May 7, 2014
[NOTE: see the updates at the bottom. In summary, there's nothing to see here and I was mistaken in posting this in the first place.]
Elsevier’s War On Access was stepped up last year when they started contacting individual universities to prevent them from letting the world read their research. Today I got this message from a librarian at my university:
The irony that this was sent from the Library’s “Open Access Team” is not lost on me. Added bonus irony: this takedown notification pertains to an article about how openness combats mistrust and secrecy. Well. You’d almost think NPG wants mistrust and secrecy, wouldn’t you? It’s sometimes been noted that by talking so much about Elsevier on this blog, we can appear to be giving other barrier-based publishers a free ride. If we give that impression, it’s not deliberate. By initiating this takedown, Nature Publishing Group has self-identified itself as yet another so-called academic publisher that is in fact an enemy of science. So what next? Anyone who wants a PDF of this (completely trivial) letter can still get one very easily from my own web-site, so in that sense no damage has been done. But it does leave me wondering what the point of the Institutional Repository is. In practice it seems to be a single point of weakness allowing “publishers” to do the maximum amount of damage with a single attack.
But part of me thinks the thing to do is take the accepted manuscript and format it myself in the exact same way as Nature did, and post that. Just because I can. Because the bottom line is that typesetting is the only actual service they offered Andy, Matt and me in exchange for our right to show our work to the world, and that is a trivial service.
The other outcome is that this hardens my determination never to send anything to Nature again. Now it’s not like my research program is likely to turn up tabloid-friendly results anyway, so this is a bit of a null resolution. But you never know: if I happen to stumble across sauropod feather impressions in an overlooked Wealden fossil, then that discovery is going straight to PeerJ, PLOS, BMC, F1000 Research, Frontiers or another open-access publisher, just like all my other work.
And that’s sheer self-interest at work there, just as much as it’s a statement. I will not let my best work be hidden from the world. Why would anyone?
Let’s finish with another outing for this meme-ready image.
David Mainwaring (on Twitter) and James Bisset (in the comment below) both pointed out that I’ve not seen an actual takedown request from NPG — just the takedown notification from my own library. I assumed that the library were doing this in response to hassle from NPG
, but of course it’s possible that my own library’s Open Access Team is unilaterally trying to prevent access to the work of its university’s researchers.
I’ve emailed Lyn Duffy to ask for clarification. In the mean time, NPG’s Grace Baynes has tweeted:
So it looks like this may be even more bizarre than I’d realised.
Further bulletins as events warrant.
OK, consensus is that I read this completely wrong. Matt’s comment below says it best:
I have always understood institutional repositories to be repositories for author’s accepted manuscripts, not for publisher’s formatted versions of record. By that understanding, if you upload the latter, you’re breaking the rules, and basically pitting the repository against the publisher.
Which is, at least, not a nice thing to do to the respository.
So the conclusion is: I was wrong, and there’s nothing to see here apart from me being embarrassed. That’s why I’ve struck through much of the text above. (We try not to actually delete things from this blog, to avoid giving a false history.)
My apologies to Lyn Duffy, who was just doing her job.
This just in from Lyn Duffy, confirming that, as David and James guessed, NPG did not send a takedown notice:
This PDF was removed as part of the standard validation work of the Open Access team and was not prompted by communication from Nature Publishing. We validate every full-text document that is uploaded to Pure to make sure that the publisher permits posting of that version in an institutional repository. Only after validation are full-text documents made publicly available.
In this case we were following the regulations as stated in the Nature Publishing policy about confidentiality and pre-publicity. The policy says, ‘The published version — copyedited and in Nature journal format — may not be posted on any website or preprint server’ (http://www.nature.com/authors/policies/confidentiality.html). In the information for authors about ‘Other material published in Nature’ it says, ‘All articles for all sections of Nature are considered according to our usual conditions of publication’ (http://www.nature.com/nature/authors/gta/others.html#correspondence). We took this to mean that material such as correspondence have the same posting restrictions as other material published by Nature Publishing.
If we have made the wrong decision in this case and you do have permission from Nature Publishing to make the PDF of your correspondence publicly available via an institutional repository, we can upload the PDF to the record.
Open Access Team
Here’s the text of the original notification email so search-engines can pick it up. (If you read the screen-grab above, you can ignore this.)
University of Bristol — Pure
Lyn Duffy has added a comment
Sharing: public databases combat mistrust and secrecy
Farke, A. A., Taylor, M. P. & Wedel, M. J. 22 Oct 2009 In : Nature. 461, 7267, p. 1053
Research output: Contribution to journal › Article
Lyn Duffy has added a comment 7/05/14 10:23
Dear Michael, Apologies for the delay in checking your record. It appears that the document you have uploaded alongside this record is the publishers own version/PDF and making this version openly accessible in Pure is prohibited by the publisher, as a result the document has been removed from the record. In this particular instance the publisher would allow you to make accessible the postprint version of the paper, i.e., the article in the form accepted for publication in the journal following the process of peer review. Please upload an acceptable version of the paper if you have one. If you have any questions about this please get back to us, or send an email directly to firstname.lastname@example.org Kind regards, Lyn Duffy Library Open Access Team.
