The giant Oklahoma Apatosaurus: OMNH 1670 redux
April 30, 2012
In the recent post on OMNH 1670, a dorsal vertebra of a giant Apatosaurus from the Oklahoma panhandle, I half-promised to post the only published figure of this vertebra, from Stovall (1938: fig. 3.3). So here it is:
And in the second comment on that post, I promised a sketch from one of my notebooks, showing how much of the vertebra is reconstructed. Here’s a scan of the relevant page from my notebook. Reconstructed areas of the vert are shaded (confusingly, using strokes going in opposite directions on the spine and centrum, and the dark shaded areas on the front of the transverse processes are pneumatic cavities), and measurements are given in mm.
Next item: is this really a fifth dorsal vertebra?
Apatosaurus louisae CM 3018 D4 and D5, in anterior (top), left lateral, and posterior views, from Gilmore (1936: plate 25).
Here are D4 and D5 of A. louisae CM 3018. They sort of bracket OMNH 1670 in terms of morphology. D4 has a broader spine, and D5 has a narrower one. The spine of D5 lacks the slight racquet-shaped expansion seen in OMNH 1670, but the overall proportions of the spine are more similar. On the other hand, the transverse processes of D4 taper a bit in anterior and posterior view, as in OMNH 1670, and unlike the transverse processes of D5 with their more parallel dorsal and ventral margins. But honestly, neither of these verts is a very good match (and the ones on either side, D3 and D6, are even worse).
Apatosaurus parvus UWGM 15556 (formerly A. excelsus CM 563) D4 (left) and D3 (right) in anterior (top), right lateral, and posterior views, from Gilmore (1936: plate 32).
Here are D3 and D4 of A. parvus UWGM 15556. D3 is clearly a poor match as well–it is really striking how much the vertebral morphology changes through the anterior dorsals in most sauropods, and Apatosaurus is no exception. D3 looks like a dorsal in lateral view, but in anterior or posterior view it could almost pass for a posterior cervical. If I was going to use the term “cervicodorsal”, indicating one of the vertebrae from the neck/trunk transition, I would apply it as far back as D3, but not to D4. That thing is all dorsal.
And it’s a very interesting dorsal from the perspective of identifying OMNH 1670. It has fairly short, tapering transverse processes. The neural spine is a bit shorter and broader, but it has a similar racquet-shaped distal expansion. I’m particularly intrigued by the pneumatic fossae inscribed into the anterior surface of the neural spine–in Gilmore’s plate they make a broken V shapen, like so \ / (or maybe devil eyes). Now, OMNH 1670 doesn’t have devil eyes on its spine, but it does have a couple of somewhat similar pneumatic fossae cut into the spine just below the distal racquet–perhaps a serially modified iteration of the same pair of fossae as in the A. parvus D4. It’s a right sod that D5 from this animal has its spine blown off–but it still has its transverse processes, and they are short and tapering as in OMNH 1670.
Apatosaurus sp. FMNH P25112, dorsal vertebrae 1-10 and sacrals 1 and 2, Riggs (1903: plate 46)
Here are all the dorsals and the first couple sacrals of FMNH P25112, which was originally described as A. excelsus but in the specimen-level analysis of Upchurch et al. 2005) comes out as the sister taxon to the A. ajax/A. parvus/A. excelsus clade. Note the striking similarity of the D5 here with D4 of the A. parvus specimen in Gilmore’s plate (until the careful phylogenetic work up Upchurch et al. 2005, that A. parvus specimen, once CM 563 and now UWGM 15556, was considered to represent A. excelsus as well). But also notice the striking similarity of D6 to OMNH 1670. It’s not quite a dead ringer–the transverse processes are longer and have weird bent-down “wingtips” (XB-70 Valkyrie, anyone?)–but it’s pretty darned close, especially in the shape of the neural spine.
So what does this all mean? First, that trying to specify the exact serial position of an isolated vertebra is nigh on to impossible, unless it’s something that is one-of-a-kind like an axis. Second, after doing all these comparos I think it’s unlikely that OMNH 1670 is a D4–those are a bit too squat across the board–but it could plausibly be either a D5 or a D6. Third, I’m really happy that it doesn’t seem to match any particular specimen better than all the rest. What I don’t want to happen is for someone to see that this vertebra looks especially like specimen X and therefore decide that it must represent species Y. As I said in the comments of the previous post, what this Oklahoma Apatosaurus material needs is for someone to spend some quality time seeing, measuring, and photographing all of it and then doing a phylogenetic analysis. That sounds like an ambitious master’s thesis or the core of a dissertation, and I hope an OU grad student takes it on someday.
If you were intrigued by my suggestion that the big Oklahoma Apatosaurus rivalled Supersaurus in size, and wanted to see a technical comparison of the two, I am happy to report that Scott Hartman has done the work for you. Here’s one of his beautiful Apatosaurus skeletal reconstructions, scaled to the size of OMNH 1670, next to his Supersaurus silhouette. This is just a small teaser–go check out his post on the subject for a larger version and some interesting (and funny) thoughts on how the two animals compare.
References
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
- Riggs, E.S. 1903. Structure and relationships of opisthocoelian dinosaurs, part I: Apatosaurus Marsh. Field Columbian Museum Publications, Geological Series 2(4): 165–196.
