Monthly Archives: December 2014

Aquilops wants to play

Here are three fun things to do with Aquilops, in descending order of how much gear they require.

Aquilops printed fossil skull

1. Print your own Aquilops fossil.

Got access to a 3D printer? Download the 3D models of the holotype skull, OMNH 34557, that we published as supplementary info with the paper, and rock out. Here’s a test print that the guys in our scientific visualization center made for me. I gotta tell you, after 18 and a half years of sauropods, it’s very satisfying to have a holotype I can shove in my pocket. UPDATE a few weeks later: read Zach Miller’s post about his 3D-printed Aquilops holotype, it’s cool.

Want a bigger challenge? If you printed it in steel or titanium, it would probably make a decent bottle opener. Just sayin’.

Aquilops paper skull assembled2. Cut and fold your own Aquilops skull.

Got access to a regular printer? Download these files, print, cut, fold, and enjoy:

Aquilops cut-and-fold – 2 small skulls. Should print 2 skulls at about life size on regular 8.5 x 11 or A4 paper. Warning: they’re small.

Aquilops cut-and-fold – 1 large skull. Warning: still not very big.

I found that regular printer paper is too flimsy to really hold the shape, so I built mine an endoskeleton (endoskull?) out of bits of cut up file folder. Just about anything would work. Teaching a course in which Aquilops could be relevant (which is all of them)? Have your students roll their own paper skulls, and use them as a springboard for talking about dinosaurs or evolution or anatomy or current events or whatever tickles your fancy.

Want a bigger challenge? My cut-and-fold skull is the epitome of laziness: I just mirror-image duplicated my lateral view and sandwiched the dorsal view in between. You could definitely make a better one, and with all of the free Aquilops data online, you have all the raw material you need. If you come up with something good, let me know in the comments and I’ll feature it in a later post.

Aquilops reconstructed skull 3D model screenshot

This is not the model, this is just a screenshot. But when you go to the link below, the 3D model will load in a window that looks just like this. Model by Garrett Stowe, copyright and courtesy of the Sam Noble Oklahoma Museum of Natural History.

3. Play with the 3D models.

No access to a printer of any sort? Well, you can still have fun with Aquilops in your browser and on your hard drive. If you want to see the holotype specimen as it looks today, there are 3D PDFs in the paper’s supplementary info. But if you haven’t been to the OMNH Aquilops page to play with the model of the complete, uncrushed skull that Garrett Stowe made, go do that now. On the same page is a 3D life restoration of Aquilops, also by Garrett Stowe. Both models are awesome, and Garrett is still working on them so they’ll be even better soon.

Want a bigger challenge? Surprise me. We made Aquilops freely available to the world, so you can take any and all of the stuff that we published – the figures from the paper, Brian Engh’s artwork, the 3D models of the fossil – and make cool new things that we haven’t thought of. C’mon, let’s play.

My neck-cartilage angle paper is out!

Arriving as an early Christmas present, and coming in just a week before the end of what would otherwise have been a barren 2014, my paper Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs is out! You can read it on PeerJ (or download the PDF).

Figure 4. Effect of adding cartilage to the neutral pose of the neck of Diplodocus carnegii CM 84. Images of vertebra from Hatcher (1901:plate III). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 2.

Figure 4: Effect of adding cartilage to the neutral pose of the neck of Diplodocus carnegii CM 84. Images of vertebra from Hatcher (1901:plate III). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 2.

Yes, that posture is ludicrous — but the best data we currently have says that something like this would have been neutral for Diplodocus once cartilage is taken into account. (Remember of course that animals do not hold their necks in neutral posture.)

The great news here is that PeerJ moved quickly. In fact here’s how the time breaks down since I submitted the manuscript (and made it available as a preprint) on 4 November:

28 days from submission to first decision
3 days to revise and resubmit
3 days to accept
15 days to publication

TOTAL 49 days

Which of course is how it ought to be! Great work here from handling editor Chris Noto and all three reviewers: Matt Bonnan, Heinrich Mallison and Eric Snively. They all elected not to be anonymous, and all gave really useful feedback — as you can see for yourself in the published peer-review history. When editors and reviewers do a job this good, they deserve credit, and it’s great that PeerJ’s (optional) open review lets the world see what they contributed. Note that you can cite, or link to, individual reviews. The reviews themselves are now first-class objects, as they should be.

