Anterior view. Dorsal is to the upper right. The neural spine and left transverse process are missing.

Here’s a closeup of the condyle. The outer layer of cortical bone is gone, allowing a glimpse of the pneumatic chambers inside the vert. The erosion of the condyle was probably inflicted post-excavation by relatively unskilled WPA workers, whose prep tools were limited to chisels, penknives, and sandpaper. Because the bones from the Kenton localities are roughly the same color as the matrix, the preparators sometimes did not realize that they were sanding into the bones until the internal structure was revealed. Bad for the completeness of this specimen, but good for pneumaticity junkies like me, because this baby is too big to be scanned by any but the largest industrial CT machines.

For other posts on the giant Oklahoma apatosaur, see:

Owl legs lie

May 12, 2017

Here is your occasional reminder of how very misleading feathers can be in understanding the true shape of an animal. An owl:

And the same owl showing a bit of leg:

And here are the two photos side by side:

We’ve often told you here on SV-POW! that necks lie. But legs lie, as well. Not to mention arms. Which is why so most of our life restorations of dinosaurs (theropods at least) probably look nothing like these animals looked in life.

Credit: I got the owl images from this Japanese page, but I have no idea where they originated. There are copies all over the Web, and figuring out which are the originals — if they’re even still up — would be a major research project. At any rate, you ought to be told that they are not my photos.

This tired old argument came up again on Twitter this evening, in light of Elsevier’s me-too announcement of a preprint archive:

Brian Nosek‏: Elsevier enters the biology #preprints space: https://www.elsevier.com/solutions/ssrn/biorn
Me: KILL IT WITH FIRE
Brian Lucey‏: I’ve used SSRN from its inception. Never ever felt it as anything but useful. That’s not changed with Elsevier.

And elsewhere in the same thread:

Me: We want preprints to be supported by community-owned initiatives that will not try to take total control.
William Gunn: Well, you said the same stuff about Mendeley and it wasn’t true then, either, so…

So what’s the problem? Mendeley and SSRN are still around, right

Yes, they are. But they continue to exist only by the grace of Elsevier. At any moment, that could change. And here’s why.

Subway is a chain of fast-food outlets that makes sandwiches. As it happens there is a branch in Cinderford, the nearest town to where I live. Which is nice.

Now everyone knows and understands that Subway is a corporation that exists to enrich its shareholders. That’s fine: no-one resents it, because it’s what it is. If the Cinderford branch makes money for them, they’ll keep it open and everyone will be happy. But if it doesn’t, then they’ll close that branch and no-one will be surprised. Because Subway’s mission is not to bring dining options to rural England, but to make money. No harm, no foul, that is just what they are.

But by the same token, Elsevier is a corporation that exists to enrich its shareholders. That’s not a controversial claim, it’s a simple statement of fact. And it’s not a criticism, it’s just recognising reality. We don’t even need to resent it: we just need to recognise it, and make our choices accordingly.

Now, from Elsevier’s perspective, Mendeley and SSRN, and indeed BioRN, are simply branches of Subway. They exist to make money for their shareholders. That’s their mission. Once more, not a criticism: just a fact.

But what this means is that the moment they are not making money, they will be shut down, just as the Cinderford branch of Subway would be. And, for that matter, just as BioMedNet, ChemWeb and ElsevierEngineering were shut down. Because Elsevier’s mission is not to further scholarship, it’s to make money. Again, not a criticism: just a fact.

What does it mean for Mendeley and SSN to “make money”? It may be that these branches of the Elsevier empire provide very little in the way of direct revenue. But someone will have run the numbers and shown that what they cost to run is less than their value to the corporation in terms of visibility, PR, drawing customers into other Elsevier products, etc. If it weren’t so, then they wouldn’t be running these services — because their responsibility is to shareholders, not scholars.

And you can bet that as soon as they day comes that they conclude Mendeley and SSRN are not paying for themselves, those services will go down in flames.