- Stovall, J.W. 1938. The Morrison of Oklahoma and its dinosaurs. Journal of Geology 46:583-600.
Inconsistent fusion in Haplocanthosaurus sacra
April 29, 2012
Matt and I have been looking in more detail at indications of maturity in sauropod skeletons, as we prepare the submission of the paper arising from our response to Woodruff and Fowler (2012) [part 1, part 2, part 3, part 4, part 5, part 6]. Here is an oddity.
Sacra of Haplocanthosaurus. Top, H. utterbacki holotype CM 879 in right lateral view, from Hatcher (1903:fig. 15). Bottom, H. priscus holotype CM 572 in left lateral view (reversed), from Hatcher (1903:pl. IV, part 3). To the same scale.
H. priscus is the type species of Haplocanthosaurus; H. utterbacki is the second species, named by Hatcher in the 1903 monograph that described the original material in detail. As previously noted, the type species is based on adult material, and the referred specimen on subadult material. This is shown by their different stages of neurocentral fusion, and corroborated by the size of the specimens as indicated in the composite illustration above.
There is a lot of fusion going on in the sacra of dinosaurs:
- sacral neural arches fused to their centra
- consecutive sacral centra fused together
- consecutive sacral neural spines fused together
- sacral lateral processes fused to ilia
As we would expect, the less mature of the two Haplocanthosaurus individuals is less fused in most respects: none of the centra were fused either to each other or their respective neural arches, and the ilium was not fused to any of the lateral processes, whereas in the adult all neural arches are fused to their centra, the five sacral centra are all fused together, and the ilium is fused to the lateral processes.
How strange, then, that the consecutive neural spines are more fused in the juvenile! Not only are spines 1, 2 and 3 fused along their entire dorsolateral length, as in the adult, but spine 4 is similarly fused. And more: the neurapophysis of spine 5 is fused to that of 4, even though the spines are not fused more ventrally.
What does this mean? Hatcher (1903:27-28) took it as indicative of species-level separation. After briefly noting that the posterior dorsal centra of H. utterbacki are more opisthocoelous than those of H. priscus, and speculating that the adult of the referred species was probably larger than that of the type, he continued:
But the most distinctive character is to be found in the sacrum which, in the present species, has the five neural spines normally coössified. The first four are cocoössified throughout their entire length, forming a long bony plate. The union between the fourth and fifth is limited to the extremities while medially [sic, presumably meaning half way up the spines] they are separated by an elongated foramen. In H. priscus only the spines of the three anterior sacrals are coössified, those of the first and second [sic, presumably intending fourth and fifth] sacrals remaining free. This difference exists notwithstanding that the type of the present species was scarcely adult, the sacral centra being neither coössified with one another nor with their neural arches. By some this character might be considered as of generic importance although I prefer to consider it as of only specific value since in all other parts of the skeleton preserved, there are no distinguishing characters which could be considered as of generic value.
At present, however, the synonymy of H. utterbacki with the type species, proposed by McIntosh and Williams (1988:22), seems to be universally accepted. If they truly belong to the same taxon then the only realistic possibility is that we are seeing individual variation in the timing of fusion. That certainly seems to have been the opinion of McIntosh and Williams (1988:14), writing about the sacrum of their own specimen, the H. delfsi holotype CMNH 10380:
As in CM 572 the short to moderately long spines of sacrals one through three are firmly united throughout, and those of sacrals four and five are firmly united to midheight. In CM 572 spines four and five are free, but this is probably an individual character because in the even younger CM 879 all five spines are united.
All of which means: we need to be really careful when drawing conclusions about taxonomy or ontogeny from individual observations of skeletal fusion.
Bonus Pneumaticity Observation: In the image at top, you’ll see that the centrum of sacral 4 in CM 879 has a couple of pneumatic fossae. For more than you probably wanted to know about those specific holes in that specific bone, see this post and the linked paper.
References
- Hatcher, J.B. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.
- McIntosh, J.S., and Williams, M. E. 1988. A new species of sauropod dinosaur, Haplocanthosaurus delfsi sp. nov., form the Upper Jurassic Morrison Fm. of Colorado. Kirtlandia 43:3-26.
- Woodruff, D.C, and Fowler, D.W. 2012. Ontogenetic influence on neural spine bifurcation in Diplodocoidea (Dinosauria: Sauropoda): a critical phylogenetic character. Journal of Morphology, online ahead of print.
SV-POW! is now (finally!) open access
April 28, 2012
It was never our intention to be so restrictive, of course. We always wanted what we write to be as widely useful as possible; but like most bloggers, we just didn’t think about what that entailed.
So now, belatedly, we are placing SV-POW! under the Creative Commons Attribution licence. This means that you can do anything with our content, subject only to giving us credit. Go nuts. We want our work to be useful. (Our use of this licence is indicated by the CC BY button at top right of all the pages.)
Note that SV-POW! is now compliant with the Budapest Open Access Initiative’s definition of open access — the only definition that matters, really, since it’s where the term “open access” was first coined. That definition is rather noble and striking:
By ‘open access’ to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”
We are applying this licence restrospectively to all the original content on the site — not just what we write from now on. To ensure that we’re on safe ground doing this, all three of us agreed on this measure, and we also obtained consent from the only (so far) guest-blogger on SV-POW!, Heinrich Mallison.
