So I came across this tweet from Laurent Gatto, who’s head of the Computational Proteomics Unit at the University of Cambridge, UK:

My immediate reaction was not to retweet. Why? Because I am not comfortable recommending rejection (or acceptance!) of something I’ve not seen. I said so, and Laurent explained the real issue:

So I have two simple questions:

First, How can this massive spending on public money possibly be confidential? What justification can there possibly be for that? And second, how can there be meaningful discussion of the offer on the table if no-one knows what it is?

And then I remembered the classic explanation of confidentiality clauses from Elsevier’s David Tempest: “we have this level of confidentiality […] Otherwise everybody would drive down, drive down, drive drive drive”.

So my first reaction was to say that if anyone comes across a leaked copy of the draft agreement, let me know and I will link to it from this post. But I am also open to hear from anyone who thinks there is a legitimate reason, that I’ve not thought of, to enforce confidentiality. So if you have a reason, please mention it in the comments. If not, but you know where there is a leaked copy, email me privately on dino@miketaylororg.uk.

One more SVP book signing

October 29, 2016

imageWe keep selling out of books, which is a nice problem to have, but still a problem for people who want books. So we’re getting a final shipment this morning, and Mark Hallett and I will be at the JHUP booth signing books, starting at 12:15 and going until we run out of either customers or books.

Many, many thanks to everyone who has gotten a book or just stopped by to chat. We’re humbled by the great response we’ve gotten.

Parting question: someone on Facebook asked if we could sign and mail bookplates for folks who can’t get to our signings. I’m cool with that, just curious about how much interest there might be. Let me know in the comments.

 

This just in: Wilson and Allain’s (2015) redescription of Rebbachisaurus garasbae, the type and only true species of Rebbachisaurus!

Wilson and Allain (2015:figure 3). Holotype of R. garasbae. Dorsal vertebra (MNHN-MRS 1958) in anterior (A), right lateral (B), posterior (C), and dorsal cross-sectional (D) views. Anterior faces top in D. Scale bar equals 20 cm.

Wilson and Allain (2015:figure 3). Holotype of R. garasbae. Dorsal vertebra (MNHN-MRS 1958) in anterior (A), right lateral (B), posterior (C), and dorsal cross-sectional (D) views. Anterior faces top in D. Scale bar equals 20 cm.

Here we see the much-admire’d dorsal vertebra that’s been on display for some time in the French National History Museum, and which we’ve seen here previously:

Jeff Wilson (left) and Ronan Allain (right), with dorsal vertebra of Rebbachisaurus.

Jeff Wilson (left) and Ronan Allain (right), with dorsal vertebra of Rebbachisaurus.

(It’s a shame that photo didn’t make it into the paper, really.)

There’s good and bad news here. The good news is obvious: this is a really important specimen, the type of a whole sauropod family, and it’s been in dire need of redescription because Lavocat’s (1954) paper did a bit of a drive-by on it. It’s great that there’s a proper description at last.

The bad news is, you can’t read it — at least, not unless you’re a JVP subscriber or at a wealthy university. It’s been a while, I think, since we wrote about a non-open access paper here at SV-POW!, and it’s funny how little we seem to have missed them. A lot of the action in vertebrate palaeo, especially for dinosaurs, seems to have moved to open access journals — especially PLOS ONE and PeerJ, but also of course the venerable Palaeontologia Electronica.

FIGURE 13. Holotype of R. garasbae. Right scapula (MNHN-MRS 1957) in medial (A) and lateral (B) views. Abbreviations: ac fo, acromial fossa; ac no, acromial notch; ac ri, acromial ridge; ss, origin of M. subscapularis. Inference of muscle attachment sites is based on comparisons with crocodile pectoral musculature (Meers, 2003). Reconstruction of distal margin of blade based on photograph of scapula in situ (Fig. 2A). Scale bar equals 20 cm.

Wilson and Allain (2015:figure 13). Holotype of R. garasbae. Right scapula (MNHN-MRS 1957) in medial (A) and lateral (B) views. Abbreviations: ac fo, acromial fossa; ac no, acromial notch; ac ri, acromial ridge; ss, origin of M. subscapularis. Inference of muscle attachment sites is based on comparisons with crocodile pectoral musculature (Meers, 2003). Reconstruction of distal margin of blade based on photograph of scapula in situ (Fig. 2A). Scale bar equals 20 cm.

