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 27, 2014
A couple of times now, I’ve pitched in an abstract for a Masters project looking at neck cartilage, hoping someone at Bristol will work on it with me co-supervising, but so far no-one’s bitten. Here’s how I’ve been describing it:
Understanding posture and motion in the necks of sauropods: the crucial role of cartilage in intervertebral joints
The sauropod dinosaurs were an order of magnitude bigger than any other terrestrial animal. Much sauropod research has concentrated on their long necks, which were crucial to their success (e.g. Sander et al. 2010). One approach to understanding neck function tries to determine neutral posture and range of motion by modelling the cervical vertebrae as a mechanical system (e.g. Stevens and Parrish 1999).
The raw material of such studies is fossilised vertebrae, but these are problematic for several reasons. The invariable incompleteness and distortion of sauropod neck fossils causes fundamental difficulties; but even given perfect fossils, the lack of preserved cartilage means that the bones are not shaped or sized as they were in life.
Ignoring cartilage has dramatic consequences for neutral posture, range of motion and even length of necks: pilot studies (Cobley 2011, Taylor 2011) found that intact bird necks are 8–12% longer than articulated sequences of their dry bones, and that figure is as high as 24% for a juvenile giraffe neck. A turkey neck postzygapophysis was 26% longer when cartilage was included than after being stripped down to naked bone.
We do not yet know how much articular cartilage sauropods had in their necks, nor even what kind of intervertebral joints they had: crocodilians have fibrocartilaginous discs like those of mammals, while birds have synovial joints, so the extant phylogenetic bracket is uninformative.
The project will involve dissection and measurement of bird and crocodilian necks, documenting the extent and shape of articular cartilage, identifying osteological correlates of fibrocartilaginous and synovial joints, and applying this data to sauropods to determine the nature of their neck joints and length of their necks, to reconstruct the lost cartilage, and to determine its effect on neutral pose and range of motion.
Following completion, we anticipate publication of the project.
Cobley, Matthew J. 2011. The flexibility and musculature of the ostrich neck: implications for the feeding ecology and reconstruction of the Sauropoda (Dinosauria: Saurischia). MSc Thesis, Department of Earth Sciences, University of Bristol. vi+64 pages.
Sander, P. Martin, Andreas Christian, Marcus Clauss, Regina Fechner, Carole T. Gee, Eva-Maria Griebeler, Hanns-Christian Gunga, Jürgen Hummel, Heinrich Mallison, Steven F. Perry, Holger Preuschoft, Oliver W. M. Rauhut, Kristian Remes, Thomas Tütken, Oliver Wings and Ulrich Witzel. 2010. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews 86:117–155. doi:10.1111/j.1469-185X.2010.00137.x
Stevens, Kent A., and J. Michael Parrish. 1999. Neck Posture and Feeding Habits of Two Jurassic Sauropod Dinosaurs. Science 284:798–800. doi:10.1126/science.284.5415.798
Taylor, Michael P., and Mathew J. Wedel. 2011. Sauropod necks: how much do we really know?. p. 20 in Richard Forrest (ed.), Abstracts of Presentations, 59th Annual Symposium of Vertebrae Palaeontology and Comparative Anatomy, Lyme Regis, Dorset, UK, September 12th–17th 2011. 37 pp. http://www.miketaylor.org.uk/dino/pubs/svpca2011/TaylorWedel2011-what-do-we-really-know.ppt
(Obviously some part of this have since been covered by my and Matt’s first cartilage paper, but plenty has not.)
I now think there are two reasons no-one’s taken up this project: first, because I wrote it as very focussed only on the question of what type of joint was present, whereas there are plenty of related issues to be investigated along the way; and second, because I wrote it as a quest to discover a specific treasure (an osteological correlate), with the implication that if there’s no treasure to be found then the project will have been a failure.
But I do think there is still plenty of important work to be done in this area, and that there’s lots of important information to be got out of comparative dissection of extant critters.
If anyone out there fancies working in this area, I’d be delighted. I’d also be happy to offer whatever advice and help I could.
Update (18 October 2014)
Somehow I’d forgotten, when I wrote this post, that I’d previously written a more detailed post about the discs-in-sauropod-necks problem. If you’re interested in the problem, you should read that.
February 9, 2014
Stop what you’re doing and go read Cameron Neylon’s blog. Specifically, read his new post, Improving on “Access to Research”.
