April 30, 2016
I love Utah. I love how much of the state is given over to exposed Mesozoic rocks. I love driving through Utah, which has a strong baseline of beautiful scenery that is frequently punctuated by the absolutely mind-blowing (Arches, Bryce Canyon, Zion, Monument Valley…). I love doing fieldwork there, and I love the museums, of which there are many. It is not going too far to say that much of what I learned firsthand about sauropod morphology, I learned in Utah (the Carnegie Museum runs a close second on the dragging-Matt-out-of-ignorance scale).
There is no easy way to say this so I’m just going to get it over with: Mike has never been to Utah.
I know, right?
But we’re going to fix that. Mike’s flying into Salt Lake City this Wednesday, May 4, and I’m driving up from SoCal to meet him. After that we’re going to spend the next 10 days driving around Utah and western Colorado hitting museums and dinosaur sites. We’re calling it the Sauropocalypse.
Why am I telling you this, other than to inspire crippling jealousy?
First, Mike and I are giving a pair of public talks next Friday evening, May 6, at the USU-Eastern Prehistoric Museum in Price. The talks start at 7:00 and will probably run until 8:00 or shortly after, and there will be a reception with snacks afterward. Mike’s talk will be, “Why giraffes have such short necks”, and my own will be, “Why elephants are so small”.
Second, occasionally people leave comments to the effect of, “Hey, if you’re ever passing through X, give me a shout.” I haven’t kept track of all of those, so this is me doing the same thing in reverse. Here’s our itinerary as of right now:
May 4, Weds: MPT flies in. MJW drives up from Cali. Stay in SLC/Provo area.
May 5, Thurs: recon BYU collections in Provo. Stay in SLC/Provo area.
May 6, Fri: drive to Price, visit USU-Eastern Prehistoric Museum, give evening talks. Stay in Price.
May 7, Sat: drive to Vernal, visit DNM. Stay in Vernal.
May 8, Sun: visit Utah Field House, revisit DNM if needed, drive to Fruita.
May 9, Mon: visit Rabbit Valley camarasaur in AM, visit Dinosaur Journey museum in PM. Go on to Moab.
May 10, Tues: drive back to Provo, visit BYU collections.
May 11, Weds: BYU collections.
May 12, Thurs: drive to SLC to visit UMNH collections, stay for Utah Friends of Paleontology meeting that evening.
May 13, Fri: BYU collections.
May 14, Sat: visit North American Museum of Ancient Life. MPT flies home. MJW starts drive home.
We’re planning lots of time at BYU because we’ll need it, the quantity and quality of sauropod material they have there is ridiculous. As for the rest, some of those details may change on the fly but that’s the basic plan. Maybe we’ll see you out there.
April 29, 2016
Here’s an awesome thing that just landed in my mailbox: the new monograph on the Thirioux dodos by Leon Claessens and his collaborators. They’ve done a better job describing what’s cool about these specimens than I could, so for the rest of this post I’m just borrowing their text from the Aves3D site, where you can view 3D models of whole dodo skeletons and many individual elements (not to mention zillions of elements from lesser, non-dodo birds):
The dodo (Raphus cucullatus) skeleton on exhibit at the Durban Natural Science Museum is one of two unique skeletons discovered and assembled more than a century ago by the amateur naturalist Etienne Thirioux. Thirioux’s two dodos are unique, not just because they are the most complete skeletons in existence, but also because they are the only two skeletons comprised of the bones of either a single individual bird (the Port Louis dodo), or the bones of (only) a few different birds (the Durban dodo). In contrast, all other known dodo skeletons are incomplete and are typically put together from separate fossil bones uncovered at a marsh called the Mare aux Songes.
The Thirioux specimens contribute greatly to our understanding of the anatomy of the extinct dodo and are the subject of a new, major monographic treatise:
Anatomy of the dodo (Raphus cucullatus L., 1758): An Osteological Study of the Thirioux specimens.
Leon P. A. M. Claessens, Hanneke J. M. Meijer, Julian P. Hume, and Kenneth F. Rijsdijk (Editors).
Society of Vertebrate Paleontology Memoir 15, Journal of Vertebrate Paleontology Vol. 35, Supplement to No. 6.
