Specimen photos with desaturated backgrounds
April 25, 2013
Generally when we present specimen photos in papers, we cut out the backgrounds so that only the bone is visible — as in this photo of dorsal vertebrae A and B of NHM R5937 “The Archbishop”, an as-yet indeterminate Tendaguru brachiosaur, in right lateral view:
But for some bones that can be rather misleading: they may be mounted in such a way that part of the bone is obscured by structure. For example — and this is a very minor case — the ventral margins of the centra in the photo above are probably slightly deeper than they appear, because the centra are slightly sunk within the plinth that holds the vertebrae upright.
So I’ve been toying with a different idea: instead of cutting the background out completely, leaving it in place but toning it down. Then the supporting structure is visible, but clearly distinct from the actual bone. (For a more extreme case, see the “Apatosaurus” minimus sacrum.)
Here’s how the image above looks if I desaturate the background:
I’m not sure what to make of this. It looks a bit strange to me, but that might only be the strangeness of unfamiliarity.
And it might not work so well (or indeed it might work better) for photos taken against a busier background.
What do you think?
What an articulated giraffe neck looks like
April 16, 2013
The cervical series of Giraffa camelopardalis angolensis FMNH 34426, articulated by Mike and me and photographed by Mike back in the summer of 2005, cropped and composited by me recently, not previously posted because there’s just too much cool stuff, man. But we’re working on it.
By the way, if you want the details on this critter:
So, this happened today
March 28, 2013
Terrifying actual cervical vertebrae of the Morrison Formation
February 17, 2013
If you found the hypothetical Amphicoelias fragillimus cervical in a recent post a bit too much to swallow, I won’t blame you. But how big do we know Morrison diplodocoid cervicals got?
The longest centrum of any specimen of anything, anywhere, is that of the cervical vertebra BYU 9024 that’s part of the Supersaurus vivianae holotype. It’s 138 cm long, which means that composited at scale with an MTSRSU, it looks like this:
This is not hypothetical. It’s an actual fossil.
(Just for the record: C8 of the Sauroposeidon holotype OMNH 53062 is slightly longer overall, at 140 cm. But that includes overhanging prezygapophyses. Its centrum is “only” 125 cm long.)
Terrifying hypothetical cervical vertebrae of the Morrison Formation
February 13, 2013
In our PeerJ neck-anatomy paper, we speculated on how long individual cervical vertebrae might have grown. Here is the relevant section:
Mere isometric scaling would of course suffice for larger animals to have longer necks, but Parrish (2006, p. 213) found a stronger result: that neck length is positively allometric with respect to body size in sauropods, varying with torso length to the power 1.35. This suggests that the necks of super-giant sauropods may have been even longer than imagined: Carpenter (2006, p. 133) estimated the neck length of the apocryphal giant Amphicoelias fragillimus Cope, 1878 as 16.75 m, 2.21 times the length of 7.5 m used for Diplodocus, but if Parrish’s allometric curve pertained then the true value would have been 2.21^1.35 = 2.92 times as long as the neck of Diplodocus, or 21.9 m; and the longest single vertebra would have been 187 cm long.
Now this speculation is shot through with uncertainty. As we’ve discussed before, at length, all estimates of Amphicoelias fragillimus length and mass are wildly speculative; and Parrish’s allometry result was extrapolated from an unconvincingly small data set. But still, these numbers are probably the best we can do with what we have.
In Diplodocus carnegii, C14 is the longest individual vertebra at 642 mm long (Hatcher 1901, p. 38). The Amphicoelias:Diplodocus size ratio of 2.21 from Carpenter and the neck allometry constant of 1.35 from Parrish suggest that the corresponding vertebra in the big boy would have been 2.92 times as long as that 642 mm, hence the 187 cm that we reported.
So what does a 187-cm long cervical vertebra look like? Scaling up from the Diplodocus carnegii C14 in Hatcher (1901: plate III) and using my good self as a scalebar, here it is:
I find that just a little bit frightening. In more ways than one.
References
- Carpenter, Kenneth. 2006 Biggest of the big: a critical re-evaluation of the mega-sauropod Amphicoelias fragillimus (Cope, 1878). New Mexico Museum of Natural History and Science Bulletin 36:131.
- Cope, Edward D. 1878. Geology and paleontology: a new species of Amphicoelias. The American Naturalist 12:563.
- Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
- Parrish, J. Michael. 2006. The origins of high browsing and the effects of phylogeny and scaling on neck length in sauropodomorphs. pp 201-224 in: Amniote paleobiology, University of Chicago Press, Chicago.
PeerJ launches today! (and we’re in it!)
February 12, 2013
Apatosaurus lousiae 1/12 scale skeleton in left antero-lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.
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.
Apatosaurus lousiae 1/12 scale skeleton in left lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.
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.
Apatosaurus lousiae 1/12 scale skeleton in dorsal view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.
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….)
Apatosaurus lousiae 1/12 scale skeleton in left postero-lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.
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
This special version of Figure 3 from our new paper goes out to Dean, who inspired it with this comment. As Tony Stark said, “It’s like Christmas, only with more…me.” Click to enWedelate.
A selection of Matt Wedels (6’2″ or 1.88m tall) with various long-necked amniotes for scale.
Diplodocus carnegii cervicals, from Hatcher (1901)
February 7, 2013
Here are cervical vertebrae 2-15 of Diplodocus carnegii in right lateral view, from Hatcher (1901: plate 3). Click to embiggen, and then just gaze in wonder for a while.
Wouldn’t that look smashing, printed, framed, and hanging on the wall?
I wonder if I will ever stop finding new interesting things to think about in this image. I doubt it.
(For a bit o’ fair-and-balanced, remember that this neck may not be complete, and that some of the neural spines are sculptures.)
Thanks to Mike for the scan.
Reference
Hatcher, John Bell. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.
A sauropod for you: Gilmore’s baby Cam
February 28, 2012
Since we’ve been a bit light on sauropods lately, here’s CM 11338, the juvenile Camarasaurus from Dinosaur National Monument, in Plate 15 from Gilmore’s 1925 monograph. It’s probably the nicest single sauropod skeleton ever found, and required only minor restoration and reposing for this wall mount at the Carnegie Museum of Natural History.
The same thing in a fake antique finish suitable for printing at 8×10″ and framing. Yes, I have done this. Make one for the sauropodophile in your life, or the non-sauropodophile you’re trying to convert.
Reference
Gilmore, Charles W. 1925. A nearly complete articulated skeleton of Camarasaurus, a saurischian dinosaur from the Dinosaur National Monument, Utah. Memoirs of the Carnegie Museum 10:347-384.
