November 6, 2014
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.
November 5, 2014
Last night, I submitted a paper for publication — for the first time since April 2013. I’d almost forgotten what it felt like. But, because we’re living in the Shiny Digital Future, you don’t have to wait till it’s been through review and formal publication to read it. I submitted to PeerJ, and at the same time, made it available as a preprint (Taylor 2014).
It’s called “Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs”, and frankly the results are weird. Here’s a taste:
A year back, as I was composing a blog-post about our neck-cartilage paper in PLOS ONE (Taylor and Wedel 2013c), I found myself writing down the rather trivial formula for the additional angle of extension at an intervertebral joint once the cartilage is taken into account. In that post, I finished with the promise “I guess that will have to go in a followup now”. Amazingly it’s taken me a year to get that one-pager written and submitted. (Although in the usual way of things, the manuscript ended up being 13 pages long.)
To summarise the main point of the paper: when you insert cartilage of thickness t between two vertebrae whose zygapophyses articulate at height h above the centra, the more anterior vertebra is forced upwards by t/h radians. Our best guess for how much cartilage is between the adjacent vertebrae in an Apatosaurus neck is about 10% of centrum length: the image above shows the effect of inserting that much cartilage at each joint.
And yes, it’s weird. But it’s where the data leads me, so I think it would be dishonest not to publish it.
I’ll be interested to see what the reviewers make of this. You are all of course welcome to leave comments on the preprint itself; but because this is going through conventional peer-review straight away (unlike our Barosaurus preprint), there’s no need to offer the kind of detailed and comprehensive comment that several people did with the previous one. Of course feel free if you wish, but I’m not depending on it.
Gilmore Charles W. 1936. Osteology of Apatosaurus, with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175–300 and plates XXI–XXXIV.
Stevens, Kent A., and J. Michael Parrish. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284(5415):798–800. doi:10.1126/science.284.5415.798
Taylor, Michael P., and Mathew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10):e78214. 17 pages. doi:10.1371/journal.pone.0078214
Fumbling towards transparency: the Royal Society’s “reject & resubmit” and submitted/published dates
July 31, 2014
Regulars will remember that nearly two years ago, I reviewed a paper for the Royal Society’s journal Biology Letters, recommended acceptance with only trivial changes (as did both other reviewers) and was astonished to see that it was rejected outright. There was an invitation to resubmit, with wording that made it clear that the resubmission would be treated as a brand new manuscript; but when the “resubmission” was made, it was accepted almost immediately without being sent to reviewers at all — proving that it was in fact a minor revision.
What’s worse, the published version gives the dates “Received August 21, 2012.
Accepted September 13, 2012″, for a submission-to-acceptance time of just 23 days. But my review was done before August 21. This is a clear falsifying of the true time taken to process the manuscript, a misrepresentation unworthy of the Royal Society, and which provoked Matt and me to declare that we would no longer provide peer-review for the Society until they fix this.
By the way, we should be clear that the Royal Society is not the only publisher that does this. For example, one commenter had had the same experience with Molecular Ecology. Misreporting the submission/revision cycle like this works to publishers’ benefit in two ways: it makes them look faster than they really are, and makes the rejection rate look higher (which a lot of people still use as a proxy for prestige).
To the Society’s credit, they were quick to get in touch, and I had what at time seemed like a fruitful conversation with Dr Stuart Taylor, their Commercial Director. The result was that they made some changes:
- Editors now have the additional decision option of ‘revise’. This provides a middle way between ‘reject and resubmit’ and ‘accept with minor revisions’. [It’s hard to believe this didn’t exist before, but I guess it’s so.]
- The Society now publicises ‘first decision’ times rather than ‘first acceptance’ times on their website.
As I noted at the time, while this is definitely progress, it doesn’t (yet) fix the problem.