February 6, 2014
In a recent comment, Doug wrote:
If I want to be a truly educated observer of Tyrannosaurus rex mounts, what 5 things should I look for in a reconstruction to assess if it is true to our current scientific understanding? I’m not talking tail dragging/upright at this point…we are well past that I hope.
If he had asked about Apatosaurus, I could have written him a novel. But it is a point of pride with me not to contribute to the over-application of human attention to T. rex; not only would it be vulgar, it would also be a waste of resources, considering how many people already have that covered. So, you theropod workers and avocational “rexperts”, we’re finally inviting you to the high table. Please, tell us–and Doug–what separates the good T. rex mounts from the crappy ones. Big piles of SV-POW! bucks will be showered on whoever brings the most enlightenment, especially if you adhere to the requested List of 5 Things format.
The comment lines are open–go!
January 15, 2014
[This is part 4 in an ongoing series on our recent PLOS ONE paper on sauropod neck cartilage. See also part 1, part 2, and part 3.]
Here’s a frequently-reproduced quote from Darwin:
About thirty years ago there was much talk that geologists ought only to observe and not theorise; and I well remember some one saying that at this rate a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!
It’s from a letter to Henry Fawcett, dated September 18, 1861, and you can read the whole thing here.
I’ve known this quote for ages, having been introduced to it at Berkeley–a copy used to be taped to the door of the Padian Lab, and may still be. It’s come back to haunt me recently, though. An even stronger version would run something like, “If you don’t know what you’re looking for, you won’t make the observation in the first place!”
For example: I started CT scanning sauropod vertebrae with Rich Cifelli and Kent Sanders back in January, 1998. Back then, I was interested in pneumaticity, so that’s what I looked for, and that’s what I found–work which culminated in Wedel et al. (2000) and Wedel (2003). It wasn’t until earlier this year that I wondered if it would be possible to determine the spacing of articulated vertebrae from CT scans. So everything I’m going to show you, I technically saw 15 years ago, but only in the sense of “it crossed my visual field.” None of it registered at the time, because I wasn’t looking for it.
A corollary I can’t help noting in passing: one of the under-appreciated benefits of expanding your knowledge base is that it allows you to actually make more observations. Many aspects of nature only appear noteworthy once you have a framework in which to see them.
So anyway, the very first specimen we scanned way back when was the most anterior of the three plaster jackets that contain the four cervical vertebrae that make up OMNH 53062, which was destined to become the holotype of Sauroposeidon. I’ve written about the taphonomy of that specimen here, and you can read more about how it was excavated in Wedel and Cifelli (2005). We scanned that jacket first because, although the partial vertebrae it contains are by far the most incomplete of the four, the jacket is a lot smaller and lighter than the other two (which weigh hundreds of pounds apiece). Right away we saw internal chambers in the vertebrae, and that led to all of the pneumaticity work mentioned above.
Happily for me, that first jacket contains not only the posterior two-thirds of the first vertebra (possibly C5), but also the front end of the second vertebra. Whoever decided to plow through the second vertebra to divide the specimen into manageable chunks in the field made a savvy choice. Way back in 2004 I realized that the cut edge of the second vertebra was not obscured by plaster, and therefore the internal structure could be seen and measured directly, which is a lot cleaner than relying on the artifact-heavy CT scans. (The CT scans are noisy because the hospital machines we had access to start to pant a bit when asked to punch x-rays through specimens this large and dense.) A figure derived from that work made it into a couple of papers and this post, and appears again above.
But that’s pneumaticity, which this post is allegedly not about. The cut through the second vertebra was also smart because it left the intervertebral joint intact.
Here are a photo of the jacket and a lateral scout x-ray. The weird rectangles toward the left and right ends of the x-ray are boards built into the bottom of the jacket to strengthen it.
And here’s a closeup of the C5/C6 joint, with the relevant radiographs and tracing. The exciting thing here is that the condyle is centered almost perfectly in the cotyle, and the zygapophyses are in articulation. Together with the lack of disarticulation in the cervical rib bundle (read more about that here and in Wedel et al. 2000), these things suggest to us that the vertebrae are spaced pretty much as they were in life. If so, then the spacing between the vertebrae now tells us the thickness of the soft tissue that separated the vertebrae in life.
