Prologue

Back when I started writing about issues in scholarly publishing, I would sometimes write about the distinction between for-profit (bad) and non-profit (good) publishers. While I still recognise this as an issue, thinking it through over the last few years has made it clear that this distinction is largely orthogonal to the one that really matters — which is between open and non-open publishers.

In fact, all four quadrants exist:

 For-profit  Non-profit
 Open  PeerJ  PLOS
 Non-Open  Elsevier  ACS

ACS may be a 501(c)(3) nonprofit organization, and PeerJ may be a private company primarily owned by two individuals — but it’s PeerJ that’s pushing openness forward, and ACS doing quite the opposite.

Logue

img_4496

Beautifully preserved cervical vertebra of Barosaurus in the prep. lab at the North American Museum of Natural Life (NAML).

I’ve found myself thinking about this recently for two reasons.

The first is that, like anyone who works on sauropods, I’ve had involvement with specimens at the Sauriermuseum Aathal (SMA), a privately owned museum in Switzerland that holds some astonishingly beautiful and complete specimens, including the Kaatedocus holotype, SMA 0009. In particular, I’ve been invited a few times to peer-review manuscripts describing SMA specimens, and I’ve always felt conflicted about this because of the SVP’s strong position on privately held specimens.

The second thing that’s pushed me to rethink the private-public distinction has been working on Barosaurus. Our experiences with specimens have been varied. Yale University was very helpful when we went to see the holotype YPM 429, and BYU really couldn’t have done more for us on our recent visit. This is what we would hope for, of course. But what we didn’t particularly anticipate is how generous and helpful the people at the commercial fossil hunters Western Paleo Labs would be. When, visiting the North American Museum of Ancient Life, we gazed in awe through their prep. lab window at their several gorgeous Barosaurus cervicals (see photo above), they invited us in to play with them. (The vertebrae, not the people.)

And that made me think about our much less satisfactory experience trying to photograph the presacrals of AMNH 6341 at the American Museum of Natural History — they are entombed in a glass case surmounted by a not-really-transparent walkway:

amnh-presacrals

Which meant that, when trying to obtain dorsal-view photographs, I had to use this technique:

amnh-photography

With results like these:

amnh-dorsal-view

Now I want to be clear that everyone we dealt with at the AMNH was as helpful as they could be. No-one that we met there was in any way obstructive. Yet the fact remains, the crucially important presacral verterbrae of the most widely recognised Barosaurus in the world were essentially impossible to study.

Worse: papers that have been published about those specimens are now essentially irreproducible, because the specimens are not really available for re-study — much as though they’d been sold to Nicolas Cage to display over his mantelpiece.

Whereas the Barosaurus vertebrae at Western Paleo Labs do seem to be available for study.

Hmm.

Just as we were mistaken in focussing primarily on the for-profit/non-profit distinction between publishers when what we really cared about was the open/non-open distinction, could it be that we’ve been misfocussing on the public/private ownership distinction when what we really care about is availability of specimens?

Is there a way to be confident about which museums will and will not always make specifimens available for study? Here’s where my knowledge cuts out, but one would think this would be the key element in museum certification. But then no doubt museum certification is done differently in different jurisdictions. Knowing that a German museum is accredited may tell you something completely different from knowing that an America museum is accredited.

So perhaps what we need is some globally recognised statement that any museum in the world can sign up to: formally committing to keep its specimens available to researchers; and comitting never to sell them to any party that has not also signed up to the statement.

Epilogue

It’s worth noting the Sauriermuseum Aathal seems, as far as I’ve ever heard, to have conducted itself in every way as we would wish. They seem pretty unambiguously to be among the good guys. More: they seem to have unilaterally done more or less what I advocated above: their website declares:

Declaration Concern: Holotypes of the fossil-collection of the Sauriermuseum Aathal.

The Sauriermuseum Aathal, Switzerland (SMA), is being recognized more and more as valuable scientific institution. We hereby state publicly the SMA policy concerning holotype specimens. We recognize the importance of these reference specimens for science, and strongly agree that they have to be available for science in perpetuity. Therefore, we declare that all holotypes present at the Sauriermuseum Aathal, Switzerland (and all new holotypes that will be described in future), will always be publicly accessible to all bona fide researchers, and will never be allowed to be sold to any private collection.

Are they one step ahead of us? And if so, should we cast off our reservations about publishing on their specimens?