A few days ago, I checked whether things have improved by looking at a recent article, and was disappointed to see that they had not. I posted two tweets:
Again, I want to acknowledge that the Royal Society is taking this seriously: less than a week later I heard from Phil Hurst at the Society:
I was rather surprised to read your recent tweets about us not fixing this bug. I thought it was resolved to your satisfaction.
Because newly published articles still only have two dates (submitted and accepted) it’s impossible to tell whether the “submitted” date is that of the original submission (which would be honest) or that of the revision, styled “a new submission” even though it’s not, that follows a “reject and resubmit” verdict.
Also: if the journals are still issuing “reject and resubmit” and then accepting the supposed new submissions without sending them out for peer-review (I can’t tell whether this is the case) then that is also wrong.
Sorry to be so hard to satisfy :-) I hope you will see and agree that it comes from a desire to have the world’s oldest scientific society also be one that leads the way in transparency and honesty.
And Phil’s response (which I quote with his kind permission):
I feel the changes we have made provide transparency.
Now that the Editors have the ‘revise’ option, this revision time is now incorporated in the published acceptance times. If on the other hand the ‘reject and resubmit’ option is selected, the paper has clearly been rejected and the author may or may not re-submit. Clearly if a paper had been rejected from another journal and then submitted to us, we would not include the time spent at that journal, so I feel our position is logical.
We only advertise the average ‘receipt to first decision’ time. As stated previously, we feel this is more meaningful as it gives prospective authors an indication of the time, irrespective of decision.
After all that recapitulation, I am finally in a position to lay out what the problems are, as I perceive them, in how things currently stand.
- Even in recently published articles, only two dates are given: “Received May 13, 2014. Accepted July 8, 2014″. It’s impossible to tell whether the first of those dates is that of the original submission, or the “new submission” that is really a minor revision following a reject-and-resubmit verdict.
- It’s also impossible to tell what “receipt to first decision” time is in the journal’s statistics. Is “receipt” the date of the revision?
- We don’t know what the journals’ rejection rates mean. Do they include the rejections of articles that are in fact published a couple of weeks later?
So we have editorials like this one from 2012 that trumpet a rejection rate of 78% (as though wasting the time of 78% of their authors is something to be proud of), but we have no idea what that number represents. Maybe they reject all articles initially, then accept 44% of them immediately on resubmission, and call that a 22% acceptance rate. We just can’t tell.
All of this uncertainly comes from the same root cause: the use of “reject and resubmit” to mean “accept with minor revisions”.
What can the Royal Society do to fix this? Here is one approach:
- Each article should report three dates instead of two. The date of initial submission, the date of resubmission, and the date of acceptance. Omitting the date of initial submission is actively misleading.
- For each of the statistics they report, add prose that is completely clean on what is being measured. In particular, be clear about what “receipt” means.
But a much better and simpler and more honest approach is just to stop issuing “reject and resubmit” verdicts for minor revisions. All the problems just go away then.
“Minor revisions” should mean “we expect the editor to be able to make a final decision based on the changes you make”.
“Major revisions” should mean “we expect to send the revised manuscript back out to the reviewers, so they can judge whether you’ve made the necessary changes”.
And “reject and resubmit” should mean “this paper is rejected. If you want to completely retool it and resubmit, feel free”. It is completely inappropriate to accept a resubmitted paper without sending it out to peer review: doing so unambiguously gives the lie to the claim in the decision letter that “The resubmission will be treated as a new manuscript”.
Come on, Royal Society. You’ve been publishing science since 1665. Three hundred and forty-nine years should be long enough to figure out what “reject” means. You’re better than this.
And once the Royal Society gets this fixed, it will become much easily to persuade other publishers who’ve been indulging in this shady practice to mend their ways, too.
July 29, 2014
I wrote this paper in 2003-4, and it was rejected without review when I submitted it back then. (For, I think, specious reasons, but that’s a whole nother discussion. Forget I mentioned it.)