I should point out here that we can’t prove that the spacing between the vertebrae is still the same as it was in life. But if some mysterious force moved them closer together or farther apart, it did so (1) without decentering the condyle of C6 within the cotyle of C5, (2) without moving the one surviving zygapophyseal joint out of contact, and (3) without disarticulating the cervical ribs. The cervical ribs were each over 3 meters long in life and they formed vertically-stacked bundles on either side below the vertebrae; that’s a lot of stuff to move just through any hypothetical contraction or expansion of the intervertebral soft tissues after death. In fact, I would not be surprised if the intervertebral soft tissues did contract or expand after death–but I don’t think they moved the vertebrae, which are comparatively immense. The cartilage probably pulled away from the bone as it rotted, allowing sediment in. Certainly every nook and cranny of the specimen is packed with fine-grained sandstone now.
Anyway, barring actual preserved cartilage, this is a best-case scenario for trying to infer intervertebral spacing in a fossil. If articulation of the centra, zygs, and cervical ribs doesn’t indicate legitimate geometry, nothing ever will. So if we’re going to use the fossils to help settle this at all, we’re never going to have a better place to start.
So, by now, you know I’m a doofus. I have been thinking about this problem literally for years and the data I needed to address it was sitting on my hard drive the entire time. One of the things I pondered during those lost years is what the best shape for a concave-to-convex intervertebral joint might be. Would the best spacing be radially constant (A in the figure above), or antero-posteriorly constant (B), or some other, more complicated arrangement? The answer in this case surprised me–although the condyle is a lot smaller in diameter than the cotyle, the anteroposterior separation between them in almost constant, as you can see in part C of the above figure.
Don’t get too worked up about that, though, because the next joint is very different! Here’s the C6/C7 joint, again in a lateral scout x-ray, with the ends of the bones highlighted. Here the condyle is almost as big in diameter as the cotyle, but it is weirdly flat. This isn’t a result of overzealous prep–most of the condyle is still covered in matrix, and I only found its actual extent by looking at the x-ray. This is flatter than most anterior dorsal vertebrae of Apatosaurus–I’ve never seen a sauropod cervical with such a flat condyle. Has anyone else?
The condyle of C6 is a bit flatter than expected, too–certainly a lot flatter than the cervical condyles in Giraffatitan and the BYU Brachiosaurus vertebrae. As we said in the paper,
It is tempting to speculate that the flattened condyles and nearly constant thickness of the intervertebral cartilage are adaptations to bearing weight, which must have been an important consideration in a cervical series more than 11 meters long, no matter how lightly built.
Anyway, obviously here the anteroposterior distance between condyle and cotyle could not have been uniform because they are such different shapes. Wacky. The zygs are missing, so they’re no help, and clearly the condyle is not centered in the cotyle. Whether this posture was attainable in life is debatable; I’ve seen some pretty weird stuff. In any case, we didn’t use this joint for estimating cartilage thickness because we had no reason to trust the results.
Kent Sanders and I had also scanned several of the smaller sauropod vertebrae from the Carnegie collection (basically, the ones that would fit in the trunk of my car for the drive back to Oklahoma). Crucially, we’d scanned a couple of sets of articulated vertebrae, CM 3390 and CM 11339, both from juvenile individuals of Apatosaurus. In both cases, the condyles and cotyles are concentric (that’s what the ‘orthogonal gaps’ are all about in the above figure) and the zygs are in articulation, just as in Sauroposeidon. These are dorsals, so we don’t have any cervical ribs here to provide a third line of evidence that the articulation is legit, but all of the evidence that we do have is at least consistent with that interpretation.
So, here’s an interesting thing: in CM 3390, above, the first dorsal is cranked up pretty sharply compared to the next one, but the condyle is still centered in the cotyle and the zygs are in articulation. Now, the vertebrae have obviously been sheared by taphonomic deformation, but that seems to have affected both vertebrae to the same extent, and it’s hard to imagine some kind of taphonomic pressure moving one vertebra around relative to the next. So I think it’s at least plausible that this range of motion was achievable in life. Using various views and landmarks, we estimate the degree of extension here somewhere between 31 and 36 degrees. That’s a lot more than the ~6 degrees estimated by Stevens and Parrish (1999, 2005). And, as we mentioned in the paper, it nicely reinforces the point made by Upchurch (2000), that flexibility in the anterior dorsals should be taken into account in estimating neck posture and ROM.
Here’s our last specimen, CM 11339. No big surprises here, although if you ever had a hard time visualizing how hyposphenes and hypantra fit together, you can see them in articulation in parts C and D (near the top of the specimen). Once again, by paging through slices we were able to estimate the separation between the vertebrae. Incidentally, the condyle IS centered in the cotyle here, it just doesn’t look that way because the CT slice is at an angle to the joint–see the lateral scout in part A of the figure to see what I mean.
So, what did we find? In Sauroposeidon the spacing between C5 and C6 is 52mm. That’s pretty darn thick in absolute terms–a shade over two inches–but really thin in relative terms–only a little over 4% of the length of each vertebra. In both of the juvenile Apatosaurus specimens, the spacing between the vertebrae was about 14mm (give or take a few because of the inherent thickness of the slices; see the paper for details on these uncertainties).
