November 5, 2014
Last night, I submitted a paper for publication — for the first time since April 2013. I’d almost forgotten what it felt like. But, because we’re living in the Shiny Digital Future, you don’t have to wait till it’s been through review and formal publication to read it. I submitted to PeerJ, and at the same time, made it available as a preprint (Taylor 2014).
It’s called “Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs”, and frankly the results are weird. Here’s a taste:
A year back, as I was composing a blog-post about our neck-cartilage paper in PLOS ONE (Taylor and Wedel 2013c), I found myself writing down the rather trivial formula for the additional angle of extension at an intervertebral joint once the cartilage is taken into account. In that post, I finished with the promise “I guess that will have to go in a followup now”. Amazingly it’s taken me a year to get that one-pager written and submitted. (Although in the usual way of things, the manuscript ended up being 13 pages long.)
To summarise the main point of the paper: when you insert cartilage of thickness t between two vertebrae whose zygapophyses articulate at height h above the centra, the more anterior vertebra is forced upwards by t/h radians. Our best guess for how much cartilage is between the adjacent vertebrae in an Apatosaurus neck is about 10% of centrum length: the image above shows the effect of inserting that much cartilage at each joint.
And yes, it’s weird. But it’s where the data leads me, so I think it would be dishonest not to publish it.
I’ll be interested to see what the reviewers make of this. You are all of course welcome to leave comments on the preprint itself; but because this is going through conventional peer-review straight away (unlike our Barosaurus preprint), there’s no need to offer the kind of detailed and comprehensive comment that several people did with the previous one. Of course feel free if you wish, but I’m not depending on it.
Gilmore Charles W. 1936. Osteology of Apatosaurus, with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175–300 and plates XXI–XXXIV.
Stevens, Kent A., and J. Michael Parrish. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284(5415):798–800. doi:10.1126/science.284.5415.798
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
September 15, 2014
The body mass should be considerably lower because the reconstructed column don’t match with published vertebrae centra lengths. 3D reconstruction also leaves too much space between vertebrae. The reconstruction body trunk is probably 15-20% longer than it really was. Check the supplementary material: http://www.nature.com/srep/2014/140904/srep06196/extref/srep06196-s1.pdf
So I did. The table of measurements in the supplementary material is admirably complete. For all of the available dorsal vertebrae except D9, which I suppose must have been too poorly preserved to measure the difference, Lacovara et al. list both the total centrum length and the centrum length minus the anterior condyle. Centrum length minus the condyle is what in my disseration I referred to as “functional length”, since it’s the length that the vertebra actually contributes to the articulated series, assuming that the condyle of one vertebra sticks out about as far as the cotyle is recessed on the next vertebra. Here are total lengths/functional lengths/differences for the seven preserved dorsals, in mm:
- D4 – 400/305/95
- D5 – 470/320/150
- D6 – 200/180/20
- D7 – 300/260/40
- D8 – 350/270/80
- D9 – 410/ – / -
- D10 – 330/225/105
The average difference between functional length and total length is 82 mm. If we apply that to D9 to estimate it’s functional length, we get 330mm. The summed functional lengths of the seven preserved vertebrae are then 1890 mm. What about the missing D1-D3? Since the charge is that Lacovara et al. (2014) restored Dreadnoughtus with a too-long torso, we should be as generous as possible in estimating the lengths of the missing dorsals. In Malawisaurus the centrum lengths of D1-D3 are all less than or equal to that of D4, which is the longest vertebra in the series (Gomani 2005: table 3), so it seems simplest here to assign D1-D3 functional lengths of 320 mm. That brings the total functional length of the dorsal vertebral column to 2850 mm, or 2.85 m.
At this point on my first pass, I was thinking that Lacovara et al. (2014) were in trouble. In the skeletal reconstruction that I used for the GDI work in the last post, I measured the length of the dorsal vertebral column as 149 pixels. Divided by 36 px/m gives a summed dorsal length of 4.1 m. That’s more than 40% longer than the summed functional lengths of the vertebrae calculated above (4.1/2.85 = 1.44). Had Lacovara et al. really blown it that badly?
