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

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 last 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 owning big databases about user behaviour.

So the outcomes of NPG’s kind offer, intentionally or not, could include anti-OA propaganda based on poor update, 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.

Aquilops in LA Times - scan

Hey, just a quick announcement this time: today’s LA Times has a nice little article on Aquilops on page A6. It’s also available online here. Good luck tracking down a hardcopy – our local Barnes & Noble doesn’t carry the LA Times (not sure which party that reflects worse on), and I got the last copy from a gas station down the street. I’m so happy that they used Brian’s artwork!

I’ll put up a better scan when I get back to work next week. Later: I did.

How bigsmall was Aquilops?

December 12, 2014

Handling Aquilops by Brian Engh

Life restoration of Aquilops by Brian Engh (CC-BY).

If you’ve been reading around about Aquilops, you’ve probably seen it compared in size to a raven, a rabbit, or a cat. Where’d those comparisons come from? You’re about to find out.

Back in April I ran some numbers to get a rough idea of the size of Aquilops, both for my own interest and so we’d have some comparisons handy when the paper came out.

Archaeoceratops skeletal reconstruction by Scott Hartman. Copyright Scott Hartman, 2011, used here by permission.

Archaeoceratops skeletal reconstruction by Scott Hartman. Copyright Scott Hartman, 2011, used here by permission.

I started with the much more completely known Archaeoceratops. The measurements of Scott Hartman’s skeletal recon (shown above and on Scott’s website – thanks, Scott!) match the measurements of the Archaeo holotype given by Dodson and You (2003) almost perfectly. The total length of Archaeoceratops, including tail, is almost exactly one meter. Using graphic double integration, I got a volume of 8.88L total for a 1m Archaeoceratops. That would come down to 8.0L if the lungs occupied 10% of body volume, which is pretty standard for non-birds. So that’s about 17-18 lbs.

Archaeoceratops and Aquilops skulls to scale

Aquilops model by Garrett Stowe, photograph by Tom Luczycki, copyright and courtesy of the Sam Noble Oklahoma Museum of Natural History.

Archaeoceratops has a rostrum-jugal length of 145mm, compared to 84mm in Aquilops. Making the conservative assumption that Aquilops = Archaeoceratops*0.58, I got a body length of 60cm (about two feet), and volumes of 1.73 and 1.56 liters with and without lungs, or about 3.5 lbs in life. The internet informed me that the common raven, Corvus corax, has an adult length of 56-78 cm and a body mass of 0.7-2 kg. So, based on this admittedly tall and teetering tower of assumptions, handwaving, and wild guesses, Aquilops (the holotype individual, anyway) was about the size of a raven, in both length and mass. But ravens, although certainly well-known, are maybe a bit remote from the experience of a lot of people, so we wanted a comparison animal that more people would be familiar with. The estimated length and mass of the holotype individual of Aquilops also nicely overlap the species averages (60 cm, 1.4-2.7 kg) for the black-tailed jackrabbit, Lepus californicus, and they’re pretty close to lots of other rabbits as well, hence the comparison to bunnies.

Of course, ontogeny complicates things. Aquilops has some juvenile characters, like the big round orbit, but it doesn’t look like a hatchling. Our best guess is that it is neither a baby nor fully grown, but probably an older juvenile or young subadult. A full-grown Aquilops might have been somewhat larger, but almost certainly no larger than Archaeoceratops, and probably a meter or less in total length. So, about the size of a big housecat. That’s still pretty darned small for a non-avian dinosaur.

Although Aquilops represents everything I normally stand against – ornithischians, microvertebrates, heads – I confess that I have a sneaking affection for our wee beastie. Somebody’s just gotta make a little plush Aquilops, right? When and if that happens, you know where to find me.

References

As I mentioned in my first post on Aquilops, I drew the skull reconstructions that appear in figure 6 of the paper (Farke et al. 2014). I’m writing this post to explain that process.

