I was struck by this bit of prevarication in Richard Van Noorden’s new piece on open access. First the set-up:

To [Michael] Eisen, the idea that research is filtered into branded journals before it is published is not a feature but a bug: a wasteful hangover from the days of print. Rather than guiding articles into journal ‘buckets’, he suggests, they could be filtered after publication using metrics such as downloads and citations, which focus not on the antiquated journal, but on the article itself.

So far, so good. And then we have this:

Alicia Wise, from Elsevier, doubts that this could replace the current system: “I don’t think it’s appropriate to say that filtering and selection should only be done by the research community after publication,” she says.

What does the weasel-word “appropriate” mean here?

Is Alicia saying that she doesn’t think what Eisen’s saying is correct? No, if that’s what she meant, she would have said so. “I don’t think it’s right to say X” is a much stronger statement.

In fact, “not appropriate” is code for “correct, but we’d rather you didn’t say it”. When you’re six years old, your parents tell you it would not be appropriate to remark on your Auntie Griselda’s wispy moustache. That doesn’t mean the moustache isn’t there. If it wasn’t there, you wouldn’t have an issue. Your parents wouldn’t need to tell you anything. By saying it’s “not appropriate”, your parents are acknowledging that, yes, Auntie G. does have a fluffy upper lip, but that they don’t want you to draw attention to it.

And in the same way, Alicia’s quote here means “Yes, filtering and selection should be done by the community after publication, but please don’t say so. That would be inconvenient for us, since our business model consists of taking money off you in exchange for bestowing illusory prestige. We want you to collude with us in perpetuating the illusion”.

Let’s not be complicit.

My thanks for Richard Van Noorden for drawing my attention to his new piece Open access: The true cost of science publishing in Nature. I wrote a detailed comment on this article, but when I went to post it, I was told “This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service”:


This news to me. No-one at Nature thought to tell me, or anything. Their system said nothing about when I logged in, nor when I started entering my comment. Just waited till I’d finished, then trashed it.

I have no idea why I am banned. How can I have, when I’ve never received any notification? I can only assume it’s for posting opinions that are at odds with what NPG would prefer we all thought — at least, in the absence of any actual data, that’s the best hypothesis I can come up with. Update 40 minutes later: turns out it was a glitch in the spam-filter. Richard got it fixed, and my comment is now up on the article.

Listen up, Nature Publishing Group: you will never get meaningful dialogue in your comments if you silently ban everyone who expresses a non-party-line opinion random people for no discernable reason. You should be aspiring to be a hub of civilised discourse on these important issues, not an echo-chamber. (If you want that, you can just go and read The Scholarly Kitchen.)

Anyway: I am paranoid enough that I copied my comment before submitting it — I’ve been screwed in too many ways by too many commenting systems to trust anything but my own. So here is that comment, stripped of its context but still IMHO important. Perhaps someone who has not been banned from commenting at Nature could post it for me?

Thanks for this useful post, Richard. I am provoked by this statement:

“Analysts estimate profit margins at 20–30% for the industry.”

Where do such low numbers come from? As is by now well known, the profit margins for the Big Four publishers (Elsevier, Springer, Wiley and Informa) are between 32.4 and 42 percent — not one of them has a margin as low as the highest end of the range you cite. Not only that, but commercial academic publishers’ profit margins continue to rise year on year.

The average profit margin among the Big Four is 36%, which means that of the $9.4 billion spent on subscriptions in 2011, $3.39 billion was simply poured down the academic drain. Note that this profit alone would be enough to pay APCs for 2.5 million PLOS ONE articles, 40% more than the world actually produced in that year.

So to spell it out, subscription profits alone would be enough to fund OA publication of ALL research, with just under a billion dollars left over to fund additional research. It’s not just idiotic that we keep paying this ludicrously inflated subscriptions, it’s iniquitous.

There’s a good, balanced piece by Stephen Pincock in the new Nature, on the question of whether early-career researchers should publish their work in open-access journals. It seems to be free to read, so take a look at Publishing: Open to possibilities.

I mention it not only because it’s a subject dear to my heart, but also because the article mentions and quotes me. (Regarding “I got quite a lot of criticism from people I respect a lot”, most of those criticisms are in the comments on this post.)