Before we can rule on that, we have to estimate how much cartilage separated the dorsal vertebrae. This is a subject of more than passing interest here at SV-POW! Towers–the only applicable data I know of are the measurements of intervertebral spacing in two juvenile apatosaurs that Mike and I reported in our cartilage paper last year (Taylor and Wedel 2013: table 3, and see this post). We found that the invertebral cartilage thickness equaled 15-24% of the length of the centra.* For the estimated 2.85-meter dorsal column of Dreadnoughtus, that means 43-68 cm of cartilage (4.3-6.8 cm of cartilage per joint), for an in vivo dorsal column length of 3.28-3.53 meters. That’s still about 15-20% shorter than the 4.1 meters I measured from the skeletal recon–and, I must note, exactly what Asier stated in his comment. All my noodling has accomplished is to verify that his presumably off-the-cuff estimate was spot on. But is that a big deal?
Visually, a 20% shorter torso makes a small but noticeable difference. Check out the original reconstruction (top) with the 20%-shorter-torso version (bottom):
FWIW, the bottom version looks a lot more plausible to my eye–I hadn’t realized quite how weiner-dog-y the original recon is until I saw it next to the shortened version.
In terms of body mass, the difference is major. You’ll recall that I estimated the torso volume of Dreadnoughtus at 32 cubic meters. Lopping off 20% means losing 6.4 cubic meters–about the same volume as a big bull elephant, or all four of Dreadnoughtus‘s limbs put together. Even assuming a low whole-body density of 0.7 g/cm^3, that’s 4.5 metric tons off the estimated mass. So a ~30-ton Dreadnoughtus is looking more plausible by the minute.
For more on how torso length can affect the visual appearance and estimated mass of an animal, see this post and Taylor (2009).
* I asked Mike to do a review pass on this post before I published, and regarding the intervertebral spacing derived from the juvenile apatosaurs, he wrote:
That 15-24% is for juveniles. For the cervicals of adult Sauroposeidon we got about 5%. Why the differences? Three reasons might be relevant: 1, taxonomic difference between Sauroposeidon and Apatosaurus; 2, serial difference between neck and torso; 3, ontogenetic difference between juvenile and adult. By applying the juvenile Apatosaurus dorsal measurement directly to the adult Dreadnoughtus dorsals, you’re implicitly assuming that the adult/juvenile axis is irrelevant (which seems unlikely to me), that the taxonomic axis is (I guess) unknowable, and that the cervical/dorsal distinction is the only one that matter.
That’s a solid point, and it deserves a post of its own, which I’m already working on. For now, it seems intuitively obvious to me that we got a low percentage on Sauroposeidon simply because the vertebrae are so long. If the length-to-diameter ratio was 2.5 instead of 5, we’d have gotten 10%, unless cartilage thickness scales with centrum length, which seems unlikely. For a dorsal with EI of 1.5, cartilage thickness would then be 20%, which is about what I figured above.
Now, admittedly that is arm-waving, not science (and really just a wordy restatement of his point #2). The obvious thing to do is take all of our data and see if intervertebral spacing is more closely correlated with centrum length or centrum diameter. Now that it’s occurred to me, it seems very silly not to have done that in the actual paper. And I will do that very thing in an upcoming post. For now I’ll just note three things:
- As you can see from figure 15 in our cartilage paper, in the opisthocoelous anterior dorsals of CM 3390, the condyle of the posterior vertebra is firmly engaged in the cotyle of the anterior one, and if anything the two vertebrae look jammed together, not drifted apart. But the intervertebral spacing as a fraction of centrum length is still huge (20+4%) because the centra are so short.