Finally, we should note the exceptions to the CC BY licence. When we’ve included material from other sources — most often figures from published papers — we do not own the copyright and can’t licence it. Similarly, all photographs of fossils held by the Natural History Museum in London are copyright the museum. If you want to re-use any of the non-original material, you’ll need to track down the copyright holders and negotiate with them.
How Elsevier can save itself, part 2: Medium
April 26, 2012
It seems the world is conveniently arranging itself for the benefit of this occasional series. Every time I am about to post an installment, something apposite happens out there. Just as I was preparing part 0, Bernstein Research’s investment report Is Elsevier Heading for a Political Train-Wreck? came out; just before part 1, Elsevier decided that the solution to their problems was to hire a PR guy; and now, as I prepare part 2, America’s richest university says publicly that it can’t afford spiralling subscription fees any more.
It’s not my intention to gloat, but the recent cascade of events must surely be giving Elsevier and other big barrier-based publishers pause for thought. A trickle of outrage has swiftly grown into a tide. That may become a tidal wave. Real change is needed to avert disaster.
Last time we looked at things that Elsevier should do right now, at no cost to itself: be explicit about terms of “sponsored articles” and non-sponsored articles; make it trivially easy to find sponsored articles; stop lying about copyright transfer; root out and destroy stupid conditions.
This time, we’ll go on to measures that probably will cost Elsevier something (though most likely not as much as they fear).
1. Change the “sponsored article” licence to CC-BY
Springer’s Open Choice is their equivalent of Elsevier’s “sponsored articles“. Except it’s not, because Springer’s version is true Budapest-compliant open access. Not only that, it’s trivially easy to tell that it’s the case, because the page simply says:
Copyright and Open Access License
If authors choose open access in the Springer Open Choice program, they will not be required to transfer their copyright; the copyright remains with the author.
NEW! Springer now permits commercial use for Open Choice, as all Open Choice articles are published under the Creative Commons Attribution (CC BY) license from January 16, 2012 onwards.
This is the right way to do it: by using a standard licence instead of writing their own terms, Springer tap into accumulated understanding of what CC BY means. And by using that particular licence, they remove all doubt about what you are and aren’t able to do with such articles. They’re freed to be used in any reasonable way, for the benefit of science.
If someone pays Elsevier $3000 to sponsor an article, it’s been paid for. There is no legitimate reason for Elsevier to take the copyright under such circumstances, and no reasonable expectation that they should be able to make more money by charging for any use of such an article. Worse, this kind of action makes Elsevier look mercenary and works directly against the partnering-with-authors impression that they otherwise try to nurture.
Special bonus: if Elsevier switch to the BOAI-compliant CC BY licence for such articles, they can stop weaseling around calling their scheme “sponsored articles”, and truthfully call the results open access. And right now, Elsevier really, really needs to be able to say that it’s supporting open access.
What does Elsevier stand to lose by doing this? A tiny revenue stream arising from people paying to actually use sponsored articles. Of course I am not privy to Elsevier’s internal accounting, so I don’t know what that amount is, but I would be amazed if it’s more than 0.01% of their revenue and pretty surprised if it was more than 0.001%. Not worth it.
2. Stop being obstructive about text-mining
When you read a published paper — say, because your library has a subscription that allows you to — you process the information that it contains and use that in your own work. Later on, you publish that work, and what you publish has benefitted from the facts that were in the papers you read. This is called research, or sometimes “standing on the shoulders of giants”, and it’s how science is made.
It’s how we’ve been doing science, in fact, since 1665. But now it’s the 21st century and we have millions of papers to read instead of a handful. Happily we have computers to do the reading for us, and in many fields they can extract important information such as use of taxonomic terms or chemical reactions. This is called text-mining. Just like when we read papers ourselves, text-mining extracts facts rather than their particular expression; and facts are not subject to copyright. So it follows that anyone who has access to papers has the right to text-mine them.
Unfortunately, Elsevier (like many other publishers) has a history of being obstructive about mining. Even when they set out to help — and to give credit, they are making an effort — it’s of the form “We are keen to arrange a teleconference with you all to discuss ways to enable text mining for academics at Cambridge University“. Which is a waste of everyone’s time: first, we want to be doing science, not making conference calls; second, it’s dumb to limit this negotiation process to one text-mining project at a time. (Even Elsevier’s own Director of Universal Access, has commented that she worries that “she might be overwhelmed by requests from others who also want text mining access“.
So this is dumb. Since other publishers (with the obvious exceptions) are equally obstructive, Elsevier has an opportunity to lead the way. They should demonstrate their commitment to open science by laying down this simple principle: if it’s been paid for (by subscription or OA), you can let computers as well as people read the information.
Again, what will this cost? Maybe a little: perhaps Elsevier have managed to negotiate contracts with some customers where they pay extra for the privilege of mining, and they’d have to forego that revenue. On the other hand, they’d be able to save a lot of money by not having to hold conference calls that involve six people at a time, including a vice president and three directors. So overall this could even be a net financial win for Elsevier.
3. Dump the “you can self-archive unless mandated to” rule
Elsevier’s Article Posting Policies state:
Elsevier believes that individual authors should be able to distribute their AAMs for their personal voluntary needs and interests, e.g. posting to their websites or their institution’s repository, e-mailing to colleagues.