Now. It’s fine if Subway run their Cinderford branch for eighteen months and then decide it’s not working out. if they close it, I can just go down the road and get a kebab or a Chinese. But it’s not fine if scholarly infrastructure vanishes, or changes its terms, or becomes available only to members, or what have you. We need to be able to rely on scholarly infrastructure. Which is why in the end it needs to be owned and run by the scholarly community.

This is why I am becoming more and more convinced of the importance of the Principles for Open Scholarly Infrastructure, which lay out the conditions for a service to be reliable, sustainable and safe from hijacking. (I expect to write more about the Principles some time soon.)

The bottom line is just this: Elsevier’s mission is money and their duty is to shareholders. But our mission is research and our duty is to the world. We and they are simply not aligned. That doesn’t mean they can’t provide and charge for useful services. But it does mean that they can’t be allowed to own and control infrastructure.

That’s why no-one should submit preprints to BioRN. Let this effort move directly from cradle to grave without passing Go. There are already plenty of good preprint options for bioscientists: PeerJ preprints, BiorXiv, arXiv’s q-bio category, the whole ASAPbio initiative) and even for palaeontologists in particular (PaleorXiv).

Use those. Don’t give Elsevier control over scholarly infrastructure.

For a long while, there has been a lot of anger among researchers and academic librarians towards the legacy publishers: the big corporations that control access to most of the world’s scholarly output. But what exactly is the problem? Let’s briefly consider several possibilities, and see if we can figure out which ones really matter.

Is it the publishers’ profit margins? As we’ve discussed before, the Big Four publishers all make profits in the region of 35% of revenue, which is more than Google (25%) or Apple (29%) make. Essentially every time you buy something from Elsevier, a third of the money goes straight into shareholders’ pockets.

But as I have previously argued, I don’t think this, in isolation, is a big problem. A company that could make a car for $500, if it sold that car for $1000, would be making a 50% profit: but that wouldn’t matter, because what we actually care about is the price we pay, not whether the price goes on costs or profits.

So is the problem with legacy publishers the sheer cost of their products (whether made up of profit or internal costs)? This is definitely an issue, and has been for a long time: the serials crisis goes back several decades. It certainly seems to be true that publishers are collecting exploitative rent on research outputs that they own, hiking up prices much faster than inflation and using underhand tactics to force renegotiation in their favour. This is underhand and destructive — but not the core of the issue.

Perhaps we get closer to the heart when we consider the provision of free labour by the authors, peer-reviewers and editors who donate their time, effort and professional expertise to enrich the publishers. No-one disputes that publishers add some value to the published work; but clearly 90% of the value is in the author’s submission, and 90% of the remainder in the volunteer-run editorial process. It sticks in the craw that the only people who benefit financially from all this are the ones who contribute least.

All of this so far has been to do with how scholarship is generated and how it then generates revenue. But maybe the real issue is what happens once it’s become a product: almost nobody can actually read the papers. To me, this is a much more fundamental issue. Whatever the academic community spends on subscriptions, the opportunity cost of all the papers we can’t read is far greater — and that is true on an enormously greater scale when we take into account the trifling matter of the world outside academia. (Bonus points: even when you can read the papers you are often limited in what you can do with them due to restrictive licences. Content-mining, data-reuse, lecture preparation, Wikipedia edits and much more are impeded by such limitations.)

But maybe even more fundamental than this is the problem that legacy publishers own and control the scholarly literature. That is the foundational truth that underlies all the other bad things I’ve listed here. They own the copyright because researchers give it to them. And so can we honestly be surprised when corporations, given a resource, then exploit it for financial gain?

The solution in the end is very, very simple: we have to stop giving them our good stuff. Just don’t. Don’t give your work to subscription-based journals. Don’t review for them. And don’t act as an editor for them. Scholarship belongs to the world, not to publishers who do the opposite of publishing. Publish your work where it benefits the world.

 

The best-preserved presacral vertebra of Vouivria damparisensis (Mannion et al. 2017: fig. 10).

New goodies out today in PeerJ: Tschopp and Mateus (2017) on the new diplodocid Galeamopus pabsti, and Mannion et al. (2017) redescribe and name the French ‘Bothriospondylus’ as Vouivria damparisensis.

