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

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

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

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

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

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

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

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

 

SO close

August 21, 2014

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

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

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

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

Bipedal Diplodocus USNM 10865 - modified from Gilmore 1932 pl 6

Diplodocus USNM 10865 - Gilmore 1932 pl 6 - cleaned up

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

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

Reference

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

I’m gathering all six parts of last year’s Tutorial 19 in one place for easy reference. Here they are:

Enjoy!

LACM Deinonychus claw

All I want to do in this post is make people aware that there is a difference between these two things, and occasionally that affects those of us who work in natural history.

In one of his books or essays, Stephen Jay Gould made the point that in natural history we are usually not dealing with whether phenomena are possible or not, but rather trying to determine their frequency. If we find that in a particular population of quail most of the birds eat ants but some avoid them, then we know some things: that quail can tolerate eating ants, that quail are not required to eat ants, and that both strategies can persist in a single population.

This idea has obvious repercussions for paleoart, especially when it comes to “long-tail” behaviors. I dealt with that in this post, and also in the comment thread to this one. But that’s not what I want to talk about today.

Sometimes it is useful to talk about things that never happen, or that have at least never occurred in the sample of things we know of. Obviously how certain you can be in these cases depends on the intensity of sampling and the inherent likelihood of a surprising result, which can be hard to judge. If you argued right now that T. rex lacked feathers because no T. rex specimens have been found with feathers, you’d most likely be wrong; it is almost certainly just a matter of time before someone finds direct evidence of feathers in T. rex, given the number of T. rex specimens waiting to be found and the strength of the indirect evidence (e.g., phylogenetic inference, analogy: ornithomimids are known to be feathered even though most specimens are found without feather impressions). If you argue that sauropods are unique among terrestrial animals in having necks more than five meters long, you’re most likely right; being wrong would imply the existence of some as-yet undiscovered land animal of sauropod size, or with seriously wacky proportions (or both), and our sampling of terrestrial vertebrates is good enough to make that extremely unlikely.

LACM baby rex snout

The reason for this post is that sometimes people confuse that last argument, which is about sampling and induction, with the argument from personal incredulity.

For example, in our no-necks-for-sex paper (Taylor et al. 2011), we included this passage:

Sauropoda also had a long evolutionary history, originating about 210 million years ago in the Carnian or Norian Age of the Late Triassic, and persisting until the end-Cretaceous extinction of all non-avian dinosaurs about 65 millions years ago. Thus the ‘necks-for-sex’ hypothesis requires that this clade continued to sexually select for exaggeration of the same organ for nearly 150 million years, a scenario without precedent in tetrapod evolutionary history.

One of the reviewers argued that we couldn’t include that section, because it was just the argument from personal incredulity writ large, like so:

There are no other known cases of X in tetrapod evolutionary history, and therefore we don’t believe that the case in question is the sole exception.

…with the second part of that unstated (by us) but implied. But we disagreed, and argued (successfully) that it was an argument based on sampling, like so:

There are no other known cases of X in tetrapod evolutionary history, and therefore it is unlikely that the case in question is the sole exception.

Now, it is perfectly fair to criticize arguments like that based on the thoroughness of the sampling and the likelihood of exceptions, as discussed above for T. rex feathers. Just don’t mistake arguments like that for arguments from personal incredulity.* On the flip side, if someone makes an argument from personal incredulity, see if the same thing can be restated as an argument about sampling. Maybe they’re correct but just expressing themselves poorly (“I refuse to believe that the moon is made out of cheese”), and maybe they’re wrong and restating things in terms of sampling will help you understand why.

* If you want to get super pedantic about it, they’re both arguments from ignorance. But one of them is at least potentially justifiable by reference to sampling. Absence of evidence is not necessarily evidence of absence, but it may get to be that way as the sampling improves (e.g., there is no evidence of planets closer to the sun than Mercury, and at this point, that is pretty persuasive evidence that no such planets exist).

LACM brachiosaur humerus with Wedels for scale

Parting shot: one thing that has always stuck in my head from Simberloff (1983) is the bit about imagining a large enough universe of possible outcomes. And I’ve always had a perverse fascination with Larry Niven’s “Down in Flames”, in which he pretty much demolished his Known Space universe by assuming that every basic postulate of that universe was false. Neither of these follow directly on from the main point of the post, but they’re not completely unrelated, either. Because I think that they yield a pretty good heuristic for how to do science: imagine what it would take for you to be wrong–imagine a universe in which you are wrong–and then go see if the thing that makes you wrong, whatever it is, can be shown to exist or to work. If not, it doesn’t mean you’re right, but it means you’re maybe less wrong, which, if we get right down to it, is the best that we can hope for.

The photos have nothing to do with the post, they’re just pretty pictures from the LACM to liven things up a little.

References

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

I was reading Stephen Curry’s excellent summary of Monday’s Royal Society’s conference on “Open access in the UK and what it means for scientific research”. One point that Stephen made is:

[David Willetts’s] argument is that pursuance of green OA leads to an unstable situation in which the cancellation of subscriptions (because readers have free access) drains the system of the funds needed to manage peer review and other publishing costs.

As an analysis of the difficulties of Green OA, this is admirably precise. But my eye was caught by that phrase “funds needed to manage peer review and other publishing costs.”

I think we should make an effort to wean ourselves off the habit of talking about “managing peer review and other publishing costs”. We all recognise that publishers do not provide peer-reviewwe do. But it’s also true that publishers don’t manage peer-review, either. Once again, we do that, by acting as unpaid academic editors.

Make-Money-online

I know that this is not news. We all know this. But a habit of speech is affording publishers a degree of credit that their efforts don’t merit, and that clouds the debate. Let’s apportion credit where it belongs.

Of course there are still “other publishing costs”. These are real and not negligible (even though PeerJ’s financial model suggests they are much less than we have sometimes assumed). It’s right that we should acknowledge that there really are publishing costs; and that whatever financial model we end up will need to pay them somehow. But let’s make an effort to be more precise about what those publishing costs are. Managing peer-review is not one of them.

Mathematician David Roberts has pointed me to a useful new five-part series by Martin Paul Eve, entitled Starting an Open Access Journal. It’s well worth a look, for how it engages with so many practicalities and how tractable he makes it all seem.

We’re actually pretty well served for open-access journals in our field (Acta Palaeontologica Polonica, Palaeontologia Electronica, PalArch’s journal of vertebrae palaeontology, soon PaleoBios, and of course PLoS ONE). But for scientists in other fields that have fewer options, starting their own journal may well be the single most effective thing they can do to advance open access. (It’s going to look pretty good on the CV, too!)

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