We are pleased to make the Thirioux dodo skeletons available to the public for viewing on Aves 3D and Sketchfab. Please enjoy these wonderful scans of the skeleton of a fascinating bird, and check back on the site frequently, as we continue to upload more new dodo bone scans each week.
for the Dodo Research Programme and the Aves 3D team
Congratulations, Leon and team, on a landmark publication. And thanks for all the free dodo visualizations!
For previous dödö-related musings, please see this pöst.
April 28, 2016
Yesterday we got a treat: the description of a new titanosaur, Sarmientosaurus musacchioi, based on some decent cervical vertebrae and an almost absurdly nice skull from the Upper Cretaceous of Argentina (Martinez et al., 2016). It was published in PLOS ONE so it’s free to the world, including a 3D PDF of the skull and some awesome visualizations. Get all that good stuff here.
I had one day’s warning about this – Brian Switek contacted me on Monday to ask if I’d be willing to lend my thoughts on the new critter for his news article for National Geographic, which you can read here. As always, I sent more stuff than he could use, so I’m recycling the long form for the rest of this post.
Brian’s first question was about how Sarmientosaurus stands out. I wrote:
Sarmientosaurus has probably the most complete and best-preserved skull of any sauropod from South America to date. It’s kind of funny – for so long we had so few good skulls from brachiosaurs and titanosaurs, and now we’re getting them, but without much of the rest of the skeleton. In North America, unquestionably the nicest Cretaceous sauropod skull is that of the brachiosaurid Abydosaurus, but all we have with the skull is a bit of the neck. Same situation now with this new titanosaur, Sarmientosaurus. I’m not complaining – great skulls without bodies are still great skulls! – but it will be nice to someday connect heads and bodies.
Also, the authors are to be commended – I don’t think anyone has ever done such a thorough job describing the skull of a sauropod dinosaur. This paper will become the standard to which all others are compared going forward.
I stand by all of that. This new paper is just ridiculous in quantity and quality of descriptive detail. Do you like technicolor sauropod palates? Here, have a technicolor sauropod palate:
The next question from Brian was about the head posture and the inference drawn by Martinez et al. (2016) that Sarmientosaurus fed at ground level. My take:
It doesn’t seem unlikely to me that Sarmientosaurus had a downward-facing snout. As for being a low grazer, I am skeptical. The inner ear usually tells us something about the alert posture of an animal, not its feeding posture. Take rhinos – some of them graze from the ground, and some of them browse up higher, but they all carry their heads the same way. Most grazers have wide snouts, whereas that of Sarmientosaurus is pointed and even a little narrower than that of Giraffatitan. That’s a curious shape for a supposed grazer.
So there are three points to unpack here. First, I chose my words deliberately in saying that the inner ear tells us “something” about the alert posture, because in fact the horizontal semicircular canals (HSCCs) aren’t great even at that. As I wrote in this post seven years ago:
Where SCCs have really attracted attention in paleontology is the “more or less” horizontal orientation of the HSCCs in living animals. Some authors have argued that if you set the HSCCs level or close to level, you can figure out how the head was oriented in life.
Well, maybe. The problem is that there is a LOT of variation around level. In birds surveyed by Duijm (1951), HSCC orientation varied by 50 degrees among taxa, from 20 degrees below horizontal to 30 degrees above. Furthermore, in humans HSCC orientation varies by up to 20 degrees among individuals. Possibly humans are weirdly variable, but it seems at least equally likely that most critters are and we’ve only discovered that variation in humans because of the huge sample size.
However you slice it, those are darn big error bars around any given head posture. That doesn’t mean that HSCC orientations in dinosaurs and other extinct vertebrates are worthless for determining posture (they may also be a source of taxonomic information). Strictly speaking, it means that preserved HSCCs can get us in the 50-degree ballpark but can’t narrow things down any further. This is one of those areas in paleontology where we’re just going to have to live with a certain amount of uncertainty, at least for now.
As far as I know, that’s all still true. But I’d love to be wrong.
