My most depressing paper

October 6, 2015

I have a new preprint up at PeerJ (Taylor 2015), and have also submitted it simultaneously for peer review. In a sense, it’s not a paper I am happy about, as its title explains: “Almost all known sauropod necks are incomplete and distorted“.

Taylor 2015: Figure 10. Manipulation of consecutive sauropod vertebrae by hand. Cervicals 2 and 3 of Giraffatitan brancai lectotype MB.R.2181 (formerly HMN SI). I attempted to articulate these two vertebrae, and empirically determine the feasible range of motion. Due to subtle distortion of the zygapophyses of these vertebrae, it was not possible to articulate C2 in a more extended position relative to C3 than shown here. Photograph by Mathew J. Wedel.

Taylor 2015: Figure 10. Manipulation of consecutive sauropod vertebrae by hand. Cervicals 2 and 3 of Giraffatitan brancai lectotype MB.R.2181 (formerly HMN SI). I attempted to articulate these two vertebrae, and empirically determine the feasible range of motion. Due to subtle distortion of the zygapophyses of these vertebrae, it was not possible to articulate C2 in a more extended position relative to C3 than shown here. Photograph by Mathew J. Wedel.

This paper has been a while coming, and much of the content will be familiar to long-time readers, as quite a bit of it is derived from three SV-POW! posts: How long was the neck of Diplodocus? (2011), Measuring the elongation of vertebrae (2013) and The Field Museum’s photo-archives tumblr, featuring: airbrushing dorsals (2014). It also uses the first half of my 2011 SVPCA talk, Sauropod necks: how much do we really know? (and the second half became the seed that grew into our 2013 neck-cartilage paper.)

So in one sense, publishing this is a bit of a mopping up exercise. But it’s also more than that, because I think it’s important to get all these observations (and the relevant literature review) down all in one place, to help us recognise just how serious the problem is. There are, to a first approximation, no complete sauropod necks in the published literature.  And the vertebrae of the necks we do have are crushed to the point where trying to articulate them is close to meaningless.

Taylor 2015: Figure 8. Cervical vertebrae 4 (left) and 6 (right) of Giraffatitan brancai lectotype MB.R.2180 (previously HMN SI), in posterior view. Note the dramatically different aspect ratios of their cotyles, indicating that extensive and unpredictable crushing has taken place. Photographs by author.

Taylor 2015: Figure 8. Cervical vertebrae 4 (left) and 6 (right) of Giraffatitan brancai lectotype MB.R.2180 (formerly HMN SI), in posterior view. Note the dramatically different aspect ratios of their cotyles, indicating that extensive and unpredictable crushing has taken place. Photographs by the author.

I’m not happy about this. But I think it’s important to face the reality and be honest with ourselves about how much we can really know about sauropod necks. There’s a lot we can do in a qualitative way, but most quantitative results are going to be swamped in supposition and error.

Reference

Taylor, Michael P. 2015. Almost all known sauropod necks are incomplete and distorted. PeerJ Preprints 3:e1767. doi:10.7287/peerj.preprints.1418v1

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Preprints are in the air! A few weeks ago, Stephen Curry had a piece about them in the Guardian (Peer review, preprints and the speed of science) and pterosaur palaeontologist Liz Martin published Preprints in science on her blog Musings of Clumsy Palaeontologist. The latter in particular has spawned a prolific and fascinating comment stream. Then SV-POW!’s favourite journal, PeerJ, weighed in on its own blog with A PeerJ PrePrint – so just what is that exactly?.

Following on from that, I was invited to contribute a guest-post to the PeerJ blog: they’re asking several people about their experiences with PeerJ Preprints, and publishing the results in a series. I started to write my answers in an email, but they soon got long enough that I concluded it made more sense to write my own post instead. This is that post.

As a matter of fact, I’ve submitted four PeerJ preprints, and all of them for quite different reasons.

Figure6-vertebra-q-composite

1. Barosaurus neck. I and Matt submitted the Barosaurus manuscript as a preprint because we wanted to get feedback as quickly as possible. We certainly got it: four very long detailed comments that were more helpful than most formally solicited peer-reviews that I’ve had. (It’s to our discredit that we didn’t then turn the manuscript around immediately, taking those reviews into a account. We do still plan to do this, but other things happened.)