C7 of Galeamopus pabsti (Tschopp and Mateus 2017: fig. 24).

Both papers are packed with interesting stuff that I simply don’t have time to discuss right now. Possibly Mike and I will come back with subsequent posts that discuss these critters in more detail. We both have a connection here besides our normal obsession with well-illustrated sauropods – Mike reviewed the Galeamopus paper, and I reviewed Vouivria. Happily, both sets of authors chose to publish the peer-review histories, so if you’re curious, you can go see what we said.

For now, I’ll just note that C7 of Galeamopus pabsti, shown above, is intriguingly similar in form to Vertebra ‘R’ of YPM 429, the ‘starship’ Barosaurus cervical (illustrated here). Mike and I spent a lot of time puzzling over the morphology of that vert before we convinced ourselves that much of its weirdness was due to taphonomic distortion and a restoration and paint job that obscured the fact that the metapophyses were missing. Given our ongoing project to unravel the wacky morphology of Barosaurus, I’m looking forward to digging into the morphology of G. pabsti in more detail.

I’ll surely irritate Mike by saying this, but my favorite figure in either paper is this one, Figure 4 from Tschopp and Mateus (2017). I can’t remember ever seeing an exploded skull diagram like this for a sauropod before, but it’s extremely helpful and I love it.

And that’s all for now. Go read these papers – they’re both substantial contributions with intriguing implications for the evolution of their respective clades. Congratulations to both sets of authors for producing such good work.

References

  • Mannion PD, Allain R, Moine O. (2017) The earliest known titanosauriform sauropod dinosaur and the evolution of Brachiosauridae. PeerJ 5:e3217 https://doi.org/10.7717/peerj.3217
  • Tschopp E, Mateus O. (2017) Osteology of Galeamopus pabsti sp. nov. (Sauropoda: Diplodocidae), with implications for neurocentral closure timing, and the cervico-dorsal transition in diplodocids. PeerJ 5:e3179 https://doi.org/10.7717/peerj.3179

Turns out that if Mike and I don’t post about sauropods for a while, people start doing it for us! This very interesting project by Tom Johnson of Loveland, Colorado, first came to my attention when Tom emailed Mark Hallett about it and Mark kindly passed it on to me. I got in touch with Tom and asked if he’d be interested in writing it up for SV-POW!, and here it is. Many thanks to Tom for his willingness to share his work with us. Enjoy! – Matt Wedel

– – – – – – – – – – – – – – – – – – – –

The sauropod formerly known as Apatosaurus in the American Museum of Natural History was the first permanently mounted sauropod dinosaur in the world, and for many years, the most famous (Brinkman 2010). The greater part of the skeleton consists of the specimen AMNH 460 from the Nine Mile Crossing Quarry north of Como Bluff, Wyoming, supplemented with bones from other AMNH specimens from Como Bluff, Bone Cabin Quarry, and with plaster casts of the forelimbs of the holotype specimen of Brontosaurus excelsus (YPM 1980) at the Yale Peabody Museum.

A herd of Brontosaurus skeleton models parading before four box covers issued between the 1950s and 1990s.

Like many aging boomer dinophiles, my dinosaur epiphany was the result of books, movies, and toys available in the 1950s, but especially a series of plastic model dinosaur skeletons that appeared around 1958. The Brontosaurus was my personal favorite, and, like the Tyrannosaurus and Stegosaurus models in the series, was very obviously based on the AMNH mount. The models were reissued at least three times over the years and can still be found either “mint in box” or more often in various stages of completion.

Apatosaurus lousiae 1/12 scale skeleton, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

The crème de la crème today, of course, is the 1:12 scale Apatosaurus skeleton model by Phil Platt, available from Gaston Design in Fruita, Colorado. A particularly nice example is the one completed and mounted by Brant Bassam of BrantWorks. The Platt skeleton is a replica in the true sense of the word. The plastic models are pretty crude in comparison, as cool as they appeared to us as kids.

