January 31, 2013
You may remember this:
…which I used to make this:
…and then this:
The middle image is just the skeleton from the top photo cut out from the background and dropped to black using ‘Levels’ in GIMP, with the chevrons scooted up to close the gap imposed by the mounting bar.
The bottom image is the same thing tweaked a bit to repose the skeleton and get rid of some perspective distortion on the limbs. The limb posture is an attempt to reproduce an elephant step cycle from Muybridge.
That neck is wacky. Maybe not as wrong as Omeisaurus, but pretty darned wrong. As I mentioned in the previous Rapetosaurus skeleton post, the cervicals are taller than the dorsals, which is opposite the condition in every other sauropod I’ve seen. All in all, I find the reposed Rapetosaurus disturbingly horse-like. And oddly slender through the torso, dorsoventrally at least. The dorsal ribs look short in these lateral views because they’re mounted at a very odd, laterally-projecting angle that I think is probably not correct. But the ventral body profile still had to meet the distal ends of the pubes and ischia, which really can’t go anywhere without disarticulating the ilia from the sacrum (and cranking the pubes down would only force the distal ends of the ilia up, even closer to the tail–the animal still had to run its digestive and urogenital pipes through there!). So the torso was deeper than these ribs suggest, but it was still not super-deep. Contrast this with Opisthocoelicaudia, where the pubes stick down past the knees–now that was a tubby sauropod. Then again, Alamosaurus has been reconstructed with a similarly compact torso compared to its limbs–see the sketched-in ventral body profile in the skeletal recon from Lehman and Coulson (2002: figure 11).
I intend to post more photos of the mount, including some close-ups and some from different angles, and talk more about how the animal was shaped in life. And hopefully soon, because history has shown that if I don’t strike while the iron is hot, it might be a while before I get back to it. For example, I originally intended this post to follow the last Rapetosaurus skeleton post by about a week. So much for that!
Like everything else we post, these images are CC BY, so feel free to take them and use them. If you use them for the basis of anything cool, like a muscle reconstruction or life restoration, let us know and we’ll probably blog it.
Earlier this month I was amazed to see the new paper by Cerda et al. (2012), “Extreme postcranial pneumaticity in sauropod dinosaurs from South America.” The title is dramatic, but the paper delivers the promised extremeness in spades. Almost every figure in the paper is a gobsmacker, starting with Figure 1, which shows pneumatic foramina and cavities in the middle and even distal caudals of Rocasaurus, Neuquensaurus, and Saltasaurus. This is most welcome. Since the 1990s there have been reports of saltasaurs with “spongy bone” in their tail vertebrae, but it hasn’t been clear until now whether that “spongy bone” meant pneumatic air cells or just normal marrow-filled trabecular bone. The answer is air cells, loads of ‘em, way farther down the tail than I expected.
Here’s why this is awesome. Lateral fossae occur in the proximal caudals of lots of neosauropods, maybe most, but only a few taxa go in for really invasive caudal pneumaticity with big internal chambers. In fact, the only other sauropod clade with such extensive pneumaticity so far down the tail are the diplodocines, including Diplodocus, Barosaurus, and Tornieria. But they do things differently, with BIG, “pleurocoel”-type foramina on the lateral surfaces of the centra, leading to BIG–but simple–camerae inside, and vertebral cross-sections that look like I-beams. In contrast, the saltasaurines have numerous small foramina on the centrum and neural arch that lead to complexes of small pneumatic camellae, giving their vertebrae honeycomb cross-sections. So caudal pneumaticity in diplodocines and saltsaurines is convergent in its presence and extent but clade-specific in its development. Pneumaticity doesn’t get much cooler than that.
But it does get a little cooler. Because the stuff in the rest of the paper is even more mind-blowing. Cerda et al. (2012) go on to describe and illustrate–compellingly, with photos–pneumatic cavities in the ilia, scapulae, and coracoids of saltasaurines. And, crucially, these cavities are connected to the outside by pneumatic foramina. This is important. Chambers have been reported in the ilia of several sauropods, mostly somphospondyls but also in the diplodocoid Amazonsaurus. But it hasn’t been clear until now whether those chambers connected to the outside. No patent foramen, no pneumaticity. It seemed unlikely that these sauropods had big marrow-filled vacuities in their ilia–as far as I know, all of the non-pneumatic ilia out there in Tetrapoda are filled with trabecular bone, and big open marrow spaces only occur in the long bones of the limbs. And, as I noted in my 2009 paper, the phylogenetic distribution of iliac chambers is consistent with pneumaticity, in that the chambers are only found in those sauropods that already have sacral pneumaticity (showing that pneumatic diverticula were already loose in their rear ends). But it’s nice to have confirmation.
