong battle to fight.”
“Provided we all recognise that open access is on its way, we can then work together to ensure that the valuable functions you [i.e. publishers] carry out continue to be properly funded.”
“The debate on open access will inform HEFCE’s planning for the research excellence process that succeeds the current one which concludes in 2014. Open access could be among the excellence criteria for qualifying articles in the future.”
That last point is crucial, of course. It ties into Harvard’s goal to “move prestige to open access“.
Very exciting times!
MOLD-A-RAMA
May 3, 2012
I’m in Chicago, visiting the Field Museum, which means two things: Brachiosaurus (see below), and Mold-A-Rama. Downstairs from the great hall, on the ground floor, they have Mold-A-Rama machines, and I cannot resist their siren song.
The Mold-A-Rama is the king of novelty souvenirs. You can keep your stamped pennies, little pewter spoons, hand-painted bells, and refrigerator magnets. None of them is worthy to sully the presence of the awesome Mold-A-Rama. You put in two dollars, and then you get to watch as this hissing, clanking 1950s machine with tubes and wires and lights actually makes your item right in front of your eyes. A few minutes later, BAM, you’re holding a hot, smelly hunk of probably carcinogenic plastic that is so fresh from the mold that it is still a bit soft. You can’t buy that kind of authenticity–except from a Mold-A-Rama.
See that red thing, newly made, still in the bowels of the machine? That is MY T. rex!
This is my first Mold-A-Rama Triceratops. I already have a T. rex from my last visit, way back in 2005, which I can now pass on to my son. I also have a Stegosaurus, a Brontosaurus (shown but not commented on here), and a Trachodon. Yeah, yeah, I know the real animals are known as Apatosaurus and Edmontosaurus these days, but I’m not talking about the real animals. I’m talking about Mold-A-Rama, and trust me, the Mold-A-Rama critters are Brontosaurus and Trachodon. They drag their tails, they live in swamps, they’re cold-blooded and they died out from racial senescence (in about 1975, I think).
Finally, because Mike will straight-up murder me if I post from Chicago without it, here’s your friendly local not-quite-fully-mature mounted holotype specimen of Brachiosaurus:
How Elsevier can save itself, part 3: Hard
May 2, 2012
These are worrying days for barrier-based publishers. In the few days since I posted part 2 of this series, we have yet another major development in the Open Access world: UK Science Minister David Willetts’ announcement that “we will make publicly funded research accessible free of charge to readers”. Exactly what form this will take is not yet clear, but the signs seem to point to an FRPAA-like universal Green-OA mandate for all research funded by the government.
What does this mean for Elsevier and their competitors? It looks to me like a swift and sudden pulling of the rug from under their feet. When Green OA becomes ubiqitous enough that researchers start looking at repositories as a first line of attack rather than the if-all-else-fails option, the need for journal subscriptions will fall away precipitously — and with it, publishers’ revenue streams.
In the face of that prospect, we now come to the third and final part of the How Elsevier Can Save Itself series. (Final, that is, apart form the forthcoming coda on how other publishers should react.) Previously we talked about easy measures and medium measures. These ones are hard. They require vision, courage, and determination.
1. Convert to Gold open access
It sounds radical; it sounds like a Won’t Ever Happen. But, really, what is the alternative? Subscription revenue is on the way out. The signs are everywhere — not just in blogs and on Twitter, but in legislation in the US, in the UK and elsewhere. Publishers reliant on subscription revenue must find another source of income or they will crash.
This may seem so obvious that it doesn’t need saying. Unfortunately for Elsevier, a there’s a steady stream of no-we’re-not-sinking denialism issuing from venues such as the Scholarly Kitchen, and because that’s what publishers want to hear, they might fall into the trap of believing it because they want to. (I have a vision of a world ten years hence when open access is all but universal; somewhere in the mid-west, Kent Anderson and David Crotty(*) have locked themselves into a underground bunker with a supply of tinned food and bottled water, and spend their days writing blog-posts to each other about how awesome the subscription-and-gatekeeper model is, and how there’s no need for change and how naive all these OA zealots are.)
Let’s assume for the moment that someone at Elsevier can see the oncoming revenue evaporation, and is making plans that go beyond “sell all my stock and get a job in another business”. What revenue streams could be brought online to replace the lost subscriptions?