Regular readers of SV-POW! might legitimately complain that my so-called advocacy consists mostly of whining about how rubbish things are. If you find that wearying (and I won’t blame you if you do), then read Cameron instead: he goes beyond critiquing what is, and sees what could be. Here is a key quote on this new post:
I did this on a rainy Saturday afternoon because I could, because it helped me learn a few things, and because it was fun. I’m one of tens or hundreds of thousands who could have done this, who might apply those skills to cleaning up the geocoding of species in research articles, or extracting chemical names, or phylogenetic trees, or finding new ways to understand the networks of influence in the research literature. I’m not going to ask for permission, I’m not going to go out of my way to get access, and I’m not going to build something I’m not allowed to share. A few dedicated individuals will tackle the permissions issues and the politics. The rest will just move on to the next interesting, and more accessible, puzzle.
Right! Open access is not about reducing subscription costs to libraries, or about slicing away the absurd profits of the legacy publishers, or about a change to business models. It’s about doing new and exciting things that simply weren’t possible before.
November 22, 2013
As a nice little perk–presumably for being early adopters and users of PeerJ–Mike and I each have been given a small number of referral codes, which will allow other folks to publish in PeerJ for free, as long as the papers are submitted by March 1, 2014. Here’s the scoop, straight from the monkey’s mouth:
If you have colleagues who would like to publish at PeerJ, then we want to give them the opportunity to try us out for free. Therefore, as a Published PeerJ Author, we are providing you with 5 unique ‘Referral Codes’ (which expire on March 1st) to distribute to your colleagues. Each code entitles the recipient to an entirely FREE PeerJ publication. They simply need to quote your referral code in the “Notes to Staff” field, when they submit to PeerJ, and as a result they will be able to publish that article for free (assuming it passes peer-review). Please disseminate these codes to colleagues who you feel will use them, but please make sure that they realize that this code is only valid for submissions made before March 1st, 2014.
Note that this is alongside the current promo wherein, if you post a preprint to PeerJ PrePrints (which is a smashing way of getting fast feedback, or at least it was for us), that manuscript can be published in PeerJ for free, as long as it is formally submitted before January 1, 2014. So if you can get the lead out before the end of the year and don’t have an allergy to fast feedback, you don’t actually need one of these codes.
So. If you’re not a PeerJ member but you have a manuscript that you’d like to send to PeerJ before the first of next March, let us know and we’ll hook you up with a referral code. If you’re fairly sure you will use one but aren’t ready to ship yet, let me know and I’ll set one aside for you, with the proviso that I can give it away if we’re getting close to the deadline and you’re not realistically going to make it.
If we get more takers than codes, we’ll figure out some fair way of choosing who gets a code, probably randomly. I will be strongly biased toward people without big paychecks* or institutional support, like grad students and postdocs. (If you’re an undergrad, you can already publish in PeerJ for free, at least for the duration of the pilot program.) So if you’re a grad student or postdoc with a serious plan to get published, speak up and you’ll go to the head of the line. So if you let us know why getting a code would benefit you, you’re more likely to get one.
* I know in academia none of us think we have big paychecks, but compared to most grad students and postdocs, those of us with steady full-time employment are living the dream. I’m trying to reach the folks for whom the $99 lifetime membership fee would be a genuine impediment.
As is apparently the usual thing now when I’m writing about PeerJ and don’t have any images of my own queued up, I’ve borrowed images from Brant Bassam’s astoundingly cool BrantWorks.com to spice up this post. Explicit permission to reproduce the images with credit can be found on this page, which is coincidentally where these images themselves are from. Get on over there and prepare to lose some time looking at sweet stuff.
Update! Five more Golden Tickets available!
As noted in the comment below, Heinrich Mallison also has five PeerJ vouchers to distribute to deserving causes. So if Matt and I run out, the options are still open. Feel free to contact Heinrich directly or to go through us if you prefer.
The LSE Impact blog has a new post, Berlin 11 satellite conference encourages students and early stage researchers to influence shift towards Open Access. Thinking about this, Jon Tennant (@Protohedgehog) just tweeted this important idea:
Would be nice to see a breakdown of OA vs non-OA publications based on career-stage of first author. Might be a wake-up call.
It would be very useful. It makes me think of Zen Faulkes’s important 2011 blog-post, What have you done lately that needed tenure?. We should be seeing the big push towards open access coming from senior academics who are established in their roles don’t need to scrabble around for jobs like early-career researchers. Yet my impression is that in fact early-career researchers are doing a lot of the pro-open heavy lifting.
Is that impression true?
We should find out.
