September 24, 2013
I woke up this morning to find its third substantial review waiting for me.
That means that this paper has now accumulated as much useful feedback in the twenty-seven hours since I submitted it as any previous submission I’ve ever made.
It’s worth reviewing the timeline here:
- Monday 23rd September, 1:19 am: I completed the submission process.
- 7:03 am: the preprint was published. It took less than six hours.
- 10:52 am: received a careful, detailed review from Emanuel Tschopp. It took less than four hours from publication, and so of course less than ten from submission.
- About 5:00 pm: received a second review, this one from Mark Robinson. (I don’t know the exact time because PeerJ’s page doesn’t show an actual timestamp, just “21 hours ago”.)
- Tuesday 24th September, about 4:00 am: received a third review, this from ceratopsian-jockey and open-science guru Andy Farke.
Total time from submission to receiving three substantial reviews: about 27 hours.
It’s worth contrasting that with the times taken to get from submission to the receipt of reviews — usually only two of them — when going through the traditional journal route. Here are a few of mine:
- Diplodocoid phylogenetic nomenclature at the Journal of Paleontology, 2004-5 (the first reviews I ever received): three months and 14 days.
- Revised version of the same paper at PaleoBios, 2005 (my first published paper): one month and 10 days.
- Xenoposeidon description at Palaeontology, 2006: three months and 19 days, although that included a delay as the handling editor sent it to a third, tie-breaking, reviewer.
- Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2008: one month and 11 days.
- Sauropod neck anatomy (eventually to be published in a very different form in PeerJ) at Paleobiology: five months and two days.
- Trivial correction to the Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2010: five months and 11 days, bizarrely for a half-page paper.
Despite the wide variations in submission-to-review time at these journals, it’s clear that you can expect to wait at least a month before getting any feedback at all on your submission at traditional journals. Even PeerJ took 19 days to get the reviews of our neck-anatomy paper back to us.
So I am now pretty such sold on the pre-printing route. As well as getting this early version of the paper out there early so that other palaeontologists can benefit from it (and so that we can’t be pre-emptively plagiarised), issuing a preprint has meant that we’ve got really useful feedback very quickly.
I highly recommend this route.
By the way, in case anyone’s wondering, PeerJ Preprints is not only for manuscripts that are destined for PeerJ proper. They’re perfectly happy for you to use their service as a place to gather feedback for your work before submitting it elsewhere. So even if your work is destined for, say, JVP, there’s a lot to be gained by preprinting it first.
September 14, 2013
Suppose you’re working on a Wealden sauropod — for example, the disturbingly Camarasaurus-like isolated dorsal vertebra NHM R2523 — and for some reason you desperately want to publish your work in Cretaceous Research.
But it’s published by Elsevier, which means that if you’re committed to open access, you have to find an exorbitant $3300 for the APC. Since Elsevier’s profit margin is 37.3%, you know that $1230.90 of your APC is going to be sliced right off the top. I’ve heard it said (but don’t have a reference for this) that barrier-based publishers spend something like 40% of their costs on marketing subscriptions. So there goes another $827.64. And because legacy publishers have to spend a fortune on paywalls, authentication systems, lawyers, spin-doctors, lobbyists and the like, that could well account for, say, half of the remainder. If that’s correct, then only $620.73 of your APC — 19% of what you give them — is actually paying for publishing services such as copy-editing, typesetting, Web hosting and archiving.
You could be forgiven for thinking that’s not the best way to spend your $3300.
it would of course be much cheaper to publish in PLOS ONE, or PeerJ, or eLife, or F1000 Research, or one of the relevant BMC journals. But let’s suppose that your heart is set on Cretaceous Research.
I don’t know how common it is for people to find themselves in this situation, but I’m guessing it crops up more often than somewhat. Often enough, maybe, that the editors wish that the journal they run was published by someone other than Elsevier.
So my question is this: who “owns” journals? For example, we know JVP could move away from T&F if they wanted — at least, when its four-year contract expires — but could Cretaceous Research move from Elsevier? Do the editorial board “own” it? Or does Elsevier? If the CR editors hypothetically wanted to keep running their journal but as (say) an open access Ubiquity Press journal with a £250 APC, would they be forced to start The New Journal of Cretaceous Research, leaving the old one to wither with no editors?
And just to be clear: this isn’t a question about Cretaceous Research, Elsevier and Ubiquity. They’re just examples. It’s about the broader problem of who controls what journals, and what the people who actually run those journals can do about it.
