As you’ll know from all the recent AMNH basement (and YPM gallery) photos, Matt and I spent last week in New York (with a day-trip to New Haven). The week immediately before that, I spent in Boston with Index Data, my day-job employers. Both weeks were fantastic — lots of fun and very productive. But they did mean that between the scheduled activities and getting a big manuscript finally submitted, I’ve been very much out of touch, and I’m only now catching up with what’s happened in The Rest Of The World while I’ve been sequestered in various basements photographing sauropod vertebrae.

Matt measuring the width across the preacetabular lobes of the fused ilia on the sacrum of the referred “Morosaurus” sp. specimen, AMNH 690, illustrated by Osborn (1094: fig 2A-E). Behold the wonder that is the Big Bone Room.

The two big events in the Open Access world while I was away were the launch of PeerJ and the release of the Finch Report. I’ll write about PeerJ in future, but today I want to say a few words on the Finch Report. I’ve deliberately not read anyone else’s coverage of the report yet, in the hope of forming an uninfluenced perspective. I’ll be very interested, once I’ve finished writing this, to see what people like Cameron Neylon, Stephen Curry and Peter Murray-Rust have said about it.

What is the Finch Report, you may ask? The introduction explains:

The report recommends actions which can be taken in the UK which would help to promote much greater and faster access, while recognising that research and publications are international. It envisages that several different channels for communicating research results will remain important over the next few years, but recommends a clear policy direction in the UK towards support for open access publishing.

So the first point to make is that it’s very good news about the overall direction. In fact, it would be easy to overlook this. The swing that’s happened over the last six months has been slow enough to miss, but the cumulative effect of myriad small shifts has been enormous: where there used to be a lot of skepticsm about open access, pretty much everyone is now accepting that it’s inevitable. (See this compilation of quotes from US congressmen, UK government ministers, publishers, editors and professors.) The questions now are about what form ubiquitous open access will take, not whether it’s coming. It is.

But there’s an oddity in that introduction which is a harbinger of something that’s going to be a recurring theme in the report:

[Open access publishing] means that publishers receive their revenues from authors rather than readers, and so research articles become freely accessible to everyone immediately upon publication.

People who have been following closely will recognise this as the definition of Gold Open Access — the scheme where the author (or her institution) pays a one-time publication fee in exchange for the publisher making the result open to the world. The other road, known as Green OA, is where an author publishes in a subscription journal but deposits a copy of the paper in a repository, where it becomes freely available after an embargo period, typically six to twelve months. That Green OA is not mentioned at this point is arguably fair enough; but that OA is tacitly equated with Gold only feels much more significant. It’s as though Green is being written out of history.

More on this point later.

Green and Gold Chrysogonum virginianum Flower 3008 by Derek Ramsey, from Wikimedia Commons.

The actual report is 140 pages long, and I don’t expect it to be widely read. But The executive summary is published as a separate document, and at 11 pages is much more digestible. And its heart is in the right place, as this key quote from p4 tells us:

The principle that the results of research that has been publicly funded should be freely accessible in the public domain is a compelling one, and fundamentally unanswerable.

Amen. Of course, that is the bedrock. But more practically, on page 3, we read:

Our aim has been to identify key goals and guiding principles in a period of transition towards wider access. We have sought ways both to accelerate that transition and also to sustain what is valuable in a complex ecology with many different agents and stakeholders.

I do want to acknowledge that this is a hard task indeed. It’s easy to pontificate on how things ought to be (I do it all the time on this blog); but it’s much harder to figure out how to get there from here. I’m impressed that the Finch group set out to answer this much harder question.

But I am not quite so impressed at their success in doing so. And here’s why. In the foreword (on page 2) we read this:

This report … is the product of a year’s work by a committed and knowledgeable group of individuals drawn from academia, research funders and publishing. … Members of the group represented different constituencies who have legitimately different interests and different priorities, in relation to the publication of research and its subsequent use.

My most fundamental issue with the report, and with the group that released it, is this. I don’t understand why barrier-based publishers were included in the process. The report contains much language about co-operation and shared goals, but the truth as we all know is that publishers’ interests are directly opposed to those of authors, and indeed of everyone else. Who does the Finch Group represent? I assumed the UK Government, and therefore the citizens of the UK — but if it’s trying to represent all the groups involved in academic activity, there’s a conflict of interests that by its nature must prevent everyone else from clearly stating what they want from publishers.