So, the pneumatic ilia in Rocasaurus, Neuquensaurus, and Saltasaurus are cool because they suggest that all the other big chambers in sauropod ilia were pneumatic as well. And for those of you keeping score at home, that’s another parallel acquisition in Diplodocoidea and Somphospondyli (given the apparent absence of iliac chambers in Camarasaurus and the brachiosaurids, although maybe we should bust open a few brachiosaur ilia just to be sure*).
* I kid, I kid.**
** Seriously, though, if you “drop” one and find some chambers, call me!
But that’s not all. The possibility of pneumatic ilia has been floating around for a while now, and most of us who were aware of the iliac chambers in sauropods probably assumed that eventually someone would find the specimens that would show that they were pneumatic. At least, that was my assumption, and as far as I know no-one ever floated an alternative hypothesis to explain the chambers. But I certainly did not expect pneumaticity in the shoulder girdle. And yet there they are: chambers with associated foramina in the scap and coracoid of Saltasaurus and in the coracoid of Neuquensaurus. Wacky. And extremely important, because this is the first evidence that sauropods had clavicular air sacs like those of theropods and pterosaurs. So either all three clades evolved a shedload of air sacs independently, or the basic layout of the avian respiratory system was already present in the ancestral ornithodiran. I know where I’d put my money.
There’s loads more interesting stuff to talk about, like the fact that the ultra-pneumatic saltasaurines are among the smallest sauropods, or the way that fossae and camerae are evolutionary antecedent to camellae in the vertebrae of sauropods, so maybe we should start looking for fossae and camerae in the girdle bones of other sauropods, or further macroevolutionary parallels in the evolution of pneumaticity in pterosaurs, sauropods, and theropods. Each one of those things could be a blog post or maybe a whole dissertation. But my mind is already thoroughly blown. I’m going to go lie down for a while. Congratulations to Cerda et al. on what is probably the most important paper ever written on sauropod pneumaticity.
- Cerda, I.A., Salgado, L., and Powell, J.E. 2012. Extreme postcranial pneumaticity in sauropod dinosaurs from South America. Palaeontologische Zeitschrift. DOI 10.1007/s12542-012-0140-6
- Janensch, W. 1947. Pneumatizitat bei Wirbeln von Sauropoden und anderen Saurischien. Palaeontographica, Supplement 7, 3:1–25.
- Osborn, H. F. 1899. A skeleton of Diplodocus. Memoirs of the American Museum of Natural History 1:191–214.
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
- 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.
April 21, 2011
[This is a guest post by frequent commenter Heinrich Mallison. Heinrich is maybe best known to SV-POW! readers for his work on digital modelling of sauropodomorphs, though that may change now that his paper on sauropod rearing mechanics is out. Read on ...]
Maybe this post should have been titled “How sauropods breathed, ate, and farted”. Or maybe not. But breathing, eating and fermenting the food will play an important role.
Last week held a special pleasure for me. I spent it in New York, digitizing sauropods bones in the American Museum of Natural History’s Big Bone Room. Treasure trove that this room is, the museum still held something even better: the opening of a new special exhibit titled The World’s Largest Dinosaurs. While all such exhibits are of general interest to me, this one is special. Mark Norell, famous palaeontologist and curator at the AMNH, had a co-curator for this exhibit, Martin Sander of Bonn University, who is the head and speaker of the German Research Foundation Research Unit FOR 533 “Sauropod Biology”. As a member of FOR 533, and having received funding for both my PhD work and my first post-doc project, I am obviously somewhat biased, so please take this into account when you read this report.
The exhibition does not show a large amount of sauropods material. Not that it wouldn’t make for a nice exhibit, as the AMNH’s Hall of Saurischian Dinosaurs doesn’t really have that many sauropods (one Apatosaurus mount, to be exact, with a mashed up Barosaurus vertebral column half-hidden away and a wonderful but obviously depressed “prosauropod”, my old friend Plateosaurus, thrown in to make up a bit for the many, many stinkin’ theropod specimens). But instead of showcasing some of the usually hidden-away bones of the AMNH collection (and believe me, there is some wonderful stuff there), it rather focuses on those parts of the animal that are usually missing: the soft tissues. “How did sauropods get so big?”, or, reversing the question: “Why did and does no other group of terrestrial vertebrates reach such gigantic body sizes?” These were the questions our research group has been busily investigating for the last six years, and the answers to these question are what the exhibit now tries to communicate to the public. And it does so quite successfully!