September 12, 2013
Paul Jump’s coverage of open-access issues in Times Higher Education continues with today’s post discussing the fallout from the new BIS report. That report says:
The Finch group, composed of representatives from publishers, universities, funders and libraries [...] was charged with determining a route to open access to which all interested parties could sign up.
There’s your problem, right there. Barrier-based publishers want the opposite to what everything else wants: to set the default to zero access. It’s fundamentally impossible to satisfy both researchers/students/doctors/businesses that want access, and publishers that want to deny them access.
The Finch Group — or BIS, if they can’t get it done — is going to have to grasp the nettle and accept that the UK’s solution on open access is going to make someone very unhappy. The only question is whether that Someone is going to be (A) barrier-based publishers, or (B) literally everyone else in the world.
September 10, 2013
I just read Mick Watson’s post Why I resigned as PLOS ONE academic editor on his blog opiniomics. Turns out his frustration with PLOS ONE is not to do with his editorial work but with the long silences he faced as an author at that journal when trying to get a bad decision appealed.
I can totally identify with that, though my most frustrating experiences along these lines have been with other journals. (yes, Paleobiology, I’m looking at you.) So here’s what I wrote in response (lightly edited from the version that appeared as a comment on the original blog).
There’s one thing that PLOS ONE could and should do to mitigate this kind of frustration: communicate. And so should all other journals.
At every step in the appeal process — and indeed the initial review process — an automated email should be sent to the author. So for the initial submission:
- “Your paper has been assigned an academic editor.”
- “Your paper has been sent out to a reviewer.”
- “An invited reviewer has declined to review; we will try another.”
- “An invited reviewer failed to accept or decline within two weeks; we will try another.”
- “A review has been submitted.”
- “A reviewer has failed to submit his report within four weeks; we are making contact again to ask for a quick response.”
- “A reviewer has failed to submit his report within six weeks; we have dropped that reviewer from this process and will try another.”
- “All reviews are in; the editor is considering the decision.”
- Decision letter.
And for the appeal:
- “Your appeal has been noted and is under consideration.”
- “We have contacted the original handling editor.”
- “The original handling editor has responded.”
- “The original handling editor has failed to respond after four weeks; we are escalating to a senior editor.”
- [perhaps] go back into some of all of the submission process.
- Decision letter.
Most if not all of these stages in the process already have workflow logic in the manuscript-handing system. There is no reason not to send the poor author emails when they happen — it’s no extra work for the editor or reviewers.
Speaking as the veteran of plenty of long-drawn-out silences from journals that I’ve submitted to, I know that getting these messages would have made a big difference to me.
September 9, 2013
You know how every time you point out a problem to legacy publishers — like when they’re caught misrepresenting their open-access offerings they explain that it’s very complicated and will take months to fix?
Here’s how that should work:
To summarise: I found a bug in the PeerJ system; I reported it in two tweets (total word-count: 32); 27 hours later, they had fixed it, and our article was showing the end-pages in its bibliography.
Are you watching, Elsevier? 27 hours.
Of course, we do realise that it’s much harder for you. PeerJ have all that manpower, those thousands of people working on their system, while you only have one or two techies, who have all sorts of other duties as well as finding bug-reports on Twitter and immediately fixing them. It’s always tough for the little guy, isn’t it?
September 9, 2013
I was at the Oklahoma Museum of Natural History in March to look at their Apatosaurus material, so I got to see the newly-mounted baby apatosaur in the “Clash of the Titans” exhibit (more photos of that exhibit in this post). How much of this is real (i.e., cast from real bones, rather than sculpted)? Most of the vertebral centra, a few of the neural arches, some of the limb girdle bones, and most of the long bones of the limbs. All of the missing elements–skull, neural arches, ribs, appendicular bits–were sculpted by the OMNH head preparator, Kyle Davies. Kyle is one of those frighteningly talented people who, if they don’t have what they need, will just freaking build it from scratch. Over the years he has helped me out a LOT with the OMNH sauropod material–including building a clamshell storage jacket for the referred scapula of Brontomerus so we could photograph it from the lateral side–so it’s about time I gave him some props.
Case in point: this sweet atlas-axis complex that Kyle sculpted for the juvenile Apatosaurus mount.