This isn’t an idle speculation:  the report itself contains various places where is suddenly says something odd, something that doesn’t quite fit, or is in conflict with the general message. It’s hard not to imagine these as having been forced into the report by the publishers at the table (according to the membership list, Bob Campbell, senior publisher at Wiley Blackwell; Steve Hall, managing director of IoP Publishing; and Wim van del Stelt, executive VP of corporate strategy at Springer). And I just don’t understand why the publishers were given a seat at the table.

And so we find statements like this, from p5:

The pace of the transition to open access has not been as rapid as many had hoped, for a number of reasons. First, there are tensions between the interests of key stakeholders in the research communications system. Publishers, whether commercial or not-for-profit, wish to sustain high-quality services, and the revenues that enable them to do so.

This is very tactfully put, if I might say so. Distilled to its essence, the is saying that while the UK government, universities, libraries, hospitals and citizens want open access, publishers want to keep the walls that give them their big profits. The bit about “high-quality services” is just a fig-leaf, and a rather transparent one at that. Reading on, still in p5:

There are potential risks to each of the key groups of players in the transition to open access: rising costs or shrinking revenues, and inability to sustain high-quality services to authors and readers.

Those all sounds like risks to the same group: publishers. And again, there is no reason I can see why these need be our problem. We know that publishing will survive in a form that’s useful to academia — the success of BioMed Central and PLoS, and the birth of ventures like eLife and PeerJ show us that — so why would it be the any part of our responsibility to make sure that the old, slow, expensive, barrier-based publishers continue to thrive?

Reading on:

Most important, there are risks to the intricate ecology of research and communication, and the support that is provided to researchers, enabling them to perform to best standards, under established publishing regimes.

I don’t understand this at all. What support? Something that publishers provide? I just don’t get what point is being made here, and can only assume that this “intricate ecology” section is one of the passages that the publishers had inserted. I wonder whether it’s a subtle attempted land-grab, trying to take the credit for peer-review? At any rate, it’s wildly unconvincing.

And so we come to the actual recommendations of the report. There are ten of these altogether, on pages 6-7, and they begin as follows:

We therefore recommend that:

i. a clear policy direction should be set towards support for publication in open access or hybrid journals, funded by APCs, as the main vehicle for the publication of research, especially when it is publicly funded;

So there it is: The Finch Report says that Gold Open Access is the way forward.

And despite my carping about publishers’ involvement in the process, and their dilution of the output, I’m pretty happy with that recommendation. Of course, there are a hundred questions about who will pay for OA (though they will be considerably less pressing in a world where $99 buy you all the publishing you can eat at PeerJ). Lots of details to be ironed out. But the bottom line is that paying at publication time is a sensible approach. It gives us what we want (freedom to use research), and provides publishers with a realistic revenue stream that, unlike subscriptions, is subject to market forces. (I will enlarge on this point in a subsequent post.)

To briefly summarise the ten recommendations:

i. Overall policy should be to move to Gold OA.
ii. Funders should provide money for Gold OA charges.
iii. Re-use rights, especially non-commercial, should be provided.
iv. Funding of subscriptions should continue during transition.
v. Walk-in access should be “pursued with vigour”
vi. We must work together to negotiate and fund licences.
vii. Subscription price negotiations should take into account the forthcoming transition to OA.
viii. Experimentation is needed on OA monographs.
ix. Repositories should be developed in “a valuable role complementary to formal publishing”.
x. Funders should be careful about mandating short embargo limits.

Mostly good stuff. I’m not happy about the emphasis on non-commercial forms of re-use in (iii), and of course walk-in access (v) is spectacularly dumb. (vi) seems a bit vacuous, but harmless I suppose — I’m not sure what point it’s trying to make.  (ix) is quietly sinister in its drive-by relegation of repositories to a subsidiary role, and of course (x) is pure publisher-food. Still, even with these caveats, the overall thrust is good.

Well, this has already gone on much longer than I intended, so I will leave further analysis for next time. For now, I am inclined to award the Finch Report a solid B+. I’ll be interested to see how that assessment stands up when I’ve read some other people’s analysis.

Just a link this time. Richard Smith was the editor of the British Medical Journal until 2004, and at one point he was chief executive of the BMJ Publishing Group. He is currently director of the United Health Group’s chronic disease initiative, and an unpaid professor at both Warwick University and Imperial College London. He’s a pretty big hitter by any standards.

Does he have the access to research that he needs?

Read his story on the BMJ blog.

This. Is. Stupid.

In their desperate scramble to retain the 32%-42% profit margins they’ve grown used to, academic publishers have told us a lot of different lies (e.g. that they provide peer-review), and repeated them so often that we’re in danger of believing them by sheer repetition.