 

Back in 2012, when Matt and I were at the American Museum of Natural History to work on Apatosaurus” minimus, we also photographed some other sacra for comparative purposes. One of them you’ve already seen — that of the Camarasaurus supremus holotype AMNH 5761. Here is another:

diplodocus-sacrum-composite

(Click through for glorious 3983 x 4488 resolution.)

This is AMNH 3532, a diplodocid sacrum with the left ilium coalesced and the right ilium helpfully missing, so we can see the structure of the sacral ribs. Top row: dorsal view, with anterior to the left; middle row, left to right: anterior, left lateral and posterior views; bottom row: right lateral view.

As a matter of fact, we’ve seen this sacrum before, too, in a photo from Matt’s much earlier AMNH visit. But only from a left dorsolateral perspective.

When we first saw this, it didn’t even occur to us that it could be anything other than good old Diplodocus. And indeed it’s a pretty good match for the same area in the CM 84/94 cast in the Museum für Naturkunde Berlin (this image extracted from Heinrich Mallison’s beautiful giant composite):

img_4853-img_4886-v3-sm-sacrum

And the general narrowness of the AMNH sacrum says Diplodocus to me. But what is that expectation of narrowness based on? When I compared the AMNH specimen with Hatcher’s (1901) ventral-view illustration in his classic Diplodocus monograph, I had second thoughts:

Hatcher (1901: fig. 9). Inferior view of sacrum and ilia of Diplodocus carnegii (No. 94), one tenth natural size; bp, public peduncle; is, ischiadic peduncle; a, anterior end; p, posterior end.

Hatcher (1901: fig. 9). Inferior view of sacrum and ilia of Diplodocus carnegii (No. 94), one tenth natural size; pp, public peduncle; is, ischiadic peduncle; a, anterior end; p, posterior end.

That is a much wider sacrum than I’d expected from Diplodocus.

So what is going on here? Is Diplodocus a fatter-assed beast than I’d realised? I am guessing not, since my expectation of narrowness has been built up across years of looking at (if not necessarily paying much attention to) Diplodocus sacra.

So could it be that CM 94, the referred specimen that Hatcher used to make up some of the missing parts of the CM 84 mount, is not Diplodocus?

Well. That is certainly now how I expected to finish this post. Funny how blogging leads you down unexpected paths. It’s a big part of why I recommend blogging to pretty much everyone. It forces you to think down pathways that you wouldn’t otherwise wander.

References

  • Hatcher, Jonathan B. 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.

 

Re-reading an email that Matt sent me back in January, I see this:

One quick point about [an interesting sauropod specimen]. I can envision writing that up as a short descriptive paper, basically to say, “Hey, look at this weird thing we found! Morrison sauropod diversity is still underestimated!” But I honestly doubt that we’ll ever get to it — we have literally years of other, more pressing work in front of us. So maybe we should just do an SV-POW! post about the weirdness of [that specimen], so that the World Will Know.

Although as soon as I write that, I think, “Screw that, I’m going to wait until I’m not busy* and then just take a single week* and rock out a wiper* on it.”

I realize that this way of thinking represents a profound and possibly psychotic break with reality. *Thrice! But it still creeps up on me.

(For anyone not familiar with the the “wiper”, it refers to a short paper of only one or two pages. The etymology is left as an exercise to the reader.)

It’s just amazing how we keep on and on falling for this delusion that we can get a paper out quickly, even when we know perfectly well, going into the project, that it’s not going to work out that way. To pick a recent example, my paper on quantifying the effect of intervertebral cartilage on neutral posture was intended to be literally one page, an addendum to the earlier paper on cartilage: title, one paragraph of intro, diagram, equation, single reference, DONE! Instead, it landed up being 11 pages long with five illustrations and two tables.

I think it’s a reasonable approximation to say that any given project will require about an order of magnitude more work than we expect at the outset.

Even as I write this, the top of my palaeo-work priority list is a paper that I’m working on with Matt and two other colleagues, which he kicked off on 6 May, writing:

I really, really want to kill this off absolutely ASAP. Like, seriously, within a week or two. Is that cool? Is that doable?

To which I idiotically replied:

IT SHALL BE SO!

A month and a bit later, the answers to Matt’s questions are clear. Yes, it’s cool; and no, it’s not doable.