Well, what are publishers good at? Managing the editorial process; proof-reading and copy-editing; page layout; consistent formatting across a brand; reliable large-scale web-hosting. Those remain valuable services which publishers could charge for.
Guess what? Charging authors for those services is Gold Open Access. It’s the only business model that might still work when Green is pervasive. (Only “might”? Yes; see below.)
2. Support the FRPAA
Wait, what? Didn’t I just say that Green-OA mandates like the FRPAA are going to Eat Elsevier’s Lunch? Yes I did; and yes they are. The thing is, there is nothing Elsevier can do to stop that. The RWA debacle should have taught them that, if they doubted it before.
So what do you do when an unstoppable enemy is charging at you? The judo move is to use that momentum to your own advantage. Or, to switch metaphors, if a train is heading down the track towards you, it’s better to hop on board than to try to stop it.
I can see that this is going to be a hard lesson for a company that’s been used to having its own way since forever. There’s a good chance that it believes in its own invincibility — its manifest destiny, if you will. You know, like Blockbuster, Borders and the News of the World.
But if Elsevier has the agility, there’s an opportunity right now to radically reposition itself as the progressive, author-friendly publisher that listens to what academics want. Given the appalling behaviour that’s got Elsevier into the current situation, it’ll take something dramatic to do that: supporting the FRPAA is the best chance they have, maybe the only chance.
3. Do it now
Here’s why I said that Gold OA is the only business model that might still work when Green is pervasive. Once Green really takes hold, there’s a danger that scholars will lose interest in journals. We’ve already seen this start to happen in maths and physics, where pre-prints on arXiv are ubiquitous. In those fields, it’s still considered valuable to get a paper into a “good journal”; but what counts most is getting your work on the pre-print server where people can see and cite it.
This danger is all the more real because of the rise of Altmetrics. A few years back when arXiv was establishing itself, journal impact factor was about the only way of getting a quick-and-dirty measurement of how “good” a paper was. That’s changing; and as it changes, it’s destroying one of the main reasons for the continuing dominance of the journal system as the primary way to share science. I don’t know how quickly Altmetrics are going to grow in influence, how well they can be designed to avoid gaming, or indeed whether the whole initiative will crash and burn. But I do know that I’m more likely to tell people that our neck-posture paper has been cited 37 times than that it was in a journal with impact factor 1.949. Because what a paper actually does is more important than where it hangs out.
So the spectre hanging over Elsevier isn’t just the destruction of their subscription model, but the possibility that by the time they get into gear and switch to Gold OA, it’ll all be over and the world will have lost interest in journals. Certainly if university libraries start redirecting their saved subscription money towards in-house publishing efforts, the chances of that will increase dramatically.
This might not happen. Inertia surrounding the journal system, and bean-counters’ ingrained love for impact factors, might be enough to keep journals alive and important, with Green OA and in-house publishing remaining second-tier. But it might. If I was Mister Elsevier, I wouldn’t be betting the farm on it.
What won’t help
A quick word on two things Elsevier could do that I have not mentioned in this series — because I don’t think they will make any difference in the long term:
- Reducing subscription prices.
- Unbundling subscriptions from their “Big Deals”.
Yes, I know that these moves would address two of the three complaints of the Cost of Knowledge boycott. But in the end I think they’re red herrings. All they do is make the current system of barriers marginally less unpalatable. And that’s like patching holes in the Titanic, because the ship is going down.
The challenge is to re-tool for a world where barriers won’t make money. Because that is not a strategy that can keep working. It just isn’t.
Can they do it?
I said at the start that, while the changes outlined in earlier posts are no-brainers, or at least only moderately difficult, these ones will require vision, courage, and determination. I think Elsevier has people with those qualities. Unfortunately, it also has a massive amount of institutional inertia. It’s hard to steer a supertanker. Even when it’s heading straight for the rocks, there are going to be plenty of people whose attitude is: heck, we’re a supertanker — we don’t need to be worried about a bunch of stinkin’ rocks.
So I’d like to think they can do it. But my head says probably not. And as Clay Shirky points out, “You’re gonna miss us when we’re gone!” is not much of a business model.
(*) My mistake: I was thinking of David Wojick here — not David Crotty, who is much more reasonable. I’m not fixing this now because it would change the interpretation of some of the comments below.
Sauropod Vertebra Picture of the Week 