December 11, 2014
As I mentioned in my first post on Aquilops, I drew the skull reconstructions that appear in figure 6 of the paper (Farke et al. 2014). I’m writing this post to explain that process.
We’ve blogged here before about the back-and-forth between paleontologists and artists when it comes to reconstructing and restoring extinct animals (example 1, example 2). Until now, I’ve always been the guy making suggestions about the art, and asking for changes. But for the Aquilops project, the shoe was on the other foot: Andy Farke was my ‘client’, and he had to coach me through drawing a basal ceratopsian skull – a subject that I was definitely not familiar with.
I started from the specimen, OMNH 34557, which is more complete than you might think at first glance. The skull is folded over about 2/3 of the way up the right orbit, so in lateral view it looks like the top of the orbit and the skull roof are missing. They’re actually present, just bent at such a sharp angle that they’re hard to see at the same time as the lateral side of the skull.
I also used a cast skull of Archaeoceratops as a reference – it’s clear from what we have of Aquilops that the two animals were pretty similar.
I started with this pencil outline on a piece of tracing paper.
And then I went right ahead and stippled the whole thing, without showing it to Andy until I was done. Yes, that was dumb. Noe the lack of sutures in this version.
I added sutures and sent it off to Andy, who sent it back with these suggested changes. At this point I realized my error: I had already spent about a day and a half putting ink on the page, and I’d have to either start all over, or do a lot of editing in GIMP. I picked the latter course, since there were plenty of areas that were salvageable.
Next I did something that I’d never done before, which is to redraw parts of the image and then composite them with the original in GIMP. Here’s are the redrawn bits.
With those bits composited in, and a few more tweaks to sutures, we got to this version, which was included in the submitted manuscript.
Then we brought Brian Engh in to do the life restorations. When Brian takes on a project, he does his homework. If you’ve seen his post on painting Aquilops, you know that all of the ferns in the Cloverly scene are based on actual fossils from the Cloverly Formation. Brian came to Claremont this summer and he and Andy and I spent most of a day at the Alf Museum looking at the specimen and talking about possible layouts for the full-body life restorations. He took a bunch of photos of the specimen while he was there, and a day or two later he sent us this diagram. He’d chopped up his photos of the skull to produce his own undistorted version to guide his painting, and in doing so he’d noticed that I had the line of the upper jaw a bit off.
That required another round of digital revisions to fix. It ended up being a lot more work than the earlier round of edits in GIMP, because so many features of the skull had to be adjusted. I ended up cutting my own skull recon into about 8 pieces and then stitching them back together one by one. Here’s what the image looked like about halfway through that process. The back of the skull, orbit, and beak are all fixed here, but the snout, cheek, and maxilla don’t yet fit together.
After a little more work, I got the whole thing back together, and this is the final version that appears in the paper. It is not perfect – the area in front of the orbit where the frontal, nasal, maxilla, and premaxilla come together is a bit dodgy, and I’m not totally happy with the postorbital. But eventually you have to stop revising and ship something, and this is what I shipped.
I did the dorsal view after the submitted version of the lateral view was finished. It went a lot faster, for several reasons:
- Most of the gross proportional issues were already sorted out from doing the lateral view first.
- The bilateral symmetry didn’t cut down on the number of dots but it did cut the conceptual workload in half.
- I did all my roughs in pencil and didn’t start inking until after we had almost all of the details hashed out.
I did have to revise the dorsal view after getting feedback from Brian about the lateral view, but that revision was pretty minor by comparison. I stretched the postorbital region and tinkered a bit with the face and the frill, and both of those steps required putting in some new dots, but it was still just one afternoon’s worth of work. Here’s the final dorsal recon:
In addition to the Life Lessons already noted in this post, I learned (or rather relearned) this important principle: if you do a big drawing and then shrink it down to column width, fine errors – a shaky line here, an ugly dot there – get pushed down below the threshold of perception. But there’s a cost, too, which is that uneven stippling becomes more apparent. I was skipping back and forth a lot between 25% image scale to see where the problem areas were, and 200% to revise the lines and dots accordingly.
All in all, it was a fun project. It was my most ambitious technical illustration to date, I learned a ton about ceratopsian skulls, and it was nice to get to make at least one substantial contribution to the paper.
Now, here’s the take-away: this is my reconstruction, and both of those words are important. “Reconstruction” because it has a lot of extrapolation, inference, and sheer guesswork included. “My” because you’re getting just one possible take on this. You can download the 3D files for the cranium and play with them yourselves. I hope that other artists and scientists will use those tools to produce their own reconstructions, and I fully expect that those reconstructions will differ from mine. I look forward to seeing them, and learning from them.
For other posts about my stippled technical illustrations, see:
Farke, A.A., Maxwell, W.D., Cifelli, R.L., and Wedel, M.J. 2014. A ceratopsian dinosaur from the Lower Cretaceous of Western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055
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.