(AAMs are “accepted author manuscripts”, defined as “the author’s version of the manuscript of an article that has been accepted for publication and which may include any author-incorporated changes suggested through the processes of submission processing, peer review, and editor-author communications”.)
So far, so good: Elsevier supports self-archiving. But it goes on:
Deposit in, or posting to, subject-oriented or centralized repositories (such as PubMed Central), or institutional repositories with systematic posting mandates is permitted only under specific agreements between Elsevier and the repository, agency or institution, and only consistent with the publisher’s policies concerning such repositories.
The page then clarifies that you’re not allowed to self-archive in response to:
Institutional, funding body or government manuscript posting policies or mandates that aim to aggregate and openly distribute the work by its researchers or funded researchers.
In other words, you’re allowed to self-archive so long as you’re not under a mandate to do so. If you’re mandated to self-archive then you’re not allowed to.
This is not just obstructive, but absurd. I’m not sure whether it’s more Kafka or Borges, but either way it makes Elsevier look dumb. The analogy that springs to mind is a stroppy toddler who likes going to the playground, but arbitrarily refuses when a parent suggests it.
It’s been pointed out many times that there is no evidence that self-archiving (“Green open access”) harms publishers in any way. Elsevier’s current policy is baseless, and makes them look both obstructive and absurd. They should fix it.
One more quote from the policy page:
We routinely analyse and modify our policies to ensure we are responding to authors’ needs and concerns, and the concerns in general of the research and scholarly communities.
That is encouraging. Let’s hope it’s true.
Probable cost to Elsevier if they fix this? Hard to evaluate, but at the moment the sum of all available evidence (i.e. none whatsoever) doesn’t give any reason to think there will be a cost at all.
4. Withdraw opposition to the FRPAA
This one is surely a no-brainer. Elsevier’s support for the RWA, both financial and rhetorical, catalysed a level of fury among researchers that’s like nothing they’ve seen before. The Cost of Knowledge boycott, which has now surpassed ten thousand signatories and is going strong, is only the tip of the iceberg. Elsevier recognised that supporting the RWA was an appalling tactical misstep, and publicly withdrew their support, resulting shortly thereafter in the RWA’s unlamented death.
So it was with something of a facepalm that, five minutes later, I saw Elsevier listed as one of the signatories on the Association of American Publishers’ letter campaigning against the FRPAA.
Seriously, Elsevier. Don’t you get it? All the researchers who hated the RWA also love the FRPAA. By publicly opposing it, you instantly undid the good that your RWA withdrawal did. Straight away, you cast yourself again as researchers’ enemy rather than partner.
Just stop it.
Cost to Elsevier: hard to calculate but probably close to zero. Cost to Elsevier of continuing to oppose the FRPAA: totally wasting the salaries of whatever PR people they hire. Because while you directly oppose what we want, no amount of PR will persuade us that you’re on our side.
5. Be open about subscription prices
No-one knows what Elsevier charge for journal subscriptions.
Even people within a university often don’t know what their own library is paying, because the librarians are forbidden to tell them.
It’s hardly surprising that this breeds an atmosphere of secrecy and distrust.
Is that what you want, Elsevier? Huh? Huh?
Again we come back to the central issue, which is trust. Elsevier is a science publisher, which means that most of its customers are scientists. Science has always been done in the open — it’s the nature of what science is. And this is becoming more and more important with the rise of open-notebook science, and of services like FigShare, DigiMorph and GenBank. That’s the atmosphere that science is happening in.
If Elsevier wants to be taken seriously by scientists, it needs to be similarly open. After all, when you keep secrets, people always assume the worst.
—
What do these measures have in common? None of them will cost Elsevier much — maybe even save them some money. These are things that should be done as a priority, as in within a month or so. They’re not hard, they just need the will to make them happen. If Elsevier don’t move quickly on these things, the door will slam shut and leave them outside.
If they do move quickly, then they’ll have made real steps towards re-casting themelves as a friend of science, and of scientists.
JVP’s new open access fee
April 25, 2012
This arrived in my inbox last week, but I’ve been too busy to blog about it until now.
Not surprisingly, I have comments.
First, this is huge news. I am certain that Taylor & Francis, which otherwise have some of the most rapacious fees in the business, are not thrilled about taking a 38% fee cut, and that they are not doing it out of the goodness of their hearts or because they want to forge a better relationship with the vertebrate paleontology community (or whatever transparent folderol they put in their public statements). Bottom line, they’re a corporation, they have a legal mandate to maximize profits for shareholders. So there are only two plausible reasons why they might be dropping the OA publication fee so sharply for JVP: because they think they’ll make more money in the long run, or because the powers-that-be at the Society of Vertebrate Paleontology fought hard for the change. I think the first reason is a non-starter, for reasons I’ll explain below, which leaves heroism from within the Society as the hypothesis I can’t falsify. Good enough for now. SVP people who helped make this happen, whoever and wherever you are, you have my heartfelt thanks. Please don’t lose sight of that if you read the rest of the post.
