Arriving as an early Christmas present, and coming in just a week before the end of what would otherwise have been a barren 2014, my paper Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs is out! You can read it on PeerJ (or download the PDF).

Figure 4. Effect of adding cartilage to the neutral pose of the neck of Diplodocus carnegii CM 84. Images of vertebra from Hatcher (1901:plate III). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 2.

Figure 4: Effect of adding cartilage to the neutral pose of the neck of Diplodocus carnegii CM 84. Images of vertebra from Hatcher (1901:plate III). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 2.

Yes, that posture is ludicrous — but the best data we currently have says that something like this would have been neutral for Diplodocus once cartilage is taken into account. (Remember of course that animals do not hold their necks in neutral posture.)

The great news here is that PeerJ moved quickly. In fact here’s how the time breaks down since I submitted the manuscript (and made it available as a preprint) on 4 November:

28 days from submission to first decision
3 days to revise and resubmit
3 days to accept
15 days to publication

TOTAL 49 days

Which of course is how it ought to be! Great work here from handling editor Chris Noto and all three reviewers: Matt Bonnan, Heinrich Mallison and Eric Snively. They all elected not to be anonymous, and all gave really useful feedback — as you can see for yourself in the published peer-review history. When editors and reviewers do a job this good, they deserve credit, and it’s great that PeerJ’s (optional) open review lets the world see what they contributed. Note that you can cite, or link to, individual reviews. The reviews themselves are now first-class objects, as they should be.

At the time of writing, my paper is top of the PeerJ home-page — presumably just because it’s the most recent published paper, but it’s a nice feeling anyway!

Screenshot from 2014-12-23 10:39:34

 

A little further down the front-page there’s some great stuff about limb function in ratites — a whole slew of papers.

Well, I’m off to relax over Christmas. Have a good one, y’all!

Despite the flagrant trolling of its title, Nature‘s recent opinion-piece Open access is tiring out peer reviewers is mostly pretty good. But the implication that the rise of open-access journals has increased the aggregate burden of peer-review is flatly wrong, so I felt obliged to leave a comment explaining why. Here is that comment, promoted to a post of its own (with minor edits for clarity):


 

Much of what is said here is correct and important. Although it would be nice if Nature could make a bit more of an effort to avoid the obvious conflict-of-interest issues that lead it to title the piece so misleadingly as an attack on open access. I am glad that so many of the other commenters on this piece saw straight through that rather snide piece of propaganda.

Only one important error of interpretation here, I think. I quote:

The rise of the open-access (OA) movement compounds this effect [i.e. the increasing number of articles needing peer-review.] The business case for online OA journals, to which authors pay submission fees, works best at high volume. And for many of these journals, submitted work is published as long as it is methodologically sound. It does not have to demonstrate, for example, the novelty or societal relevance that some traditional journals demand.

The implication is that journals of this kind (PLOS ONE, PeerJ, the various Frontiers journals) increase the total peer-review burden. In fact, the exact opposite is the case. They greatly reduce the the total amount of peer reviewing.

It’s an open secret that nearly every paper eventually gets published somewhere. Under the old regime, the usual approach is to “work down the ladder”, submitting the same paper repeatedly to progressively less prestigious journals until it reached one that was prepared to publish work of the supplied level of sexiness. As a result, many papers go through four, five or more rounds of peer-review before finally finding a home. Instead, such papers when submitted to a review-for-soundness-only venue such as PLOS ONE require only a single round of review. (Assuming of course that they are indeed methodologically sound!)

The rise of review-for-soundness-only journals (“megajournals”) is an unequivocal improvement in the scientific publishing landscape, and should be welcomed by all parties: authors, who no longer have to submit to the monumental waste of time and effort that is the work-down-the-ladder system; readers, who get access to new research much more quickly; and editors and reviewers who no longer have to burn hours re-reviewing and re-re-reviewing perfectly good papers that have already been repeatedly rejected for a perceived lack of glamour.

Matt’s post yesterday was one of several posts on this blog that have alluded to Clay Shirky’s now-classic article How We Will Read [archived copy]. Here is the key passage that we keep coming back to:

Publishing is not evolving. Publishing is going away. Because the word “publishing” means a cadre of professionals who are taking on the incredible difficulty and complexity and expense of making something public. That’s not a job anymore. That’s a button. There’s a button that says “publish,” and when you press it, it’s done.

In ye olden times of 1997, it was difficult and expensive to make things public, and it was easy and cheap to keep things private. Privacy was the default setting. We had a class of people called publishers because it took special professional skill to make words and images visible to the public. Now it doesn’t take professional skills. It doesn’t take any skills. It takes a WordPress install.