I haven’t touched the manuscript since then (except to single-space it for submission as a preprint). It’s ten years old. That’s a problem because it’s an analysis of a database of dinosaur diversity, and as everyone knows, the rate of recognising new dinosaurs has gone through the roof. That’s the reason I never made any attempt to update and resubmit it: dinosaur diversity is a fast-moving target, and each time through the submit-reject cycle takes long enough for the data to be outdated.
So much for the history. Now the question: how should I cite this paper? Specifically, what date should I give it? If I cite it as from 2004, it will give the misleading impression that the paper has been available for ten years; but if I cite it as from 2014, it will imply that it’s been worked on at some point in the last ten years. Both approaches seem misleading to me.
At the moment, I am citing it as “Taylor (2014 for 2004)”, which seems to more or less capture what’s meant, but I don’t know whether it’s an established convention. Is there an established convention?
Releated: where in mv publications list should it appear? At present I am sorting it under 2014, since that’s when it came out; but should it be under 2004, when it was written? I guess publication date is the one to go far — after all, it’s not unusual even now for papers to spend a year or more in press, and it’s the later (publication) date that’s cited.
Help me out. How should this be done?
- Taylor, Michael P. 2014 (written in 2004). A survey of dinosaur diversity by clade, age, place of discovery and year of description. PeerJ PrePrints 2:e434v1. doi: 10.7287/peerj.preprints.434v1
I was reading a rant on another site about how pretentious it is for intellectuals and pseudo-intellectuals to tell the world about their “media diets” and it got me thinking–well, angsting–about my scientific media diet.
And then almost immediately I thought, “Hey, what am I afraid of? I should just go tell the truth about this.”
And that truth is this: I can’t tell you what forms of scientific media I keep up with, because I don’t feel like I am actually keeping up with any of them.
Papers – I have no systematic method of finding them. I don’t subscribe to any notifications or table of contents updates. Nor, to be honest, am I in the habit of regularly combing the tables of contents of any journals.
Blogs – I don’t follow any in a timely fashion, although I do check in with TetZoo, Laelaps, and a couple of others every month or two. Way back when we started SV-POW!, we made a command decision not to list any sites other than our own on the sideboard. At the time, that was because we didn’t want to have any hurt feelings or drama over who we did and didn’t include. But over time, a strong secondary motive to keep things this way is that we’re not forced to keep up with the whole paleo blogosphere, which long ago outstripped my capacity to even competently survey. Fortunately, those overachievers at Love in the Time of Chasmosaurs have a pretty exhaustive-looking set of links on their sidebar, so globally speaking, someone is already on that.
The contraction in my blog reading is a fairly recent thing. When TetZoo was on ScienceBlogs, I was over there all the time, and there were probably half a dozen SciBlogs that I followed pretty regularly and another dozen or so that I at least kept tabs on. But ScienceBlogs burned down the community I was interested in, and the Scientific American Blog Network is sufficiently ugly (in the UI sense) and reader-unfriendly to not be worth my dealing with it. So I am currently between blog networks–or maybe past my last one.
Social Media – I’m not on Twitter, and I tend to only log into Facebook when I get an interesting notice in my Gmail “Social” folder. Sometimes I’m not on FB for a week or two at a time. So I miss a lot of stuff that goes down there, including notices about new papers. I could probably fix that if I just followed Andy Farke more religiously.
What ends up happening – I mainly find papers relevant to specific projects as I execute those projects; each new project is a new front in my n-dimensional invasion of the literature. My concern is that in doing this, I tend to find the papers that I’m looking for, whereas the papers that have had the most transformative effect on me are the ones I was not looking for at the time.
Beyond that, I find out about new papers because the authors take it on themselves to include me when they email the PDF out to a list of potentially interested colleagues (and many thanks to all of you who are doing that!), or Mike, Darren, or Andy send it to me, or it turns up in the updates to my Google Scholar profile.