Now, here’s an interesting thing: we can try to estimate the intervertebral spacing in an adult Apatosaurus in two ways–by scaling up from the juvenile apatosaurus, or by scaling sideways from Sauroposeidon (since a big Apatosaurus was in the same ballpark, size-wise)–and we get similar answers either way.
Scaling sideways from Sauroposeidon (I’m too lazy to write anymore so I’m just copying and pasting from the paper):
Centrum shape is conventionally quantified by Elongation Index (EI), which is defined as the total centrum length divided by the dorsoventral height of the posterior articular surface. Sauroposeidon has proportionally very long vertebrae: the EI of C6 is 6.1. If instead it were 3, as in the mid-cervicals of Apatosaurus, the centrum length would be 600 mm. That 600 mm minus 67 mm for the cotyle would give a functional length of 533 mm, not 1153, and 52 mm of cartilage would account for 9.8% of the length of that segment.
Scaling up from the juveniles: juvenile sauropods have proportionally short cervicals (Wedel et al. 2000). The scanned vertebrae are anterior dorsals with an EI of about 1.5. Mid-cervical vertebrae of this specimen would have EIs about 2, so the same thickness of cartilage would give 12mm of cartilage and 80mm of bone per segment, or 15% cartilage per segment. Over ontogeny the mid-cervicals telescoped to achieve EIs of 2.3–3.3. Assuming the cartilage did not also telescope in length (i.e., didn’t get any thicker than it got taller or wider), the ratio of cartilage to bone would be 12:120 (120 from 80*1.5), so the cartilage would account for 10% of the length of the segment–almost exactly what we got from the based-on-Sauroposeidon estimate. So either we got lucky here with our tiny sample size and truckloads of assumptions, or–just maybe–we discovered a Thing. At least we can say that the intervertebral spacing in the Apatosaurus and Sauroposeidon vertebrae is about the same, once the effects of scaling and EI are removed.
Finally, we’re aware that our sample size here is tiny and heavily skewed toward juveniles. That’s because we were just collecting targets of opportunity. Finding sauropod vertebrae that will fit through a medical-grade CT scanner is not easy, and it’s just pure dumb luck that Kent Sanders and I had gotten scans of even this many articulated vertebrae way back when, since at the time we were on the hunt for pneumaticity, not intervertebral joints or their soft tissues. As Mike has said before, we don’t think of this paper as the last word on anything. It is, explicitly, exploratory. Hopefully in a few years we’ll be buried in new data on in-vivo intervertebral spacing in both extant and extinct animals. If and when that avalanche comes, we’ll just be happy to have tossed a snowball.
- Stevens, K.A. and Parrish, J.M. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284: 798-800. [Free subscription required]
- Stevens, Kent A., and J. Michael Parrish. 2005. Neck posture, dentition, and feeding strategies in Jurassic sauropod dinosaurs. pp. 212-232 in: Virginia Tidwell and Ken Carpenter (eds.), Thunder Lizards: the Sauropodomorph Dinosaurs. Indiana University Press, Bloomington, Indiana. 495 pp.
- Taylor, Michael P., and Mathew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10): e78214. 17 pages. doi:10.1371/journal.pone.0078214 [PDF]
- Upchurch, P. 2000. Neck posture of sauropod dinosaurs. Science 287: 547b.
- Wedel, M.J. 2003b. The evolution of vertebral pneumaticity in sauropod dinosaurs. Journal of Vertebrate Paleontology 23:344-357.
- Wedel, M.J. 2007. Aligerando a los gigantes (Lightening the giants). ¡Fundamental! 12:1-84. [in Spanish, with English translation]
- Wedel, M.J., and Cifelli, R.L. 2005. Sauroposeidon: Oklahoma’s native giant. Oklahoma Geology Notes 65 (2):40-57.
- Wedel, M.J., R.L. Cifelli and R.K. Sanders. 2000. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4): 343-388.
November 3, 2013
As I mentioned a few days ago, Matt and I have a couple of papers in the new PLOS ONE Sauropod Gigantism collection. We were each lead author on one and second author on the other, so for convenience’s sake we’ll refer to them as my paper (Taylor and Wedel 2013c on neck cartilage) and Matt’s paper (Wedel and Taylor 2013b on caudal pneumaticity.)
Mine is very simple in concept (although it ended up at 17 pages and 23 figures). It’s all about addressing one of the overlooked variables in reconstructing the postures of the necks of sauropods (and indeed of all tetrapods). That is, the spacing between consecutive vertebrae, and the effect this has on “neutral pose”.
The concept of “neutral pose” goes back to the DinoMorph work of Stevens and Parrish (1999). They defined it (p. 799) as follows: “We determined the neutral poses for each animal, wherein the paired articular facets of the postzygapophyses of each cervical vertebra were centered over the facets of the prezygapophyses of its caudally adjacent counterpart.”