Can we please put an end to this one? Researchers do not have the access they need.

Caudal pneumaticity in saltasaurines. Cerda et al. (2012: fig. 1).

Earlier this month I was amazed to see the new paper by Cerda et al. (2012), “Extreme postcranial pneumaticity in sauropod dinosaurs from South America.” The title is dramatic, but the paper delivers the promised extremeness in spades. Almost every figure in the paper is a gobsmacker, starting with Figure 1, which shows pneumatic foramina and cavities in the middle and even distal caudals of Rocasaurus, Neuquensaurus, and Saltasaurus. This is most welcome. Since the 1990s there have been reports of saltasaurs with “spongy bone” in their tail vertebrae, but it hasn’t been clear until now whether that “spongy bone” meant pneumatic air cells or just normal marrow-filled trabecular bone. The answer is air cells, loads of ‘em, way farther down the tail than I expected.

Caudal pneumaticity in diplodocines. Top, transverse cross-section through an anterior caudal of Tornieria, from Janensch (1947: fig. 9). Bottom, caudals of Diplodocus, from Osborn (1899: fig. 13).

Here’s why this is awesome. Lateral fossae occur in the proximal caudals of lots of neosauropods, maybe most, but only a few taxa go in for really invasive caudal pneumaticity with big internal chambers. In fact, the only other sauropod clade with such extensive pneumaticity so far down the tail are the diplodocines, including Diplodocus, Barosaurus, and Tornieria. But they do things differently, with BIG, “pleurocoel”-type foramina on the lateral surfaces of the centra, leading to BIG–but simple–camerae inside, and vertebral cross-sections that look like I-beams. In contrast, the saltasaurines have numerous small foramina on the centrum and neural arch that lead to complexes of small pneumatic camellae, giving their vertebrae honeycomb cross-sections. So caudal pneumaticity in diplodocines and saltsaurines is convergent in its presence and extent but clade-specific in its development. Pneumaticity doesn’t get much cooler than that.

Pneumatic ilia in saltasaurines. Cerda et al. (2012: fig. 3).

But it does get a little cooler. Because the stuff in the rest of the paper is even more mind-blowing. Cerda et al. (2012) go on to describe and illustrate–compellingly, with photos–pneumatic cavities in the ilia, scapulae, and coracoids of saltasaurines. And, crucially, these cavities are connected to the outside by pneumatic foramina. This is important. Chambers have been reported in the ilia of several sauropods, mostly somphospondyls but also in the diplodocoid Amazonsaurus. But it hasn’t been clear until now whether those chambers connected to the outside. No patent foramen, no pneumaticity. It seemed unlikely that these sauropods had big marrow-filled vacuities in their ilia–as far as I know, all of the non-pneumatic ilia out there in Tetrapoda are filled with trabecular bone, and big open marrow spaces only occur in the long bones of the limbs. And, as I noted in my 2009 paper, the phylogenetic distribution of iliac chambers is consistent with pneumaticity, in that the chambers are only found in those sauropods that already have sacral pneumaticity (showing that pneumatic diverticula were already loose in their rear ends). But it’s nice to have confirmation.

So, the pneumatic ilia in Rocasaurus, Neuquensaurus, and Saltasaurus are cool because they suggest that all the other big chambers in sauropod ilia were pneumatic as well. And for those of you keeping score at home, that’s another parallel acquisition in Diplodocoidea and Somphospondyli (given the apparent absence of iliac chambers in Camarasaurus and the brachiosaurids, although maybe we should bust open a few brachiosaur ilia just to be sure*).

* I kid, I kid.**

** Seriously, though, if you “drop” one and find some chambers, call me!

Pectoral pneumaticity in saltasaurines. Cerda et al. (2012: fig. 2).

But that’s not all. The possibility of pneumatic ilia has been floating around for a while now, and most of us who were aware of the iliac chambers in sauropods probably assumed that eventually someone would find the specimens that would show that they were pneumatic. At least, that was my assumption, and as far as I know no-one ever floated an alternative hypothesis to explain the chambers. But I certainly did not expect pneumaticity in the shoulder girdle. And yet there they are: chambers with associated foramina in the scap and coracoid of Saltasaurus and in the coracoid of Neuquensaurus. Wacky. And extremely important, because this is the first evidence that sauropods had clavicular air sacs like those of theropods and pterosaurs. So either all three clades evolved a shedload of air sacs independently, or the basic layout of the avian respiratory system was already present in the ancestral ornithodiran. I know where I’d put my money.