The centrepiece is a full-sized, fleshed out model of a sauropod (Mamenchisaurus hochuanensis), but on one side the skin and superficial musculature has been cut away. The visitor can see the neck vertebrae, the trachea, the carotid artery, and the ribcage. And the ribcage is also a projection area, on which a video is played that shows the internal organs and how they work.
With a voice-over that explains the actions in simple terms, the principle of the avian-style unidirectional lung and the air sacs is explained (albeit with a small error, as lung physiologist and FOR 533 member Steve Perry was quick to point out – the AMNH has promised to fix things), as well as the basic principles of sauropod reproduction (high number of offspring). Many things are not said or shown here, which is a good thing as it allows for the normal short attention span of the average museum visitor for one piece of exhibit. Instead, interesting stuff like how much fodder a sauropod needed per day (or even per hour), a comparison of a sauropod’s and an elephant’s heart, and of a giraffe’s and a sauropod’s neck vertebra (wow, how light the sauropod one is!) are explored at small science stations spread around the room. I won’t go into a detailed description here, you can find that elsewhere on the web. The AMNH did a blogger’s preview a while ago, and invited the press for a press conference and walk-through of the exhibit with the chance to interview the scientists present on Wednesday, so much info has already been plastered all over the web. Instead, I’ll just show you some pics and talk a bit about the concept of the exhibition, and how various issues were handled that can make or break a show.
One thing is how to catch the attention of visitors and direct it to the content of the exhibit. You don’t want people just going “aw, sh*t! That is one HUGE bone/animal!” and wandering off into the next room. If you want to educate them (and that, may I remind you, is the central purpose of a museum exhibit), you need to get them interested in stuff. Get them to read texts, look at stuff (not just let their eyes wander across it for a few seconds), try to get their brains going. The sauropod exhibit manages this by, first of all, being behind a closed door you can’t see through. Usually, the AMNH halls are accessible either through an open doorway, or in a few cases through glass doors. Secondly, the exhibit, especially the rather confined area you enter first, is dark. Very dark. Again a marked contrast to the AMNH’s usually well-lit halls. Just a few plants greet the visitor, and it takes a second to adjust to the dark – enough time to look around a bit and notice the neck and head of Argentinosaurus (fleshed out model) above.
Next, the visitor is channeled along, with only a very few specimens to catch his attention. Well done, because these few pieces (sauropod leg, Komodo dragon skeleton, human skeleton, etc.) focus on getting the main message across (sauropods = way larger than everything else), aided by the largest animals (or their silhouettes) or various groups painted on the wall. Only once the message has been driven home, as I could detect from the comments I overheard, are the visitors released into the main area that contains the sauropod model and the various detail exhibits around it.
The next thing is giving people time to check things out. If you herd them too much, they will get driven along by the masses. That’s why the larger, opener area around the sauropod model and the smaller bits around it works so well: people can sit down to see the projected videos on the sauropod belly, or they can drift around from one specimen or science station to the next.
The stations are not just glass cabinets with some bones in them. Instead, at many of them you can DO things. One allows you to measure either an adult or baby sauropod femur or your own, and then calculate how heavy a sauropod of that size was. At another you can pump a sauropod’s and an elephant’s lung. One I liked very much simply had an unpainted sauropod model, and two sets each (adult and children height) of oculars. One showed a colorful “show-off” version, the other a “camouflage” one. “Which one is true? We don’t know!” is how I’d paraphrase the text that goes with it. One that innocently hides in the corner is among the most impressive: a 5 ½ ft cube (1.7 m, for the civilized) made from Plexiglas filled with sauropod food. A serving sufficient for one day! On it, also, the various plant groups available in the Mesozoic were rated for various factors, getting an easily understood rating in stars. That’s another big thing: make things easily understandable, visualize them!
With all these things well done, there remains only one more thing: make things fun for kids! And the AMNH did just that by adding a kids’ dinosaur dig. OK, it is one of those cheesy things where you use brushes and stuff to brush sand off fossils (cast), but it was done well enough that kids lined up like there was no tomorrow.