Second, there’s the difference between alert posture and feeding posture. Go watch horses graze – the skull is practically vertical while they’re feeding, but that’s not the orientation you get from the HSCCs. So if I’m skeptical about ignoring the error bars around HSCC orientation to determine alert posture, I’m even more skeptical about trying to infer feeding posture from them. Also, the rhino point – we have an extant group with closely related taxa where one is a grazer (white rhino, Ceratotherium) and one is a browser (black rhino, Diceros). They hold their heads about the same. So feeding preference will not necessarily be reflected in normal, non-feeding head posture.Third, muzzle shape. Most grazers have wide mouths, but as I said in the email to Brian – and as this figure shows – the snout of Sarmientosaurus is narrower than that of Giraffatitan, and I don’t think anyone is seriously proposing that Giraffatitan was a grazer. So if Sarmientosaurus was more committed to low-level feeding than more basal titanosauriforms, its face was evolving in the wrong direction. Just sayin’.
(Incidentally, I am hugely in favor of figures like 33 and 34 in Martinez et al., 2016, which make it easy to compare the new critter to a selection of reference taxa. I wish everyone would do this all the time.)Finally (final for the purposes of the interview), Brian noted that in the media sauropods are often depicted as all being pretty much the same, and he asked what made Sarmientosaurus stand out. My response:
Until now, the skulls we’ve found of basal titanosauriforms – brachiosaurs and relatives – and more derived titanosaurs haven’t looked much alike. To me Sarmientosaurus is cool because it bridges that gap. From the top and the front the skull looks a lot like those of Brachiosaurus and Giraffatitan – really wide, pretty big teeth, long toothrow. But from the side, the smaller nostrils and long snout have obvious similarities to more derived titanosaurs like Nemegtosaurus. And they phylogenetic analysis confirms that, which is nice. But you can take one look at this thing and say, “Yeah, cool, we’ve been waiting for someone like you.”
The lateral views of titanosauriform skulls in the above figure nicely illustrate my point. If you took the Giraffatitan skull in A and the Tapuiasaurus skull in F and did a 50% morph between them, you’d get something pretty darned close to Sarmientosaurus. And about halfway between Giraffatitan and the really derived saltasaurids is where the phylogenetic analysis puts Sarmientosaurus. The gestalt of the skull nicely reflects the animal’s relationships, which does not always happen.
Oh, there are cervical vertebrae, too, and a seriously weird ossified tendon that is apparently not a cervical rib, but those will keep for another post.
The take-home here is that although I disagree with the authors on a few points of paleobiological interpretation, the Sarmientosaurus fossils are spectacular and Martinez et al. (2016) have done a tremendous job of describing and illustrating them. And the paper is free to anyone who wants it, as it should be. One of the great delights of the last few years has been watching PLOS ONE and PeerJ become the preferred outlets for high-quality descriptive work on dinosaurs.
Now if we can just find more of this thing!
Martínez RDF, Lamanna MC, Novas FE, Ridgely RC, Casal GA, Martínez JE, et al. (2016) A Basal Lithostrotian Titanosaur (Dinosauria: Sauropoda) with a Complete Skull: Implications for the Evolution and Paleobiology of Titanosauria. PLoS ONE 11(4): e0151661. doi:10.1371/journal.pone.0151661
In this short series on the moral dimensions of open (particularly open access), we’ve considered why this is important, the argument that zero marginal cost should result in zero price, the idea that the public has a right to read what it paid for, the very high profit margins of scholarly publishers, and the crucial observation that science advances best and fastest when we can build on each other’s work with minimal friction. I’d like to bring the series to a close by asking this question: if we want change, who is responsible for bringing it about?
Often, those most committed to open-access ideals are students and early-career researchers. But we may feel that those just starting out on their careers are the ones with most to lose (or with the least to gain) if they make pro-open stands such as only publishing their work in open-access journals, or agitating for change at their institutions.
Perhaps the responsibility lies with those who have already acquired positions in academia? There are two problems with that. One is that even an academic who has a job wants to present the best possible case for promotion — and, when it’s available, for tenure. The other is that even those who are fully secure and happy in their posts do much of their work in collaboration with Ph.D students and postdocs, and may feel that they owe it to those younger collaborators not to make their paths more difficult by insisting on open access.
Perhaps, then, the responsibility for change lies with senior academics who hold influential administrative roles, having graduated past the point of doing their own research? There are the people with the most power to bring about change, and with the least likelihood of losing out. Yet these people earned their roles by excelling under the old system of paywalled papers and journal prestige as a surrogate for evaluating quality. Is it reasonable to expect these people to turn against the very system that gave them such success?
And we can hardly expect the turkeys who work for legacy publishers to vote for Christmas.