It’s no secret that I am done with JVP (and Palaeontology, and the Journal of Paleontology, not that I’ve ever had a paper in that last one) until they become fully open access journals — and no, a hybrid OA option doesn’t cut it. I’m glad to have that notch on my bedpost, but I don’t feel any need to go back there.

But what I’d forgotten, or perhaps never really registered, is how terribly old-fashioned JVP papers look. No-one is disputing the journal’s high editorial standards or the importance of the work published there; but their tiny fonts, cumbersome two-column layout, and low-resolution black-and-white figures located bizarrely distant from the relevant text all make it feel like a journal badly in need of an overhaul for the 21st Century. I’m not sure what plans the Society has (it’s been years since I was a member) but I’d love to see JVP reinvented as a full-colour open-access journal, primarily online with printed copies only for those who want to pay for them. We’ll see.

Wilson and Allain (2015:figure 5). Holotype of R. garasbae. Computed tomography (CT) scans of the dorsal vertebra (MNHN-MRS 1958). A–E, transverse sections; F– G, frontal sections. Abbreviations: acpl, anterior centroparapophyseal lamina; cpol, centropostzygapophyseal lamina; cprf, centroprezygapophyseal fossa; ct, cotyle; lat. spol, lateral spinopostzygapophyseal lamina; med. cprl, medial centroprezygapophyseal lamina; med. spol; medial spinopostzyga- pophyseal lamina; nc, neural canal; pc, pleurocoel; pcdl, posterior centrodiapophyseal lamina; podl, postzygodiapophyseal lamina; posl, postspinal lamina; poz, postzygapophysis; prpl, prezygoparapophyseal lamina; prsl, prespinal lamina; prz, prezygapophysis; sc, subcamerae; spdl, spinodiapophy- seal lamina; se, septum; tpol, intrapostzygapophyseal lamina. Scale bar equals 10 cm for CT images.

Wilson and Allain (2015:figure 5). Holotype of R. garasbae. Computed tomography (CT) scans of the dorsal vertebra (MNHN-MRS 1958). A–E, transverse sections; F– G, frontal sections. Abbreviations: acpl, anterior centroparapophyseal lamina; cpol, centropostzygapophyseal lamina; cprf, centroprezygapophyseal fossa; ct, cotyle; lat. spol, lateral spinopostzygapophyseal lamina; med. cprl, medial centroprezygapophyseal lamina; med. spol; medial spinopostzygapophyseal lamina; nc, neural canal; pc, pleurocoel; pcdl, posterior centrodiapophyseal lamina; podl, postzygodiapophyseal lamina; posl, postspinal lamina; poz, postzygapophysis; prpl, prezygoparapophyseal lamina; prsl, prespinal lamina; prz, prezygapophysis; sc, subcamerae; spdl, spinodiapophyseal lamina; se, septum; tpol, intrapostzygapophyseal lamina. Scale bar equals 10 cm for CT images.

It’s great that Wilson and Allain had the Rebbachisaurus vertebrae CT-scanned, showing just how crazily lightly they are built: see figure 13, especially part A, above. But I have to admit to finding it strange that a 34-page paper that deals in detail with sauropod pneumaticity doesn’t cite anything by either Brooks Britt or our own Matt Wedel — surely the two people who have done the most important work in this area, certainly the most foundational work.

My 2009 paper (Taylor 2009, duh) does get a mention — not, this time, to disagree with me on the generic separation of Giraffatitan from Brachiosaurus, to but to acknowledge its recognition of the spinoparapophyseal lamina (SPPL) that occurs in D?8 of the Giraffatitan paralectotype MB.R.2181 (formerly HMN SII) and has now been recognised also in Rebbachisaurus.

Anyway, this is an important new paper, very well illustrated (apart from the annoyingly avoidable lack of colour) and with typically careful and exhaustive descriptions. It’s going to be very helpful, and it’s reawakened an idea that I once had …

… but that’s for another time.

References

In my blog-post announcing Haestasaurus as the new generic name for the misassigned species “Pelorosaurusbecklesii, I briefly surveyed the three phylogenetic analyses in the paper. Of the third — the one based on the Mannion et al. (2013) Lusotitan matrix using both discrete and continuous characters — I wrote that it …

… recovers Haestasaurus as a titanosaur — as sister to Diamantinasaurus and then Malawisaurus, making it a lithostrotian well down inside Titanosauria.