The thing is, I think that’s … kind of OK. The upshot is that we end up writing reasonably substantial papers, which is after all what we’re meant to be trying to do. If the reasonably substantial papers that end up getting written aren’t necessarily the ones we thought they were going to be, well, that’s not a problem. After all, as I’ve noted before, my entire Ph.D dissertation was composed of side-projects, and I never got around to doing the main project. That’s fine.

In 2011, Matt’s tutorial on how to find problems to work on discussed in detail how projects grow and mutate and anastamose. I’m giving up on thinking that this is a bad thing, abandoning the idea that I ought to be in control of my own research program. I’m just going to keep chasing whatever rabbits look good to me at the time, and see what happens.

Onwards!

AMNH 460 skeleton model 2

In a recent post I showed some photos of the mounted apatosaurine at the American Museum of Natural History in New York, AMNH 460, which Tschopp et al. (2015) regarded as an indeterminate apatosaurine pending further study.

A lot of museums whose collections and exhibits go back to the late 19th and early 20th centuries have scale model skeletons and sculptures that were used to guide exhibit design. I have always been fascinated by these models, partly because they’re windows into another era of scientific research and science communication, and partly because they’re just cool – basically the world’s best dinosaur toys – and I covet them. In my experience, it is very, very common to find these treasures of history buried in collections, stuck up on top of specimen cabinets, or otherwise relegated to some out-of-the-way corner where they won’t be in the way. I know that exhibit space is always limited, and these old models often reflect ideas about anatomy, posture, or behavior that we now know to be mistaken. But I am always secretly thrilled when I see these old models still on exhibit.

AMNH T rex skeleton model

The AMNH has a bunch of these things, because Henry Fairfield Osborn was crazy about ’em. He not only used 2D skeletal reconstructions and 3D model skeletons to guide exhibit design, he published on them – see for example his 1898 paper on models of extinct vertebrates, his 1913 paper on skeleton reconstructions of Tyrannosaurus, and his 1919 paper with Charles Mook on reconstructing Camarasaurus. That genre of scientific paper seems to have disappeared. I wonder if the time is right for a resurgence.

So in a glass case at the feet of AMNH 460 is a model – I’d guess about 1/12 or 1/15 scale – of that very skeleton. You can tell that it’s a model of that particular skeleton and not just some average apatosaur by looking carefully at the vertebrae. Apatosaurines weren’t all stamped from quite the same mold and the individual peculiarities of AMNH 460 are captured in the model. It’s an amazing piece of work.

AMNH 460 skeleton model

The only bad thing about it is that – like almost everything behind glass at the AMNH – it’s very difficult to photograph without getting a recursive hell of reflections. But at least it’s out where people can see and marvel at it.

Oh, and those are the cervical vertebrae of Barosaurus behind it – Mike and I spent more time trying to look and shoot past this model than we did looking at it. But that’s not the model’s fault, those Barosaurus cervicals are just ridiculously inaccessible.

So, memo to museums: at least some of us out here are nuts about your old dinosaur models, and where there’s room to put them on exhibit, they make us happy. They also give us views of the skeletons that we can’t get otherwise, so they serve a useful education and scientific purpose. More, please.

References

Osborn, H. F. (1898). Models of extinct vertebrates. Science, New Series, 7(192): 841-845.

Osborn, H.F. (1913). Tyrannosaurus, restoration and model of the skeleton. Bulletin of the American Museum of Natural History, 32: 91-92, plates 4-6.

Osborn, H. F., & Mook, C. C. (1919). Characters and restoration of the sauropod genus Camarasaurus Cope. From type material in the Cope Collection in the American Museum of Natural History. Proceedings of the American Philosophical Society, 58(6): 386-396.

AMNH 460 left anterolateral view

Apatosaurines on the brain right now.

I’ve been thinking about the question raised by Jerry Alpern, a volunteer tour guide at the AMNH, regarding the recent Tschopp et al. (2015) diplodocid phylogeny. Namely, if AMNH 460 is now an indeterminate apatosaurine, pending further study, what should the museum and its docents tell the public about it?

Geez, Apatosaurus, it’s not like we’re married!

I think it’s a genuinely hard problem because scientific and lay perspectives on facts and hypotheses often differ. If I say, “This animal is Apatosaurus“, that’s a fact if I’m talking about YPM 1860, the genoholotype of Apatosaurus ajax; it would continue to be a fact even if Apatosaurus was sunk into another genus (as Brontosaurus was for so long). We might call that specimen something else, but there would always be a footnote pointing out that it was still the holotype of A. ajax, even if the A. part was at least temporarily defunct – the scientific equivalent of a maiden name.* For every other specimen in the world, the statement, “This animal is Apatosaurus” is a hypothesis about relatedness, subject to further revision.