But I also feel obliged to respond to a couple of points in the article, and since it doesn’t seem to have comments enabled, a short post here seems to be appropriate.

First, there’s this quote from Rob Brooks:

Impact factors still pretty much rule. A lot of people — grant committees, administrators and even referees — can’t assess quality. All they can do is count or pseudo-quantify. They count the number of papers you’ve got and count the impact factors of the papers and make a little metric, rather than just reading the papers.

My response: are there really referees who can’t assess quality? Do we really have situations where you submit a paper for peer-review, and the referees evaluate its quality — and recommend acceptance or rejection — not on the basis of the quality of the science, but on the impact factors of other journals you’ve published in?

If that’s true, then those referees should get out of science, now. Or, no — wait — it’s too late for that. They are already out of science. But they should stop pretending to be scientists and go work in McDonald’s.

By contrast, Robert Kiley of the Wellcome Trust is a beacon of sanity:

Many funders are looking beyond a journal’s brand name. “If you come to Wellcome for a grant,” he says, “we make it clear that funding decisions are based on the intrinsic merit of the work, and not the title of the journal in which an author’s work is published.” Kiley points to the policies of the UK programme for assessing research quality, the Research Excellence Framework, which stated in July 2012 that no grant-review sub-panel “will make any use of journal impact factors, rankings, lists or the perceived standing of publishers in assessing the quality of research outputs”

Pincock then discusses the open-access citation advantage:

Whether [open access] translates into higher citation rates is up for debate. In 2010, a meta-analysis found 27 studies showing that open-access articles had more citations than papers behind paywalls — up to 600% more, depending on the field — and four that found no open-access advantage.

I would not describe that as “up for debate”. I would describe it “has been analysed in detail and the jury is in”. As noted previously here on SV-POW! and in my submission to the House of Commons, Swan’s data says that on average open-access articles are cited 2.76 times as often as non-open.

The most misleading part of the article, though, is this you-get-what-you-pay-for assertion:

According to Carl Bergstrom, an evolutionary biologist at the University of Washington in Seattle, there tends to be a positive correlation between an open-access journal’s fees and its score in a system he co-developed that rates journals according to the number of citations they receive, with citations from highly ranked journals weighted more heavily.

However, the actual results show at best an extremely weak correlation, with very wide confidence intervals. (I find it baffling that the page doesn’t give numbers for these important measures.) Someone wanting to summarise these findings in a few words would do better to state that there is essentially no correlation between influence and price.

Apart from these caveats, the article is good, and presents multiple perspectives with little bias — to Nature‘s credit. It’s well worth reading.


So, this happened today

March 28, 2013

Big Bend Alamosaurus cervical J with Matt for scale


Another raw photo from the road.

The Morrison fossils from the Oklahoma panhandle were dug up and prepped out by  WPA workers in the 1930s, and their preparation toolkit consisted of hammers, chisels, pen-knives, and sandpaper. (Feel free to take a minute if you need to get your nausea under control.) And whereas most Morrison fossils are much darker than the surrounding matrix, in the Oklahoma panhandle the bone and matrix are about the same color. Sometimes the prep guys didn’t know they’d gone too deep until they sanded into the trabecular bone. Or in this case, into the air spaces in the condyle of this anterior dorsal of Apatosaurus.

Still, we have lots of anterior dorsals of Apatosaurus, and very few we can see inside, and they’re too darned big to scan, so this gives us useful information that a more perfect specimen would not. So I salute you, underemployed dude from eighty-odd years ago. Thanks for showing me something cool.

OMNH 1331 is my new hero

March 24, 2013

Here’s an update from the road–get ready for some crappy raw images, because that’s all I have the time or energy to post (with one exception).

OMNH 1331

Here’s OMNH 1331. It’s just the slightly convex articular end off a big vertebra, collected near Kenton, Oklahoma, in 1930s by one of J. Willis Stovall’s field crews. I measured the preserved width at 45 cm using a tape measure, and at 44.5 in GIMP using the scale bar in the photo, which is up on a piece of styrofoam so it’s about the same distance from the camera as the rim of the vertebra (i.e, about 8 feet–as high as I could get and still shoot straight down). So whether your distrust runs to tape measures or scale bars in photos, I am prepared to argue that this sucker is roughly 45 cm wide.