Overall, the exhibit gets two big thumbs up from me. If you make it to NY while it is on, or to any of its future stations, go see it! However, as FOR 533 member Steve Perry was quick to point out: if you’re in it only for the size, you’ll be disappointed! Aside from a few isolated bones, not much of the largest dinosaurs (Argentinosaurus and Amphicoelias) is to be seen in bone. It is the biological details that matter! But don’t get me started about the tail musculature, especially the caudofemoralis, of the big model.
And then, there is the other thing about it that is closely tied to shameless self-promotion: the AMNH did not produce a catalogue or anything similar. Instead, the latest book from the “Life of the Past” series (Editor: James Farlow) of Indiana University Press was presented at the press conference. The lucky reporters all even got a free copy! The title is Biology of the Sauropod Dinosaurs: Understanding the Life of Giants, edited by N. Klein, K. Remes, C. T. Gee and P. M. Sander. And by now, I am sure, you have figured out who the authors are … It is intended to be a summary of the research findings of the first (and part of the second) funding period of FOR 533, and yours truly has two chapters in it. The first doesn’t really give much new information; most is already contained in my two papers here and here. The second, however, presents novel research that didn’t make it into the AMNH exhibit. But hey, why spoil the surprise – go and buy our book!) Overall, it is quite a technical book, so laypeople beware, but we did try to make the research as accessible as possible while retaining a high standard. For the even more technically minded there is the summary of our research group’s work (which cost the DFG ~€6.000.000) to be found in Sander et al. 2010. However, reading that paper is not half as much fun as the book, or the exhibit.
- Sander, P. Martin, Andreas Christian, Marcus Clauss, Regina Fechner, Carole T. Gee, Eva-Maria Griebeler, Hanns-Christian Gunga, Jürgen Hummel, Heinrich Mallison, Steven F. Perry, Holger Preuschoft, Oliver W. M. Rauhut, Kristian Remes, Thomas Tütken, Oliver Wings and Ulrich Witzel. 2010. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews 86:117-155. doi:10.1111/j.1469-185X.2010.00137.x
February 26, 2011
Sorry for the very short post. We have some longer stuff planned, but we’ve been too busy to kick it out this week, and I wanted to leave you with something cool to ponder over the weekend. Here’s the ilium of Giraffatitan overlaid on that of Brontomerus, scaled to the same acetabulum diameter (Giraffatitan is HMN J1, left ilium, modified from Janensch 1961: pl. E, fig. 2; Brontomerus is of course OMNH 66430 from Taylor et al. 2011:fig. 2).
And here’s the same thing comparing Rapetosaurus and Brontomerus (Rapetosaurus is holotype FMNH PR 2209, left ilium, modified from Curry Rogers 2009: fig. 39B). This one was tricky to scale because the ilial margin of the acetabulum is so different in the two taxa.
Here is the same trick performed with the ilium of the canonical pretty basal neosauropod Camarasaurus — specifically, Camarasaurus supremus AMNH 5761 Il. 1, left ilium, modified from Osborn and Mook (1921: fig. 87). In this case, the proportions are so very different that it’s hard to make a meaningful superimposition: we tried to scale to equal acetabulum size, but probably that of the Camarasaurus was proportionally larger than in the other taxa illustrated in this post. Still, here it is:
Finally, in response to Paul Barrett’s comment on a subsequent article, here is a superimposition of the ilium of Alamosaurus on that of Brontomerus:
(Sorry about the poor quality of this one, but the only figure I could find of a complete Alamosaurus ilium was the line-drawing in Lehman and Coulson (2002:fig. 8) — none of the standard descriptive works seem to illustrate a complete or near-complete ilium.)
We had a figure like these in an early draft of the paper, but we ditched it because we felt that doing a broader comparative figure would be more valuable. But I like the kick in the brainpan that these overlays provide.
- 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.
- Janensch, Werner. 1961. Die Gliedmaszen und Gliedmaszengurtel der Sauropoden der Tendaguru-Schichten. Palaeontographica, suppl. 7 (1), teil 3, lief. 4: 177-235.
- Lehman, Thomas M. and Alan B. Coulson. 2002. A juvenile specimen of the sauropod dinosaur Alamosaurus sanjuanensis from the Upper Cretaceous of Big Bend National Park, Texas. Journal of Paleontology 76(1):156-172.
- Osborn, Henry Fairfield, and Charles C. Mook. 1921. Camarasaurus, Amphicoelias and other sauropods of Cope. Memoirs of the American Museum of Natural History, n.s. 3:247-387, and plates LX-LXXXV.