Now for the not-so-good news. If you’re an author, you want your work to be read as widely as possible, so OA is in your best interests, period. There are OA journals that are free to publish in, like Paleodiversity, PalArch’s JVP, and Acta Palaeontological Polonica, and of course PLoS ONE gives waivers to authors who can’t pay their $1350/article publication fee. But let’s say that you have grant money or departmental funds to pay OA publication fees. Would you choose to pay $2000/article for OA publication in JVP? Let’s look at some criteria you might want to consider:
- Article length: limited in JVP, unlimited in PLoS ONE.
Color figures: not free in JVP, free in PLoS ONE.[Note the correction below from Paul Barrett: colour figures are now free in JVP PDFs — a charge is only made for printing colour.]- Impact factor: 2.241 for JVP (retrieved from here), 4.411 for PLoS ONE.
- Rejection criteria: your work has to be scientifically sound and also pass some threshold of general interest or importance at JVP; at PLoS ONE it just has to be scientifically sound.
- Publication speed: there is a lag-time between when your manuscript is accepted at JVP and when it is made public. Admittedly JVP moves pretty fast right now for paper journal, and you’re unlikely to wait more than 2 or 3 months. But PLoS ONE is faster still, posting your paper almost immediately after it’s accepted.
And of course the elephant in the room:
- Cost: $2000 for OA publication in JVP, $1350 for PLoS ONE.
So, to sum up, if you send your paper to JVP it will have to be shorter and have fewer figures that will be in black and white unless you choose to pay extra for color reproduction, the selection criteria are more stringent but the impact factor is much lower (for now), and you’ll have to wait a bit longer–but at least you’ll get to pay half again as much for worse performance in all of these areas. That’s why this can’t be some kind of long-term strategy by Taylor & Francis to get more business–doing that requires undercutting your competitors, not overcharging and under-delivering. They’re practically driving potential authors towards PLoS with pitchforks and torches.
So, although I applaud the good folks in the Society for getting a concession this big from Taylor & Francis, the publisher’s service to us is still a joke, because it is so markedly inferior but costs so much more. It’s like completing a 50-yard pass in American football…from halfway back in your own end zone. Hell of a play, dude. Hell of a play. But you’re still on the wrong side of the field.
What next? Well, the good news is that the Society has been getting concessions from Taylor & Francis, so in the short term we should keep pushing for T&F to give us an OA option that is actually competitive. This is a step in the right direction, but it is just a step, and we are way behind the curve here.
In the long term, I think we should think very hard about the Society’s mission. The full version can be found here, but the central kernel is, “The object of the society is to advance the science of vertebrate paleontology.” Allowing a for-profit, barrier-based publisher to put our science behind a paywall in order to enrich its shareholders is simply not consistent with that object. It doesn’t advance the science, it hurts our authors, and it hurts the people who need access to our work but can’t afford it. We should demand better. We must demand better, if we are to be true to our mission.
Update
Note that Paul Barrett, one of the Senior Editors of JVP and Co-Chair of the SVP Publications Committee, explains below that the discount on OA fees was offered by Taylor and Francis rather than negotiated by the SVP as we assumed. Matt has asked for clarification on how this went down (once, twice), but Paul says that he can’t go further into the discussions about JVP’s negotiations as there are legal and commercial implications.
The giant Oklahoma Apatosaurus: OMNH 1670
April 25, 2012
Left: the Queen of England, 163 cm. Middle, the Oklahoma apatosaur dorsal, 135 cm. Right, classic “big Apatosaurus” dorsal, 106 cm. To scale.
Something I’ve always intended to do but never gotten around to is posting on some of the immense Apatosaurus elements from the Oklahoma panhandle. Here’s one of the most impressive, OMNH 1670, an isolated dorsal. Notice that the tip of the neural spine is ever-so-shallowly bifurcated, which in Apatosaurus indicates a D4, D5, or D6. The low parapophyses and fat transverse processes are similar to D4, but Apatosaurus D4s usually have somewhat broader spines, so I’m guessing this thing is a D5. These things vary and I could easily be off by a position in either direction.
Next to it is D5 of CM 3018, the holotype specimen of Apatosaurus louisae (from Gilmore 1936: plate 25), which has served as the basis for many of the published mass estimates of the genus Apatosaurus. OMNH 1670 is 135 cm tall, compared to 106 cm for D5 of CM 3018. If the rest of the animal scaled the same way, it would have been 1.27^3 = 2 times as massive. Mass estimates for CM 3018 are all over the map, from about 18 tons up to roughly twice that, so the big Oklahoma Apatosaurus was probably in Supersaurus territory, mass-wise, and may have rivaled some of the big titanosaurs (Update: see the two giant diplodocids square off in a cool follow-up post by Supersaurus wrangler Scott Hartman). Here’s a fun rainy-day activity: take any skeletal reconstruction of Apatosaurus, clone it in Photoshop or GIMP, scale it up by 27%, and park it next to the original. It looks a lot bigger. So I’m continually surprised that Apatosaurus is so rarely mentioned in the various roundups of giant sauropods, both in the technical literature and in popular articles online. This vertebra was figured by Stovall (1938)–if I get inspired, I’ll dig up that figure and post it another day (hey, look, I did!).
Fun fact: in Apatosaurus the tallest (most posterior) dorsals are 1.3-1.5 times as tall as D5 (Gilmore 1936: 201). So D10 from this individual was probably between 1.7 and 2 meters tall–not quite in Amphicoelias fragillimus territory but getting closer than I’ll bet most people suspected.