… and of course as SV-POW! itself demonstrates, it doesn’t even need a WordPress install — you can just use the free online service.

This passage has made a lot of people very excited; and a lot other people very unhappy and even angry. There are several reasons for the widely differing responses, but I think one of the important ones is a pun on the word “publish”.

When Shirky uses the word, he is talking  about making something public, available to the world. Which after all is its actual meaning.

But when academics use the word “publish” they usually mean something quite different — they mean the whole process that a research paper goes through between submission and a PDF appearing in a stable location (and in some cases, copies being printed). That process involves many other aspects besides actual publishing — something that in fact Shirky goes straight on to acknowledge:

The question isn’t what happens to publishing — the entire category has been evacuated. The question is, what are the parent professions needed around writing? Publishing isn’t one of them. Editing, we need, desperately. Fact-checking, we need. For some kinds of long-form texts, we need designers.

And this is dead on target. Many writers need editors[*], to varying degrees. Fact-checking could be equated with peer-review, which we pretty much all agree is still very important. Most academic publishers do a certain amount of design (although I suspect that in the great majority of cases this is 99% automatic, and probably involves human judgement only in respect of where to position the illustrations).

But due to the historical accident that it used to be difficult and costly to make and distribute copies, all those other tasks — relatively inexpensive ones, back in the days when distribution was the expensive thing — have become bundled with the actual publishing. With hilarious consequences, as they say. You know, “hilarious” in the sense of “tragic, and breathtakingly frustrating”.

funny-sad-truck-head-down

That’s why we’re stuck in an idiot world where, when we need someone to peer-review our manuscript, we usually trade away our copyright in exchange (and not even to the people who provide the expert review). If you stop and think about that for a moment, it makes absolutely no sense. When I recently wrote a book about Doctor Who, I had several people proofread it, but I didn’t hand over copyright to any of them. My ability to distribute copies was not hobbled by having had independent eyes look it over. There is no reason why it should have, and there is no reason why our ability to distribute copies of our academic works should be limited, either.

What we need is the ability to pay a reasonable fee for the services we need —  peer-review, layout design, reference linking — and have the work published freely.

Well, wouldja lookit that. Looks like I just invented Gold Open Access.

Is publishing just a button? Yes. Making things public is now trivial to do, and in fact much of what so-called publishers now do is labouring to prevent things from being public. But we do need other things apart from actual publishing — things that publishers have historically provided, for reasons that used to make sense but no longer do.

Exactly what those things are, and how extensive and important they are, is a discussion for another day, but they do exist.

 

[*] Note: the whole issue of academic publishing is further confused by another pun, this one on the word “editor”. When Shirky refers to editors, he means people who sharpen up an author’s prose — cutting passages, changing word choices, etc. Academic editors very rarely do that, and would be resented if they did. In our world, an “editor” is usually the nominally independent third party who solicits and evaluates peer-reviews, and makes the accept/reject decision. Do we need editors, in this academic sense? We’ll discuss that properly another time, but I’ll say now that I am inclined to think we do.

metaphor

…is not actually about scholarly publication. It’s Steve Albini’s keynote address at Melbourne’s Face the Music conference. It’s about the music industry, and how the internet transformed it from a restrictive, top-down oligarchy that mostly benefited middlemen into a more open, level, vibrant ecosystem where artists can get worldwide exposure for free, and yet are often compensated better than they were under the old system. Go read it, and then think about this:

Once the music world met the internet, the problem of getting information from musicians (authors) to listeners (readers) didn’t require any central planning to solve. What little building needed to happen was taken care of by people who were just happy to let the internet work the way it was designed to, and the way it works the most naturally: it makes sharing information almost effortless. Publishers (record labels) still exist, because they offer certain conveniences, but few people are under the delusion that they are necessary.

dead horse

Over here in academia, we’ve already spent more than a decade wringing our hands over how to manage the shift from a barrier-based publishing world to one based on OA. We’ve put so much time and effort and thought into the problem of how to “save” or “transform” scholarly publishing. Why do we do that? Why not just walk away? Publishing is a button, and anything that we do to lend it any more importance–anything we feed it, in terms of time, effort, energy, or regard–is wasted. Wasted because we deliberately ignore the new reality in favor of propping up a system that performed a job that no-one needs done anymore. I keep wondering when the hell we’re all going to wake up, and start sharing our work the way that musicians and listeners share digital music.