OMNH 1331 internal structure

There’s admittedly not a ton of morphology here, but the size and the fact that the other side is hollow and has a midline bony septum show that it is a pneumatic vertebra from a sauropod, and given that the quarry it’s from was chock-full of Apatosaurus, and liberally salted with gigantic Apatosaurus, I feel pretty good about calling it Apatosaurus.

OMNH 1331 cloned and flipped

To figure out how wide the articular face was when it was intact, I duplicated the image and reversed it left-to-right in GIMP, which yields an intact max width of about 49 cm. That is friggin’ immense.

If we make the maximally conservative assumption that this is the largest centrum in the whole skeleton of a big Apatosaurus, then it has to be part of a dorsal vertebra. Here are the max diameters of the largest dorsal centra in some big mounted apatosaurs, taken from Gilmore (1936). The number in parentheses is how many percent bigger OMNH 1331 is.

  • A. louisae CM 3018 – 36.5 cm (34%)
  • A. parvus UWGM 15556 – 36.5 cm (34%)
  • A. sp. FMNH P25112 – 41 cm (20%)

OMNH 1331 lateral view

However, this might not be part of a dorsal vertebra. For one thing, it’s pretty convex, and Apatosaurus dorsals sometimes have a little bump but they’re pretty close to amphiplatyan, at least in the posterior half of the series. For another, I think that smooth lower margin on the right in the photo above is part of the rim of a big pneumatic foramen, but it’s waaay up high and pretty medial on the centrum, opening more dorsally than laterally, which I have seen a lot in anterior caudal vertebrae. Finally, Jack McIntosh went through the OMNH collections years ago and his identifications formed the basis for a lot of the catalogue IDs, and this thing is catalogued as the condyle off the back end of a proximal caudal.

Here are the max diameters of the largest caudal centra in those same mounted apatosaurs, again taken from Gilmore (1936). Once again, the number in parentheses is how many percent bigger OMNH 1331 is.

  • A. louisae CM 3018 – 30 cm (63%)
  • A. parvus UWGM 15556 – 32.5 cm (51%)
  • A. sp. FMNH P25112 – 39 cm (26%)

(Aside: check out the skinny rear end on A. louisae. ‘Sup with that?)

So whatever vert it’s part of, OMNH 1331 is damn big bone from a damn big Apatosaurus. There are lots of other big Apatosaurus vertebrae in the OMNH collections, like OMNH 1670, but OMNH 1331 is the largest centrum that I know of in this museum. Which is why you’re getting a post about most of one end of a centrum in the wee hours of the morning–it’s most of one end of an awesome centrum. And it pains me when people do comparison figures of big sauropod vertebrae, or lists of the “Top 10 Largest Sauropods”, and put in stuff like Argentinosaurus and Puertasaurus and Supersaurus, but leave out Apatosaurus. It was legitimately huge, and it’s time the world realized that.

For more on the giant Oklahoma Apatosaurus, see:


Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.

As I noted in a comment on the previous post, titanosaurs have stupid cervicals.

As evidence, here is as gallery of titanosaur cervicals featured previously on SV-POW!.

1. From Whassup with your segmented lamina, Uberabatitan ribeiroi?, an anterior cervical of that very animal, from Salgado and Carvalho (2008: fig. 5). As well as the titular segmented lamina, note the ridiculous ventral positioning of the cervical rib. It’s like it’s trying to be Apatosaurus, but it just doesn’t have the chops.


2. From Mystery of the missing Malawisaurus vertebra, this alleged vertebra of that taxon from Jacobs et al. (1993:fig. 1), which completely fails to resemble all the other cervicals subsequently described from Malawisaurus (see the earlier post for details). Note the crazy sail-like neural spine and super-fat parapophyseal stump.


3. From Futalognkosaurus was one big-ass sauropod, this completely insane posterior cervical vertebra of Futalognkosaurus in right anterolateral view, with Juan Porfiri (175 cm) for scale. It’s super-tall — much taller than it is wide, and seemingly taller than it is long.

Posterior cervical vertebra of Futalognkosaurus in right anterolateral view; Juan Porfiri (175 cm) for scale

4. From Ch-ch-ch-changes, cervical 11 of Rapetosaurus, from Curry Rogers (2009:fig. 5). Notice how tiny the centrum is compared with the tall superstructure, and how the neural spine has such a distinct peak. Weird.