It turns out that everyone, no matter what their career stage or what their role in the world of scholarly communication, has a legitimate reason to say “No, it shouldn’t be my responsibility”.
And that being so, there is only one possible answer to the question “Who should take responsibility?” That answer is, “I should”. Whoever I am.
From my own unique position on the fringes of academia, I take responsibility to do what little I can to bring about the changes that the world needs in how science is communicated. From his position as a postdoc, Jon Tennant does what he can. From her first academic job, Erin McKiernan does what she can. From his relatively secure academic post, Matt Wedel does what he can. From his position running a highly visible and successful lab, Mike Eisen does what he can. And in his powerful role as Rector of the University of Liège, Bernard Rentier does what he can.
It’s simply no use any one of us shrugging and saying “What can I do?” At the same time, it’s also true that, for most of us, what we can do is not very much. But the crucial truth is that by each of us doing what we can, we have done great work over the last decade in pushing towards the world we now live in: where open access is no longer seen as a fringe concern of naive idealists, but is the model used by the world’s biggest and most cited academic journal, where it’s required by 500 university policies and national policies in the USA, UK and many other countries, and where I am proud to say that my own discipline of vertebrate palaeontology now seems to happen primarily in open-access journals.
So we can give ourselves a pat on the back. Go right ahead, do it now — I’ll wait.
But there is an enormous amount still to do. Gold open access is absurdly overpriced. Green open access remains subject to delays, deliberately imposed by reprehensible embargoes. The obsession with journal rank continues. Open data policies remain rare, and are not well enforced. Barrier-based publishing continues to dominate by volume of published papers. Text and data mining initiatives are repeatedly stymied by publisher who bar access even to subscribers. Much of what is published as “open access” is under restrictive licences that pointlessly prohibit many ways of using the work. And there are myriad other related issues still to be resolved, such as the wastefulness of traditional pre-publication peer-review.
How can we fix all these problems?
The same same way we got to where we are now with open access. By each one of us doing what we can to advance sane, efficient, inexpensive, moral means of scientific communication in whatever role we find ourselves. No one of us can fix this. But every one of us can make a contribution.
This blog is nine years old. Since Matt and I are both still enjoying it, there’s no reason think it won’t still be going in another nine years. Strange as it is to imagine SV-POW! in 2025, I hope I can look forward to writing then in an environment where scholarly paywalls are seen as anachronistic and laughable, where publication is faster and more transparent, where data is routinely re-used, and where researchers are evaluated according to the quality of their work, not according to the brand-name they attach to it.
 By the way, I might note that the OA advocates I’ve known as students all seem to have gone on to good postdocs, and the OA advocates I’ve known as postdocs all seem to have gone on to find jobs in academia. I’m not sure what to make of that observation, but I’ll just leave it here.
 It’s certainly true that the most useful descriptive papers are now always in OA journals, where there are no arbitrary limits on length or number of illustrations, or colour fees.
Several drinks later, they all die and somehow become skeletonised, and that’s how they all land up on a table in my office:
Top left: pieces of monitor lizard Varanus exanthematicus. Cervical vertebrae 1-7 on the piece of paper, femora visible above them, bits of feet below them. Awaiting reassembly. The whole skeleton is there.
Top right, on a plate on top of some lizard bits: skull, cervicals and feet of common pheasant Phasianus colchicus. The skull has come apart, and I can’t figure out how to reattach the quadrates. One of the feet is cleanly prepped out and waiting to be reassembled, while the other retains some skin for now.
Bottom left: skull and anterior cervicals of red fox Vulpes vulpes. Lots of teeth came out during the defleshing process, and will need to be carefully relocated and glued after the skull has finished drying out.
Bottom right: skull and anterior cervicals of European badger Meles meles. The skull is flat-out awesome, and by far my favourite among my mammal skulls. If tyrannosaurs were medium-sized fossorial mammals, they’d have badgers’ skulls for sure. A few teeth that came out have been glued into place; once the glue is dry, this skull is done.
April 13, 2016
the whole idea is idiotic.
Plagiarism is “presenting someone else’s work or ideas as your own“. So self-plagiarism is presenting your own work or ideas as your own. Which is nonsense.
Can we please abandon this unhelpful and misleading phrase?
Note added subsequently, in response to Snarky Mᶜ̵Snarkface’s tweet: my real point is that discussion of the practice is actively confused by the use of this misleading term for it.