One of the more fundamental flaws in Stevens and Parrish (1999) is the assumption that animals habitually rest their necks in neutral pose — an assumption that is unsupported by evidence and, as it turns out, false (Vidal et al. 1986, Taylor et al. 2009). But let’s leave that aside for the moment, and consider what neutral pose actually represents.
The fact that there is even such a thing as neutral articulation between two consecutive vertebrae is due to there being three points of contact between those vertebra: as with the legs of a tripod, three points is the minimum number you need to fix an object in three-dimensional space. Two of these points are at the zygapophyses, as noted in the original definition above. The third point is the articulation between the centra.
The centrum has been curiously overlooked in discussions of neutral pose, but needless to say its length is crucial in establishing what is neutral. In the image above, if the centrum was longer, then the angle between the consecutive vertebrae would need to be raised in order to keep the zygapophyses articulated.
And of course it was longer in life, because of the cartilage in between the consecutive centra. (The use of the more specific term “osteological neutral pose” goes some way to recognising that tissues other than bone have been overlooked, but the problem has not really been addressed or even properly acknowledged in published works before our paper.)
You simply can’t ignore cartilage when modelling neck postures and expect to get anything resembling a meaningful result. That is, presumably, the reason why the habitual posture of rabbits in life exceeds the most extended posture we were able to obtain when manipulating dry vertebrae of a hare: compare Vidal et al. (1986: fig. 4) with Taylor et al. (2009: fig. 1).
How big is the effect? That depends on the thickness of the cartilage and the height of the zygapophyses above the center of rotation. Here is an illustration that we should have put in the paper, but which inexplicably neither of us thought of:
Here’s some elementary trigonometry. Suppose the intervertebral cartilage is x distance thick at mid-height of the centra, and that the height of the zygs above this mid-height point (the magenta line) is y. The triangle between the middle of the condyle of the posterior vertebra, the middle of the cotyle of the anterior one and the zygapophyseal articulation is near enough a right-angled triangle as makes no odds.
Consider the angle θ between the green lines. Sin(θ) = opposite/hypotenuse = x/y, and by similarity, the additional angle of inclination of the anterior vertebra is also θ.
But for small angles (and this is generally a small angle), sin(θ) ≈ θ. So the additional inclination in radians = cartilage thickness divided by zygapophyseal height. For example, in vertebrae where the zygs are 23 cm above the mid-height of the centra, adding 4 cm of intervertebral cartilage adds about 4/23 = 0.174 radians = 10 degrees of extra inclination. (That’s pretty similar to the angle in the illustration above. Eyeballing the cartilage thickness and zyg height in the illustration suggests that 23:4 ratio is about right, which is a nice sanity-check of this method.)
At this point, I am cursing my own stupidity for not putting this diagram, and the very simple calculation, into the paper. I guess that can happen when something is written in a hurry (which to be honest this paper was). The formula is so simple — and accurate enough within tolerances of inevitable measurement error — that we really should have used it all over the place. I guess that will have to go in a followup now.
Anyway — next time, we’ll address this important related question: how thick, in fact, was the cartilage between the cervicals of sauropods?
- Stevens, Kent A., and J. Michael Parrish. 1999. Neck Posture and Feeding Habits of Two Jurassic Sauropod Dinosaurs. Science 284:798-800.
- Taylor, Michael P., and Matthew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10): e78214. 17 pages. doi:10.1371/journal.pone.0078214 [PDF]
- Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2):213-230. [PDF]
- Vidal, Pierre Paul, Werner Graf and Alain Berthoz. 1986. The orientation of the cervical vertebral column in unrestrained awake animals. Experimental Brain Research, 61:549-559. doi:10.1007/BF00237580
- Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi:10.1371/journal.pone.0078213 [PDF]
April 4, 2013
Because I am preparing this paper from PLOS ONE, with its stupid numbered-references system, I am finally getting to grips with a reference-management system. Specifically, Zotero, which is both free and open source, which means it can’t be taken over by Elsevier.
As a complete Zotero n00b, I’ve run into a few issues that more experienced users will no doubt find laughable. Here are two of them. I need to cite Greg Paul’s classic 1988 paper on the skeletal reconstruction of Giraffatitan:
Paul, Gregory S. 1988. The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2(3):1-14.
When I render this using Zotero’s PLOS ONE style, it comes out as:
Paul GS (1988) The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2: 1–14.
So the first problem is, how can I get Giraffatitan to be set in italics?
And the second one, which is arguably more important, is how can I get the issue number included? I undertsand that PLOS ONE referencing style omits the issue-numbers by preference, since they are often redundant, with the pages of each volume being numbered consecutively across volumes. But Hunteria is one of those journals (PaleoBios is another) that resets page-numbers at the start of each issue. As a result, Hunteria volume 2 had at least three page 14s, one in each of its issues, so that issue number is a crucial part of the reference.
Help me, SV-POW! readers — you’re my only hope.