- Taylor, Michael P., Mathew J. Wedel and Richard L. Cifelli. 2011. A new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA. Acta Palaeontologica Polonica 56(1):75-98. doi: 10.4202/app.2010.0073
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.)
December 14, 2010
Over at his truly unique blog Paleo Errata, Jeff Martz is claiming that Stereopairs Are Cool. This assertion he supports with the following figure that he put together, showing a set of five stereopairs of a Longosuchus braincase:
Unfortunately, I am one of those who can’t “see” stereopairs, so these images are uninformative to me — or, at least, no more informative than your average inch-wide braincase photo.
So how else can we envisage the stereo information in these pairs of photos that Jeff took? My favourite way is using red-cyan anaglyphs — those goofy 3d images that you look at through 3d glasses. To compare, I did this to Jeff’s image. The process is simple: take two copies of the stereopair image, cut out all the right-eye views from one set and all the left-eye views from the other, then edit the colour levels of both layers. In one, take the red right down to zero, so you only have blue+green=cyan; in the other take the green and blue down so you only have red. Then stack one layer on top of the other and change its mode to “Lighten only”. Export the result as a JPEG and you get this result:
Armed with my red-cyan glasses (which, remember, I got as a freebie with a Lego catalogue), I can now make out the 3d structure really easily. Positives for the anaglyph approach:
- The 3D image is much easier to see
- The result takes up less space on the page
- Most importantly, the size limitation is removed: I have some beautiful whole-screen anaglyphs (e.g. Archbishop cervical, wallaby skull), whereas stereograms are restricted to a couple of inches’ separation.
The downside is, of course, that you need special equipment to see them –albeit equipment so laughably minimal that Amazon.com will sell you THREE PAIRS for $1.39, you cheap gits. But for those of who who are too poor to find $1.39, and who don’t have two friends with whom you can form an ad-hoc 3D-glasses buying consortium at a cost of $0.47 each, there is one further approach: a low-rent technique that I call a “wigglegram” for want of a better term. Here it is:
I discovered this approach by accident, when flipping through a bunch of photographs that I’d taken of, I think, the Archbishop. As a matter of policy, I take most of my photos twice, so that if I shake slightly or the auto exposure gets it wrong, I have a good copy that I can retain. I was trying to decide which of two nearly identical pictures to keep. But as it happened, I’d moved the camera slightly to the side between taking the first and the second, so as I skipped back and forth between them, I was seeing two slightly different perspectives.
So there you have it: three different ways to visualise 3d structure, each built from the same basic set of photos. They each have their merits, and I hope we’ll increasingly see more of all three of them, as we move into the Shiny Digital Future, and arbitrary limits on manuscript length and numbers of figures get lifted.
I leave y0u with an actual application of all this. Matt and I have, for some time, been working on a manuscript about caudal pneumaticity in sauropods, and we wanted to include a brief survey of which genera it’s been reported in. Among the candidates was Saltasaurus, which has a candidate pneumatic caudal vertebra that was illustrated thus by Powell (2003: plate 53, part 3):
Matt can “see” stereograms, and insisted that the dark patch on the side of the centrum is a pneumatic fossa. I wasn’t so sure, and in fact we got into quite an argument over whether or not to include this specimen in our list. The argument was neatly concluded when I had the obvious idea of converting Powell’s stereogram into an anaglyph:
As soon as I saw this, I recognised what the structure is: the crescent moon-shaped dark patch is indeed a deep, invasive fossa, and the broad, roughly circular object above it and to the right is a lumpen lateral process sticking right out into the camera (and partially hiding the fossa). So Matt was right, the vertebra is pneumatic, and a beautiful friendship was saved by the power of red-cyan anaglyphys. Yay!
- Powell, Jaime E. 2003. Revision of South American Titanosaurid dinosaurs: palaeobiological, palaeobiogeographical and phylogenetic aspects. Records of the Queen Victoria Museum 111: 1-94.
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.
June 11, 2010
By now you’ve probably heard that the entire UC system is threatening to boycott the Nature Publishing Group over unsustainable business practices.*
First, a few links to get you up to speed.
- The original letter, which was an in-house UC document that leaked (possibly deliberately, certainly understandably) and then propagated through academia like the proverbial brushfire.
- Nature Publishing Group’s initial response, which accused the UC of distorting several issues.
- The UC’s rebuttal, which showed that, in fact, they had not, and that NPG was guilty of far worse distortions.