- Transferring these numbers to Dreadnoughtus only results in 4.3-6.8 cm of cartilage between adjacent vertebrae, which does not seem unreasonable for a 30- or 40-ton animal with dorsal centra averaging 35 cm in diameter. If you asked me off the cuff what I thought a reasonable intervertebral spacing was for such a large animal, I would have said 3 or 4 inches (7.5 to 10 cm), so the numbers I got through cross-scaling are actually lower than what I would have guessed.
- Finally, if I’ve overestimated the intervertebral spacing, then the actual torso length of Dreadnoughtus was even shorter than that illustrated above, and the volumetric mass estimate would be smaller still. So in going with relatively thick cartilage, I’m being as generous as possible to the Lacovara et al. (2014) skeletal reconstruction (and indirectly to their super-high allometry-derived mass estimate), which I think is only fair.
- Gomani, Elizabeth M. 2005. Sauropod dinosaurs from the Early Cretaceous of Malawi, Africa. Palaeontologia Electronica 8(1):27A (37 pp.)
- Lacovara, Kenneth J.; Ibiricu, L.M.; Lamanna, M.C.; Poole, J.C.; Schroeter, E.R.; Ullmann, P.V.; Voegele, K.K.; Boles, Z.M.; Egerton, V.M.; Harris, J.D.; Martínez, R.D.; Novas, F.E. (September 4, 2014). A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina. Scientific Reports. doi:10.1038/srep06196.
- 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 Vertebrate Paleontology 29(3):787-806.
- 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
July 18, 2013
Readers with long memories might recall that, nearly two years ago, we published annotated skeletal reconstructions of Camarasaurus and of Tyrannosaurus, with all the bones labelled. At the time, I said that I’d like to do an ornithischian, too.
Well, here it is at last, based on Marsh’s (1891) classic reconstruction of Triceratops:
Click through for the full-sized version (2076 by 864 pixels), which — like the other two — you are welcome to print out and hang on your wall as a handy reference, or to use in teaching. (Marsh’s original is out of copyright; I hereby make my modified version available under the CC By 3.0 licence.)
February 12, 2013
Today our paper on sauropod neck anatomy is formally published in PeerJ.
There’s not much new to say about the paper, since we posted it to arXiv last year and told the world about it then (post 1, post 2, post 3). Although a lot more attractive in form, this version is almost identical in content, modulo some changes requested by the PeerJ reviewers, and some changes to the figures to make sure every part of every figure was CC BY or otherwise in the public domain. Many thanks to everyone who gave us permission to use their images, especially Scott Hartman, who is rapidly getting to be the go-to person for this sort of thing just by doing good work and being a nice guy.
The big news, of course, is not the paper but the outlet. We’re excited about PeerJ because it promises to be a game-changer, for lots of reasons. Mike has a nice article in the Guardian today about the thing that is getting the most attention, which is the cost to publish. I blogged about it last fall, when I bought the max bling lifetime membership–for about one-tenth of the OA publication fee for a single article from one of the big barrier-based publishers.
Then there’s turnaround time: for our paper, a mere 72 days, including both submission day (Dec. 3) and publication day (Feb. 12). My fastest turnaround before this was 73 days for my sauropod nerve paper, but that was from submission to posting of the accepted manuscript, not publication of the final version of record. Prior to that I’d had a couple of papers published within six months of submission, but that was definitely the exception rather than the rule. And sadly, I’ve had several situations now where a paper languished in peer review for six months.
And that brings me to peer review–the real “peer” in PeerJ. When you sign up a lifetime membership, you agree to review one paper a year for them to keep your membership active. Certainly not a crushing amount of work, especially since I’ve been averaging 5 or 6 reviews a year for much less congenial outlets.
I’ve seen this from both sides now, since I was tapped to review a manuscript for PeerJ back in December. The first thing I liked is that they asked for the review back within 10 days. That’s just about right. I can see a thorough review taking three days (not working straight through, obviously, but taking time to carefully read, digest, look stuff up, and compose the review), and a busy academic maybe needing a week to find that kind of time. If one is too busy to get it done within 10 days, better to just be honest, say that, and decline the review. There is certainly no reason to let reviewers have manuscripts for four to six weeks, let alone the three to four months that was standard when I got into this business.