April 28, 2012
Given the huge amount we’ve written about open access on this blog, it may come as a surprise to realise that the blog itself has not been open access until today. It’s been free to read, of course, but in the absence of an explicit licence statement, the default “all rights reserved” has applied, which has meant that technically you’re not supposed to do things like, for example, using SV-POW! material in course notes.
It was never our intention to be so restrictive, of course. We always wanted what we write to be as widely useful as possible; but like most bloggers, we just didn’t think about what that entailed.
So now, belatedly, we are placing SV-POW! under the Creative Commons Attribution licence. This means that you can do anything with our content, subject only to giving us credit. Go nuts. We want our work to be useful. (Our use of this licence is indicated by the CC BY button at top right of all the pages.)
Note that SV-POW! is now compliant with the Budapest Open Access Initiative’s definition of open access — the only definition that matters, really, since it’s where the term “open access” was first coined. That definition is rather noble and striking:
By ‘open access’ to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”
We are applying this licence restrospectively to all the original content on the site — not just what we write from now on. To ensure that we’re on safe ground doing this, all three of us agreed on this measure, and we also obtained consent from the only (so far) guest-blogger on SV-POW!, Heinrich Mallison.
Finally, we should note the exceptions to the CC BY licence. When we’ve included material from other sources — most often figures from published papers — we do not own the copyright and can’t licence it. Similarly, all photographs of fossils held by the Natural History Museum in London are copyright the museum. If you want to re-use any of the non-original material, you’ll need to track down the copyright holders and negotiate with them.
December 14, 2011
This year, I missed The Paleo Paper Challenge over on Archosaur Musings — it was one of hundreds of blog posts I missed while I was in Cancun with my day-job and then in Bonn for the 2nd International Workshop on Sauropod Biology and Gigantism. That means I missed out on my annual tradition of promising to get the looong-overdue Archbishop description done by the end of the year.
But this year, Matt and I are going to have our own private Palaeo Paper Challenge. And to make sure we heap on maximum pressure to get the work done, we’re announcing it here.
Here’s the deal. We have two manuscripts — one of them Taylor and Wedel, the other Wedel and Taylor — which have been sitting in limbo for a stupidly long time. Both are complete, and have in fact been submitted once and gone through review. We just need to get them sorted out, turned around, and resubmitted.
(The Taylor and Wedel one is on the anatomy of sauropod cervicals and the evolution of their long necks. It’s based on the last remaining unpublished chapter of my dissertation, and turned up in a modified form as my SVPCA 2010 talk, Why Giraffes Have Such Short Necks. The Wedel and Taylor one is on the occurrence and implications of intermittent pneumaticity in the tails of sauropods, and turned up as his SVPCA 2010 talk, Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.)
We’re going to be realistic: we both have far too much going in (incuding, you know, families) to get these done by the end of 2011. But we have relatively clear Januaries, so our commitment is that we will submit by the end of January 2012. If either of us fails, you all have permission to be ruthlessly derisive of that person.
… and in other news …
Some time while we were all in Bonn, the SV-POW! hit-counter rolled over the One Million mark. Thanks to all of your for reading!
October 31, 2011
Back when Darren and I did the Xenoposeidon description, we were young and foolish, and only illustrated the holotype vertebra NHM R2095 in four aspects: left and right lateral, anterior and posterior. No dorsal or ventral views.
Also, because the figure was intended for Palaeontology, which prints only in greyscale, I stupidly prepared the figure in greyscale, rather than preparing it in colour and then flattening it down at the last moment. (Happily I’d learned that lesson by the time we did our neck-posture paper: although it was destined for Acta Palaeontologia Polonica, which also prints in greyscale, and though the PDF uses greyscale figures, the online full-resolution figures are in colour.)
As if that wasn’t dumb enough, I also composited the four featured views such that the two lateral views were adjacent, and above the anterior and posterior views — so it wasn’t easy to match up features on the sides and front/back between the views. Since then, I have landed on a better way of presenting multi-view figures, as in my much-admire’d turkey cervical and pig skull images.
So, putting it all together, here is how we should have illustrated illustrated Xenoposeidon back in 2007 (click through for high resolution):
(Top row: dorsal view, with anterior facing left; middle row, from left to right: anterior, left lateral, posterior, right lateral; bottom row, ventral view, with anterior facing left. As always with images of NHM-owned material, this is copyright the NHM.)
Of course, if we’d published in PLoS ONE, then this high-resolution (4775 x 4095), full colour image could have been the published one rather than an afterthought on a blog somewhere. But we didn’t: back then, we weren’t so aware of the opportunities available to us now that we live in the Shiny Digital Future.
In other news, the boys and I all registered Xbox Live accounts a few days ago. I chose the name “Xenoposeidon”, only to find to my amazement that someone else had already registered it. But “Brontomerus” was free, so I used that instead.
May 10, 2011
People who’ve been paying especially close attention may have noted than on four separate occasions in the last eighteen months, I’ve casually referred to our old buddy HMN SII as the paralectotype specimen of Giraffatitan brancai. (Butchering a wallaby, photographing big bones, How fat was Camarasaurus, and baby giraffe neck, in case you were wondering.)