NB: if you try to use the scale bar lying on the centrum of OMNH 1670 to check my numbers, you will get a wonky answer. The problem is that the vertebra is so large that it is almost impossible to get far enough back from it (above it, in this case, since it is lying on a padded pallet) to get a shot free from distortion due to parallax. For this shot, the pallet with the vert was on the floor, and I was standing on top of the tallest ladder in the OMNH collections, leaning out over the vert to get centered over the prezygapophyses, and shooting straight down–in other words, I had done everything possible to minimize the visual distortion. But it still crept in. Anyway, trust the measurements, which I–and presumably Gilmore–made with a good old reliable tape measure.
References
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
- Stovall, J.W. 1938. The Morrison of Oklahoma and its dinosaurs. Journal of Geology 46:583-600.
Harvard’s library can’t afford journal subscriptions
April 23, 2012
Harvard University is probably the single richest school on the planet. Its endowment in 2011 was the biggest in the USA, at $31.728 billion — over 60% more than the next highest (Yale, at $19.374 billion).
It’s also in with a good shout as the best university in the world — the current Times Higher Education ranking has it equal second, behind only Cal Tech, level with Stanford, and ahead of Oxford, Princeton and Cambridge.
If any university should be able to pay all its journal subscriptions without problems, it’s Harvard.
So this memorandum, published last Tuesday, came as quite a shock:
To: Faculty Members in all Schools, Faculties, and Units
From: The Faculty Advisory Council
Date: April 17, 2012
RE: Periodical SubscriptionsWe write to communicate an untenable situation facing the Harvard Library. Many large journal publishers have made the scholarly communication environment fiscally unsustainable and academically restrictive. … Some journals cost as much as $40,000 per year, others in the tens of thousands. Prices for online content from two providers have increased by about 145% over the past six years, which far exceeds not only the consumer price index, but also the higher education and the library price indices. …
The Faculty Advisory Council to the Library, representing university faculty in all schools and in consultation with the Harvard Library leadership, reached this conclusion: major periodical subscriptions, especially to electronic journals published by historically key providers, cannot be sustained: continuing these subscriptions on their current footing is financially untenable. … Costs are now prohibitive.
Yes, you read it right. The world’s richest university can’t afford journal subscriptions. If anyone ever doubted that subscription prices had run wild, that the academic publishers who control access to the research we generate are out of control, this should dispel any remaining illusions that all is well with the current model.
Happily, the Harvard advisory council does not limit itself to whining, but has concrete suggestions for researchers (and also for the library). The actions they recommend for researchers on their staff are:
- Archive all their own papers as Green Open Access.
- Submit to open-access journals; “move prestige to open access”.
- Resign from editorial boards of non-OA journals if they won’t convert.
- Ask professional societies to take control of publishing in their fields.
- Recruit colleagues to join them in these measures.
The deal here is that Open Access is not a fringe issue any more. It’s not just something that idealistic young researchers like to shout about. It’s a major part of the strategy of one — several, actually — of the world’s top universities. I’d argue that it’s been a moral imperative for a long time. Now Open Access has become an economic imperative, too. (Anyone who doubts that it’s much, much cheaper than the subscription model should check out the numbers in my recent article at The Scientist: it seems to come out at about one eighth of the cost.)
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For more analysis of Harvard’s public statement, see Harvard: we have a problem at Stephen Curry’s Reciprocal Space, and “No, we can’t” at the Library Loon’s Gavia Libraria. (The latter is particularly interesting because it offers a librarian’s perspective rather than the much more familiar researcher’s perspective.)
How Elsevier can save itself, part 1: Easy
April 22, 2012
Last time we looked at the state Elsevier has got itself into, and how it needs to make significant changes to regain the trust of researchers (and librarians for that matter).
By coincidence, literally as I was writing that, Elsevier’s Liz Smith tweeted:
I clicked through and looked at the advert:
Can you help us tell our story? We’re looking for someone who is part community manager, part brand manager and part journalist to be in charge of an exciting new website that will help us communicate more effectively and consistently with the research community.
You’ll establish and implement a content strategy for the site, to make sure that we’re talking about the many positive things happening at Elsevier.
This is worth doing — as Richard Poynder pointed out back in January, Elsevier needs to get out more, and hiring someone whose job is just that can’t hurt. But I hope no-one at Elsevier thinks that it will be enough to “make sure that we’re talking about the many positive things happening at Elsevier”.
The problems run much deeper than that.
So I’m going to discuss some of the things that Elsevier needs to actually do. By that I mean, not just talking more effectively about what’s happening already, but changes that need to made.
This post will address the easy ones — things that Elsevier should do right now, without even thinking about it. We’re talking here about things that will have pretty much no cost, and will start to make Elsevier look like people we can do business with.
1. Be explicit about “sponsored article” terms
I’m starting with this one to give Elsevier a head start, since it seems they’ve fixed this now. As of a few weeks ago, the sponsored article page has a link to a Sponsored Articles – User Rights page which spells out important details about what you are and are not allowed to do with a sponsored article.
(For the moment I am not interested in what those terms are — we’ll discuss how they are and are not satisfactory in the next article. I am just interested in whether we can find out what the terms are.)
Why am I mentioning this in How Elsevier Can Save Itself when it’s a problem they’ve already fixed? Two reasons.
