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.

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

 

dodo-skeleton-flipped

Hey, remember this? Your bound-for-PeerJ manuscript is like our Mauritian friend here, and the March 1 deadline is approaching like a hungry sailor with a club. So if you still want a voucher, let me know ASAP.

Today (12th February) is the one-year anniversary of the first PeerJ papers! As Matt put it in an email this morning:

Hard to believe it’s been a year already. On the other hand, it’s also hard to believe that it’s only been a year. PeerJ is just such an established part of my worldview now.

That’s exactly right. PeerJ has so completely rewritten the rule-book (on price, speed and quality of service) that now when I’m thinking about new papers I’m going to write, the question I ask myself is no longer “Where shall I send this?” but “Is there any reason not to send it to PeerJ?”

dorsals-ab-composite

Dorsals A and B (probably D8 and D9) of NHM R5937, “The Archbishop”, a still-undescribed brachiosaurid sauropod from the Upper Jurassic Tendaguru Formation of Tanzania, which I will get done this year, and which is destined for PeerJ. Top row: dorsal view with anterior to the right. Bottom row, from left to right: left lateral, posterior, right lateral, anterior.

Yesterday in the comments of a post on The Scholarly Kitchen, Harvey Kane asked me “I am curious as to where you get the notion that publishing OA is less expensive and in some way “better” than the traditional model?” My reply was (in part):

My notion that OA publishing yields better results than traditional is rooted in the online-only nature of articles, which allows them to ignore arbitrary limits on word-count, number of figures, use of colour, etc., and to exploit online-only formats such as video, 3d models, CT-slice stacks, etc. In my own field of vertebrate palaeontology, it’s now routine to see in PLOS ONE descriptive articles that are many times more comprehensive than their equivalents in traditional journals — see for example the recent description of the frog Beelzebufo.

Of course there is nothing specific to open-access about this: there is no technical reason why an online-only subscription journal shouldn’t publish similarly detailed articles. But my experience so far has been that they don’t — perhaps because they are tied to the mindset that pages and illustrations are limited resources.

For Beelzebufo in PLOS ONE, read baby Parasaurolophus in PeerJ, which we described as “the world’s most open-access dinosaur“. This paper is 83 pages of technicolour goodness, plus all the 3d models you can eat. And the crazy thing is, this sort of detail in descriptive papers is not even exceptional any more — see for example the recent description of Canardia in PLOS ONE, or this analysis of croc respiration in PeerJ

Years ago, I said that in the Archbishop descriptions I wanted to raise the bar for quality of illustration. Well, I’ve taken so long over getting the Archbishop done that the bar has been raised, and now I’m scrambling to catch up. Certainly the illustrations even in our 2011 description of Brontomerus are starting to look a bit old-fashioned.

And of course, the truly astonishing thing about PeerJ is that it does this so very cheaply. Because I’m already a member (which cost me $99), the Archbishop description is going to be free to me to publish this year. (This year for sure!) If we also get our Barosaurus neck preprint published properly this year,then I’ll have to find $100 to upgrade my Basic membership to Enhanced. That’s cheap enough that it’s not even worth going through the hassle of trying to get Bristol to pay for me. And if I ever hit a year when I publish three or more papers, I’ll upgrade once more (for another $100) to the Investigator plan and then that’s it: I’m done paying PeerJ forever, however many papers I publish there. (Matt jumped straight to the all-you-can-eat plan, so he wouldn’t even have to think about it ever again.)

Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view. (Taylor and Wedel 2013b: figure 6)


Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view. (Taylor and Wedel 2013b: figure 6)

PeerJ’s pricing is making PLOS ONE’s $1350 APC look distinctly old-fashioned; and the $3000 charged by the legacy publishers (for a distinctly inferior product) is now frankly embarrassing. You might expect that as such low prices, PeerJ’s quality of service would suffer, but that’s not been our experience: editing, reviewing, typesetting and proofing for our neck-anatomy paper were all up there with the best we’ve received anywhere.

And it’s great to see that it’s not just minor researchers like Matt and me who are persuaded by PeerJ: they’ve now accumulated a frankly stellar list of 20 universities (so far) with institutional plans for researchers to publish there. When I say “stellar” I mean that the list includes Harvard, MIT, Cambridge, Berkeley, Stanford, Johns Hopkins, UCL, Carnegie Mellon, Duke … the list goes on.

We can only hope that the next year, and the next ten and twenty, are as successful for PeerJ as the first has been; and that other New Generation publishers will join it in pushing the field forward.

I leave the last word to Matt:

I’m getting Vicki a lifetime membership for Valentine’s Day. Because I’m a romantic.

She’s a lucky, lucky woman.

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