My mistake! I was working from the result of an earlier version of that analysis. In the final version included in the paper, things are rather different:

Fig 17. Strict consensus tree (LCDM). A strict consensus tree based on the 17 most parsimonious trees generated by analysis of the Mannion et al. [18] LCDM with the revised scores for Haestasaurus and the addition of six new characters. GC values (multiplied by 100) are shown in square brackets for all nodes where these values are greater than 0. Abbreviations: Brc, Brachiosauridae; Dd, Diplodocoidea. N.B. the tree topology shown here means that the clades defined by Brachiosaurus+Saltasaurus (Titanosauriformes) and Andesaurus+Saltasaurus (Titanosauria) are identical. See main text for details.

Upchurch et al. (2015: Fig 17). Strict consensus tree (LCDM).
A strict consensus tree based on the 17 most parsimonious trees generated by analysis of the Mannion et al. [18] LCDM with the revised scores for Haestasaurus and the addition of six new characters. GC values (multiplied by 100) are shown in square brackets for all nodes where these values are greater than 0. Abbreviations: Brc, Brachiosauridae; Dd, Diplodocoidea. N.B. the tree topology shown here means that the clades defined by Brachiosaurus+Saltasaurus (Titanosauriformes) and Andesaurus+Saltasaurus (Titanosauria) are identical. See main text for details.

As you can see, Haestasaurus is indeed a titanosaur in this analysis — but not a derived one at all. In fact, it’s part of the most basal clade of titanosaurs, along with Janenschia and Dongbeititan. In this tree, we have a really nice, big Brachiosauridae, containing 19 OTUs split fairly evenly between two subclades.

[Side-note: Upchurch et al. (2015) uses phylogenetic definitions that I’m not crazy about. I prefer the arrangement that I followed in my brachiosaur paper (Taylor 2009), in which Titanosauriformes = Brachiosauridae + Titanosauria is a node-stem triplet. Hopefully, some time soon, the wretched PhyloCode will finally be implemented, and we’ll be in a position to nail down a single set of definitions for the whole community to use.]

Anyway, the upshot of all this is that all three phylogenetic analyses in the paper return Haestasaurus as a pretty basal macronarian, and on the balance of evidence it’s likely not a titanosaur after all. (That’s why the name “Haestatitan“, which was in some earlier drafts of the paper, was changed to Haestasaurus. Kind of a shame, given how mundane -saurus names are, but probably the wisest course of action.)

What is the takeaway lesson from this? It’s not just “Haestasaurus is not a derived titanosaur”. It’s that all our phylogenetic hypotheses are just that — hypotheses. Papers that publish only a single cladogram are always at risk of being misinterpreted as conveying much more certainty than they really do, and Paul and Phil are to be commended for including the whole messy story in this paper. The position of Haestasaurus shifts around far too easily for us to have a strong sense of what it is, and it’s good that the paper makes that clear.

(It also makes me glad that way back in Taylor and Naish (2007), I and Darren didn’t give a more precise position of Xenoposeidon than that it’s probably some kind of neosauropod. And even that is not something I would put money on.)

References

I have sent this message to David Loydell and Beris Cox, the editors of the Palaeontographical Society’s monograph series. (Update: and to Steve Donovan, secretary of the society.)


Dear Palaeontographical Society,

I was delighted to see that Adam Smith and Roger Benson’s new monograph on the plesiosaur Rhomaleosaurus thorntoni is now out, as shown on Adam’s publications page. This is a long-awaited work on an important specimen.

But when I asked Adam to send me a copy of the PDF, I was surprised to find that he doesn’t have one, and doesn’t expect to be given one. Is this correct?

If so, can you please explain the society’s reasoning?

I would like to publish your response on my blog, https://svpow.com/, as others will also be interested in this. May I please have your permission to do so?

Many thanks,

Dr. Michael P. Taylor
Department of Earth Sciences
University of Bristol
Bristol BS8 1RJ

Reference

Smith A.S. and Benson R.B.J. 2014. Osteology of Rhomaleosaurus thorntoni (Sauropterygia: Rhomaleosauridae) from the Lower Jurassic (Toarcian) of Northamptonshire, England. Monograph of the Palaeontographical Society 168(642):1–40 and plates 1–35.

Update 1 (two hours later)

David Loydell is no longer an editor for the Monographs of the Palaeontographical Society. Instead, I am writing to Steve Donovan, Secretary of the Palaeontographical Society.

