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”:

banned-from-nature

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

DSCN1178

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:

Reference

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.

uberabatitan-cervicals-copy

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.

malawisaurus-1993

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! 

CurryRogers2009-rapetosaurus-fig9-C9

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.

References