Rapetosaurus cervical

5. From Talking about sauropods on The Twenty-First Floor, cervical 9 of the same Rapetosaurus individual, from Curry Rogers (2009:fig. 9). The neural spine is a completely different shape from that of C11, but that is presumably mostly due to damage. One of the interesting things here is the apparent lack of pneumatic foramina in the centrum. They’re there somewhere: Curry Rogers (2009:1054) writes “In cervical vertebrae 9, 11, and 12, the centrum bears an elongate shallow pneumatic fossa with two anterior pneumatic foramina surrounded by sharp, lip-like boundaries.” But they are hard to make out! 


The meta-oddity here is that the cervicals of the four titanosaur genera pictures here are all so different from each other. What does this mean?

Probably only that Titanosauria is a huge, disparate, long-lived clade that encompasses far more morphological variation than (say) Diplodocidae. It’s a truism that we don’t, even now, really have a handle on titanosaur phylogeny — every new study that comes out seems to recover a dramatically different topology — so our perception of the clade is really as a big undifferentiated blob. In contrast, the division of Diplodocoidea into Rebbachisaurids, Dicraeosaurids and Diplodocids (plus some odds and ends) is nicely established and easy to think about.

So. Lots of work to be done on titanosaurs.


Mounted Alamosaurus in Dallas 1

Next week I’m going to visit the Perot Museum of Nature and Science in Dallas, Texas, to see their big Alamosaurus (these photos were kindly provided by Ron Tykoski of the Perot Museum, with permission to post). See that sweet string of cervical vertebrae in front of the mounted skeleton? A photo of those same vertebrae when they were still in the ground was featured in the post “How big was Alamosaurus?” three and a half years ago. Happily now they are out of the ground, prepped, and on display, and Tony Fiorillo and Ron Tykoski are working on getting them and some other new Alamosaurus material described.

Mounted Alamosaurus in Dallas 2

Here’s another view of that mount. You may be wondering, first, how legit is it, and second, how big is it? Happily, I have answers for you. In email messages with permission to cite, Ron Tykoski wrote,

The Alamosaurus skeletal mount by RCI  in the photos is based upon scaling the Smithsonian and UT Austin material to match the size of our cervicals here in Dallas.  There were enough overlapping parts between the pieces at the three institutions to get the proportions pretty nicely supported.

I ran across your SV-POW thread on ‘How big was Alamosaurus?’ back when you first posted it in ‘09.  You ought to be pleased to know that you came remarkably close to the eventual size of the skeleton we wound up with.  The full skeleton RCI generated (again, based off scaling to the Dallas verts) is 84ft long, about 16ft at the shoulder (I dropped a tape measure from the 1st dorsal neural spine to the floor during skeleton construction and got 480cm-490cm), and a neck + head of about 25ft.  The overall length and neck length were provided by RCI after fabrication and assembly.   That shoulder height is a bit suspect though based on the positioning of the pectoral girdle in the mount, relative to the ribcage and vert column.   I think the head currently is posed about 25ft or so off the floor, but I can’t verify that (I didn’t get into the scissor-lift to check that at the time).  This skeleton actually played a role in determining the size of the hall in which it is installed.  We decided early in the planning phase for the building that this skeleton would be the centerpiece for the hall.  As a result, the ceilings for this floor had to be made extra-high, and the mid-room support pillars designed out to accommodate the skeleton and still clear all the HVAC, sprinkler heads, and other necessities.

That’s all pretty fantastic–both that we have enough of Alamosaurus to do a pretty rigorous full skeletal mount, and that the beast was legitimately pretty darned big. Ron goes on:

One correction to the story on SV-POW, the Dallas cervical series consists of only 9 verts, not 10.  There may have been frags or something that made folks think there was a 10th at the anterior end of the series when first found, but I’ve never seen evidence of it in our collection.  This may be supported by the fact that the verts were given letter designations in the field (that we still use), and are identified as verts B through J, from anterior to posterior.