- A Chronicle of Higher Education piece that has some very interesting quotes on the UC side.
- Of all the blogging that has been done on this, the now-infamous Fight Club post seems to be getting the most link-love and discussion, and deservedly so.
- This post and those that follow at The Book of Trogool have some good analysis and more scrumptious links. Also at ScienceBlogs, Janet Stemwedel considers this from the standpoint of junior researchers who need high-profile pubs to survive, and with her usual thoughtfulness and humanity.
* It doesn’t matter whose side you’re on, it’s pretty clear that a 7% markup every year is not sustainable for academic libraries whose budgets are flat, if they’re lucky, or more likely declining. If it really costs NPG 7% more each year to maintain their web access, then they’re doing something wrong. So who does this serve, other than NPG shareholders?
Some of the more interesting points that have come up in the ensuing discussions:
As noted by Janet Stemwedel, it would be very nice if the UC would issue a statement that good scholarship on the part of faculty will be recognized and rewarded no matter where it’s published. I am wholeheartedly in agreement with that, and am only sad that it took something like this to force the issue out into the open. Good work is good work, and the people who need it will generally find it. A lot of the battle over OA is getting hidebound administrators to stop thinking with their pseudoheads and find non-retarded ways to assess the output of their faculty. It shouldn’t be part of the battle over OA, because impact factors are orthogonal to publication model (and to the quality and lasting value of the work). But we all know that publications in Cell, Nature, and Science are the ticket to grants, promotions, and tenure. PLoS is successfully driving a wedge into this, but the battle is far from over.
More than one commenter has noted that there is probably some schadenfreude going on here, as faculty who feel like they are under the gun to publish in high-rejection-rate journals get to fight back a little, and as faculty who are being forced to take pay cuts, furloughs, etc., get to shift their anger from university-internal targets to a visible and little-loved external enemy. I think both hypotheses are accurate, and I suppose that it is not 100% fair for NPG to get pasted with more hate than they have coming, but I don’t really care, because the level of hate they have legitimately earned is already extremely high. In some of the online discussions about the future of newspapers–or rather, the lack of a future for newspapers–someone, somewhere, made the point that when you gouge people for decades, you shouldn’t be surprised when they stand aside and refuse to rescue you as you crash and burn. To my massive irritation, I can’t find that quote right now, but it’s exactly appropriate here. A lot of faculty wouldn’t pee in Nature‘s mouth if its teeth were on fire–and now they may get the chance to withhold that pee.
I’ve seen a few comments to the effect that the proposed boycott would never come to pass because the UC could not get junior faculty, who need those CNS pubs, to play ball. I wouldn’t bet that way. In my experience, junior faculty are far more likely to be attuned to the injustices of the high-stakes, for-profit journal world, and thus the ones most likely to understand what is actually at stake, and to have little sympathy for an outfit that they see as an unsympathetic career gatekeeper. If there is faculty resistance, I expect it to come from tenured folks who’ve benefited from having an inside track at Nature. (I know, I know, everyone from Nature on down claims that the “inside track” is a myth, but does anyone actually believe that?)
Many have noted Keith Yamamoto’s SDFy comments at the end of the Chronicle article: “In many ways it doesn’t matter where the work’s published, because scientists will be able to find it”. All I have to add here is “Hell yeah!” and “Bang on!”
For my part, I’d like to point out something that I have not seen widely discussed, but which seems like it ought to be. A not-for-profit organization–like, say, PLoS–has to maintain its infrastructure, pay its employees, and deliver a service. A corporation has all of those demands, plus the mandate to make a profit. So people can whine all they want that open access publishers still have to charge to do the same work as commercial publishers and that the work will cost about the same, but at the end of the day the commercial publisher is in business to make a profit, and PLoS is in business to make science. Absolutely, we should stop letting commercial publishers sell our own fat asses back to us. We should definitely stop paying any for-profit publisher to line its shareholders’ pockets at our expense. Screw them and the horse they rode in on; that is our freakin’ horse.
The big noise on the Dinosaur Mailing List at the moment is this thread about Rob Gay’s newly self-published book Notes on Early Mesozoic Theropods, which you can buy from print-on-demand house lulu.com. (You can also pay to download a PDF if you prefer.)