There’s loads more interesting stuff to talk about, like the fact that the ultra-pneumatic saltasaurines are among the smallest sauropods, or the way that fossae and camerae are evolutionary antecedent to camellae in the vertebrae of sauropods, so maybe we should start looking for fossae and camerae in the girdle bones of other sauropods, or further macroevolutionary parallels in the evolution of pneumaticity in pterosaurs, sauropods, and theropods. Each one of those things could be a blog post or maybe a whole dissertation. But my mind is already thoroughly blown. I’m going to go lie down for a while. Congratulations to Cerda et al. on what is probably the most important paper ever written on sauropod pneumaticity.

References

  • Cerda, I.A., Salgado, L., and Powell, J.E. 2012. Extreme postcranial pneumaticity in sauropod dinosaurs from South America. Palaeontologische Zeitschrift. DOI 10.1007/s12542-012-0140-6
  • Janensch, W. 1947. Pneumatizitat bei Wirbeln von Sauropoden und anderen Saurischien. Palaeontographica, Supplement 7, 3:1–25.
  • Osborn, H. F. 1899. A skeleton of Diplodocus. Memoirs of the American Museum of Natural History 1:191–214.

From the collections of the American Museum of Natural History, I give you the sacrum and fused ilia of “Apatosaurusminimus AMNH 675, as correctly identified by Steve P in a comment to the previous post:

"Apatosaurus" minimus sacrum with fused ilium, right lateral view

As Steve P rightly pointed out, AMNH 675 was designated as Brontosaurus sp. by Osborn (1904), and made the type of Apatosaurus minimus by Mook (1917).

It’s been known for some time that whatever this is, it’s not Apatosaurus — see for example McIntosh (1990a:398), McIntosh (1990b:59) and Upchurch et al. (2004:298). But what actually is it? Well, at the moment, no-one knows. Matt and I now have a manuscript in prep that we hope will somewhat elucidate this question. More to come on this specimen, most likely.

References

McIntosh, John S. 1990a. Sauropoda. In The Dinosauria, pp. 345–401. Berkeley and Los Angeles: University of California Press.

McIntosh, John S. 1990b. Species Determination in Sauropod Dinosaurs with Tentative Suggestions for the Their Classification. In Dinosaur Systematics: Approaches and Perspectives, pp. 53–69. Cambridge: Cambridge University Press.

Mook, Charles C. 1917. Criteria for the determination of species in the Sauropoda, with description of a new species of Apatosaurus. Bulletin of the American Museum of Natural History 38:355-360.

Osborn, Henry F. 1904. Manus, sacrum, and caudals of Sauropoda. Bulletin of the American Museum of Natural History 20:181-190.

Upchurch, Paul, Paul M Barrett, and Peter Dodson. 2004. Sauropoda” In The Dinosauria, 2nd Edition, pp. 259–322. Berkeley and Los Angeles: University of California Press.

A couple of posts back, when Matt was talking about turtle laminae, he included a photo of me in front of the skeleton of the giant turtle Archelon. Also in that photo is the tripod I was using — if you want to call it that — a tripod of altogether startling inadequacy. Here it is again, this time in the collections of the AMNH:

(Bonus SV-POW! points for anyone who can tell me what taxon or specimen I am working on. Sorry, Heinrich, you’re disqualified, since you already know.)

Why did we use such a poor tripod? Matt was planning to bring a proper one, but at the last minute decided to downsize his luggage by taking one small enough to fit into a smaller bag — in fact, it’s the tripod that came free with a telescope he recently bought. Not a good move: it was too short for many of the shots we wanted to take, too flimsy to properly stabilise the camera in many situations, and didn’t have enough degrees of freedom to let us get every shot we wanted from the best position.

Still, it was better than nothing, and we did contrive to get all the specimen photos we needed.

At the end of the week, when we finished up in collections and went to catch our taxi to the airport, Matt left the tripod behind. I emailed our AMNH host Carl Mehling to explain:

Matt deliberately left behind his tripod — it’s on the desk where we had the pelvic elements. He has much better tripods at home, and regrets the false economy of bringing that lighter and less stable one. But we figured it would be better than nothing for the use of anyone who turns up in collections with no tripod at all, so please feel free to make it available to visitors. Matt asks only that it be known as “The Mathew J. Wedel Memorial Tripod”.

Carl replied:

Thanks so much for the tripod – I KNOW it will come in handy!

My response:

Ah, sorry about this but my client insists that it must be known by its full title The Mathew J. Wedel Memorial Tripod at all times. If necessary, you may abbreviate it to TMJWMT on second and subsequent mentions.