Figure1-diversity-by-phylogeny

2. Dinosaur diversity. Back in 2004 I submitted my first ever scientific paper, a survey of dinosaur diversity broken down in various ways. It was rejected (for what I thought were spurious reasons, but let it pass). The more time that passed, the more out of date the statistics became. As my interests progressed in other directions, I reached the point of realising that I was never going to get around to bringing that paper up to date and resubmitting it to a journal. Rather than let it be lost to the world, when I think it still contains much that is of interest, I published it as a pre-print (although it’s not pre- anything: what’s posted is the final version).

figure3-CM3018-juxtaposition

3. Cartilage angles. Matt and I had a paper published on PLOS ONE in 2013, on the effect that intervertebral cartilage had on sauropod neck posture. Only after it was published did I realise that there was a very simple way to quantify the geometric effect. I wrote what was intended to be a one-pager on that, planning to issue it as a sort of erratum. It ended up much longer than expected, but because I considered it to be material that should really have been in the original PLOS ONE paper, I wanted to get it out as soon as possible. So as soon as the manuscript was ready, I submitted it simultaneously as a preprint and onto the peer-review track at PeerJ. (It was published seven weeks later.)

cladogram

4. Apatosaurine necks. Finally, I gave a talk at this year’s SVPCA (Symposium on Vertebrate Palaeontology and Comparative Anatomy), based on an in-progress manuscript in which I am second author to Matt. The proceedings of the symposium are emerging as a PeerJ Collection, and I and the other authors wanted our paper to be a part of that collection. So I submitted the abstract of the talk I gave, with the slide-deck as supplementary information. In time, this version of the preprint will be superseded by the completed manuscript, and eventually (we hope) by the peer-reviewed paper.

So the thing to take away from this is that there are lots of reasons to publish preprints. They open up different ways of thinking about the publication process.

Wouldn’t it be great if, after a meeting like the 2015 SVPCA, there was a published set of proceedings? A special issue of a journal, perhaps, that collected papers that emerge from the work presented there.

Of course the problem with special issues, and edited volumes in general, is that they take forever to come out. After the Dinosaurs: A Historical Perspective conference on 6 May 2008, I got my talk on the history of sauropod research written up and submitted on 7 August, just over three months later. It took another five and a half months to make it through peer-review to acceptance. And then … nothing. It sat in limbo for a year and nine months before it was finally published, because of course the book couldn’t be finalised until the slowest of the 50 or so authors, editors and reviewers had done their jobs.

Taylor (2010: fig. 4). Marsh's reconstructions of Brontosaurus. Top: first reconstruction, modified from Marsh (1883, plate I). Bottom: second reconstruction, modified from Marsh (1891, plate XVI).

Taylor (2010: fig. 4). Marsh’s reconstructions of Brontosaurus. Top: first reconstruction, modified from Marsh (1883, plate I). Bottom: second reconstruction, modified from Marsh (1891, plate XVI).

There has to be a better way, doesn’t there?

Rhetorical question, there. There is a better way, and unsurprisingly to regular readers, it’s PeerJ that has pioneered it. In PeerJ Collections, papers can be added at any time, and each one is published as it’s ready. Better still, the whole lifecycle of the paper can (if the authors wish) be visible from the collection. You can start by posting the talk abstract, then replace it with a preprint of the complete manuscript when it’s ready, and finally replace that with the published version of the paper once it’s been through peer-review.

Take a look, for example, at the collection for the 3rd International Whale Shark Conference (which by the way was held at the Georgia Aquarium, Atlanta, which has awesome whale sharks on view.)

pb-120306-whaleshark-843p.photoblog900

As you can see from the collection (at the time of writing), only one of the constituent papers — Laser photogrammetry improves size and demographic estimates for whale sharks — has actually been published so far. But a dozen other papers exist in preprint form. That means that the people who attended the conference, saw the talks and want to refer to them in their work have something to cite.

The hot news is that Mark Young and the other SVPCA 2015 organisers have arranged for PeerJ to set up an SPPC/SVPCA 2015 Collection. I think this is just marvellous — the best possible way to make a permanent record of an important event.

The collection is very new: at the time of writing, it hosts only five abstracts (one of them ours). We’re looking forward to seeing others added. Some of the abstracts (including ours) have the slides of the talk attached as supplementary information.

talk-title-page

Although I’m lead author on the talk (because I prepared the slides and delivered the presentation), this project is really Matt’s baby. There is a Wedel et al. manuscript in prep already, so we hope that within a month or two we’ll be able to replace the abstract with a complete manuscript. Then of course we’ll put it through peer-review.