The interesting thing about about this book is that it contains nomenclatural acts — specifically it names the new theropod Kayentavenator elysiae. But is this act valid according to the ICZN? Opinions differ. The fact that the work was self-published is irrelevant — the Code simply doesn’t care about that. Beyond this, in the book itself, Gay contends that:
Those that are concerned about the naming of a new genus in this format should not be. The availability and distribution requirements are more than met—the relevant institutions have received a copy for their records. In addition “Notes on Early Mesozoic Theropods” will remain available to all who wish to purchase it online, as well as those stores that chose to carry it, for the foreseeable future—far surpassing the availability of many other high profile publications to those anywhere on the globe.
He feels that this satisfies the relevant articles of the code:
8.1. Criteria to be met. A work must satisfy the following criteria:
- 8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,
- 8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and
- 8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies.
The first thing to say is that Gay would have done himself a favour if his preface had discussed these articles specifically and explained how he felt they were fulfilled: by making only the more general statement above, he’s left matters more open to discussion; or at least forfeited the opportunity to get in a good, strong, opening statement in the inevitable debate.
My own feeling, based on a couple of years on the ICZN mailing list and having witnessed many such discussions between the Commissioners and other specialist nomenclaturists, is that a print-on-demand publication like this does not meet requirement 8.1.3 (“simultaneously obtainable copies by a method that assures numerous identical and durable copies”) — it’s because of this requirement that PLoS ONE has had to adopt its frankly rather silly policy of printing 50 hardcopies of each article it publishes that contains nomenclatural acts, rather than just printing copies on demand for anyone who wants them.
[There has also been some talk on the list about whether this book counts as published under Article 8.6, "Works produced after 1999 by a method that does not employ printing on paper", but there's no room for debate about that. That Article states that such a work "must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself", which is not the case for this book.]
But the real question is: so what? The Commission will never produce a ruling on this — it just doesn’t do that, unless presented with a formal petition to conserve a subsequently published name for the same taxon. So in practice, whatever the code says, the reality is that the validity of the name Kayentavenator elysiae will — like the validity of all other names — be determined by whether and how it actually gets used in subsequent work.
In short, it comes down to this: when the next paper comes out on that animal, will it use Gay’s name, or will the worker in question erect his own name for the same animal and claim that it has priority as the first validly published name?
And that in turn comes down to — let’s be frank — the personality of that next worker. We all know of scientists whose goal seems to be to get their name on as many publications and taxa as possible; we all know others who are more concerned with giving credit where it’s due. It seems strange that something like the effective validity of a zoological name should be determined by a personality, but that’s how it looks.
As a side-issue, the way I read this is that Gay has done himself a huge disfavour by charging a fee to download the PDF version of his book. If he wants his work to be accepted, then the best way is to make sure anyone who is remotely interested can get get hold of it with minimal inconvenience and at zero cost. It may seem odd, but the truth is that Kayentavenator elysiae‘s chances of survival are dependent far more on marketing than on any other factor; so the PDFs should be made freely and easily available.
The sky is falling! The sky is falling!
Tim Williams was one of several commenters on the DML to make this point:
This is a HUGE concern. Especially because advances in technology mean that self-publication is now much cheaper than it used to be. All you need is a computer and a printer, and off you go.
This has been true for some time. If anything, it’s surprising that we don’t see a lot more rogue taxonomy than we do, especially in a field as charismatic as dinosaur palaeontology. For some reason, extant animals seem (so far) to have suffered much more from this than we have — see for example Raymond Hoser, whose self-published taxonomic works have been widely referred to as “taxonomic vandalism” and whose name has been used in the term “Hoser taxonomy”.
I think we’re deluding ourselves if we think this isn’t coming to dinosaur palaeo.
The widely expressed fear is that “anyone, regardless of knowledge and abilities, will be able to create valid taxa without any restraints” (Dan Chure to the DML). Because “when it comes to what constitutes a published work, Article 8 of the ICZN Code is so vague and permissive that it is laughably easy to meet the criteria” (Tim Williams again).
Unfortunately, it’s not a simple matter of tightening the language up. Even if the ICZN didn’t move so agonisingly slowly, it’s not really possible to give a rigorous definition of “valid publication”. You could come up with whatever form of words you wanted, and I (if I were sufficiently unethical) could find a way to make an end-run around it.
In particular, requiring peer-review (while a step in the right direction) would not solve the problem: then you have to define what “peer-review” means, and as we’ve seen in certain articles published in in-house journals in recent years, that concept is also slippery.