But in my Big Brachiosaur Bonanza (Taylor 2009:788), I nominated HMN SII as the lectotype of this species. So why all this paralectotype stuff? Well, what I wrote in the paper was:
The original type specimen, “Skelett S” (Janensch, 1914:86) was subsequently found (e.g., Janensch, 1929:8) to consist of two individuals, which were designated SI (the smaller) and SII (the larger and more complete). Janensch never explicitly designated these two specimens as a syntype series or nominated either specimen as a lectotype; I therefore propose HMN SII as the lectotype specimen of Brachiosaurus brancai.
But in May last year, I got an email from Mark Konings, a dinosaur enthusiast from the Netherlands, pointing out (more politely than I deserved) that I’d got this wrong. In fact, Janensch did nominate a lectotype — the wrong one, SI, but we’re stuck with it. He did this in a paper on skulls (Janensch 1935-1936:151), which is why I overlooked it. (Well, that and the fact that he rather inconsiderately wrote in German.)
Once I’d been shown my mistake, I realised that the only thing to do was formally correct it in JVP, where the original article had been, so I sent them the shortest and most boring manuscript I’ve ever written (and it is up against some pretty stiff competition in the “most boring” category). And that manuscript was published today (Taylor 2011), fixing my dumb mistake.
Many thanks to Mark for spotting this!
- Janensch, Werner. 1935-36. Die Schadel der Sauropoden Brachiosaurus, Barosaurus und Dicraeosaurus aus den Tendaguru-Schichten Deutsch-Ostafrikas. Palaeontographica 2 (Suppl. 7) 2:147-298.
- Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrae Paleontology 29(3):787-806.
- Taylor, Michael P. 2011. Correction: a re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrae Paleontology 31(3):727.
March 30, 2011
This tutorial is based on all the things that I stupidly forgot to do along the way of tearing down the juvenile giraffe neck that Darren, John Conway and I recently got to take to pieces. At half a dozen different points in that process, I found myself thinking “Oh, we should have done X earlier on!” So it’s not a tutorial founded on the idea that I know how this should be done; it’s about how I am only now realising how it should be done, off the back of my dumb mistakes.
What you want is to get the maximum possible information out of your specimen. At each stage of preparation, information is lost — a necessary evil, because of course at the same time new information becomes available. So don’t miss anything early on.
The whole neck
If you’re lucky, you’ll get the complete, intact neck to work with. (Ours was not quite intact, having been skinned, and lost an indeteminate amount of superficial muscle and ligament in the process.) So before you start cutting, photograph the neck in dorsal, ventral, lateral, anterior and posterior aspects.
Next, you want to measure the neck:
- total mass
- total length, front of atlas to back of last centrum.
- maximum flexion (i.e. downwards bend)
- maximum extension (i.e. upwards bend)
- maximum deflection (i.e. lateral bend)
These last three are hard to do, because “maximum” flexion, extension and deflection are not exact things. You can always push or squeeze or bend a bit harder. These are the unpleasantly messy aspects of working with animals rather than robots — most kinds of tissue are flexible and resilient. You just have to do the best you can, and supplement your measurements with photographs of the neck bent in each direction.
Now you’re ready to start taking that baby apart. Get the skin off, then redo all your photos and redo all your measurements — yes, even total length, even though you “know” removing the skin can’t affect that. Because you don’t know what you don’t know. Does removing the skin affect the maximum range of movement? How much of the neck’s total mass was due to the skin? Weigh the skin as well: does its mass added to that of the deskinned neck add up to that of the intact neck? If not, is the discrepancy due to blood loss?
Once the skin is off, you can start removing muscles. Ideally, you want to identify each muscle as you go, and remove them one by one, so that you leave the major ligaments behind. In practice this is harder than it sounds, because the muscles in real necks are, inconveniently, not clearly delineated and labelled like the ones in books. Still, going slowly and carefully, it’s often possible to avoid cutting actual muscles but just the fascia between them, which allows you remove complete muscles. Done well, this can leave in place not only the nuchal ligament running along the top of all the neural spines, but the shorter ventral ligaments joining adjacent vertebrae.
As you’re doing this, you want to avoid damaging the intercentral joints and the zygapophyseal capsules, so far as possible. You’ll probably find it easy to preserve the former, which are tough, but harder not to accidentally damage at least some of the latter. You want to keep them intact as far as possible, so you can see how the react when you manipulate the neck. (Do these manipulations gently, or you’ll tear those capsules.)
Now that the skin and muscles are both off — at least, so far as you can remove the muscles, which will not be completely — you can redo all your photos and redo all your measurements again. Yes, all of them. Because you just can’t tell what you’re going to be interested in later, and curse yourself for missing.