In a comment on the last post, Mark Robinson asked an important question:

You linked to the preprint of your The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines submission – does this mean that it has not yet been formally published?

As so often in these discussions, it depends what we mean by our terms. The Barosaurus paper, like this one on neck cartilage, is “published” in the sense that it’s been released to the public, and has a stable home at a well known location maintained by a reputable journal. It’s open for public comment, and can be cited in other publications. (I notice that it’s been cited in Wikipedia). It’s been made public, which after all is the root meaning of the term “publish”.

On the other hand, it’s not yet “published” in the sense of having been through a pre-publication peer-review process, and perhaps more importantly it’s not yet been made available via other channels such as PubMed Central — so, unlike say our previous PeerJ paper on sauropod neck anatomy, it would in some sense go away if PeerJ folded or were acquired by a hostile entity. But then the practical truth is of course that we’d just make it directly available here on SV-POW!, where any search would find it.

In short, the definition of what it means for a paper to be “published” is rather fluid, and is presently in the process of drifting. More than that, conventions vary hugely between fields. In maths and astronomy, posting a preprint on arXiv (their equivalent of PeerJ Preprints, roughly) pretty much is publication. No-one in those fields would dream of not citing a paper that had been published in that way, and reputations in those fields are made on the basis of arXiv preprints. [Note: I was mistaken about this, or at least oversimplified. See David Roberts’ and Michael Richmond’s comments below.]

Maybe the most practical question to ask about the published-ness or otherwise of a paper is, how does it affect the author’s job prospects? When it comes to evaluation by a job-search panel, or a promotion committee, or a tenure board, what counts? And that is a very hard question to answer, as it depends largely on the institution in question, the individuals on the committee, and the particular academic field. My gut feeling is that if I were looking for a job in palaeo, the Barosaurus preprint and this cartilage paper would both count for very little, if anything. But, candidly, I consider that a bug in evaluation methods, not a problem with pre-printing per se. But then again, it’s very easy for me to say that, as I’m in the privileged position of not needing to look for a job in palaeo.

For Matt and me, at least as things stand right now, we do feel that we have unfinished business with these papers. In their present state, they represent real work and a real (if small) advance in the field; but we don’t feel that our work here is done. That’s why I submitted the cartilage paper for peer-review at the same time as posting it as a preprint (it’s great that PeerJ lets you do both together); and it’s why one of Matt’s jobs in the very near future will be getting the Barosaurus revised in accordance with the very helpful reviews that we received, and then also submitted for peer-review. We do still want that “we went through review” badge on our work (without believing it means more than it really does) and the archiving in PubMed Central and CLOCKSS, and the removal of any reason for anyone to be unsure whether those papers “really count”.

But I don’t know whether in ten years, or even five, our attitude will be the same. After all, it changed long ago in maths and astronomy, where — glory be! — papers are judged primarily on their content rather than on where they end up published.

 

SO close

August 21, 2014

Bipedal Diplodocus USNM 10865 - modified from Gilmore 1932 pl 6 - v2

I have often argued that given their long hindlimbs, massive tail-bases, and posteriorly-located centers of mass, diplodocids were basically bipeds whose forelimbs happened to reach the ground. I decided to see what that might look like.

Okay, now obviously I know that there are no trackways showing sauropods actually getting around like this. It’s just a thought experiment. But given how close the center of mass of Diplodocus is to the acetabulum, I’ll bet that this pose was achievable in life. If diplodocids had just pushed the CM a few cm farther back, they might have dispensed with forelimbs entirely, or done something different with them, like re-evolved grasping hands.

Image modified from Gilmore (1932: plate 6). Here’s a horizontal-necked bipedal Diplodocus and the original pose:

Bipedal Diplodocus USNM 10865 - modified from Gilmore 1932 pl 6

Diplodocus USNM 10865 - Gilmore 1932 pl 6 - cleaned up

UPDATE the next day: I had forgotten that Niroot had already done a bipedal Apatosaurus, and a much more convincing one than mine. Go see it.

UPDATE the next week: Well, heck. Looks like the primary value of this post was so that people would remind me of all the other places the same idea has already been covered better. As you can see from the comment thread, Mike blogged about this at the WWD site, Scott Hartman drew it, and Heinrich Mallison showed that it was plausible. Sheesh, I suck.

Reference

  • Gilmore, C. W. 1932. On a newly mounted skeleton of Diplodocus in the United States National Museum. Proceedings of the United States National Museum 81, 1-21.