Here’s one possible experimental design: take a random sample of 100 Ph.D students, 100 post-docs, 100 early-career researchers in tenure-track jobs and 100 tenured researchers. For each of them, analyse their last ten years of publications and determine what proportion are paywalled, what proportion are free to read (e,g, on arXiv or in an all-rights-reserved IR), and what proportion are true (BOAI-compliant) open access.
An alternative approach would be to randomly sample 1000 open-access papers (from PLOS and BMC journals, for example), and 1000 paywalled papers (from Elsevier and Springer, say) and find the career-stage of their authors. I’m not sure which approach would be better?
Who is going to do this?
I think it would be a nice, tractable first project for someone who wants to get into academic research but hasn’t previously published. It would be hugely useful, and I’m guessing widely cited. Does anyone fancy it?
September 23, 2013
I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!
I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:
Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.
Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.
If the PrePrint successfully passes these checks, it will be made public.
You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.
Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).
Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.
And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.
I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.
Now here’s what we’d like:
We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.
So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.
Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.
- Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
- Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1
Last Tuesday Mike popped up in Gchat to ask me about sauropod neck masses. We started throwing around some numbers, derived from volumetric estimates and some off-the-cuff guessing. Rather than tell you more about it, I should just paste our conversation, minimally edited for clarity and with a few hopefully helpful links thrown in.
* R. McNeill Alexander (1985, 1989) did estimate the mass of the neck of Diplodocus, based on the old Invicta model and assuming a specific gravity of 1.0. Which was a start, and waaay better than no estimate at all. Still, let’s pretend that Mike meant “tried based on the actual fossils and what we know now about pneumaticity”.
The stuff about putting everything off until April is in there because we have a March 31 deadline to get a couple of major manuscripts submitted for an edited thingy. And we’ve made a pact to put off all other sciencing until we get those babies in. But I want to blog about this now, so I am.
Another thing Mike and I have been talking a lot about lately is the relation between blogging and paper-writing. The mode we’ve seen most often is to blog about something and then repurpose or rewrite the blog posts as a paper. Darren paved the way on this (at least in our scientific circle–people we don’t know probably did it earlier), with “Why azhdarchids were giant storks“, which became Witton and Naish (2008). Then last year our string of posts (starting here) on neural spine bifurcation in Morrison sauropods became the guts–and most of the muscles and skin, too–of our in-press paper on the same topic.
But there’s another way, which is to blog parts of the science as you’re doing them, which is what Mike was doing with Tutorial 20–that’s a piece of one of our papers due on March 31.
Along the way, we’ve talked about John Hawks’ model of using his blog as a place to keep his notes. We could, and should, do more of that, instead of mostly keeping our science out of the public eye until it’s ready to deploy (which I will always favor for certain projects, such as anything containing formal taxonomic acts).
And I’ve been thinking that maybe it’s time for me–for us–to take a step that others have already taken, and do the obvious thing. Which is not to write a series of blog posts and then decide later to turn it into a paper (I wasn’t certain that I’d be writing a paper on neural spine bifurcation until I had written the second post in that series), but to write the paper as a series of blog posts, deliberately and from the outset, and get community feedback along the way. And I think that the sauropod neck mass project is perfect for that.
Don’t expect this to become the most common topic of our posts, or even a frequent one. We still have to get those manuscripts done by the end of March, and we have no shortage of other projects waiting in the wings. And we’ll still post on goofy stuff, and on open access, and on sauropod stuff that has nothing to do with this–probably on that stuff a lot more often than on this. But every now and then there will be a post in this series, possibly written in my discretionary blogging time, that will hopefully move the paper along incrementally.
Alexander, R.M. 1985. Mechanics of posture and gait of some large dinosaurs. Zoological Journal of the Linnean Society, 83(1): 1-25.
Alexander, R.M. 1989. Dynamics of Dinosaurs and Other Extinct Giants. Columbia University Press.
- Hutchinson, J.R., Bates, K.T., Molnar, J., Allen, V., and Makovicky, P.J. 2011. A computational analysis of limb and body dimensions in Tyrannosaurus rex with implications for locomotion, ontogeny, and growth. PLoS ONE 6(10): e26037. doi:10.1371/journal.pone.0026037
- Taylor, M.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.
- Wedel, M.J., and Taylor, M.P. In press. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. PalArch’s Journal of Vertebrate Paleontology.
- Witton, M.P., and Naish, D. 2008. A reappraisal of azhdarchid pterosaur functional morphology and paleoecology. PLoS ONE 3(5): e2271. doi:10.1371/journal.pone.0002271