First, because it took an incredibly long time to get them to make these terms clear: see previous articles one, two, three, three and a half, four.
Second, the terms are still not completely clear, in that they don’t say who has the copyright in the article. (It’s Elsevier, by the way, not the author, but we’ll talk about that in the next part.)
This is in contrast to, for example, Springer’s “Open Choice” page, which is crystal clear about both copyright ownership and access conditions in just 55 words of a page that fits on a single sheet of A4.
2. Be explicit about non-sponsored article terms
I have little idea at the moment exactly what I’m allowed to do with regular non-sponsored articles. I am affiliated with the University of Bristol and have off-campus access via Shibboleth and an intermittently functional VPN, so I assume I am allowed to download ScienceDirect articles. But I don’t know whether, for example, I’m allowed to email copies to colleagues who should have access but don’t from off-campus; or whether I’m allowed to text-mine the articles that I have access to; or, if so, what I am allowed to do with the results.
To be fair, there is a fairly hefty document on Authors’ Rights & Responsibilities, but that is addressed much more to the authors of articles than to their users.
Immediate Update. It turns out I was looking in the wrong place: the information doesn’t seem to be on elsevier.com, but it is on sciencedirect.com, where it can be reached by a Terms and Conditions link on almost every page. Those terms and conditions are very restrictive, but again we’ll discuss that next time. The important thing is to make sure they are very easy to find.
3. Make it trivially easy to find sponsored articles
When I was first trying to discover the terms of “sponsored articles”, one approach I took was to go to Cretaceous Research, an Elsevier journal, try to find a sample sponsored article, and see what it said about itself.
Well, I couldn’t do it. The Advanced Search page has fields for subject, date-range and more, but no “limit to sponsored articles” or similar checkbox.
There are lots of reasons people might want to find sponsored articles, and I can’t think of any good reasons why Elsevier might not want them to. So this should be made very easy. (Apart from anything else, it’s about the best way to advertise the journal.)
Not providing a searching option makes it look as though Elsevier want to hide sponsored articles — to stop people from getting full value from them. That perception, whether accurate or not, needs to be dealt with.
4. Stop lying about copyright transfer
This page in the Author’s Rights area discusses a question that comes up a lot:
Why does Elsevier request transfer of copyright?
The research community needs certainty with respect to the validity of scientific papers, which is normally obtained through the editing and peer review processes. The scientific record must be clear and unambiguous. Elsevier believes that, by obtaining copyright transfer, it will always be clear to researchers that when they access an Elsevier site to review a paper, they are reading a final version of the paper which has been edited, peer-reviewed and accepted for publication in an appropriate journal. This eliminates any ambiguity or uncertainty about Elsevier’s ability to distribute, sub-license and protect the article from unauthorized copying, unauthorized distribution, and plagiarism.
This is flagrant nonsense. No-one — no-one — evaluates the trustworthiness or validity of a paper on the basis of who owns the copyright. No-one.
So whatever the true reason for copyright transfer, we know it’s not to make it “clear to researchers that when they access an Elsevier site to review a paper, they are reading a final version of the paper.”
When Elsevier tells us things that we know are not true, how can they expect us to believe anything else they say?
5. Root out and destroy and stupid conditions
You sometimes hear stories like this one: an inter-library loan facility where the librarian is sent a PDF, but publisher restrictions do not not allowed it be forwarded to the patron. Instead, the librarian has to print the PDF out, destroy the original, scan the printout and send the scan to the patron.
Are these stories true? I don’t know. If they are, is Elsevier the publisher concerned? I don’t know. But Elsevier needs to make sure of that. At this point, any such stupidities will be discovered, and trumpeted, and ridiculed.
The same goes for any other equally dumb edge-cases. If they exist, someone’s going to find them. Better for Elsevier that it be one of their own people, and that they fix it ASAP.
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What do these measures have in common? None of them will cost Elsevier anything. These are things that should be done as soon as humanly possible, by which I mean “within the next week” rather than “we’ll set up a group to look into it, and report back at the next six-monthly management meeting”.
These measures are about transparency and sanity. They are the kinds of changes that will start to put some trust back in place. Being up-front and clear about what the access situation is will start to chip away at the sense that Elsevier has something to hide. Getting rid of palpable lies about copyright transfer will be a start towards enabling us to believe Elsevier when they tell us other things. None of this is enough to make an enemy into a friend; but it will at least help us to feel we’re facing an honourable enemy. (Of course, there is a lot more that researchers need from Elsevier beyond that baseline. We’ll look into that next time.)
Please do shout in the comments if I’ve missed any zero-cost transparency or sanity measures that should have been listed here.
How Elsevier can save itself, part 0: Introduction
April 20, 2012
Background
Today has seen the release of a Bernstein Research investment report by Claudio Aspesi, entitled Reed Elsevier: Is Elsevier Heading for a Political Train-Wreck? It contains some stark warnings to potential investors:
Elsevier’s original support for the RWA has triggered a rising level of support for open mandates, in turn escalating an obscure bill into both a public policy debate on dissemination of publicly-funded research as well as an unwelcome scrutiny into the finances of Elsevier.
And:
Another controversy, this time around text mining, is brewing in the background, and could possibly further escalate the issues triggered by the RWA debacle.