Most fish, amphibians, and other non-amniote tetrapods only have a single specialized vertebra for attaching to the skull. But amniotes have two: a ring- or doughnut-shaped first cervical vertebra (the atlas) that articulates with the occipital condyle(s) of the skull, and a second cervical vertebra (the axis) that articulates with the atlas and sometimes with the skull as well. Mammals have paired occipital condyles on the backs or bottoms of our skulls, so our skulls rock up and down on the atlas (nodding “yes” motion), and our skull+atlas rotates around a peg of bone on the axis called the odontoid process or dens epistrophei (shaking head “no” motion). As shown in the photos and diagrams below, the dens of the axis is actually part of the atlas that fuses to the second vertebra instead of the first. Also, reptiles, including dinosaurs and birds, tend to have a single ball-shaped occipital condyle that fits into the round socket formed by the atlas, so their “yes” and “no” motions are less segregated by location.
Anyway, the whole shebang is often referred to as the atlas-axis complex, and that’s the reconstructed setup for a baby Apatosaurus in the photo above. In addition to making a dull-colored one for the mount, Kyle made this festive version for the vert paleo teaching collection. Why so polychromatic?
Because in fact he built two: the fully assembled one two photos above, and a completely disassembled one, some of which is shown in this photo (I had to move the bigger bits out of the tray so they wouldn’t block the key card at the back). I originally composed this post as a tutorial. But frankly, since Kyle did all of the heavy lifting of (a) making the thing in the first place, (2) making a color-coded key to it, and (d) giving me permission to post these photos, it would be redundant to walk through every element. So think of this as a self-study rather than a tutorial.
Oh, all right, here’s a labeled version. Note that normally in an adult animal the single piece of bone called the atlas would consist of the paired atlas neural arches (na1) and single atlas intercentrum (ic1), and would probably have a pair of fused cervical ribs (r1). Everything else would be fused together to form the axis, including the atlas pleurocentrum (c1), which forms the odontoid process or dens epistrophei (etymologically the “tooth” of the axis).
Here’s the complete Romer (1956) figure from the key card, with a mammalian atlas-axis complex for comparison. Incidentally, the entire book this is drawn from, Osteology of the Reptiles, is freely available online.
And here’s the complete Gilmore (1936) figure. Sorry for the craptastic scan–amazingly, this one is NOT freely available online as far as I can tell, and Mike and I have been trying to get good scans of the plates for years. Getting back on topic, single-headed atlantal cervical ribs have been found in several sauropods, especially Camarasaurus where several examples are known, so they were probably a regular feature, even though they aren’t always preserved.
Also, as noted in this post, it is odd that in this specimen of Apatosaurus the cervical ribs had not fused to the first two vertebrae, even though they normally do, and despite the fact that the vertebrae had fused to each other, even though they normally don’t. Further demonstration, if any were needed, that sauropod skeletal fusions were wacky.
For comparison to the above images, here is the atlas-axis complex in the synapsid Varanops, from Campione and Reisz (2011: fig. 2C).
Those proatlas thingies are present in some sauropods, but that’s about all I know about them, so I’ll say no more for now.
There is a good overview of the atlas-axis complex with lots of photos of vertebrae of extant animals on this page.
Previous SV-POW! posts dealing with atlantes and axes (that’s right) include:
- A fused atlas and axis in Apatosaurus
- Yet more uninformed noodling on the future of scientific publishing and that kind of thing
- Another mystery: embossed laminae and “unfossae”
- Tutorial 15: the bones of the sauropod skeleton
- Campione, N.E. and Reisz, R.R. 2011. Morphology and evolutionary significance of the atlas−axis complex in varanopid synapsids. Acta Palaeontologica Polonica 56 (4): 739–748.
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11: 175-300.
- Romer, A.S. 1956. Osteology of the Reptiles. University of Chicago Press, Chicago. 772 pp.
September 6, 2013
We’re just back from SVPCA 2013 in Edinburgh. The first part of the meeting was held at the Royal Society of Edinburgh, but on Friday we moved to the National Museums Scotland. Which is awesome. And free to the public. The design process for the museum seems to have been, “Okay, let’s get one of, oh, every interesting thing in the world, and put it right here.” We have tons more photos of amazing things from the museum, and maybe we’ll get around to posting them sooner or later, but today I have other things to do.
Like make fun of Mike. And talk about vomiting dinosaurs.
