Ending on a high note
December 31, 2012
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.
What would happen if I publicly posted the reviews I receive?
December 23, 2012
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.]
Welcome Kaatedocus: this is how to illustrate a sauropod
December 20, 2012
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:
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):
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 description 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:
And here is a posterior vertebra — possibly also C14 — of the Barosaurus holotype YPM 429, in dorsal and right lateral views:
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 Ornithopsis — whatever 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
What has higher energy output than a hummingbird?
December 17, 2012
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”?
Umbaran Starfighter vs. Apatosaurus cervical, round 3
December 16, 2012
Just sayin’:
![gallery15[1]](https://web.archive.org/web/20211109041817im_/https://svpow.files.wordpress.com/2012/12/gallery151.jpg?w=960&h=540)
vs.
(From here.)
Update
The rest of the Umbaran Starfighter Saga:
- Was the Umbaran Starfighter from Clone Wars inspired by an Apatosaurus vertebra? (Dec. 13, 2012)
- Heck, yes, the Umbaran Starfighter from Clone Wars was inspired by an Apatosaurus vertebra (Dec. 15, 2012)
- Umbaran Starfighter update (Jan. 4, 2013)
- CONFIRMED: the Umbaran Starfighter is an Apatosaurus cervical (Jan. 21, 2013)
Heck, yes, the Umbaran Starfighter from Clone Wars was inspired by an Apatosaurus vertebra
December 15, 2012
Yesterday, Matt showed you this starship from the Star Wars universe:
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, 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:
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:
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:
- Was the Umbaran Starfighter from Clone Wars inspired by an Apatosaurus vertebra? (Dec. 13, 2012)
- Umbaran Starfighter vs. Apatosaurus cervical, round 3 (Dec. 16, 2012)
- Umbaran Starfighter update (Jan. 4, 2013)
- CONFIRMED: the Umbaran Starfighter is an Apatosaurus cervical (Jan. 21, 2013)
One argument in favour of CC BY
December 14, 2012
[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.
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.
Update, January 21, 2013: YES, it was! Scroll down for links to the entire saga.
Because it’s doing a hell of an impression of one, if not. It’s got the huge cervical rib loops (wings), bifurcated neural spine (top fins), and even a condyle on the front of the centrum (cockpit pod). About all it’s missing are the zygapophyses and the cervical ribs themselves.
Some actual Apatosaurus cervicals for comparison, from previous posts:
Apatosaurus ajax NSMT-PV 20375, cervical vertebrae 3, 6 and 7 in anterior and posterior views. Modified from Upchurch et al. (2005: plate 2)
Apatosaurus parvus CM 563/UWGM 15556 cervicals 7, 5, 4 and 3 in anterior and right lateral views, from Gilmore (1936:pl. 31)
Various Apatosaurus cervicals–see Wedel and Sanders (2002) for specimen numbers and sources.
And of course Mike’s magisterial work photographing the Apatosaurus ajax holotype YPM 1860 cervical:
More on the Umbaran Starfighter here.
The complete Umbaran Starfighter Saga–at least as told on SV-POW!:
- Was the Umbaran Starfighter from Clone Wars inspired by an Apatosaurus vertebra? (Dec. 13, 2012)
- Heck, yes, the Umbaran Starfighter from Clone Wars was inspired by an Apatosaurus vertebra (Dec. 15, 2012)
- Umbaran Starfighter vs. Apatosaurus cervical, round 3 (Dec. 16, 2012)
- Umbaran Starfighter update (Jan. 4, 2013)
- CONFIRMED: the Umbaran Starfighter is an Apatosaurus cervical (Jan. 21, 2013)
For other Star Wars/paleontology crossovers, please see:
The sauropods of Star Wars: Special Edition
and–mostly as shameless self-promotion since the paleo link is pretty tenuous:
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.
- Upchurch, P., Tomida, Y., and Barrett, P.M. 2005. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs No. 26. Tokyo. ISSN 1342-9574.
- Wedel, M.J., and Sanders, R.K. 2002. Osteological correlates of cervical musculature in Aves and Sauropoda (Dinosauria: Saurischia), with comments on the cervical ribs of Apatosaurus. PaleoBios 22(3):1-6.
What would happen if I placed my manuscripts in the Public Domain?
December 13, 2012
We know that most academic journals and edited volumes ask authors to sign a copyright transfer agreement before proceeding with publication. When this is done, the publisher becomes the owner of the paper; the author may retain some rights according to the grace or otherwise of the publisher.
Plenty of authors have rightly railed against this land-grab, which publishers have been quite unable to justify. On occasion we’ve found ways to avoid the transfer, including the excellent structured approach that is the SPARC Author Addendum and my tactic of transferring copyright to my wife.
Works produced by the U.S. Federal Government are not protected by copyright. For example, papers written by Bill Parker as part of his work at Petrified Forest National Park are in the public domain.