At the time of writing, my paper is top of the PeerJ home-page — presumably just because it’s the most recent published paper, but it’s a nice feeling anyway!

Screenshot from 2014-12-23 10:39:34

 

A little further down the front-page there’s some great stuff about limb function in ratites — a whole slew of papers.

Well, I’m off to relax over Christmas. Have a good one, y’all!

My early Christmas present: a dead corn snake

A friend’s daughter owned a pet corn snake, and a hamster. About a month ago, the former got into the latter’s cage — and in a reversal of the usual course of such events, sustained some nasty injuries. As snakes often do, it struggled to recover, and the wound seems to have necrotised.

This morning I got an email from the friend saying that the snake had died, and asking whether I would like it. I managed to restrain my enthusiasm for long enough to express condolences to the daughter; and an hour later, the snake was delivered!

IMG_1861-cleaned

Here it is — as with all these images, click through for the full resolution. I’ve learned that it’s difficult to measure the length of a snake — they don’t lay out straight in the way that you’d like, even when they’re dead — but as best I can make out, it’s 120 cm long. It weighs 225 g, but don’t tell Fiona I used the kitchen scales.

The hamster wound is very apparent, just behind the neck, on the left hand side. Here’s the head and neck in close-up:

IMG_1847-cleaned

Ouch — very nasty. It can’t have been pleasant watching a pet linger on with a wound like that.

He (or she? How do you sex a snake?) was a handsome beast, too. Here’s the head. You can easily make out the individual large scales covering it, and make out some of the shape of the skull.

IMG_1852-cleaned

The skulls of snakes are beyond weird. Here is one from an unspecified non-venomous snake at Skulls Unlimited (i.e. probably not a corn snake):

variants_large_3861

Hopefully at some point I’ll be able to show you my own snake’s skull. In the mean time, this guy says he has a corn-snake skull, but the photography’s not very good.

Finally, here is my snake, mouth open, showing the pterygoid teeth on the roof of the mouth:

IMG_1857-cleaned

What next? It seems clear that bugging is the only realistic way to free up the skeleton, and this may be the specimen that persuades me to invest in a proper colony of dermestids rather than just relying on whatever inverts happen to wander past.

It might be worth trying to skin and gut the snake first. Gutting will be easy; skinning might be very difficult. I think that removing the skin from the skull without damaging the very delicate bones might be impossible. Can dermestids cope with snake skin?

I’m taking advice!

 

My new paper on Haplocanthosaurus is out

Foster and Wedel 2014 fig 3 - dorsals

Fig. 3. MWC 8028, Haplocanthosaurus dorsal vertebrae. A. Lateral view of dorsal centrum with bottom edge of lateral pneumatic fossa preserved. B. Dorsal view of same centrum as in A, showing the median septum between the paired lateral fossae. C. Lateral view of dorsal centrum with smaller segment of the lateral pneumatic fossa margin preserved. D. Dorsal view of same centrum as in C, again showing the median septum and paired lateral fossae. E. Lateral view of dorsal centrum with partial pleurocoel preserved. F. Cross-sectional (posterior) view of same dorsal as in E. G. Dorsal neural spines in lateral (top) and anterior or posterior (center, bottom) views. Scale bars = 10 cm.

Right on the heels of Aquilops last week, my paper with John Foster on the new specimen of Haplocanthosaurus from Snowmass, Colorado, was just published in Volumina Jurassica. I’ll have more to say about it later, but right now I am up against a deadline on a big project and I need to go work on that. I’m only popping up here to note two quick things.

First, if you’re not familiar with Volumina Jurassica – and I wasn’t, before this project – it’s a free-to-access* journal that publishes papers on all aspects of the Jurassic. The current issue is specifically dedicated to the Jurassic formations of the American West. There’s a lot of interesting stuff in there, but of special interest to SV-POW! readers will be the paper by Cary Woodruff and John Foster on the legendary and possibly apocryphal Amphicoelias fragillimus.

* But not truly open access since the journal claims to retain exclusive rights to distribute the papers. That seems like a quaint affectation now that the internet is here, but whatever – at least they let anyone download the PDF for free, which is primarily what I care about.