This groovy stuffed fulmar, Fulmarus glacialis, is shown in the act of puking, which it does to dissuade predators. And probably everyone else. I am reliably informed by Darren that this is unrealistic fulmar vomit, and that the real thing is more of a thin stream, like the world’s nastiest water gun, which can be directed with considerable accuracy. Note to self: don’t piss off the fulmars.
Last year cemented “drawing goofy sauropods down at the pub” as a regular SVPCA Thing. So one night I was out with Mike and Darren and paleoartist Bob Nicholls, who is famous around these parts as the creator of the Greatest. Paleoart. Ever. I did a goofy sketch in my notebook illustrating the “defensive vomit” hypothesis, which Brian Engh and I cooked up during this alligator dissection. More on that another time, maybe. Anyway, after bashing out a fairly pathetic sauropod-puking-on-theropod scene, I passed the notebook to Bob and said, “Make this not suck”. Which he did. (Seriously, if you could see my original scrawl, you’d be the one throwing up.)
So now I have an original Bob Nicholls sketch–heck, the world’s first Wedel-Nicholls artist collaboration!–in my notebook, of one of evolution’s most majestic successes responding appropriately to a vulgar, overstudied theropod. Bob drew it right in front of me and I got to drink good beer while I watched him work.
And that, more or less, is why I attend SVPCA.
I couldn’t sign off without giving you another version of Giant Irish Mike, with the background cropped out so he can be dropped right into posters, slide shows, and other works of science and art. I really, really hope that he turns up in conference talks and other presentations in the months and years to come. If so, send us a photo documenting his miraculous apparition and we’ll show it to the world.
September 6, 2013
Those familiar with Lull (1919: plate II: figure 2) will recognise this as “vertebra Q” of the Barosarus lentus holotype YPM 429, in ventral view.
Stay tuned for more exciting Barosaurus-related news!
Lull, R. S. 1919. The sauropod dinosaur Barosaurus Marsh. Memoirs of the Connecticut Academy of Arts and Sciences 6:1-42 and plates I-VII.
September 4, 2013
I recently handled the revisions on a paper that hopefully will be in press very soon. One of the review comments was “Be very careful not to make ad hominem attacks”.
I was a bit surprised to see that — I wasn’t aware that I’d made any — so I went back over the manuscript, and sure enough, there were no ad homs in there.
There was criticism, though, and I think that’s what the reviewer meant.
Folks, “ad hominem” has a specific meaning. An “ad hominem attack” doesn’t just mean criticising something strongly, it means criticising the author rather than the work. The phrase is Latin for “to the man”. Here’s a pair of examples:
- “This paper by Wedel is terrible, because the data don’t support the conclusion” — not ad hominem.
- “Wedel is a terrible scientist, so this paper can’t be trusted” – ad hominem.
What’s wrong with ad hominem criticism? Simply, it’s irrelevant to evaluation of the paper being reviewed. It doesn’t matter (to me as a scientist) whether Wedel strangles small defenceless animals for pleasure in his spare time; what matters is the quality of his work.
Note that ad hominems can also be positive — and they are just as useless there. Here’s another pair of examples:
- “I recommend publication of Naish’s paper because his work is explained carefully and in detail” — not ad hominem.
- “I recommend publication of Naish’s paper because he is a careful and detailed worker” — ad hominem.
It makes no difference whether Naish is a careful and detailed worker, or if he always buys his wife flowers on their anniversary, or even if he has a track-record of careful and detailed work. What matters is whether this paper, the one I’m reviewing, is good. That’s all.
As it happens the very first peer-review I ever received — for the paper that eventually became Taylor and Naish (2005) on diplodocoid phylogenetic nomenclature — contained a classic ad hominem, which I’ll go ahead and quote:
It seems to me perfectly reasonable to expect revisers of a major clade to have some prior experience/expertise in the group or in phylogenetic taxonomy before presenting what is intended to be the definitive phylogenetic taxonomy of that group. I do not wish to demean the capabilities of either author – certainly Naish’s “Dinosaurs of the Isle of Wight” is a praiseworthy and useful publication in my opinion – but I question whether he and Taylor can meet their own desiderata of presenting a revised nomenclature that balances elegance, consistency, and stability.
You see what’s happening here? The reviewer was not reviewing the paper, but the authors. There was no need for him or her to question whether we could meet our desiderata: he or she could just have read the manuscript and found out.
(Happy ending: that paper was rejected at the journal we first sent it to, but published at PaleoBios in revised form, and bizarrely is my equal third most-cited paper. I never saw that coming.)