Ending on a high note

December 31, 2012

Dicraeosaurus by Brian Engh

We’ve gotten a few complaints this year about how much time we’ve spent talking about open access instead of dinosaurs. Brian Engh is in the more-dinosaurs faction, but he doesn’t just whinge about our non-dino coverage, he does something about it. He writes:

here’s the deal:

when sv-pow becomes more discussion about human things and less discussion about ancient monsters i bombard your email with whatever crappy unfinished dino-drawings i got lying around. you have my permission to do with these as you wish, however if they end up on SV-POW i will be happy and feel i’m doing my part to combat humans.

Awesome.

Happy new year, sauropod fans. Enjoy this rearing Dicraeosaurus courtesy of Brian.

After the authors’ own work, the biggest contribution to a published paper is the reviews provided, gratis, by peers. When peer-review works as it’s supposed to, they add significant value to the final paper. But the actual reviews are never seen by anyone except the authors and the handling editor.

This is bad for several reasons.

First, good reviewers don’t get the credit they deserve. That’s unfair on those who do a good job — who generously invest a lot of time and effort in others’ work.

Second, bad reviewers don’t get the blame they deserve. That leaves them free to act in bad faith: blocking papers by people they don’t like, or whose work is critical of their own; or just doing a completely inadequate job. Because there are no negative consequences for doing a bad job, people have no external incentive to straighten up and fly right.

Third, the effort that goes into reviewing is largely wasted. Often the reviews themselves are significant pieces of work (that’s certainly true when I’m the one giving the review) and the wider community could benefit from seeing them. Frequently reviews contain extended discussion, not only of the paper’s subject matter but of scientific philosophy such as approaches to taxonomy or narrative structure.

Fourth, editors’ decisions remain unexplained. Most editors handle manucripts efficiently and fairly, but there are cases when this isn’t the case — as for example when I was one of three reviewers who wholeheartedly recommended acceptance but the editor rejected the paper. Even discussing that situation was difficult, because the reviews in question were not available for the world to read.

Fifth, and more general than any of the above, the reviewing process is opaque to the world. In times past, logistical reasons such as lack of space in printed journals meant that the sausage-machine approach to the review process was the only feasible one: no-one wants to see what goes into the machine or what goes on inside, we only want the final product. But we live in an increasingly open world, and consensus is that pretty much all processes benefit from openness.

There are various initiatives under way to change the legacy system of reviewing, including F1000 Research and the eLife decision-letter system. But at the moment only a small minority of papers are submitted to such venues.

What to do about the others?

And so I found myself wondering … what would happen if I just unilaterally posted the reviews I receive? I already make pages on this site for each of my published papers (example): it would be easy to extend those pages by also adding:

  • The submitted version of the manuscript
  • All the reviews I received
  • The editor’s decision letter
  • My response letter to the editor
  • The final published paper.

I know this is “not done”. My question is: why not? Is there an actual reason, other than inertia? Wouldn’t we all be better off if this was standard operating procedure?

[Note that this is orthogonal to reviewer anonymity. As it happens, I think that is also a bad thing, but it's independent of what I'm proposing here. I could post an unsigned review as-is, without revealing who wrote it even if I knew.]

A couple of days ago, a paper by Tschopp and Mateus (2012) described and named a new diplodocine from the Morrison Formation, Kaatedocus siberi, based on a beautifully preserved specimen consisting of a complete skull and the first fourteen cervical vertebrae.

Unfortunately, the authors chose to publish their work in the Journal of Systematic Palaeontology, a paywalled journal, which means that most of you reading this will be unable to read the actual paper — at least, not unless you care enough to pay £27 for the privilege.

So you’ll just have to take my word for it when I tell you that it’s a fine, detailed piece of work, weighing in at 36 pages. It features lavish illustrations of the skull, but we won’t trouble you with those. The vertebrae are illustrated rather less comprehensively, though still better than in most papers:

x

Tschopp and Matteus (2012: figure 9). A, Photograph and B, drawings of the mid-cervical vertebrae of the holotype of Kaatedocus siberi (SMA 0004). Photograph in lateral view and to scale, CV 8 shown in the drawings is indicated by an asterisk. Drawings of CV 8 (B) in dorsal (1), lateral (2), ventral (3), posterior (4) and anterior (5) views. Scale bars = 4 cm.

It should be immediately apparent from these lateral views that the vertebra are rather Diplodocus-like. But the hot news is that there is a great raft of free supplementary information, including full five-orthogonal-view photos of all fourteen vertebrae!