We’ve blogged here before about the back-and-forth between paleontologists and artists when it comes to reconstructing and restoring extinct animals (example 1, example 2). Until now, I’ve always been the guy making suggestions about the art, and asking for changes. But for the Aquilops project, the shoe was on the other foot: Andy Farke was my ‘client’, and he had to coach me through drawing a basal ceratopsian skull – a subject that I was definitely not familiar with.

Aquilops skull - Farke et al 2014 figure 3

I started from the specimen, OMNH 34557, which is more complete than you might think at first glance. The skull is folded over about 2/3 of the way up the right orbit, so in lateral view it looks like the top of the orbit and the skull roof are missing. They’re actually present, just bent at such a sharp angle that they’re hard to see at the same time as the lateral side of the skull.

Archaeoceratops lateral

I also used a cast skull of Archaeoceratops as a reference – it’s clear from what we have of Aquilops that the two animals were pretty similar.

Aquilops skull lateral 1 - outline

I started with this pencil outline on a piece of tracing paper.

Aquilops skull lateral 2 - rough stipple

And then I went right ahead and stippled the whole thing, without showing it to Andy until I was done. Yes, that was dumb. Noe the lack of sutures in this version.

Aquilops skull lateral 3 - rough stipple marked up

I added sutures and sent it off to Andy, who sent it back with these suggested changes. At this point I realized my error: I had already spent about a day and a half putting ink on the page, and I’d have to either start all over, or do a lot of editing in GIMP. I picked the latter course, since there were plenty of areas that were salvageable.

Aquilops skull lateral 4 - redrawn bits

Next I did something that I’d never done before, which is to redraw parts of the image and then composite them with the original in GIMP. Here’s are the redrawn bits.

Aquilops skull lateral 5 - penultimate version

With those bits composited in, and a few more tweaks to sutures, we got to this version, which was included in the submitted manuscript.

Aquilops skull lateral 6 - beak curvature issue

Then we brought Brian Engh in to do the life restorations. When Brian takes on a project, he does his homework. If you’ve seen his post on painting Aquilops, you know that all of the ferns in the Cloverly scene are based on actual fossils from the Cloverly Formation. Brian came to Claremont this summer and he and Andy and I spent most of a day at the Alf Museum looking at the specimen and talking about possible layouts for the full-body life restorations. He took a bunch of photos of the specimen while he was there, and a day or two later he sent us this diagram. He’d chopped up his photos of the skull to produce his own undistorted version to guide his painting, and in doing so he’d noticed that I had the line of the upper jaw a bit off.

Aquilops skull lateral 7 - partly revised

That required another round of digital revisions to fix. It ended up being a lot more work than the earlier round of edits in GIMP, because so many features of the skull had to be adjusted. I ended up cutting my own skull recon into about 8 pieces and then stitching them back together one by one. Here’s what the image looked like about halfway through that process. The back of the skull, orbit, and beak are all fixed here, but the snout, cheek, and maxilla don’t yet fit together.

Aquilops skull lateral 8 - final published version

After a little more work, I got the whole thing back together, and this is the final version that appears in the paper. It is not perfect – the area in front of the orbit where the frontal, nasal, maxilla, and premaxilla come together is a bit dodgy, and I’m not totally happy with the postorbital. But eventually you have to stop revising and ship something, and this is what I shipped.

Aquilops dorsal recon lineup for SV-POW

I did the dorsal view after the submitted version of the lateral view was finished. It went a lot faster, for several reasons:

  • Most of the gross proportional issues were already sorted out from doing the lateral view first.
  • The bilateral symmetry didn’t cut down on the number of dots but it did cut the conceptual workload in half.
  • I did all my roughs in pencil and didn’t start inking until after we had almost all of the details hashed out.

