Getting to grips with a reference-manager: two problems
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.
SV-POW! is now (finally!) open access
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.
Necks, I win; tails, Wedel loses –or– The SV-POW! Palaeo Paper Challenge
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.
Brachiosauridae incertae sedis NMH R5937, "The Archbishop", dorsal neural spine C, probably from an anterior dorsal vertebra. Top row: dorsal view, anterior to top; middle row, left to right: anterior, left lateral, posterior, right lateral; bottom row: ventral view, anterior to bottom.
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!
Xenoposeidon in all its glory
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.
At last it can be told!
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.)
Giraffatitan brancai paralectotype HMN SII in the justly underrated left posteroventrolateral view, slightly obscured by a bit of Boring Old Diplodocus neck
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!
References
- 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.
Tutorial 13: how to dissect a neck
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.
Cervical vertebra 5 of two-week-old giraffe: left column, anterior; middle column, top to bottom, dorsal, left lateral, posterior, all with anterior to the left; right column, posterior
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.
Skinning
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?
Stripping muscle
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.
John (left) and Darren (right) removing muscle from the giraffe neck (in right lateral aspect), while keeping ligaments intact
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.
Stripping ligament
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.)
I’m stupid
February 20, 2011
Earlier this evening, while I was editing an SV-POW! article that we plan to release on Wednesday, I (Mike) inadvertently hit the Publish button rather than Save Draft as I’d intended. I was able to quickly undo the posting, but it’s possible that some of you may have seen Wednesday’s article prematurely, especially if you use an RSS reader that happened to cache that page during the brief period that it was available.
I am asking you all, please, to limit the damage from my stupidity by not discussing that article or its subject at all until Wednesday. Please don’t even say what it was about.
Thanks for understanding.
I do not dare behold it
January 14, 2011
By a curious coincidence, today’s Bob The Angry Flower cartoon is all about the Archbishop description.
But, hey, at least I got my confession in early — I was officially the first participant to fail the 2010 Paleo Project Challenge.
THIS year, for sure!
The hitherto hidden half of BMNH R46870
July 12, 2009
It’s no secret – at least, not if you’re a regular SV-POW! reader – that the Lower Cretaceous Wealden Supergroup of southern England includes more than its fair share of enigmatic sauropod remains (see Mystery sauropod dorsals of the Wealden part 1, part 2, part 3). Poor taxonomic decisions, a dearth of adequate descriptive literature, and (perhaps) the vague concept that sauropod diversity in the Lower Cretaceous of Europe must be low have combined to prevent adequate appraisal. Recent comments on Wealden sauropods have been provided by Naish et al. (2004), Naish & Martill (2007), Taylor & Naish (2007) and Mannion (2008).
One of the most interesting Wealden sauropods – and I mean ‘interesting’ in an entirely subjective, historiographical sense – is Chondrosteosaurus gigas. This taxon has a rather confusing history that I don’t want to repeat here. The type series consists of two cervical vertebrae: BMNH R46869 and BMNH R46870 (and it is BMNH R46870, despite the occasional use in the literature of ’46780′). We’ve looked at BMNH R46869 before. This time round I want to briefly talk about BMNH R46870. Anyone familiar with the literature on Wealden sauropods will know that this specimen was sectioned and polished. However, to date, only half of BMNH R46870 has been published (Owen 1876, plate V; Naish & Martill 2001, text-fig. 8.4), on both occasions as a mirror-image of the actual specimen. Previously unreported is that both halves of the specimen were polished, and both are in the Natural History Museum’s collection today. And here they are, shown together for the first time ever. I screwed up on the lighting, so sorry for the poor image quality [images © Natural History Museum, London].
A little bit of science has been done on this specimen. Chondrosteosaurus has had a mildly controversial history: it’s been suggested at times to be a camarasaur, but its camellate interior show that it’s a titanosauriform. Because the exact ratio of bone to air can be measured, the specimen lends itself particularly well to an Air Space Proportion analysis of the sort invented by Matt. Indeed, Matt did some ASP work on the figured half of BMNH R46870 in his thesis, finding an ASP of 0.70 (Wedel, Phd thesis, 2007). The average ASP of sampled neosauropod vertebrae is 0.61, and an ASP of 0.70 for the mid-centrum (as opposed to the condyle or cotyle) is most similar to the values present in camarasaurs and brachiosaurs. Mid-centrum ASP values of titanosaurs seem to be lower (Wedel, Phd thesis, 2007).
Anyway, more on Wealden sauropods – hopefully, a lot more – in the future.
References
- Mannion, P. 2008. A rebbachisaurid sauropod from the Lower Cretaceous of the Isle of Wight, England. Cretaceous Research 30, 521-526.
- Naish, D. & Martill, D. M. 2001. Saurischian dinosaurs 1: Sauropods. In Martill, D. M. & Naish, D. (eds) Dinosaurs of the Isle of Wight. The Palaeontological Association (London), pp. 185-241.
- Naish, D. & Martill, D. M. 2007. Dinosaurs of Great Britain and the role of the Geological Society of London in their discovery: basal Dinosauria and Saurischia. Journal of the Geological Society, London, 164, 493-510.
- Naish, D., Martill, D. M., Cooper, D. & Stevens, K. A. 2004. Europe’s largest dinosaur? A giant brachiosaurid cervical vertebra from the Wessex Formation (Early Cretaceous) of southern England. Cretaceous Research 25, 787-795.
- Owen, R. 1876. Monograph on the fossil Reptilia of the Wealden and Purbeck Formations. Supplement 7. Crocodilia (Poikilopleuron). Dinosauria (Chondrosteosaurus). Palaeontographical Society Monographs, 30, 1-7.
- Taylor, M. P. & Naish, D. 2007. An unusual new neosauropod dinosaur from the Lower Cretaceous Hastings Beds Group of East Sussex, England. Palaeontology 50, 1547-1564.