I hope plenty of other SVPCA 2015 speakers will do the same. Even those who, for whatever reason, don’t want to publish their work in PeerJ, can use the collection as a home for their abstracts and preprints, then go off and submit the final manuscript elsewhere.

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

Recently, I published an old manuscript of mine as a PeerJ Preprint.

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?

References

Today, available for the first time, you can read my 2004 paper A survey of dinosaur diversity by clade, age, place of discovery and year of description. It’s freely available (CC By 4.0) as a PeerJ Preprint. It’s one of those papers that does exactly what it says on the tin — you should be able to find some interesting patterns in the diversity of your own favourite dinosaur group.

Fig. 1. Breakdown of dinosaur diversity by phylogeny. The number of genera included in each clade is indicated in parentheses. Non-terminal clades additionally have, in square brackets, the number of included genera that are not also included in one of the figured subclades. For example, there are 63 theropods that are neither carnosaurs nor coelurosaurs. The thickness of the lines is proportional to the number of genera in the clades they represent.

Taylor (2014 for 2004), Figure 1. Breakdown of dinosaur diversity by phylogeny. The number of genera included in each clade is indicated in parentheses. Non-terminal clades additionally have, in square brackets, the number of included genera that are not also included in one of the figured subclades. For example, there are 63 theropods that are neither carnosaurs nor coelurosaurs. The thickness of the lines is proportional to the number of genera in the clades they represent.

“But Mike”, you say, “you wrote this thing ten years ago?”

Yes. It’s actually the first scientific paper I ever wrote (bar some scraps of computer science) beginning in 2003. It’s so old that all the illustrations are grey-scale. I submitted it to Acta Palaeontologica Polonica way back on on 24 October 2004 (three double-spaced hard-copies in the post!) , but it was rejected without review. I was subsequently able to publish a greatly truncated version (Taylor 2006) in the proceedings of the 2006 Symposium on Mesozoic Terrestrial Ecosystems, but that was only one tenth the length of the full manuscript — much potentially valuable information was lost.

My finally posting this comes (as so many things seem to) from a conversation with Matt. Off work sick, he’d been amusing himself by re-reading old SV-POW! posts (yes, we do this). He was struck by my exhortation in Tutorial 14: “do not ever give a conference talk without immediately transcribing your slides into a manuscript”. He bemoaned how bad he’s been at following that advice, and I had to admit I’ve done no better, listing a sequence of old my SVPCA talks that have still never been published as papers.

The oldest of these was my 2004 presentation on dinosaur diversity. Commenting on this, I wrote in email: “OK, I got the MTE four-pager out of this, but the talk was distilled from a 40ish-page manuscript that was never published and never will be.” Quick as a flash, Matt replied:

If I had written this and sent it to you, you’d tell me to put it online and blog about how I went from idea to long paper to talk to short paper, to illuminate the process of science.

And of course he was right — hence this preprint.

Fig. 2. Breakdown of dinosaurian diversity by high-level taxa. "Other sauropodomorphs" are the "prosauropods" sensu lato. "Other theropods" include coelophysoids, neoceratosaurs, torvosaurs (= megalosaurs) and spinosaurs. "Other ornithischians" are basal forms, including heterodontosaurs and those that fall into Marginocephalia or Thyreophora but not into a figured subclade.

Taylor (2014 for 2004), Figure 2. Breakdown of dinosaurian diversity by high-level taxa. “Other sauropodomorphs” are the “prosauropods” sensu lato. “Other theropods” include coelophysoids, neoceratosaurs, torvosaurs (= megalosaurs) and spinosaurs. “Other ornithischians” are basal forms, including heterodontosaurs and those that fall into Marginocephalia or Thyreophora but not into a figured subclade.

I will never update this manuscript, as it’s based on a now wildly outdated database and I have too much else happening. (For one thing, I really ought to get around to finishing up the paper based on my 2005 SVPCA talk!) So in a sense it’s odd to call it a “pre-print” — it’s not pre anything.

Despite the data being well out of date, this manuscript still contains much that is (I think) of interest, and my sense is that the ratios of taxon counts, if not the absolute numbers, are still pretty accurate.

I don’t expect ever to submit a version of this to a journal, so this can be considered the final and definitive version.

References