I later learned from Tony Fiorillo that the vertebrae were labelled B through J in the field in case anything anterior to B turned up, but nothing did, so the ‘A’ placeholder went unused. That reminds me of the search in the mid-1800s for the hypothetical planet Vulcan (not the one you’re thinking of) between Mercury and the Sun, which I bring up for no reasons other than that hypothetical planets are cool, and if you’re exploring, it’s worth keeping an open mind about what might yet turn up.

There’s more to say about the size of Alamosaurus–we haven’t even covered the big material described by Fowler and Sullivan (2011) yet–but I’m not going to say a whole lot right now, since I’m going to see the Big Bend material in Dallas in just a few days. Watch this space.


Fowler, D.W. and Sullivan, R.M. 2011. The first giant titanosaurian sauropod from the Upper Cretaceous of North America. Acta Palaeontologica Polonica 56 (4): 685–690.

The problem

I find myself reading a lot recently about “portable peer-review” — posts like Take me as I am, and my paper as it is? by scicurious at Neurotic Physiology, which excellently diagnoses a terrible, wasteful problem in scientific publishing:

My papers don’t often get in with minor revisions. Often I’ve got a ridiculously puffed head about my own work (apparently), and send them to places which reject them out of hand, or suggest major revisions and piles of new experiments which we just cannot do for various reasons. Then the paper ends up shuttled around. Send it in, wait 3 months, get rejected. Reformat (+2 mo or even more depending on collaborators and how much other crap you’ve got on your plate at the time) and send it out again. Years go by. In the meantime, suggested reviewers begin to hate me and I run out of new ones (only so many people in the field!).

I really wish there was a way to get out of this. This sort of thing contributes to the long lag times and slowness of scientific advance.

What a waste! What a drag on the progress of science! What a ridiculous situation we’re got ourselves into, with our chasing-after-prestigious-journals games.

An inadequate solution

The solution proposed by scicurious is:

You submit a paper to a large umbrella of journals of several “tiers”. It goes out for review. The reviewers make their criticisms. Then they say “this paper is fine, but it’s not impactful enough for journal X unless major experiments A, B, and C are done. However, it could fit into journal Y with only experiment A, or into journal Z with only minor revisions”.

As an incremental improvement on the current system, this is good, if rather impractical to implement.

But it doesn’t go nearly far enough. It still wastes time by going to multiple journals, probably with different formatting requirements, requiring assessment (albeit more lightweight) by several editors. And it does all that in the name of getting a designer label onto the paper by placing it in a “good” journal.

What are we, fourteen?

High-school kids are dumb enough to judge other kids by how fashionable their clothes are, by the labels on them, by whether they’re the clothes other kids think are cool.

Have we really not got beyond that?

The ugly truth

Trying to get into “good” journals is an idiot game. (Notice I don’t say “an idiot’s game” — more on this distinction below.) Although the political and bean-counting value of getting into Nature is huge, the scientific value of getting into Nature is zero. A paper in Nature is literally no better at all than the same paper would be in PLOS ONE. (In fact, it’s probably less good, because it will be butchered to fit the draconian space requirements.) Spending time and effort in trying to get a given piece of research into Nature is just about the least useful thing that can be done for that research.

I think deep down everyone knows this. But of course scientists still waste innumerable hours formatting their work first for Nature, then for Science when it gets rejected, then for PNAS when it gets rejected again, and so on “down the ladder”. But that direction is only “down” by agreement. And the reason of course is because it’s widely (though not universally) believed that wearing these designer clothes is the way to get jobs and grants. That’s why people who are not idiots play this idiot game.

(Thanks heavens for funders and assessors who explicitly state that the journal a work is published in has no effect on how it’s evaluated. You can find such statements from The Wellcome Trust, and regarding the Research Excellence Framework (REF). I want to see more granting and evaluation bodies make similar statements, and I look forward to seeing a university hiring policy that says the same.)

A better way

Happily for me, I don’t need a job or a grant, so I have the luxury of standing on the sidelines, shaking my head sagely yet smugly at the ridiculous manouevres happening on the pitch.

I admit to my shame that I have played the getting-into-a-good-journal game in the past, just because I blindly copied what I saw my colleagues doing without really thinking about it. One result is that our neck-anatomy paper was needlessly held up for more than four yearsNo-one benefits from these delays. They are a completely avoidable net loss for science.