Go right ahead. Remove the short ligaments, and do your best to get the nuchal ligament off all in one chunk — not quite as easy as it sounds, because it doesn’t just sit on top of the neural spines, but sort of encloses them. Measure the nuchal ligament at rest, then stretch it out as far as you can and measure it extended. Calculate how far it stretched as a proportion of the rest length. Compare this with what you learned from Alexander (1989:64-65). Hmm. Interesting, no?
You can guess what’s coming now: redo all your photos and redo all your measurements yet again. You should find that the total length is the same, but who knows what you might find about changing flexibility? Also, your progressive sequence of mass measurements will tell you what proportion of the whole neck was skin, muscle, ligament, etc.
Separating the vertebrae
This sounds like it should be easy, but it’s not. The zygapophyses will come apart very easily, but the centra will be held firmly together with very dense connective tissue which has be cut carefully away, piece by piece, with the blade of a scalpel worked between the condyle of one vertebra and the cotyle of the next. (I’m writing here about a giraffe neck, but I’m confident the same will be true of other artiodactyls and maybe most mammals; bird necks are different.)
Once you’ve got the vertebrae separate, photograph each vertebra separately, from each of the cardinal directions. Also, measure each vertebra separately — especially for centrum length, but you may as well get all the major measurements. These measurements will include the cartilage caps at the front and back of each centrum. (This is the step that I most regret missing out.)
Articulate the vertebrae in “neutral pose” by keeping the centra in full contact and rotating each intercentral joint about its midpoint until the corresponding zygapophyses are maximally overlapped. What does this pose look like? How does it compare to the animal’s habitual pose in life? (If possible, compare with the pose shown by an X-ray of the live animal, since necks lie.)
Articulate the vertebrae in positions of “maximal” flexion, extension and deflection by keeping the centra in full contact and rotating each intercentral joint about its midpoint until the corresponding zygapophyses are displaced to a degree of your choosing. Try it with the zygs allowed to slide until they are 50% disarticulated, then with 75% disarticulation, then displacing until they are just past the point of contacting each other. Photograph all these poses and measure their deflection. Compare these variant poses with those obtained when the vertebrae were still joined together, and when the ligaments, muscles and skin were still in place. What degree of zygapophyseal disarticulation best matches the whole-neck bending ability? How does this vary along the neck? How does that this compare with what you may have been led to expect in the literature. Hmm.
Using your earlier photos of the whole neck’s bending profile, arrange the vertebrae in the exact same pose. How much do the zygapophyses disarticulate in these poses? As you rotate the joints about the articulation of their centra, do the zygs just slide neatly past each other, or do they move far apart from each other as the neck bends? Interesting, yes?
Cleaning the vertebrae
Have you recorded all the information you need from the intact vertebrae with their cartilage in place? If you’re sure, then …
Lightly simmer the vertebrae for an hour or so, then remove the excess flesh by hand and using a toothbrush. Repeat as needed to get them clean. If you can do this really carefully — I couldn’t — you may be able to keep the cartilage firm, and firmly articulated with the bone. (Bugging the vertebrae is probably a better approach for this purpose, but I find it hard to be that patient.)
Once the vertebrae have dried out — and especially, once their cartilage is dry — re-measure each vertebra. Does the drying of the cartilage affect the centrum length?
Simmer the vertebrae again and gently peel off the cartilage caps at the front and back of each centrum. Re-measure the centra: how long are they now? What proportion of each centrum’s length was cartilage?
Articulate all the centra in a straight line, and measure the total length. How does this compare with the whole-neck length you started with? [Crib-sheet answer for our baby giraffe: 41 cm vs. a whole-neck length of 51 cm. Expect a closer match if you're dealing with an adult animal,which will have proportionally less cartilage.]
Articulate the vertebrae in “neutral pose” as you did back when the individual vertebrae were complete. How does the new “neutral pose” compare with the old one? With habitual life posture? Huh. Makes you think, doesn’t it?
Nearly done …
Articulate the vertebrae in positions of “maximal” flexion, extension and deflection as you did before, and compare your results with those from when the vertebrae were complete with their cartilage caps. Well! Who’d have thought?
Now remember that the fossils we have of, say, sauropod cervicals are those of the dry bone only, with no cartilage. Think about how different the “neutral pose” and range of movement would be if we had the intact vertebrae with their cartilage.
Dammit all, I’ve given the game away
As I wrote this article, I found myself giving away more and more of a paper I’ve been planning to write, in which I go through essentially this process with a couple of necks, ideally from very different clades, and write up the results. Say, a giraffe, an ostrich and a croc. The extent to which the dry-bone postures and flexibility vary from those of the live animals would give us a reasonable starting point for thinking about how life postures and flexibility of sauropods might have varied from what we’d deduce from the dry bones alone.
Wouldn’t that be a great little paper?
Well, I might still write it when I find the time, but I won’t stand in the way of anyone else who wants to plough straight in and just get it done. (You might mention me in the acknowledgements if you do.)