So far, this combination of ad hoc and half-assed methods seems to be working, although it does mean that I have unfairly outsourced much of my paper discovery to other people without doing much for them in return. When I say that it’s working, I mean that I don’t get review comments pointing out that I have missed important recent papers. I do get review comments saying that I need to cite more stuff,* but these tend to be papers that I already know of and maybe even cited already, just not in the right ways to satisfy the reviewers.**
* There is a sort of an arrow-of-inevitability thing here, in that reviewers almost always ask you to cite more papers rather than fewer. Only once ever have I been asked to cite fewer sources, and that is when I had submitted my dinosaur nerve paper (Wedel 2012) to a certain nameless anatomy journal that ended up not publishing it. One of the reviewers said that I had cited several textbooks and popular science books and that was poor practice, I should have cited primary literature. Apparently this subgenius did not realize that I was citing all of those popular sources as examples of publications that held up the recurrent laryngeal nerve of giraffes as evidence for evolution, which was part of the point that I was making: giraffe RLNs are overrated.
** My usual sin is that I mentally categorize papers in one or two holes and forget that a given paper also mentioned C and D in addition to saying a lot about A and B. It’s something that vexes me about some of my own papers. I put so much stuff into the second Sauroposeidon paper (Wedel et al. 2000b) that some it has never been cited–although that paper has been cited plenty, it often does not come up in discussions where some of the data presented therein is relevant, I think because there’s just too much stuff in that paper for anyone (who cares about that paper less than I do) to hold in their heads. But that’s a problem to be explored in another post.
The arborization of science
Part of the problem with keeping up with the literature is just that there is so much more of it than there was even a few years ago. When I first got interested in sauropod pneumaticity back in the late 90s, you were pretty much up to speed if you’d read about half a dozen papers:
- Seeley (1870), who first described pneumaticity in sauropods as such, even if he didn’t know what sauropods were yet;
- Longman (1933), who first realized that sauropod vertebrae could be sorted into two bins based on their internal structures, which are crudely I-beam-shaped or honeycombed;
- Janensch (1947), who wrote the first ever paper that was primarily about pneumaticity in dinosaurs;
- Britt (1993), who first CTed dinosaur bones looking for pneumaticity, independently rediscovered Longman’s two categories, calling them ‘camerate’ and ‘camellate’ respectively, and generally put the whole investigation of dinosaur pneumaticity on its modern footing;
- Witmer (1997), who provided what I think is the first compelling explanation of how and why skeletal pneumaticity works the way it does, using a vast amount of evidence culled from both living and fossil systems;
- Wilson (1999), who IIRC was the first to seriously discuss the interplay of pneumaticity and biomechanics in determining the form of sauropod vertebrae.
Yeah, there you go: up until the year 2000, you could learn pretty much everything important that had been published on pneumaticity in dinosaurs by reading five papers and one dissertation. “Dinosaur pneumaticity” wasn’t a field yet. It feels like it is becoming one now. To get up to speed today, in addition to the above you’d need to read big swaths of the work of Roger Benson, Richard Butler, Leon Claessens, Pat O’Connor (including a growing body of work by his students), Emma Schachner (not on pneumaticity per se, but too closely related [and too awesome] to ignore), Daniela Schwarz, and Jeff Wilson (and his students), plus important singleton papers like Woodward and Lehman (2009), Cerda et al. (2012), Yates et al. (2012), and Fanti et al. (2013). Not to mention my own work, and some of Mike’s and Darren’s. And Andy Farke and the rest of Witmer, if you’re into cranial pneumaticity. And still others if you care about pneumaticity in pterosaurs, which you should if you want to understand how–and, crucially, when–the anatomical underpinnings of ornithodiran pneumaticity evolved. Plus undoubtedly some I’ve forgotten–apologies in advance to the slighted, please prod me in the comments.
You see? If I actually listed all of the relevant papers by just the authors I named above, it would probably run to 50 or so papers. So someone trying to really come to grips with dinosaur pneumaticity now faces a task roughly equal to the one I faced in 1996 when I was first trying to grokk sauropods. This is dim memory combined with lots of guesswork and handwaving, but I probably had to read about 50 papers on sauropods before I felt like I really knew the group. Heck, I read about a dozen on blood pressure alone.