The second thing I liked is that they gave me the option to sign the review (which is almost always implicitly present, whether reviewers take advantage of it or not), and they gave the authors of the manuscript the option to publish my review alongside the paper. I love that. It means that, for the first time ever*, maybe the time and effort I put into the review will not disappear without a trace after I send it off. (It is astonishingly wasteful that we write these detailed technical critiques and then consign them to never be seen by any but a handful of people.) And it had a salutary effect on my reviewing. I always strive to be thoughtful and constructive in my reviews, but the knowledge that this review might be published for the world to see made me a lot more careful, both in what I said and how I said it. Hopefully, the authors I reviewed for will opt to publish my review, so you will be able to judge for yourself whether I succeeded–I’ll keep you posted on that. UPDATE: Hooray! The paper is out, and it’s a beaut, and the authors did publish the review history, which is excellent. The paper is Schachner et al. (2013), “Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria”, the reviews by Pat O’Connor and myself and the author responses and the editor’s letters are all available by clicking the “Peer review history” link on the sidebar, and you should go read all of it right now.
* There are a bare handful of other outlets that publish reviews alongside papers, but I’ve never been tapped to review for them, so this was my first experience with a peer review that might be published.
Naturally Mike and I took the maximum openness option and had our reviews and all the rest of the paper trail published alongside our paper, and I intend to do this every time from here on out. As far as I’m concerned, the benefits of open peer review massively outweigh those from anonymous peer review. There will always be a few jackasses in the world, and if openness itself doesn’t force better behavior out of them, at least they’ll be easier to identify and route around in an open world. Anyway, to see our reviews, expand ‘Author and article information’ at the top of this page, and click the link in the green box that says, “The authors have chosen to make the review history of this article public.”
One happy result of this will manifest in just a few weeks. Bunny-wrangler and sometime elephant-tracker Brian Kraatz and I co-teach a research capstone course for the MS students at WesternU, and one of the things we cover is peer review. Last year I had to dig up a couple of my reviews that were sufficiently old and anonymous that no harm could come from sharing them with the students, but even so, they only got half the story, because I no longer had the manuscripts and couldn’t have shared them if I had. This year I’ll be able to point the students at PeerJ and say, “Go look. There’s the back-and-forth. That’s how we do this. Now you know.”
Science, process and product alike, out in the open, freely available to the world: that’s why I’m proud to be a member of PeerJ.
(And I haven’t even mentioned the preprint server, or all the thought the PeerJ team put into the graphic design of the papers themselves, or how responsive the production team was in helping us get the finished product just right, or….)
The pictures in this post have nothing to do with our paper, other than showing off one of the beautiful products of the factors we discuss therein. The images are all borrowed from Brant Bassam’s amazing BrantWorks, which we will definitely be discussing more in the future. Explicit permission to reproduce the images with credit can be found on this page. Thanks, Brant!
UPDATE: Bonus Figure
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.
April 30, 2012
In the recent post on OMNH 1670, a dorsal vertebra of a giant Apatosaurus from the Oklahoma panhandle, I half-promised to post the only published figure of this vertebra, from Stovall (1938: fig. 3.3). So here it is:
And in the second comment on that post, I promised a sketch from one of my notebooks, showing how much of the vertebra is reconstructed. Here’s a scan of the relevant page from my notebook. Reconstructed areas of the vert are shaded (confusingly, using strokes going in opposite directions on the spine and centrum, and the dark shaded areas on the front of the transverse processes are pneumatic cavities), and measurements are given in mm.
Next item: is this really a fifth dorsal vertebra?
