June 30, 2015
You know what’s wrong with scholarly publishing?
Wait, scrub that question. We’ll be here all day. Let me jump straight to the chase and tell you the specific problem with scholarly publishing that I’m thinking of.
There’s nowhere to go to find all open-access papers, to download their metadata, to access it via an open API, to find out what’s new, to act as a platform for the development of new tools. Yes, there’s PubMed Central, but that’s only for work funded by the NIH. Yes, there’s Google Scholar, but that has no API, and at any moment could go the way of Google Wave and Google Reader when Google loses interest.
Instead, we have something like 4000 repositories out there, balkanised by institution, by geographical region, and by subject area. They have different UIs, different underlying data models, different APIs (if any). They’re built on different software platforms. It’s a jungle out there!
As researchers, we don’t need 4000 repos. You know what we need? One Repo.
Hey! That would be a good name for a project!
I’ve mentioned before how awesome and pro-open my employers, Index Data, are. (For those who are not regular readers, I’m a palaeontologist only in my spare time. By day, I’m a software engineer.) Now we’re working on an index of green/gold OA publishing. Metadata of every article across every repository and publisher. We want it to be complete, in the sense that we will be going aggressively for the long tail as opposed to focusing on some region or speciality, or things that are easily harvestable by OAI-PMH or other standards. We want it to be of a high, consistent quality in terms of metadata. We want it to be up to date. And most importantly, we want it to be fully open for all and any kind of re-use, by any other actor. This will include downloadable data files, OAI-PMH access, search-retrieve web services, embeddable widgets and more. We also envisage a Linked Data representation with a CRUD interface that allows third parties to contribute supplemental information, entity reconciliation, tagging, etc.
Instead of 4000 fragments, one big, meaty chunk of data.
Because we at Index Data have spent the last ten years helping aggregators and publishers and others getting access to difficult-to-access information through all kinds of crazy mechanisms, we have a unique combination of the skills, the tools, and the desire to pursue this venture.
So The One Repo is born. At the noment, we have:
- Harvesting set up for an initial set of 20 repositories.
- A demonstrator of one possible UI.
- A whitepaper describing the motivation and some of the technical aspects.
- A blog about the project’s progress.
- An advisory board of some of the brightest, most experienced and wisest people in the world of open access.
We’ve been flying under the radar for the last month and a bit. Now we’re ready for the world to know what we’re up to.
The One Repo is go!
March 9, 2014
Although it would be nice to think that our site views have octupled in the last day because of Mike’s fine and funny posts about what search terms bring people to SV-POW!, the real reason is that we were blessed by incoming links from both pages of this Cracked.com article.
Now, as any person who has ever accomplished anything whatsoever knows, it is super-important to avoid Cracked.com or you’ll still be up 23 hours from now reading, “6 Mind-Blowing Ways that Comedy Writers are Secretly Destroying Your Productivity”. (I’m kidding, that article doesn’t really exist–but if it did, I’m sure it would consist entirely of descriptions and links to six other Cracked articles). But that’s only true because most of the articles there hit the sweet spot at the intersection of funny, surprisingly informative, mercifully short, and well-written. Crack.com would be a more honest URL, but I assume it was taken.
Anyway, I’d like to return the favor, so here’s a list of the 6 SV-POW! Posts Most Likely to Blow the Minds of Cracked.com Readers. If I missed some goodies or recommended some stinkers, let me know–the comment thread is open.
Who doesn’t want to read about the bizarre real-world mystery surrounding what might have been the world’s largest dinosaur? If you’re not sold, consider that the picture above shows a single vertebra that was–or at least might have been–seven and a half feet tall.
The mercifully short version of this much longer post, in which I consider the consequences of the world’s largest animals having the world’s longest cells.
Weapons-grade anatomical pedantry.
Yes, there is a ship in Star Wars: The Clone Wars that is basically a flying dinosaur vertebra. It took us about five weeks to unravel that story–the post linked above has links to the rest of the saga.
Our original linkbait post. Don’t miss the shorter follow-up with more critters.