Journals know this, and have clauses in their copyright transfer agreements to deal with it. For example, Elsevier’s template agreement has a box to check that says “I am a US Government employee and there is no copyright to transfer”, and the publishing agreement itself reads as follows (emphasis added):
Assignment of publishing rights
I hereby assign to <Copyright owner> the copyright in the manuscript identified above (government authors not electing to transfer agree to assign a non-exclusive licence) and any supplemental tables, illustrations or other information submitted therewith that are intended for publication as part of or as a supplement to the manuscript (the “Article”) in all forms and media (whether now known or hereafter developed), throughout the world, in all languages, for the full term of copyright, effective when and if the article is accepted for publication.
So journals and publishers are already set up to deal with public domain works that have no copyright. And that made me wonder why this option should be restricted to U.S. Federal employees.
What would happen if I just unilaterally place my manuscript in the public domain before submitting it? (This is easy to do: you can use the Creative Commons CC0 tool.)
Once I’d done that, I would be unable to sign a copyright transfer agreement. Not merely unwilling — I wouldn’t need to argue with publishers, “Oh, I don’t want to sign that”. It would be simpler than this. It’s would just be “There is no copyright to transfer”.
What would publishers say?
What could they say?
“We only publish public-domain works if they were written by U.S. federal employees”?
Where do formatted references come from?
December 12, 2012
It’s an oddity to me that when publishers try to justify their existence with long lists of the valuable services they provide, they usually skip lightly over one of the few really big ones. For example, Kent Anderson’s exhausting 60-element list omitted it, and it had to be pointed out in a comment by Carol Anne Meyer:
One to add: Enhanced content linking, including CrossREF DOI reference linking, author name linking cited-by linking, related content linking, updates and corrections linking.
(Anderson’s list sidles up to this issue in his #28, “XML generation and DTD migration” and #29, “Tagging”, but doesn’t come right out and say it.)
Although there are a few journals whose PDFs just contain references formatted as in the manuscript — as we did for our arXiv PDF — nearly all mainstream publishers go through a more elaborate process that yields more information and enables the linking that Meyer is talking about. (This is true of the new kids on the block as well as the legacy publishers.)
The reference-formatting pipeline
When I submit a manuscript with formatted reference like:
Taylor, M.P., Hone, D.W.E., Wedel, M.J. and Naish, D. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285(2):150–161. doi:10.1111/j.1469-7998.2011.00824.x
(as indeed I did in that arXiv paper), the publisher will take that reference and break it down into structured data describing the specific paper I was referring to. It does this for various reasons: among them, it needs to provide this information for services like the Web Of Knowledge.
Once it has this structured representation of the reference, the publication process plays it out in whatever format the journal prefers: for example, had our paper appeared in JVP, Taylor and Francis’s publication pipeline would have rendered it:
Taylor, M. P., D. W. E. Hone, M. J. Wedel, and D. Naish. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285:150–161.
(With spaces between multiple initials, initials preceding surnames for all authors except the first, an “Oxford comma” before the last author, no italics for the journal name, no bold for the volume number, the issue number omitted altogether, and the DOI inexplicably removed.)
What’s needed in a submitted reference
Here’s the key point: so long as all the relevant information is included in some format (authors, year, article title, journal title, volume, page-range), it makes no difference how it’s formatted. Because the publication process involves breaking the reference down into its component fields, thus losing all the formatting, before reassembling it in the preferred format.
And this leads us the key question: why do journals insist that authors format their references in journal style at all? All the work that authors do to achieve this is thrown away anyway, when the reference is broken down into fields, so why do it?
And the answer of course is “there is no good reason”. Which is why several journals, including PeerJ, eLife, PLOS ONE and certain Elsevier journals have abandoned the requirement completely. (At the other end of the scale, JVP has been known to reject papers without review for such offences as using the wrong kind of dash in a page-range.)
Like so much of how we do things in scholarly publishing, requiring journal-style formatting at the submission stage is a relic of how things used to be done and makes no sense whatsoever in 2012. Before we had citation databases, the publication pipeline was much more straight-through, and the author’s references could be used “as is” in the final publication. Not any more.
How far can we go?
All of this leads me to wonder how far we can go in cutting down the author burden of referencing. Do we actually need to give all the author/title/etc. information for each reference?
In the case of references that have a DOI, I think not (though I’ve not yet discussed this with any publishers). I think that it suffices to give only the DOI. Because once you have a DOI, you can look up all the reference data. Go try it yourself: go to http://www.crossref.org/guestquery/ and paste my DOI “10.1111/j.1469-7998.2011.00824.x” into the DOI Query box at the bottom of the page. Select the “unixref” radio button and hit the Search button. Scroll down to the bottom of the results page, and voila! — an XML document containing everything you could wish to know about the referenced paper.
And the data in that structured document is of course what the publication process uses to render out the reference in the journal’s preferred style.
Am I missing something? Or is this really all we need?