Here’s where I think this is going. Ultimately, the validity or otherwise of names is always decided by the working taxonomic (and more broadly biological) community. Until recently, the broader community has been able to delegate the process to journals in most cases, because it was easy to see what a “journal” was: it had a publisher, it was printed on glossy paper, and it came out on a regular schedule. It was easy to see whether a given work was in a journal or not.
That is changing very fast. By most of the criteria above, PLoS ONE is not a “journal” (no publisher but itself, no printing on paper, and no regular schedule) yet I don’t think anyone is going to claim it’s not a journal. Although I think PLoS ONE is a wonderful thing (I’ll be sending my own work there), one of its deleterious side-effects is that it, along with Palaeontologia Electronica and others, has shifted people’s ideas of what is “published”. One can easily imagine, say, a museum setting up its own PLoS-like journal — maybe a reputable one, maybe a less reputable one. From there it’s a short slide to a department, a small group or even an individual setting up his own journal. We have to face the facts that (A) it’s going to be hard to say what is and isn’t a “journal” and (B) we have no way of checking, in general, that “peer-review” is meaningful and adequate.
So I see only two possible paths.
One is that names will get published here, there and everywhere — ultimately even on blogs (although we don’t plan to go down that path here on SV-POW!) — and it will be up to the community to determine what is and isn’t counted as valid.
The other possibility is that a formal name-registration database like ZooBank comes swinging in to save the day, and only registered names are considered valid (or only registered names and those published before, say, 2012).
Unfortunately, ZooBank seems to be the only candidate registration system in town, and it’s in trouble: grotesquely underfunded, the work of basically one person, consequently well behind schedule and by no means ready technically or organisationally to do what it’s intended to do. (I mean no criticism of any individual in saying this, but those are the facts.)
The way forward?
It seems that nomenclatural anarchy is inevitable unless something like ZooBank takes off rapidly. So if I were rich and influential, one of the main things I’d be doing would be to pour that money and influence into ZooBank, getting it up to speed as soon as possible and making sure the infrastructure is in place to handle a lot of regsitrations really quickly. Because the current de facto approach of delegating the assessment of legitimacy to journals is on the way out: I give it less than ten years.
But given that science is chronically underfunded, and zoology funded less than most sciences, and zoological nomenclature less than most of the rest of the zoology, I am not optimistic than this can be made to fly. the bottom line for ZooBank is that it’s not anyone’s full-time or primary job; and until it is, there’s always going to be something else more urgent that pushes out this work that is merely important. (Actually it’s urgent, too, but because the deadlines are soft rather than hard, the urgency isn’t apparent — we’ll just all wake up one day and find that they’ve passed.)
I’m not happy about it, but my prediction is: nomenclatural anarchy. For sure, names published in JVP will start out with a better chance than names published in print-on-demand books at lulu.com, but that’s going to become a sliding scale rather than the clear black-and-white distinction we’ve been used to.
How bad is it?
I don’t know. The truth is that lots of nomenclatural decisions are made by the community already, and somehow we all seem to survive. I recently demonstrated, I thought conclusively, that the species formerly known as “Brachiosaurus” brancai cannot be considered congeneric with the Brachiosaurus type species B. altithorax, and must be considered to belong to its own genus Giraffatitan (Taylor 2009); but whether that reassignment is adopted is for the community to decide over the next few years. I was disappointed to see that Chure et al. (2010), for poorly explained reasons, rejected this name; and I was pleased to see that Sander et al. (2010) accepted it. But only time will tell whether it sticks. And yet, somehow, we survive despite all this uncertainty.
Will it be so terrible if, in the same way, the published works of the community determine which nomenclatural acts are considered validly published? Maybe not.
- Chure, Daniel, Brooks B. Britt, John A. Whitlock and Jeffrey A. Wilson. 2010. First complete sauropod dinosaur skull from the Cretaceous of the Americas and the evolution of sauropod dentition. Naturwissenschaften (online preprint). doi:10.1007/s00114-010-0650-6
- 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.
- Sander, P. Martin, Andreas Christian, Marcus Clauss, Regina Fechner, Carole T. Gee, Eva-Maria Griebeler, Hanns-Christian Gunga, Jürgen Hummel, Heinrich Mallison, Steven F. Perry, Holger Preuschoft, Oliver W. M. Rauhut, Kristian Remes, Thomas Tütken, Oliver Wings and Ulrich Witzel. 2010. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews. 43 pages. doi: 10.1111/j.1469-185X.2010.00137.x
- Taylor, Michael P. 2009a. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.