Here is just one of them, C6, in glorious high resolution (click through for the full awesome):

tjsp_a_746589_sup_30911353

Now, folks, that is how to illustrate a sauropod in 2012! The goal of a good descriptive paper is to be the closest thing possible to a proxy for the specimen itself, and you just can’t do that if you don’t illustrate every element from multiple directions. By getting this so spectacularly right, Tschopp and Matteus have made their paper the best illustrated sauropod descriptions for 91 years. (Yes, I am talking about Osborn and Mook 1921.)

It’s just a shame that all the awe-inspiring illustrations are tucked away in supplementary information rather than in the paper itself. Had the paper been published in a PLOS journal, for example, all the goodness could have been in one place, and it would all have been open access.

Is Kaatedocus valid?

There’s a bit of a fashion these days for drive-by synonymisation of dinosaurs, and sure enough no sooner had Brian Switek written about Kaatedocus for his new National Geographic blog than comments started cropping up arguing (or in some cases just stating) that Kaatedocus is merely Barosaurus.

It’s not. I spent a lot of time with true Barosaurus cervicals at Yale this summer, and those of Kaatedocus are nothing like them. Here is Tschopp and Mateus’s supplementary figure of C14:

tjsp_a_746589_sup_30912152

And here is a posterior vertebra — possibly also C14 — of the Barosaurus holotype YPM 429, in dorsal and right lateral views:

IMG_0441

IMG_0430

Even allowing for a certain amount of post-mortem distortion and “creative” restoration, it should be immediately apparent that (A) Barosaurus is much weirder than most people realise, and (B) Kaatedocus ain’t it.

There may be more of a case to be made that Kaatedocus is Diplodocus — but that’s the point: it there’s a case, then it needs to be actually made, which means a point-by-point response to the diagnostic characters proposed by the authors in their careful, detailed study based on months of work with the actual specimens.

There seems to be an idea abroad at the moment that it’s somehow more conservative or sober or scientific to assume everything is a ontogenomorph of everything else — possibly catalysed by the Horner lab’s ongoing “Toroceratops” initiative and subsequent cavalier treatment of Morrison sauropods — maybe even by the Amphidocobrontowaassea paper. Folks, there is no intrinsic merit in assuming less diversity. Historically, the Victorian sauropod palaeontologists of England did at least as much taxonomic damage by assumptions of synonymy (everything’s Cetiosaurus or Ornithopsiswhatever that is) as they did by raising new taxa. The thing to do is find the hypothesis best supported by evidence, not presupposing that either splitting or lumping is a priori the more virtuous course.

Sermon ends.

Morrison sauropod diversity

As we’ve pointed out a few times in our published work, sauropod diversity in the Kimmeridgian-Tithonian in general, and in the Morrison Formation in particular, was off-the-scale crazy. There’s good evidence for at least a dozen sauropod genera in the Morrison, and more than fifteen species. Kaatedocus extends this record yet further, giving us a picture of an amazing ecosystem positively abundant with numerous species of giant animals bigger than anything alive on land today.

Sometimes you’ll hear people use this observation as a working-backwards piece of evidence that Morrison sauropods are oversplit. Nuh-uh. We have to assess taxonomy on its own grounds, then see what it tells us about ecosystem. As Dave Hone’s new paper affirms (among many others), Mesozoic ecosystem were not like modern ones. We have to resist the insidious temptation to assume that what we would have seen in the Late Jurassic is somehow analogous to what we see today on the Serengeti.

Hutton’s (or Lyell’s) idea that “the present is the key to the past” may be helpful in geology. But despite its roots as a branch of the discipline, the palaeontology we do today is not geology. When we’re thinking about ancient ecosystems, we’re talking about palaeobiology, and in that field the idea that the present is the key to the past is at best unhelpful, at worst positively misleading.

Sermon ends.

But isn’t the Kaatedocus holotype privately owned?

You’ve had two sermons already, I’m sure we can all agree that’s plenty for one blog post. I will return to this subject in a subsequent post.

Sermon doesn’t even get started.

References

Osborn, Henry Fairfield, and Charles C. Mook. 1921. Camarasaurus, Amphicoelias and other sauropods of Cope. Memoirs of the American Museum of Natural History, n.s. 3:247-387, and plates LX-LXXXV.

Tschopp, Emanuel, and Octávio Mateus. 2012. The skull and neck of a new flagellicaudatan sauropod from the Morrison Formation and its implication for the evolution and ontogeny of diplodocid dinosaurs. Journal of Systematic Palaeontology. doi:10.1080/14772019.2012.746589

I happened to be browsing Gerald L. Woods superb Guinness Book of Animal Facts and Feats (3rd edition) this morning, and happened across this fragment on page 76:

Not surprisingly, hummingbirds have the highest energy output per unit of weight of any living warm-blooded animal.

The wording struck me as strange: highest of any living warm-blooded animal? Is Wood just being redundant here, or is he implying that there are cold-blooded animals with a higher mass-specific metabolic rate? The idea seems inherently contradictory, doesn’t it?