What I want to look at this time is the efficiency of sharing: as Glyn Moody pointed out on Twitter, the more people share, the more others can build on it, then share, then build — and so on. The work each of us does becomes easier, and better, and more productive, because of the work others have already done. We become partners in the great enterprise of research.
This is hardly a novel observation, of course. Isaac Newton famously said it best, in a letter to Robert Hooke on 15 February 1676. Although he was not by nature a modest man, he made the rather brilliant observation: “If I have seen further it is by standing on the shoulders of giants”.
But the great thing about this is that the quote itself stands on the shoulders of a giant — it’s a modified version of an earlier observation by John of Salisbury (1120 – October 25 1180), who wrote:
Bernard of Chartres used to say that we were like dwarfs seated on the shoulders of giants. If we see more and further than they, it is not due to our own clear eyes or tall bodies, but because we are raised on high and upborne by their gigantic bigness.
And as Johnny-boy makes clear, he was also not the originator of this profound observation — it was due to Bernard of Chartres, who died shortly after John of Salisbury was born.
What’s happened here? Newton has not merely lifted John-of-S.’s quote: he has substantially improved on it. Newton’s version is pithier and more striking: there’s good reason why it’s the version everyone quotes. He built on the earlier work of J.-of-Salisbury, and the yet earlier work of B.-of-C., to make something new and valuable.
And this of course is the whole purpose of scholarly communication. It’s why we have academic publishers: to make it possible for us to progress our fields by standing on each other’s shoulders.
Unfortunately, the publishers are mostly standing on our toes.
No-one intended this. No-one started an academic publisher for the money (at least, not until recently), but out of genuine desire to advance scholarship. In the pre-Internet era, journals were simply the state of the art for disseminating information. And since each printed copy of a journal cost money to make and distribute, a fee was quite properly charged for each copy. There was no alternative.
All that changed with the advent of the Internet in general, and the World Wide Web in particular. Now that the Web is used for so many things — commerce, media streaming, blogging, auctions, cat photos — it’s easy to forget what it was invented for. But we needn’t forget, because we have archived copies of the very first email ever sent by Tim Berners-Lee about this new “World Wide Web” thingy that he had come up with:
Yes, folks, you read it right. The whole purpose of the Web was to enable the free sharing of scholarly publications. It was a technology given to the world for the betterment of information sharing.
Viewed in this light, it’s clear that open access is nothing more than the Web working right. And the continuation of printed-on-paper journal limitations by other means (i.e. paywalls) constitutes a deliberate impediment to all the advances we could be making now that the technology has improved.
By happy coincidence, Peter Murray-Rust has blogged just today about some of those possible advances — in this case, based on content mining:
We have already shown that mining detects errors in the literature which can be put right – indeed our technology could be valuable in the reviewing and editing of material for publication. Another is the sheer scale – we could mine the whole literature for – say – breeding grounds and create systematic maps. That brings benefits. But there are also dangers – it may pinpoint endangered areas or species. But this is the inevitable challenge of the Digital Century – we have to learn how to live with and manage massive new knowledge.
(The bolding of the last part is mine, not Peter’s.)
We’re facing the possibility of such an enormous amount of new knowledge that one of the challenges we will be presented with is how to live with it. We have the technology to stand on the shoulders of millions of giants simultaneously. What a great problem to have! And how tragic when 20th-Century technology actively prevents us from reaching this state.
This shoulders-of-giants argument regarding Open is a very positive one. I like that. Some pro-open arguments can be rather negative: “publishers make too much profit”, “the public shouldn’t be prevented from reading what it paid for” and so on. But this one is wholly positive: open access, and open scholarship in general, enables us to do much more!
I’ve leave the last word to Cameron Neylon, and a blog-post that I have often cited as a vision of our possible future: Network Enabled Research: Maximise scale and connectivity, minimise friction:
We need to get as much material online as fast as we can. We need to connect it up, to make it discoverable, to make sure that people can find and understand and use it. And we need to ensure that once found those resources can be easily transferred, shared, and used. And used in any way – at network scale the system is designed to ensure that resources get used in unexpected ways. At scale you can have serendipity by design, not by blind luck.
Let’s not accept systems and conventions that prevent this happening.
[ Finish up with part 5: whose responsibility is this?]