Foster and Wedel 2014 fig 4 - sacrum

Fig. 4. Sacra of Haplocanthosaurus.  A. MWC 8028, sacrum in right lateral view. B. MWC 8028, close-up of S4 and S5 centra highlighting pneumatic fossae. C. MWC 8028 with divisions between the vertebrae overlaid. D. CM 879, sacrum in right lateral view with divisions between the vertebrae overlaid. E. CM 572 in right lateral view, after Hatcher (1903c: plate 4). B–E are not shown at the same scale, scale bar for A = 20 cm. Note that the neural arches in CM 572 were restored during preparation, and the sacral neural spines as shown here are probably lower than they would have been in life.

Second, the figure resolution in the PDF of the Haplocanthosaurus paper is not stellar, so as is the case with almost all of our papers, the full-color, high-resolution figures are available at the paper’s page on the sidebar.

Gotta run.

For our previous posts on Haplocanthosaurus, go here; for those on Amphicoelias, including Mike’s very popular, “How big was Amphicoelias fragillimus? I mean, really?”, go here.

References

Why I feel horrible about Nature‘s article-sharing initiative

I wrote last week that I can’t support Nature’s new broken-access initiative for two reasons: practically, I can’t rely on it; and philosophically I can’t abide work being done to reduce utility.

More recently I read a post on Nature’s blog: Content sharing is *not* open access and why NPG is committed to both. It’s well worth reading: concise, clear and helpful. The key point they make is that “This is not a step back from open access or an attempt to undermine it. We see content sharing as an additional offering to open access, not instead of it”. But do read the article, as it provides useful background on NPG’s moves towards open access.

So NPG do look pretty much like the good guys here. They are not taking anything away; they are adding a thing that no-one is obliged to use; and they are carefully not claiming that this thing is something it’s not. What’s not to like? Surely at worst this has to have net zero value, yes?

Well, no.

The first thing is that for me the value is not more than zero, because articles that might evaporate at any moment are simply not of value to me as a researcher. If I am going to cite them, I need to have permanent copies, so I can check back on what I meant.

All right — but doesn’t that leave the value at least no less than zero?

Well, it depends. When I wrote last year about the travesty that is “walk-in access” — the ridiculous idea that you can physically go to a special magic building to use their anointed computers to read documents your own computer is perfectly capable of reading — I speculated:

I can only assume that was always the intention of the barrier-based publishers on the Finch committee that came up with this initiative: to deliver a stillborn access initiative that they can point to and say “See, no-one wants open access”.

It’s easy to imagine barrier-based publishers making the same point when take-up of NPG’s broken access is low. That’s one possible bad outcome that would make the broken-access offer a net negative.

Another, much more serious, one would the fragmentation of the literature into multiple mutually incompatible subsets. In this dystopia, you’d have to read NPG papers on ReadCube, Elsevier papers using Mendeley, and so on. As Peter Murray-Rust noted:

Maybe we’ll shortly return to the browser-wars “this paper only viewable on Read-Cube”. If readers are brainwashed into compliance by technology restrictions our future is grim.

Say what you want about PDFs — and there is plenty to dislike about them — the format is at least defined by an open standard: anyone can write software to read and display it, and lots of different groups have created implementations. The idea of papers that can only be read by a specific program (almost certainly a proprietary one) is a horrifyingly retrograde one.

And here’s a third possible bad consequence. ReadCube is one of those applications that “phones home” — it tracks what you read. NPG say that this data is anonymised, but the opportunities for abuse are obvious. Suppose you look up a lot of papers about cancer and find that your health insurance premiums have gone up. You read papers about communist theory, and can’t get a place at the university you thought was keen to take you. Right now, this isn’t happening (so NPG assure us) but history does not give us reason to be optimistic about corporations that own big databases about user behaviour.

So the outcomes of NPG’s kind offer, intentionally or not, could include anti-OA propaganda based on poor uptake, fragmentation of the literature into technically incompatible subsets, and violation of researcher privacy.

Not a pretty prospect.

But here’s why I feel even worse about this: pointing it out feels like throwing a generous offer back in the faces of the people who made it. When I read Timo Hannay’s visionary exposition of what broken access is meant to achieve, and Steven Inchcoombe and Grace Baynes clear explanation of what it is and isn’t, I see good people honestly trying to do good work, and I hate to be so negative about it.

So my heartfelt apologies to Timo, Steven and Grace; but I gotta call ’em like I see ’em, and to me broken access looks like an offer with very low value, and carrying several significant threats.

What I would really like to see from NPG — an unequivocal good that I could celebrate unreservedly — would be for them to make all their articles properly open access (CC By) after one year. That would be a genuine and valuable contribution to the progress of research.