I did have to revise the dorsal view after getting feedback from Brian about the lateral view, but that revision was pretty minor by comparison. I stretched the postorbital region and tinkered a bit with the face and the frill, and both of those steps required putting in some new dots, but it was still just one afternoon’s worth of work. Here’s the final dorsal recon:

Aquilops dorsal skull reconstruction - final published version

In addition to the Life Lessons already noted in this post, I learned (or rather relearned) this important principle: if you do a big drawing and then shrink it down to column width, fine errors – a shaky line here, an ugly dot there – get pushed down below the threshold of perception. But there’s a cost, too, which is that uneven stippling becomes more apparent. I was skipping back and forth a lot between 25% image scale to see where the problem areas were, and 200% to revise the lines and dots accordingly.

All in all, it was a fun project. It was my most ambitious technical illustration to date, I learned a ton about ceratopsian skulls, and it was nice to get to make at least one substantial contribution to the paper.

Now, here’s the take-away: this is my reconstruction, and both of those words are important. “Reconstruction” because it has a lot of extrapolation, inference, and sheer guesswork included. “My” because you’re getting just one possible take on this. You can download the 3D files for the cranium and play with them yourselves. I hope that other artists and scientists will use those tools to produce their own reconstructions, and I fully expect that those reconstructions will differ from mine. I look forward to seeing them, and learning from them.

For other posts about my stippled technical illustrations, see:

Reference

Farke, A.A., Maxwell, W.D., Cifelli, R.L., and Wedel, M.J. 2014. A ceratopsian dinosaur from the Lower Cretaceous of Western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Today sees the description of Aquilops americanus (“American eagle face”), a new basal neoceratopsian from the Cloverly Formation of Montana, by Andy Farke, Rich Cifelli, Des Maxwell, and myself, with life restorations by Brian Engh. The paper, which has just been published in PLOS ONE, is open access, so you can download it, read it, share it, repost it, remix it, and in general do any of the vast scope of activities allowed under a CC-BY license, as long as we’re credited. Here’s the link – have fun.

Obviously ceratopsians are much more Andy’s bailiwick than mine, and you should go read his intro post here. In fact, you may well be wondering what the heck a guy who normally works on huge sauropod vertebrae is doing on a paper about a tiny ceratopsian skull. The short, short version is that I’m here because I know people.

OMNH 34557, the holotype of Aquilops

OMNH 34557, the holotype of Aquilops

The slightly longer version is that OMNH 34557, the holotype partial skull of Aquilops, was discovered by Scott Madsen back in 1999, on one of the joint Cloverly expeditions that Rich and Des had going on at the time (update: read Scott’s account of the discovery here). That the OMNH had gotten a good ceratopsian skull out of Cloverly has been one of the worst-kept secrets in paleo. But for various complicated reasons, it was still unpublished when I got to Claremont in 2008. Meanwhile, Andy Farke was starting to really rock out on ceratopsians at around that time.

For the record, the light bulb did not immediately go off over my head. In fact, it took a little over a year for me to realize, “Hey, I know two people with a ceratopsian that needs describing, and I also know someone who would really like to head that up. I should put these folks together.” So I proposed it to Rich, Des, and Andy in the spring of 2010, and here we are. My role on the paper was basically social glue and go-fer. And I drew the skull reconstruction – more on that in the next post.

One of the world's smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale.

One of the world’s smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale. Copyright Leah Vanderburg, courtesy of the Sam Noble Oklahoma Museum of Natural History.

Anyway, it’s not my meager contribution that you should care about. I am fairly certain that, just as Brontomerus coasted to global fame on the strength of Paco Gasco’s dynamite life restoration, whatever attention Aquilops gets will be due in large part to Brian Engh’s detailed and thoughtful work in bringing it to life – Brian has a nice post about that here. I am very happy to report that the three pieces Brian did for us – the fleshed-out head that appears at the top of this post and as Figure 6C in the paper, the Cloverly environment scene with the marauding Gobiconodon, and the sketch of the woman holding an Aquilops - are also available to world under the CC-BY license. So have fun with those, too.