No more. I am done with having my work rejected for spurious (i.e. non-scientific reasons). I’m only planning on submitting to journals that don’t do that. I reject the idiot notion that the natural lifecycle of a piece of work involves multiple submissions-review-reject cycles. From now on, my cycle is: do some work, write it up, submit it, see it published, move on to the next thing.

And note that “move on to the next thing” is a crucial step here. What really burns me is not the four-year delays on the papers I mentioned above, but all the other work that I’ve not done because I’ve been buggering about, excuse my French, with the corpses of these long-dead projects instead of getting the next thing done. And if that’s true for me, I bet it’s true for you, as well. Yes, you, reading this!

As of now, except in exceptional circumstances, my plan is only to submit to venues where I know scientifically sound work will be accepted. That means “megajournals” like PLOS ONE, PeerJ and (I don’t know, I will look into it) maybe some or all BMC journals. It also means edited volumes that I’m invited to contribute to (though they have their own issues). It probably also means certain other journals, such as PalArch, though they don’t make it explicit (and it would be good if they did).

Three clarifications

First clarification: to be clear, I am not arrogant enough to think this means I will never again have a paper rejected. No doubt there will be occasions where I’ve made significant scientific errors, and reviewers will have to point those out and recommend rejection. I don’t mind that: it’s peer-review actually doing its job, and I’d rather fix those mistakes before publication. What I’m done with is rejections on the basis of “not impacty enough for this journal”, or the often equally specious “not a good fit”.

Second clarification: I don’t absolutely rule out exceptions. There might be occasions where, say, an impact-selective journal announces plans to put out a special volume that I want to be part of. I might submit to that; then again, I might not. I’ll judge it as it comes. But the point is, any exceptions will be exceptions. When I start thinking “where shall I send this?”, my list won’t start with Palaeontology and JVP. I’m glad to have got those notches on my bedpost, but I don’t feel any great need to go back to them.

Third clarification: I do understand that others might not be in a position to make the same leap. I am 99.7% certain that Darren won’t, for example, as he is convinced of the absolute necessity of Science‘n’Nature papers to advance his career. Matt, on the other hand, can and I think will — he’s got a tenure-track job at a university that he likes, has no plans to move on, and doesn’t need “prestigious” papers for his tenure case, only good ones.

(It pained me to have to make that distinction. What a stupid world, where “prestigious papers” and “good papers” are not synonymous, and don’t even overlap that much.)

But for people who, like me, don’t need to have an eye on the possible job-power of “prestige”, it seems obviously better to do what advances science best and fastest. And what a tragedy that advancing science isn’t what gets jobs.

Wedel and Taylor 2013 bifurcation Figure 7 - small Diplodocus cervical

Figure 7. BYU 12613, a posterior cervical of Diplodocus or Kaatedocus in dorsal (top), left lateral (left), and posterior (right) views. It compares most favourably with C14 of D. carnegii CM 84/94 (Hatcher, 1901: plate 3) despite being only 42% as large, with a centrum length of 270 mm compared to 642 mm for C14 of D. carnegii.

The original version of the PDF of our new paper (Wedel and Taylor 2013) had a couple of obvious errors: Kaatedocus was misspelled in the caption to Figure 7 (as Kaatedocu), and the submission date was given as June 24, 2012, not the correct date of June 14. Both of these errors were introduced during the editorial handling, so I politely asked  if they could be fixed, and thanks to the kind offices of the folks at PalArch, now they have been. However, to avoid confusion (or perhaps propagate it, depending on your feelings), the corrected PDF has a different filename. The original version will continue to be available at:


and the corrected version (with an extra ‘1’ on the end of the filename) is at:


Two things:

  • I will go around changing the links here and elsewhere (FigShare, etc.) to the new version, but I probably won’t have time today, as I have an all-afternoon community outreach at the local public library to help organize.
  • I realize that some people, including possibly my coauthor, will hate this because now we have created some uncertainty about which is the version of record. So we’re not going to ask for any more changes, no matter how egregious the errors we find (and we are certain to find a few more, that’s just the nature of the beast); as far as I’m concerned, the second corrected version is the final version. Also, the changes made are tiny and don’t affect the science at all, so it’s not like we’ve moved any important goalposts here.

If you have strong feelings about this either way, feel free to sound off in the comments.