A deliberately goofy post in which I wax poetic about the largest predatory dinosaur claws ever discovered.
So, that was a big pile of superlatives and Star Wars. If you’re hungry for more substantial fare, you might start with our Tutorials page or our Things to Make and Do series on dissecting and skeletonizing modern animals. We also blog a lot about the evils of obstructive publishers and the need for open access to the scientific literature–you can find those posts on our Shiny Digital Future page.
A parting shot in my desperate quest for attention: this Star Wars ship flying around in the background in Firefly and Serenity is at least partly my fault–full story here. Oh, and my co-blogger Mike Taylor has written an insightful and affordable book about Doctor Who; read about it here.
March 11, 2013
For a paper that I and Matt are preparing, we needed to measure the centrum length of a bunch of turkey cervicals. That turns out to be harder than you’d think, because of the curious negative curvature of the articular surfaces.
Above is a C7 from a turkey: anterior view on the left; dorsal, left lateral and ventral views in the middle row; and posterior on the right. As you can see from the anterior, dorsal and ventral views, the anterior articular surface is convex dorsoventrally but concave transversely; and as you can see from the lateral view, the posterior face is concave dorsoventrally and convex transversely.
This means you can’t just put calipers around the vertebra. If you approach the vertebra from the top or bottom, then the upper or lower lip of the posterior articular surface will protrude past the centre of the saddle, and give you too long a length. If you approach from the side, the same will happen with the left and right lips of the anterior articular surface.
What are we trying to measure anyway?
But this raises the question of what it is we’re trying to measure. I said “we needed to measure the centrum length of a bunch of turkey cervicals”, but what exactly is centrum length? Why shouldn’t the upper and lower lips of the posterior articular surface count towards it?
What does centrum length mean?
The problem doesn’t only arise with bird cervicals. The same issue arises in measuring more sensible and elegant vertebrae, such as our old friend HMN SII:C8, or MB.R.2181:C8 as we must now learn to call it.
Although the back of the vertebra is nice and simple here — it’s obvious what line we’re measuring to at the back — we have three choices of where the “front” of the vertebra is, and a case can be made for any of them as being “the length of the vertebra”.
The longest measurement (here marked “T” for “total length”) goes to the front of the prezygapophyseal rami. The next one (“C” for “centrum length”) goes to the anteriormost point of the condyle. The distinction is important: as noted recently, the longest vertebra in the world belongs to Sauroposeidon if we use total length, but to Supersaurus if we use centrum length.
But in life, most of the condyle would be buried in the cotyle of the preceding vertebra. So should it count towards the length of the vertebra? If you consider a string of articulated vertebrae, the buried condyles don’t contribute to the overall length of the neck. So Matt and I call the length from the posterior margin of the condyle to the posterior margin of the cotyle the functional length (marked “F” above), which I believe is a new term.
Another way to think of the functional length is the distance from a given point on a vertebra (in this case the posterior margin of the cotyle) to the same point on the adjacent vertebra:
For our current project, Matt and I are interested in how the lengths of individual vertebrae contribute to total neck length, so for our purposes, functional length is definitely what we want.
By the way, Janensch is the only author I know of to have even recognised the importance of functional length. The measurement tables on pages 39 and 44 have columns for “Gesamtlänge des Wirbels ab Vorderende per Präzygapophyse”, “Gesamtlänge der Wirbel-Körpers in 1/2 Höhe” and “Länge der Wirbel-körpers ohne Condylus in 1/2 Höhe” — that is, “Total length of the vertebra from the anterior end of the prezygapophysis”, “Total length of the centrum measured at mid-height” and “Length of the centrum minus condyle at mid-height”. This is typical of his careful and methodical approach. Kudos!
Hey! I thought this was about turkeys
And so it is. Here is the functional length measurement for a turkey cervical:
It’s the shortest anteroposterior distance between the two articular surfaces.
Measuring functional length
Matt and I chatted about this at some length, and I am ashamed to say that we thought through all sorts of complicated solution involving subtracting measurements from known scaffold length and suchlike.