Finally, I need to thank a couple of people. Steve Henriksen, our Vice President for Research here at Western University of Health Sciences, provided funds to commission the art from Brian. And Gary Wisser in our scientific visualization center used his sweet optical scanner to generate the hi-res 3D model of the skull. That model is also freely available online, as supplementary information with the paper. So if you have access to a 3D printer, you can print your own Aquilops – for research, for teaching, or just for fun.

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Next time: Aquilöps gets röck döts.

Reference

Farke, A.A., Maxwell, W.D., Cifelli, R.L., and Wedel, M.J. 2014. A ceratopsian dinosaur from the Lower Cretaceous of Western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055

It’s been a week since Nature announced what they are now calling “read-only sharing by subscribers” — a much more accurate title than the one they originally used on that piece, “Nature makes all articles free to view” [old link, which now redirects]. I didn’t want to leap straight in with a comment at the time, because this is a complex issue and I felt it better to give my thoughts time to percolate.

Meanwhile, other commentators have weighed in, and have mostly been pretty negative. John Wilbanks described it as “canonization of a system that says a small number of companies not only do control the world’s knowledge, but should control all the world’s knowledge”; Ross Mounce characterised it as “beggar access”; Peter Murray-Rust says “Nature’s fauxpen access leaves me very sad and very angry”. Perhaps surprisingly, Michael Eisen is more temperate, asking whether Nature’s policy is “a magnanimous gesture or a cynical ploy”, and concluding only “At the end of the day, this is a pretty cynical move”.

I am a bit more optimistic (although as you will see, still not really happy).

First of all, let’s say clearly that this is a step in a good direction. Nature‘s papers are now at least somewhat easier for regular people to get hold of, and that is to be applauded. Even if Mike Eisen’s cynical reading is correct, it’s still a net good.

But — and it’s a big but — I have a huge problem with the use of ReadCube, or any equivalent, to provide a crippled form of access. Rather than Ross’s term “beggar access”, which focusses on the need to get a subscriber to share a link, I think the best term to describe what Nature is offering here is “broken access”. Broken by deliberately locking the content into the ReadCube jail, to prevent printing, downloading, copy-pasting, etc.

My issue with this is two-fold: both practical and philosophical. Practically, PDFs are very far from perfect, but there’s a lot we can do with them (including printing, downloading, copy-pasting, etc.) Most crucially, when I download a PDF, I have it forever. I can refer back to it whenever I need it, without depending on a third party. It becomes part of my research toolkit. I know it’s not going to vanish when my back is turned.

By contrast, we never know when we’re going to be able to read these Nature papers. Certainly not when we’re offline. Maybe not when there’s a service outage. Probably not after the end of the one-year pilot. And you can’t build research on something that you can’t rely on existing. It’s not real.

But the philosophical issue is really burns is that ReadCube exists precisely in order to take away functionality. Its purpose is to make access limited, ephemeral, unreliable and less useful. And I find that offensive. The idea of doing work to remove functionality hurts me. The idea of all those clever people doing all that hard work to take functionality away. It’s wrong. It’s burning value.

So I end up feeling conflicted about the new Nature policy. It is a forward step; but one that I literally don’t ever see myself taking advantage of. A much more useful policy (to me anyway) would be to keep new articles under lock and key, but make them truly open after, say, a year. Because for a scientist, usefulness trumps timeliness.

Finally, Matt makes this point:

Nature papers are short, typically 5 pages or fewer. With big, modern monitors, you can usually get away with screen-shotting a whole page in one go, or in two takes and the world’s easiest GIMP stitch at worst. So by not allowing people to download the PDFs, all they’ve done is ensure that the people who really need their own offline copy will have to waste maybe 15 minutes assembling one. So the ‘barrier’ they’ve put up is low and crossable, it’s just annoying. Is that what Nature wants to be known for, annoying their users to death?
It’s a real issue. For many people, their main impression of Nature is now going to be “that journal where you have the read the papers in that weird UI where you can’t do anything”.
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