I was interested in skeletal illustrations I have seen of Tyrannosaurus rex, which compare the completeness of various specimens by showing the actual bones included by coloring them red. A 2005 study of Apatosaurus by Upchurch et. al. examined eleven of the most complete Apatosaurus individuals, and I was interested to see the actual bones known for each specimen. Using published descriptions, red markers, and copies of a skeletal silhouette of Apatosaurus (permission obtained from the artist), I prepared a comparison of the most completely known Apatosaurus specimens. It was clear, of course, that Apatosaurus louisae (CM 3018) is the most complete specimen of the Apatosaurus/Brontosaurus group. But it also was apparent that old AMNH 460 included a substantial portion of the skeleton, even if it is a composite.

I grabbed some additional markers and, using the illustration of the mount in William Diller Matthew’s popular book Dinosaurs (Matthew 1915, fig. 20, which I trust is in the public domain by now), I color-coded the bones according to the composition as listed in Matthew’s (1905) article:

  • AMNH 460, Nine-Mile Crossing Quarry: 5th, 6th, 8th to 13th cervical vertebrae; 1st to 9th dorsal; 3rd to 19th caudal; all ribs; both coracoids; “parts of” sacrum and ilia; both ischia and pubes; left femur and astragalus; and “part of” the left fibula. RED
  • AMNH 222, Como Bluff: right scapula, 10th dorsal vertebra, right femur and tibia. GREEN
    (Visitors to AMNH: you can see the rest of AMNH 222 under the feet of the hunched-over Allosaurus)
  • AMNH 339, Bone Cabin Quarry: 20th to 40th caudal vertebrae. LIGHT BLUE
  • AMNH 592, Bone Cabin Quarry: metatarsals of the right hind foot. VIOLET
  • YPM 1980, Como Bluff: left scapula, forelimb long bones (casts). YELLOW
  • The remaining parts of the skeleton are either modeled in plaster or are unspecified (“a few toe bones”). BLACK

It occurred to me that I might have sufficient spare parts of old ITC and Glencoe Brontosaurus models to create a three-dimensional version. I did, and painting prior to assembly definitely made the job easier.

There are obviously limitations to using Matthew’s (1915) reconstruction (e.g., only 13 cervicals) and the model (12 cervicals). It is also not clear from Matthew’s description how much of the sacrum and ilia were restored. Nevertheless, the painted model does provide a colorful, if crude, visualization of the composition of the composite.

Here are some more photos of the finished product:

A view from the front of the model, compared with a historical AMNH photo of the forelimbs and pelvic girdle.

Long considered a specimen of Brontosaurus excelsus or Apatosaurus excelsus, AMNH 460 was referred to Apatosaurus ajax by Upchurch et. al. in 2005. In the most comprehensive analysis of diplodocid phylogeny to date, Tschopp et. al. (2015) found AMNH 460 to be an “indeterminate apatosaurine” pending a “detailed analysis of the specimen.” What to call it? Oh, yeah, that’s been covered in another post!

This is a nostalgia shot for the old brontophiles. Notice that the Triceratops is entering the lake for a swim!

Tom Johnson with the mounted skeleton of Amphicyon, a Miocene “bear-dog”,
in the Raymond Alf Museum of Paleontology in Claremont, California.

References

  • Brinkman , Paul D. (2010). The Second Jurassic Dinosaur Rush, University of Chicago Press, 2010.
  • Matthew, William Diller, (1905). “The Mounted Skeleton of Brontosaurus,” The American Museum Journal, Vol. V, No. 2, April.
  • Matthew, W.D. (1915). Dinosaurs, With Special Reference to the American Museum Collections, American Museum of Natural History, New York.
  • Tschopp, Emanuel, Octávio Mateus, and Roger Benson. (2015). “A Specimen-Level Phylogenetic Analysis and Taxonomic Revision of Diplodocidae (Dinosauria, Sauropoda).” Ed. Andrew Farke. PeerJ 3 (2015): e857.
  • Upchurch, P., Tomida, Y., 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 (Tokyo) 26 (118): 1–156.