It took us a stupidly long to to arrive at the very obvious solution, which is just to modify the calipers to have a “tooth” that can protrude into the concavity of the anterior articulation between its left and right lips. Easily done with a flat-ended screw and a blob of wood glue:
With the measurements of all the vertebrae in my series, I can now fairly confidently expect that the sum of the individual lengths will come out at about the length of the complete neck.
You know, unless intervertebral cartilage turns out to be important or something.
- Janensch, Werner. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3:27-93.
1. Matt and I are so used to opisthocoelous sauropod presacrals that when we’re talking about vertebrae — any vertebrae — we tend to say “condyle” and “cotyle” for the anterior and posterior articular surfaces, no matter what their morphology. When talking about crocodile cervicals or titanosaur caudals, we’re even likely to say ridiculous things like “the condyle is concave and the cotyle is convex”. Nonsense, of course: condyle means “A rounded prominence at the end of a bone, most often for articulation with another bone.” What we should say is “the condyle is at the back and the cotyle is in front”.
Update, January 21, 2013: YES, it was! Scroll down for links to the entire saga.
Because it’s doing a hell of an impression of one, if not. It’s got the huge cervical rib loops (wings), bifurcated neural spine (top fins), and even a condyle on the front of the centrum (cockpit pod). About all it’s missing are the zygapophyses and the cervical ribs themselves.
Some actual Apatosaurus cervicals for comparison, from previous posts:
And of course Mike’s magisterial work photographing the Apatosaurus ajax holotype YPM 1860 cervical:
More on the Umbaran Starfighter here.
The complete Umbaran Starfighter Saga–at least as told on SV-POW!:
- Was the Umbaran Starfighter from Clone Wars inspired by an Apatosaurus vertebra? (Dec. 13, 2012)
- Heck, yes, the Umbaran Starfighter from Clone Wars was inspired by an Apatosaurus vertebra (Dec. 15, 2012)
- Umbaran Starfighter vs. Apatosaurus cervical, round 3 (Dec. 16, 2012)
- Umbaran Starfighter update (Jan. 4, 2013)
- CONFIRMED: the Umbaran Starfighter is an Apatosaurus cervical (Jan. 21, 2013)
For other Star Wars/paleontology crossovers, please see:
and–mostly as shameless self-promotion since the paleo link is pretty tenuous:
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
- Upchurch, P., Tomida, Y., and Barrett, P.M. 2005. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs No. 26. Tokyo. ISSN 1342-9574.
- Wedel, M.J., and Sanders, R.K. 2002. Osteological correlates of cervical musculature in Aves and Sauropoda (Dinosauria: Saurischia), with comments on the cervical ribs of Apatosaurus. PaleoBios 22(3):1-6.
Needless to say, one of the things I love most about Paco’s Brontomerus artwork is that it’s a rare and welcome example of the much neglected Sauropods Stomping Theropods school of palaeo-art.
When I reviewed the examples I know of, I was a bit disappointed to find that they number only five. Here they are, in chronological order.
First, we have this gorgeous sketch by Mark Hallett, showing Jobaria (here credited as “unnamed camarasaurid”) quite literally stomping on Afrovenator:
To the best of my knowledge, this has never actually been published — I found it on Dave Hone’s Archosaur Musings, in the interview with Hallett. Mark tells me that this was a concept sketch of possible main art for Paul Sereno’s North African dinosaur article, Africa’s Dinosaur Castaways in the June 1996 issue of National Geographic (Sereno 1996) — three years before Jobaria was described (Sereno et al. 1999); but for some inexplicable reason, it wasn’t used.
It seems incredible to think that there was no published, or even completed but unpublished, sauropod-stomping-theropod art before the mid-1990s, but I’ve not yet found any. I thought that Bakker might have come up with something in The Dinosaur Heresies (Bakker 1986) or The Bite of the Bronto (Bakker 1994); but I flipped through both and I don’t see anything relevant. Anyone know of anything earlier?
The next entry on my list is Luis Rey’s striking Astrodon, carrying away a raptor that bit off more than it could chew.