* This is going to sound kinda horrible, but when one partner in a marriage takes the other’s surname, that’s a nomenclatural hypothesis about the future of the relationship.

Apatosaurine cervicals are the best cervicals.

Apatosaurine cervicals are the best cervicals.

Fuzzy science

Things that look fairly solid and unchanging from a distance – specifically, from the perspective of the public – often (always?) turn out to be fairly fuzzy or even arbitrary upon closer inspection. Like what is Apatosaurus (beyond the holotype, I mean) – or indeed, what is a planet.** There is no absolute truth to quest for here, only categories and hypotheses that scientists have made up so that we can have constructive conversations about the crazy spectrum of possibilities that nature presents us. We try to ground those categories and hypotheses in evidence, but there will always be edge cases, and words will always break down if you push them too hard. Those of us who work on the ragged frontier of science tend to be fairly comfortable with these inescapable uncertainties, but I can understand why people might get frustrated when they just want to know what the damned dinosaur is called.

** Triton, the largest body orbiting Neptune, is almost certainly a captured Kuiper Belt object, and it’s bigger than Pluto. Moon or planet? Probably best to say a former dwarf planet currently operating as a satellite of Neptune – but that’s a mouthful (and a mindful, if you stop to think about it), not a short, convenient, easily-digestible label. Any short label is going to omit important information. This is related to the problem of paper title length – below some threshold, making something shorter means making it incomplete.

What I would say

I suppose the short version that is most faithful to the Tschopp et al. results is:

This skeleton (AMNH 460) might be Apatosaurus or Brontosaurus or a third, new thing – scientists aren’t sure yet.

A reasonable follow-up sentence – and an answer to the inevitable “Why not?” – would be:

They have to look at 477 anatomical details for lots of skeletons and weigh all the evidence, and that takes time.

Personally, if I was talking to museum visitors I would lean in conspiratorially and say:

If you want to call it Apatosaurus or Brontosaurus, go ahead – those are both ‘live’ hypotheses, and even the world’s experts on this problem can’t tell you that you’re guessing the wrong way – at least not yet.

And if there was a kid in the group, I’d add:

Maybe you’ll be the one to figure it out!

What would you say?

My neck is fat.

My neck is fat.

P.S. I wouldn’t change the signage. It could still turn out to be Apatosaurus, and the Tschopp et al. results do not lend themselves to easy label-ification.

P.P.S. With some modification for taxonomy, all of this applies to the Field Museum diplodocid FMNH P25112 as well.

Reference

Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ3:e857 https://dx.doi.org/10.7717/peerj.857

Brontosaurus, the animal formerly known as Apatosaurus, the animal formerly known as Brontosaurus.

YPM 1980: Brontosaurus excelsus, the animal formerly known as Apatosaurus excelsus, the animal formerly known as Brontosaurus excelsus.

Today is a good day for sauropod science. Since we’re not getting this up until the afternoon, you’ve probably already seen that Emanuel Tschopp and colleagues have published a monstrous specimen-level phylogenetic analysis of Diplodocidae and, among other things, resurrected Brontosaurus as a valid genus. The paper is in PeerJ so you can read it for free (here).

I’ve already been pinged by lots of folks asking for my thoughts on this. I know that the return of Brontosaurus is what’s going to catapult this paper into the spotlight, but I hope what everyone takes away from it is just what a thorough piece of work it is. I’ve never seen so many phylogenetic characters illustrated so well. It sets a new standard, and anyone who wants to overturn this had better roll up their sleeves and bring a boatload of data. I’m also very, very happy that it’s open-access so everyone in the world can see it, use it, question it, tear it apart or build on it. Getting Brontosaurus back is just gravy. Although, being pro-brontosaur enough to have named a dinosaur in honor of Brontosaurus, I’m also pretty happy about that. If you need a quick guide to who’s who now, A. ajax and A. louisae are still Apatosaurus, and B. excelsus, B. yahnahpin (formerly Eobrontosaurus), and B. parvus (originally Elosaurus) are all Brontosaurus. For more details, go read the paper.

A louisae from Wikipedia - full

Apatosaurus lousiae CM 3018: still Apatosaurus. Photo from Wikipedia.