And yet even out here on the crazy-eyed, axe-wielding fringe of the OA movement, we are still conservative. Zen Faulkes published a paper on his blog, and he did it 26 months ago, which is a near eternity in the Shiny Digital Future (it’s 13.4% of the lifespan to date of Google). Mike and I have admired that move, and talk about it, but we haven’t done it. Why not? We could even solicit peer reviews from people we know to be tough but fair reviewers. We all do unpaid editorial and review work for publishers, why not for each other directly? It’s like we’re thinking, “Okay, okay, I’ll review this paper, but only if there’s a publisher somewhere that will benefit from my unpaid labor!”

I suppose that for us, one answer is that PeerJ has given us other options that are just as easy as blogging, like posting preprints. So I am a bit torn: I like PeerJ, I support it, I have several papers in the pipeline that I’m planning on sending there. It offers certain conveniences, like sticking DOIs on everything for us, and tracking all of our metrics. But do we need PeerJ? I wonder if it is just the methadone that will help ease us out of our sad addiction to publishers.

Okay we get it already

Bonus observation: don’t just translate Albini’s thoughts on music to scholarly publishing, also try doing the reverse. It becomes pretty clear that the central theme of The Scholarly Kitchen is, “How will poor, helpless music listeners survive without all the middlemen to tell them what to listen to? They’ll be so lost.” Keep polishing that brass, guys, and thanks for the patronization!

The photos are of the dodo skeleton in the Yorkshire Museum, which I saw at SVPCA back in September. If you’re a dodo-phile like me, you should consider supporting Leon Claessens’s, Kenneth Rijsdijk’s, and Hanneke Meijer’s quest to better understand the skull and feeding mechanics of dodos. Their crowdfunding campaign runs through the end of the year–please go check it out.

When Susie Maidment presented her in-progress research at SVP in Berlin last week, someone came in late, missed her “no tweeting, please” request, and posted a screenshot of the new work (since deleted).

On the back of that, Susie started an interesting thread in which it became apparent that people have very different assumptions. She, and Marc Jones, and others, were assuming that if you don’t tell people not to tweet, then they’ll know not to. Meanwhile, I, and Björn Brembs, and others were assuming the opposite: unless someone says not to tweet, you’re good to go.

Obviously this state of affairs is a recipe for disaster.  We’re all going to find ourselves giving presentations where we assume the audience will be doing one thing, but at least some audience members are assuming the other.

So the first thing to say is that we should be explicit about our expectations. My talk at SVPCA this year contained this slide:

tweet-this-talk

I’m going to get into the habit of including something like this every time. Similarly, people who don’t want material from their talks appearing on Twitter should say so.

The second thing is that conferences should state their default policies (always of course allowing individual authors to override them). Someone at, say, SVP, should know from the registration material either that it’s OK to tweet unless told not to, or that it’s not OK to tweet unless told that it is. I think it’s reasonable that different conferences would lean in different directions on this.

The third thing is in the absence of other guidance, it’s better not to tweet. I feel a bit uncomfortable about this because it goes against my pro-open tendencies, but it’s a matter of failing safe. If I want you to tweet my talk but but I forget to say so and there is no conference-wide policy (or the conference policy is No Tweeting), then you won’t tweet it, and that is a missed opportunity –but I’ll live. But if Susie doesn’t want you to tweet but forgets to say so, and you do, then she will be unhappier. (For example, in the present case, Susie is hoping for a media splash, which could be diluted if knowledge of the new finding is already leaking out.

To summarise:

  • Individual presenters should say what they want.
  • The conference should provide a default policy
  • If the absence of both, fail safe by not tweeting.

That’s what I think, anyway. What do you think?

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.

 

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:

Taylor (2014:figure 3). Effect of adding cartilage to the neutral pose of the neck of Apatosaurus louisae CM 3018. Images of vertebra from Gilmore (1936:plate XXIV). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 1. If the slightly sub-horizontal osteological neutral pose of Stevens and Parrish (1999) is correct, then the cartilaginous neutral pose would be correspondingly slightly lower than depicted here, but still much closer to the elevated posture than to horizontal. (Note that the posture shown here would not have been the habitual posture in life: see discussion.)

Taylor (2014:figure 3). Effect of adding cartilage to the neutral pose of the neck of Apatosaurus louisae CM 3018. Images of vertebra from Gilmore (1936:plate XXIV). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 1. If the slightly sub-horizontal osteological neutral pose of Stevens and Parrish (1999) is correct, then the cartilaginous neutral pose would be correspondingly slightly lower than depicted here, but still much closer to the elevated posture than to horizontal. (Note that the posture shown here would not have been the habitual posture in life: see discussion.)

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.

References

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. 2014. Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs. PeerJ PrePrints 2:e588v1 doi:10.7287/peerj.preprints.588v1

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

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