I wondered whether he might have insect flight in mind?

Am I making a mistake in conflating “energy output” with “metabolic rate”?

 

Just sayin':

gallery15[1]

vs.

apato-growth-series

(From here.)

Update

The rest of the Umbaran Starfighter Saga:

Yesterday, Matt showed you this starship from the Star Wars universe:

UmbaranStarfighter-SWE

And asked whether it’s based on a cervical vertebra of Apatosaurus.

Absolutely it is. It can’t be just a coincidence. Matt showed a lot of useful orthogonal views of various Apatosaurus cervicals in the last post, but here’s a a nice informative oblique view which is similar (though not identical) to that of the Umbaran ship:

apatosaurus-ajax-holotype--YPM-1860--left-anterolateral-DSCN5946

Apatosaurus ajax holotype YPM 1860, cervical vertebra of unspecified position but probably from around the middle of the neck, in left anterolateral view. This is the same vertebra that appears in the last three photos in Matt’s post.

(Because the vertebra photo was taken from higher up than the starfighter image, the condyle/cockpit appears lower on the vertebra. That is basically an effect of perspective rather than a difference in proportions.)

The questions for me are twofold: which Apatosaurus vertebra is it based on, and who did it?

What vertebra is it based on?

In some ways, the cervical that it most resembles is this classic: C?8 of the Apatosaurus excelsus holotype YPM 1980:

Ostrom and McIntosh (1966:plate 12) -- Brontosaurus excelsus YPM 1980 cervical 8

This one resembles the starfighter in the very deep cervical rob loops — deep even for Apatosaurus — and in the small, high condyle. It also resembled the ship in the absence of neural-spine metapophyses (due to breakage, not taxonomically significant variation, alas). The result of their absence is that the “upper wings” (i.e. postzygapophyseal rami) are swept up, out and back, as in the ship.

But in other respects it’s very different — notably the very elongate prezyg rami (an effect exaggerated by the breakage) and the more or less parallel trajectories of the top and bottom margins of the loop.

Another candidate would be the one that appears in the top left part of figure 7 (“the freak gallery”) from our recent neck-anatomy paper on arXiv:

This on is rather bulky for a model for the ship, but does have a less wrong shape of the cervical rib loops. And the damage that blew off both the prezygs and the metapophyses leaves the isolated “wings” on the top, just as in the ship.

I think the best model I can find for the starfighter is probably C8 of the Apatosaurus louisae holotype CM 3018, which Gilmore illustrated beautifully in his 1936 monograph but which unfortunately I only have as this bad scan:

Gilmore1936-plateXXIV-C8

It has good, deep cervical-rib loops; a definite bend from the fairly lateral upper part to the more ventrally inclined lateral part; a high, fairly small condyle; and a definite bulges where the parapophysis fuses with the cervical ribs, corresponding to the weapons pods of the starfighter.

And yet, and yet …

I can’t shake the feeling that I’ve seen another Apatosaurus vertebra somewhere that is a more or less perfect fit for the ship. But I can’t remember where I saw it. Come to that, I can’t think what specimen it could be from, if not one of those that Matt and I have shown in these posts.

Anyone?

Whose work is it?

The other mystery is — whose work is this design, and where did he or she get the shape from? In a comment on the last post, I said to Matt that “one can hardly help but suspect that Jarrod did it on your instruction”. (Jarrod is an old friend of Matt’s who works in digital effects for film and TV.) But  Matt insists it’s none of his doing — and I must say that if it had been in any way his work, he would have been shouting about it long before now.

So how did it happen?

Anyone know?

Update

The Umbaran Starfighter is an Apatosaurus vertebra–check out the rest of the saga:

[Originally written as a comment on Martin Coward's blog, but I thought the point was worth making as its own post.]

Here’s my take on the widely used Creative Commons Attribution licence (CC BY) in contrast to more restrictive CC licences such as the Non-Commercial variant (CC BY-NC).

It may be true, as Martin suggests, that CC BY-NC is better for the author than CC BY. But authors are part of a community, and it’s unquestionably better for the broader community that CC BY be used. It’s better for society that commercial applications of the author’s research be allowed and encouraged.

research-to-money

So long as researchers are funded by that broader community, it’s fair that funders should be able to mandate the more permissive licence, which is better for society. If we kick back against that — if we say it’s not enough to be paid to do research, we also want a slice of the commercial uses of our work — we only perpetuate society’s ivory-tower stereotype of academics who think the world owes them a living.

So while there is certainly an argument to be made that CC BY is also better for the researcher, I think that whether that’s true or not, simple justice requires that no additional restrictions be placed on such work.

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