Carl’s reply:

I can engrave it in the Lab and apply a B72/India Ink/B72 sandwich acronym/monogram on it. I will also construct an archival museum mount for it and put a security chip in its brain.

That’s when Matt himself weighed in:

Oh, and be sure that when the tripod is not in use it is stored in an airtight positive pressure chamber full of an inert gas. It should also be polished twice daily with the down of a hatchling bald eagle (fresh down each time, naturally). Finally, the tripod itself should be listed as an author on any publications that include photos taken with it. Please send a runner to my office in California to confirm that these instructions will be carried out to the letter.

The runner hasn’t arrived yet (to my knowledge) but I think we can take it as read that Carl will comply with these very reasonable conditions.

So, folks! If ever you’re working in the AMNH big-bone room, and you find you’ve forgotten your tripod … you might just be lucky enough to be allowed use of the Mathew J. Wedel Memorial Tripod!

Sometimes you just can’t make this stuff up.

You may recall a story from the Onion Our Dumb Century book, allegedly from 1904, about the skeleton of Satan being discovered in Wyoming. Mike used his occult powers to put together this scan from freely available online sources:

If you scrutinize the above image carefully, you’ll see that ‘Satan’ is an Allosaurus (I’m no theropod booster, but I always thought that was a little harsh on T. rex).

Why am I telling you this? Because last week Mike and I were toiling in the big bone room in the basement of the AMNH when we came across AMNH 666.

It’s an ilium. (Of course it would have to be an appendicular element. Vertebrae are from on high [or dorsal, if you prefer].)

Of Allosaurus!

The stomach-churning color here could be a manifestation of diabolical power, or just what happens when you try to photograph a pink specimen label on a yellow-orange forklift.

After this harrowing encounter, we cleansed our bodies, minds, and souls with street-vendor hot dogs and The Avengers.* That particular mode of exorcism may not be the most effective–I felt distinctly dodgy that evening. But the next day we received illumination at the Altar of Sauropod Awesomeness and were soon back to what we jokingly refer to as normal.

* The best way to see The Avengers is by going up to the observation deck of the Empire State Building shortly beforehand, so big swathes of the Manhattan skyline will still be in your mental RAM during the big final battle. I understand it’s not an option for everyone.

Folks, I just got this email from open-access guru Peter Suber (quoted with permission):

I get ominous warnings when I try to visit your blog at http://svpow.com/. The warning in the browser says, “Malicious website blocked”. The warning in a separate pop-up says, “The Web page you are attempting to visit…could potentially harm your computer.”

Both warnings are from Trend Micro, which came factory installed on my Windows-based Dell laptop. I’ve found it reliable in the past.

Has anyone else seen this? Is it something we should be worried about? Does anyone know what we can do to stop it?

(BTW., for what it’s worth I can assure anyone else who’s seeing this warning that it can be ignored. There’s no malware here.)

 

Here’s a cool skeleton of the South American pleurodire Podocnemis in the Yale Peabody Museum.

What’s that you’re hiding in your neck, Podocnemis?

Laminae! Here’s a closeup:

The laminae run from the transverse processes to the prezygapophyses and the centrum, which I reckon makes them analogues of the PRDLs and ACDLs of sauropods.

As long as I’m posting on Peabody turtles, here’s Archelon. It’s not bad, if you’re into that sort of thing. Which Mike clearly ain’t, but for a good reason, which will be revealed soon.

For more info on vertebral laminae in extant non-dinosaurs, see this post and the lower left paragraph on page 212 of this paper.

Secretary bird:

Matt pointed out to me something that in retrospect is obvious, though I’d never thought about it before: the eyelashes of birds are not homologous with ours, since mammals’ eyelashes are modified hairs and birds don’t have hair. Instead, their lashes are modified feathers. It would be interesting to see both kinds of eyelash under a microscope and compare.

It certainly looks as though these “feathers” are simple unbranched filaments — much like the earliest protofeathers found on so many of those wacky Chinese raptors. I wonder how closely they resemble the ancestral state?

Check this baby out:

I know, I know what you’re thinking. “Enough with the vulgar overexposed skull of this beast, Taylor”, you cry: “Show us its zygapophyses!”

But of course.

This is from the anterior part of the tail, in right lateral view: the vertebrae that you see here are the third to seventh of those that carry chevrons.

The hot news here is of course that sperm whales go to all the bother of developing zygapophyses, right up at the top of their neural arches, down in a region of the body where they don’t come close to articulating and are of no conceivable use.

Anyone know why? Care to hazard a guess?

For previous adventures in the Harvard Museum of Natural History, see here (monotremes) and here (bird eggs).

 

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