This appeared in Tom Holtz’s outstanding encyclopedia (Holtz 2007), which I highly recommend for every interested layman, including but not limited to bright kids. The image also turned up, with Luis’s permission, in the publicity for Xenoposeidon — notably in The Sun, one of Britain’s most downmarket, lowest-common-denominator tabloids, where it was a pleasant surprise indeed.
I just love the expression on the raptor’s face. He’s going HOLY CRAP!, and his buddies are all like, Hey, dude, c’mon, we were only playing! But Astrodon‘s all, Nuh-uh, you started this, I’m going to finish it.
Next up, and a year, later, we have this moody just-going-about-my-business Camamasaurus, squishing theropod eggs, nests and babies in a casual sort of way, as though he’s saying “Well, you should have got out of my way”:
As it happens, this one was done for me, by Mark Witton. It was intended as an illustration for a “Fossils Explained” article that I was going to do for Geology Today on the subject of (get ready for a big surprise): sauropods. In fact, I am still going to do it. But since it’s been two and a bit years since I got the go-ahead from the editor, I’m hardly in a position to complain that Mark gave the image to Dave Martill and Darren when they suddenly needed artwork to publicise the findings of their Moroccan expedition. (Since then, the Mail seems to have re-used this picture pretty much every time they have a story about dinosaurs — even when that story is complete and utter crap.)
I don’t mind too much about this Witton original being whisked away from me, because shortly afterwards Mark went on to provide me with a much better piece — the beautifully wistful Diplodocus herd scene that we used in the publicity for our neck-posture paper.
And, amazingly, that brings us up to date. The next relevant artwork that I know of was Paco’s glorious Brontomerus life restoration, which you’ve already read all about. Just to vary things a bit, this is the second of the two renders — the one that wasn’t in the paper itself:
So is that the end of the story for now? Happily, not quite. Emily Willoughby produced this alternative Brontomerus restoration on the very day the paper came out!
I’m not going to claim that this is close to the quality of the other four pieces in this article, but you have to admire the speed of the work. Emily wrote most of the initial Wikipedia entry for Brontomerus, and produced this picture to illustrate it. At first when I saw this, I thought Emily had misunderstood the paper as indicating powerful retractors, so that the drawing had Brontomerus kicking backwards like a horse. But when I looked closely I realised it’s kicking outwards, thanks to the enlarged abductors. Neat.
A question and a challenge
I’d like to end this post with a question and a challenge. First, the question: what other pieces of palaeoart have I missed that feature sauropods handing theropods their arses? There have to be others — right?
And the challenge: I’d love it if those of you who are artists were to fix this terrible hole in the fabric of reality? I’d love to see new and awesome art on the timeless theme of sauropods stomping theropods. How about it? If any of you have influence with the Art Evolved people, you might try seeing whether you can get them to join in the challenge. It would be awesome to see a whole new crop of these pieces!
- Bakker, Robert T. 1986. The Dinosaur Heresies: New Theories Unlocking The Mystery of the Dinosaurs and Their Extinction. Morrow, New York. 481 pages.
- Bakker, Robert T. 1994. The Bite of the Bronto. Earth 3 (6): 26-35.
- Holtz, Thomas R., Jr., and Luis V. Rey. 2007. Dinosaurs: The Most Complete, Up-to-Date Encyclopedia for Dinosaur Lovers of All Ages. Random House, New York. 432 pages.
- Sereno, Paul C. 1996. Africa’s dinosaur castaways. National Geographic 189(6):106-119.
- Sereno, Paul C., Allison L. Beck, Didier. B. Dutheil, Hans C. E. Larsson, Gabrielle. H. Lyon, Bourahima Moussa, Rudyard W. Sadleir, Christian A. Sidor, David J. Varricchio, Gregory P. Wilson and Jeffrey A. Wilson. 1999. Cretaceous Sauropods from the Sahara and the Uneven Rate of Skeletal Evolution Among Dinosaurs. Science 282:1342-1347.
 If you want to call it that.