My personal feelings aside, a lot of people are asking how solid is this generic re-separation. I haven’t read the entire paper yet – it’s 299 pages long, for crying out loud – but the separation of Brontosaurus and Apatosaurus seems solid enough. Tschopp et al. didn’t do it lightly, they justify their decision in detail. I don’t hold with the idea that just because two taxa are sisters, means that they cannot be separated generically. As usual in phylogenetic taxonomy, it comes down to what we decide as a community constitutes “diagnosably distinct”. Tschopp et al. have actually put some thought into what that might mean here, and whether you agree with them or not, they’ve at least made all of their evidence and reasoning explicit. That’s both an opportunity and a challenge for critics: an opportunity to pin down exactly where and why you may disagree, and a challenge to do exactly that. You can’t just sit back and say, “I think the analysis is flawed” or “I wouldn’t have coded that character that way” (well, you can, but if that’s all you say, no-one is obliged to take that kind of lazy, drive-by criticism seriously). There are 477 characters here, most of them illustrated, for 81 OTUs, and a lot of post-hoc discussion of the results. So whether you agree with the authors or not, in whole or in part, both fans and critics should dig in and build on this work. Is it the last word on diplodocid taxonomy? Of course not. But it does move the field forward significantly, and the Tschopp et al. should be applauded for that.

There’s a lot more in there than just bringing back Brontosaurus. “Diplodocus” hayi is elevated to its own genus, Galeamopus. Neither of those things are super surprising. There have been rumors since the 90s at least that Brontosaurus might be coming back, and everyone has known for a while that D. hayi was a bit wonky. I was also not surprised to see Australodocus returned to Diplodocidae – when I saw the type material in 2011, it looked diplodocid to me (based on some characters I’ll have to unpack in some other post). More surprising to me are the sinking of Dinheirosaurus into Supersaurus, the finding that Tornieria is not particularly close to Diplodocus, and the uncertain positions of AMNH 460, the American Museum mount, which is an indeterminate apatosaurine pending further study, of FMNH 25112, the Field Museum “Apatosaurus”, which might not even be an apatosaurine at all(!). In several cases, Tschopp et al. come right out and say that X is going to need further study, so if you want to work on sauropods and you’re stuck for project ideas, go see what needs doing.

AMNH mounted Apatosaurus with Taylor for scale

AMNH 460: we don’t know who this is anymore.

As I was scanning the paper again while composing the last paragraph, I almost fell down the rabbit hole. So much interesting stuff in this paper. Even if all you care about is morphology, the hundred or so figures illustrating the phylogenetic characters ought to keep you happy for a very long time. I look forward to reading through the vertebral characters in detail and seeing what I’ve been missing all these years.

I’m contractually obliged to point out that the authors chose to publish the complete peer-review history of the paper, so you can see what the editor (Andy Farke) and reviewers had to say. As always, I think this transparency (and credit for the reviewers) is great for science, and I can’t wait until it’s the norm at more journals.

FMNH 25112 formerly Apatosaurus

FMNH 25112: what even IS that thing?

In addition to the paper, there’s also an interview with lead author Emanuel Tschopp on the PeerJ blog, and a nice shout-out for SV-POW!

Parting shot: why did Tschopp et al. get different results than anyone had previously? Because they used more specimens and more taxa – more data full stop. That’s also why their paper warrants serious consideration. It’s serious work. Let’s go stand on their shoulders.

Reference

Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ 3:e857 https://dx.doi.org/10.7717/peerj.857

Better

AMNH T. rex mount, photo by Mike Taylor.

In a recent comment, Doug wrote:

If I want to be a truly educated observer of Tyrannosaurus rex mounts, what 5 things should I look for in a reconstruction to assess if it is true to our current scientific understanding? I’m not talking tail dragging/upright at this point…we are well past that I hope.

If he had asked about Apatosaurus, I could have written him a novel. But it is a point of pride with me not to contribute to the over-application of human attention to T. rex; not only would it be vulgar, it would also be a waste of resources, considering how many people already have that covered. So, you theropod workers and avocational “rexperts”, we’re finally inviting you to the high table. Please, tell us–and Doug–what separates the good T. rex mounts from the crappy ones. Big piles of SV-POW! bucks will be showered on whoever brings the most enlightenment, especially if you adhere to the requested List of 5 Things format.

The comment lines are open–go!