Here are D4 and D5 of A. louisae CM 3018. They sort of bracket OMNH 1670 in terms of morphology. D4 has a broader spine, and D5 has a narrower one. The spine of D5 lacks the slight racquet-shaped expansion seen in OMNH 1670, but the overall proportions of the spine are more similar. On the other hand, the transverse processes of D4 taper a bit in anterior and posterior view, as in OMNH 1670, and unlike the transverse processes of D5 with their more parallel dorsal and ventral margins. But honestly, neither of these verts is a very good match (and the ones on either side, D3 and D6, are even worse).
Here are D3 and D4 of A. parvus UWGM 15556. D3 is clearly a poor match as well–it is really striking how much the vertebral morphology changes through the anterior dorsals in most sauropods, and Apatosaurus is no exception. D3 looks like a dorsal in lateral view, but in anterior or posterior view it could almost pass for a posterior cervical. If I was going to use the term “cervicodorsal”, indicating one of the vertebrae from the neck/trunk transition, I would apply it as far back as D3, but not to D4. That thing is all dorsal.
And it’s a very interesting dorsal from the perspective of identifying OMNH 1670. It has fairly short, tapering transverse processes. The neural spine is a bit shorter and broader, but it has a similar racquet-shaped distal expansion. I’m particularly intrigued by the pneumatic fossae inscribed into the anterior surface of the neural spine–in Gilmore’s plate they make a broken V shapen, like so \ / (or maybe devil eyes). Now, OMNH 1670 doesn’t have devil eyes on its spine, but it does have a couple of somewhat similar pneumatic fossae cut into the spine just below the distal racquet–perhaps a serially modified iteration of the same pair of fossae as in the A. parvus D4. It’s a right sod that D5 from this animal has its spine blown off–but it still has its transverse processes, and they are short and tapering as in OMNH 1670.
Here are all the dorsals and the first couple sacrals of FMNH P25112, which was originally described as A. excelsus but in the specimen-level analysis of Upchurch et al. 2005) comes out as the sister taxon to the A. ajax/A. parvus/A. excelsus clade. Note the striking similarity of the D5 here with D4 of the A. parvus specimen in Gilmore’s plate (until the careful phylogenetic work up Upchurch et al. 2005, that A. parvus specimen, once CM 563 and now UWGM 15556, was considered to represent A. excelsus as well). But also notice the striking similarity of D6 to OMNH 1670. It’s not quite a dead ringer–the transverse processes are longer and have weird bent-down “wingtips” (XB-70 Valkyrie, anyone?)–but it’s pretty darned close, especially in the shape of the neural spine.
So what does this all mean? First, that trying to specify the exact serial position of an isolated vertebra is nigh on to impossible, unless it’s something that is one-of-a-kind like an axis. Second, after doing all these comparos I think it’s unlikely that OMNH 1670 is a D4–those are a bit too squat across the board–but it could plausibly be either a D5 or a D6. Third, I’m really happy that it doesn’t seem to match any particular specimen better than all the rest. What I don’t want to happen is for someone to see that this vertebra looks especially like specimen X and therefore decide that it must represent species Y. As I said in the comments of the previous post, what this Oklahoma Apatosaurus material needs is for someone to spend some quality time seeing, measuring, and photographing all of it and then doing a phylogenetic analysis. That sounds like an ambitious master’s thesis or the core of a dissertation, and I hope an OU grad student takes it on someday.
If you were intrigued by my suggestion that the big Oklahoma Apatosaurus rivalled Supersaurus in size, and wanted to see a technical comparison of the two, I am happy to report that Scott Hartman has done the work for you. Here’s one of his beautiful Apatosaurus skeletal reconstructions, scaled to the size of OMNH 1670, next to his Supersaurus silhouette. This is just a small teaser–go check out his post on the subject for a larger version and some interesting (and funny) thoughts on how the two animals compare.
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
- Riggs, E.S. 1903. Structure and relationships of opisthocoelian dinosaurs, part I: Apatosaurus Marsh. Field Columbian Museum Publications, Geological Series 2(4): 165–196.
- Stovall, J.W. 1938. The Morrison of Oklahoma and its dinosaurs. Journal of Geology 46:583-600.