August 26, 2009
Was this just a half-lame attempt to fulfill our titular mandate whilst plugging my new astronomy blog? Of course it was (and I just did it again!). Doesn’t mean you lot are off the hook for figuring out what it is. So here’s another image with more views. You have a week. Don’t let me down.
Oh, and to sweeten the pot, 351 SV-POW!bucks to the person who first figures it out.
UPDATE: Too late, suckers! In a stunning move, Phil Mannion won the contest basically right out of the gate. The vertebra is indeed a cervical of Paluxysaurus (image below from Rose, 2007). Good job, Phil!
Well, now you’re hosed–the contest is over and you’re not due for another post for nearly a week. What to do, what to do? Assuming that you’re all caught up on your Tet Zoo reading, you might want to check out Save Your Breath For Running Ponies. It’s not just a paleo blog, but it has a lot of paleo in it, including lots of smack talk to whatever critter has been in the news lately. For example, see the recent post, “It’s not all mindless sex with beautiful women, placoderm”. This makes SYBFRP sort of the FU, Penguin of paleo.
OR you could discuss the question I posed in the comments: why does “this anterior cervical of Paluxysaurus look so much like Euhelopus, DGM Serie B, etc. The posterior cervicals look like Sauroposeidon, not exactly the same, but lots of similarities. The juxtaposition blew my mind ten years ago, and it still does. Your thoughts are welcome.” They still are.
March 22, 2009
Isn’t this a beauty?
What is it, you ask? We will never know. A friend of mine pointed me to a forthcoming fossil auction by I. M. Chait, and as I scrolled through all the crappy ornithopod skeletons and suchlike, my eye was caught by this bone, described as a “Diplodocus dorsal bone”, from the Bone Cabin quarry in Wyoming. “The dorsal bone most likely came from close to the back of the head[?!]”.
Whatever it is, it ain’t Diplodocus: the metapophyses are too low, the intraspinal trough is not deep enough, the diapophyses are too high up, they’re laterally rather than ventrolaterally inclined, the hyposphene is way too big and too triangular, the centrum is subquadrangular rather than ovoid, the centropostzygapophyseal laminae are absent … I could go on. If you don’t believe me, here is the complete set of Dipodocus carnegii dorsals, from Hatcher (1901: plate VIII): posterior to anterior running from left to right; anterior, posterior and right lateral views from top to bottom.
Not even close.
So what actually is the for-sale vertebra? Of course there is only so much you can say from a single photograph, but it looks very much as though this is something new, as yet undescribed. Unknown to science, in fact. I say that largely because of the those bizarre dorsolaterally oriented struts which extend from the sides of the neural arch to meet and merge with the diapophyses. I don’t recall ever having seen anything like that. In general proportions, too, this vertebra is distinctly odd.
Unknown to science it is, and unknown to science it will remain — if, as seems likely, some rich idiot buys this as a trophy to sit on his cocktail bar. Hence the righeous fury alluded to in the title: so far as the wider world is concerned, so far as our understanding of Morrison Formation ecological diversity is concerned, so far as our understanding of sauropod disparity is concerned, this vertebra might just as well have stayed in the ground.
If anyone reading this blog is a rich benefactor, then just maybe this vert could be rescued: bought by someone who appreciates its scientific significance, and donated to an accredited museum, where it can be properly reposited and scientifically studied. So if any of you out there have $5000 to spare and fancy a decent chance at getting a sauropod named after you, you know what to do.
I’ve hestitated about publishing this post, because of the danger that it will become sufficiently widely known to push the price up. The last thing I want is to make more money for the fossil dealers responsible for taking this thing out of the hands of scientists. But I figured it’s worth the risk. Let’s hope I’m right.
[To be absolutely clear: I. M. Chait did not solicit me to write this, neither do they even know about it, and I am pretty sure they would not be happy about it if they did.]
- Hatcher, Jonathan Bell. 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.
Update (23 March 2009)
We have heard from an SV-POW! reader who is looking into buying this specimen and donating it to a museum. Which would be awesome. (I won’t mention his or her name at this stage until he or she authorises me to do so.) That being so, please no-one else try the same thing — we last thing we want is for two readers to get into a bidding war!