(Note to self: this is probably a good argument for writing a review paper on dinosaur pneumaticity, possibly in collaboration with some of the folks mentioned above–sort of a McIntosh  for the next generation.)
When I wrote the first draft of this post, I was casting about for a word to describe what is going on in science, and the first one that came to mind is “fragmentation”. But that’s not the right word–science isn’t getting more fragmented. If anything, it’s getting more interconnected. What it’s really doing is arborizing–branching fractally, like the blood vessels in the image at the top of this post. I think it’s pointless to opine about whether this is a good or bad thing. Like the existence of black holes and fuzzy ornithischians, it’s just a fact now, and we’d better get on with trying to make progress in this new reality.
How do I feel about all this, now that my little capillary of science has grown into an arteriole and threatens to become a full-blown artery? It is simultaneously exhilarating and worrying. Exhilarating because lots of people are discovering lots of cool stuff about my favorite system, and I have a lot more people to bounce ideas around with than I did when I started. Worrying because I feel like I am gradually losing my ability to keep tabs on the whole thing. Sound familiar?
Conclusion: Help a brother out
Having admitted all of this, it seems imperative that I get my act together and establish some kind of systematic new-paper-discovery method, beyond just sponging off my friends and hoping that they’ll continue to deliver everything I need. But it seems inevitable that I am either going to have to be come more selective about what I consume–which sounds both stupid and depressing–or lose all of my time just trying to keep up with things.
Hi, I’m Matt. I just arrived here in Toomuchnewscienceistan. How do you find your way around?
- Britt, B. B. 1993. Pneumatic postcranial bones in dinosaurs and other archosaurs. Ph.D. dissertation, University of Calgary, Calgary, 383 pp.
- Cerda, I.A., Salgado, L., and Powell, J.E. 2012. Extreme postcranial pneumaticity in sauropod dinosaurs from South America. Palaeontologische Zeitschrift. DOI 10.1007/s12542-012-0140-6
- Fanti, F., Cau, A., Hassine, M., and Contessi, M. 2013. A new sauropod dinosaur from the Early Cretaceous of Tunisia with extreme avian-like pneumatization. Nature Communications 4:2080. doi:10.1038/ncomms3080
- Longman, H. A. 1933. A new dinosaur from the Queensland Creta- ceous. Memoirs of the Queensland Museum 10:131–144.
- McIntosh, John S. 1990. Sauropoda. pp. 345-401 in: D. B. Weishampel, P. Dodson and H. Osmólska (eds.), The Dinosauria. University of California Press, Berkeley and Los Angeles.
- Seeley, H. G. 1870. On Ornithopsis, a gigantic animal of the pterodactyle kind from the Wealden. Annals and Magazine of Natural History, Series 4, 5 279-283.
- Wilson, J. A. 1999. A nomenclature for vertebral laminae in sauropods and other saurischian dinosaurs. Journal of Vertebrate Paleontology 19, 639-653.
- Witmer, L.M. 1997. The evolution of the antorbital cavity of archosaurs: a study in soft-tissue reconstruction in the fossil record with an analysis of the function of pneumaticity. Society of Vertebrate Paleontology Memoir 3:1-73.
- Woodward, H.N., and Lehman, T.M. 2009. Bone histology and microanatomy of Alamosaurus sanjuanensis (Sauropoda: Titanosauria) from the Maastrichtian of Big Bend National Park, Texas. Journal of Vertebrate Paleontology 29(3):807-821.
- Yates, A.M., Wedel, M.J., and Bonnan, M.F. 2012. The early evolution of postcranial skeletal pneumaticity in sauropodomorph dinosaurs. Acta Palaeontologica Polonica 57(1):85-100. doi: http://dx.doi.org/10.4202/app.2010.0075