And most importantly, this conclusion:
Adding acrimonious relationships with the research community to the difficult ones it already has with academic librarians looks self-defeating. We believe that Elsevier needs to rethink altogether how it thinks of researchers as customers, or it could end up, in a few years, facing the same hostility it encounters with much of the academic librarian community.
I’m not here to gloat. I mention this report only as the timely backdrop to a short series of posts that I’ve been planning to write for a few weeks now.
State of the nation
It should now be clear to everyone who’s been paying attention that Elsevier has got itself into a rotten position. No-one trusts it or likes it. Even people who act as associate editors for its journals seem to be feeling that that’s something to be a bit apologetic about rather than something to declare proudly. The feeling has grown stronger and more widespread — the Cost of Knowledge boycott is now closing in on 10,000 signatories — and all but the most head-in-the-sand types are now being forced to recognise that the distrust, dislike and resolution is real and significant, and that it’s not going away.
Every time I’ve got into conversation with an actual Elsevier employee (Liz Smith, Tom Reller) they’ve been friendly, reasonable and polite — and I should add, rather forbearing, when you think of how much I’ve had to say against their employer. But there’s often an undertone of hurt. I don’t know if I’m over-interpreting, but it seems to me that Elsevier employees feel mystified and a bit put out that all this hostility has arisen suddenly. But of course, it hasn’t really been sudden at all. It’s been building for many years. Elsevier has been shielded from having to take the anger seriously because its power in the marketplace has let them bulldoze right over the dissatisfaction. Now that the dam is finally breaking it’s catastophic.
Matt has explained in detail why no-one trusts Elsevier any more in an outstanding post that I urge all scholarly publisher employees to read if they don’t understand how things have got so bad. To (over-)summarise Matt’s analysis, scientists are trained to see dishonesty as a permanent stain, whereas in business a certain amount of dishonesty is expected. So things like the fake journals are a huge deal to scientists, while the career businessmen at the helm of Elsevier can’t necessarily see what all the fuss is about. Because of half a dozen big things and a thousand small things, Elsevier has lost the trust of both librarians and researchers.
These posts are about how Elsevier can win back the trust it’s lost. I think that’s the only way it can survive in the medium and long term.
Why do I care whether Elsevier survives?
Elsevier as it is today? I don’t. But there has be a core of something worth saving in a company with that much experience, with so many skilled people. It can be done. Same goes for Springer, Wiley, Blackwell and the rest. In the end it’s up to each publisher whether it’s prepared to embrace the necessary changes (both cosmetic and radical), or whether it’ll keep chasing short-term megaprofits at the cost of sliding into irrelevance.
And the world needs a flourishing ecosystem of different publishers. Much as I admire PLoS, a PLoS monoculture in publishing wouldn’t be in anyone’s best interests. We need competition between multiple publishers to drive prices down and services up, to keep everyone on their toes.
So if Elsevier can make themselves a part of that, so much the better for them.
What Elsevier needs to do
I’m planning to post five articles in this series — most of them pretty short.
- This one is the introduction.
- in part 1, I will discuss the easy things that Elsevier can and should do without even thinking about it. Things that they should do now.
- Part 2 will talk about changes that will probably hurt them a little more to make, but which still need to be done as soon as possible.
- In Part 3, I’ll look at the deeper changes that will be necessary in the medium and long term
- Finally, I’ll top off the series with a few words about other barrier-based for-profit publishers [not yet written].
Stay tuned! And, Elsevier folks: please do chip in with comments.
Barosaurus lentus AMNH 6341 dorsal sequence
April 18, 2012
I’ve been thinking about Barosaurus lately.
<homer>Mmmm … Barosaurus …</homer>
The best (and only, really) good recent treatment of Barosaurus is in John McIntosh’s chapter of the 2005 IUP Thunder Lizards volume. The main weakness of that chapter is that, while a lot of material is illustrated, the figures are rather small and not particularly well reproduced — and, in the case of the two-page spread of dorsal vertebrae, monumentally confusing:
Barosaurus lentus AMNH 6341 dorsal vertebrae 1 to 9 (A-I) in anterior, left side, and posterior views. From McIntosh (2005:fig. 2.5)
Quick! find the fourth dorsal in posterior view! [˙ʇɟǝן ɯoʇʇoq ʇɐ s,ʇı :ɹǝʍsuɐ]
To get a better sense of the variation along the column, I scanned the two pages, loaded them into GIMP, joined them together, cleaned up the “white” of the background while retaining all the contrast I could, then moved each of the 27 illustrations to its own layer. Then I was able to rearrange them to my liking, align them, and produce this modified version:
Barosaurus lentus AMNH 6341 dorsal vertebrae 1 to 9 in anterior (top), left lateral (middle), and posterior (bottom) views. Modified from McIntosh (2005:fig. 2.5)
So here it is for anyone else who finds it useful.
(One character that varies sequentially is of course the degree of neural spine bifurcation. But we won’t be flogging that dead horse any more — we’re done blogging, and the paper is in prep.)
References
- McIntosh, J.S. 2005. The genus Barosaurus Marsh (Sauropoda, Diplodocidae); pp. 38-77 in Virginia Tidwell and Ken Carpenter (eds.), Thunder Lizards: the Sauropodomorph Dinosaurs. Indiana University Press, Bloomington, Indiana, 495 pp.