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

 

As promised, some thoughts on the various new brachiosaur mass estimates in recent papers and blog-posts.

Back in 2008, when I did the GDI of Giraffatitan and Brachiosaurus for my 2009 paper on those genera, I came out with estimates of 28688 and 23337 kg respectively. At the time I said to Matt that I was suspicious of those numbers because they seemed too low. He rightly told me to shut up and put my actual results in the paper.

More recently, Benson et al. (2014) used limb-bone measurements to estimate the masses of the same individuals as 56000 and 34000 kg. When Ian Corfe mentioned this in a comment, my immediate reaction was to be sceptical: “I’m amazed that the two more recent papers have got such high estimates for brachiosaurs, which have the most gracile humeri of all sauropods“.

So evidently I have a pretty strong intuition that Brachiosaurus massed somewhere in the region of 35000 kg and Giraffatitan around 30000 kg. But why? Where does that intuition come from?

I can only assume that my strongly held ideas are based only on what I’d heard before. Back when I did my 2008 estimate, I probably had in mind things like Paul’s (1998) estimate of 35000 kg for Brachiosaurus, and Christiansen’s (1997:67) estimate of 37400 for Giraffatitan. Whereas by the time the Benson et al. paper came out I’d managed to persuade myself that my own much lower estimates were right. In other words, I think my sauropod-mass intuition is based mostly on sheer mental inertia, and so should be ignored.

I’m guessing I should ignore your intuitions about sauropod masses, too.

References

How disruptive is PeerJ?

February 21, 2013

Matt and I were discussing “portable peer-review” services like Rubriq, and the conversation quickly wandered to the subject of PeerJ. Then I realised that that seems to be happening with all our conversations lately. Here’s a partial transcript.

Mike: I don’t see portable peer-review catching on. Who’s going to pay for it unless journals give an equal discount from APCs? And what journal is going to do that when they get the peer-review done for free anyway? If I was Elsevier, I wouldn’t say “OK, we’ll accept your external review and give you a $700 discount”, I’d charge the full $3000 and get two more free reviews done.

Plus, you know, I can get all the peer-review I want, free of charge, at PeerJ.

Matt: Yeah, that was pretty much my take. Even as I was sending that I thought about adding, “I wonder if this is one more thing that PeerJ will kill.” Only ‘abort’ is more the verb I want, in that I don’t see this ever getting off the ground anyway.

Mike: I think the world at large has yet to realise what a black hole PeerJ is, in the sense that it’s warping all the space near it. Pretty much every time I have any thought at all about scholarly publishing now, that thought it swiftly followed by “… or, wait, I should just use PeerJ for that.”

Matt: Exactly. It makes me think that we may be discovering the contours of that space-warping effect for some time, in that we’re used to one model, and that, among all the other things PeerJ does, it quacks something like that old model so we tend to think of it as a very cool duck, and not the freakin’ tyrannosaur that is going to eat scholarly publishing.

Also makes me think of that Paul Graham thing about noticing that the door is open, and there being a lag between the freedom to do something and the adoption of that newly facilitated action or behavior.

Interesting times.

New thought: assuming PeerJ does not implode, will the established powers try to start PeerJ-alikes, and if so, what will they charge (amount), and what will they charge for (lifetime membership? decadal? annual? per 1000 pages published?).

Mike: Sweet metaphor. It’s true. It’s qualitatively different from other journals in two respects.

First, the APC is literally an order of magnitude less — and at that point, a quantitative difference becomes qualitative. Someone like [NAME REDACTED] would worry about paying $1350 to PLOS ONE, but didn’t even stop and think before saying, yeah, I’ll do that.

Second, the lifetime membership changes the game for all subsequent submissions. Now when you have a manuscript ready to go, your question isn’t going to be “where shall I send this?”, it’s going to be “is there are compelling reason not to send this to PeerJ?”

Legacy publishers won’t start PeerJ-alikes because they can’t. As noted in many SV-POW! posts, Elsevier takes about $5000 for each article they put behind a paywall. Slice away the 40% profit and you get $3000 which not coincidentally is what they charge as an APC. They have old, slow, encumbered systems and processes and top-heavy organisation. At $3000 they are only breaking even. They can’t compete at a PLOS-like $1350 level and they can’t even think about competing at PeerJ levels. If they offered a lifetime membership they’d have to ask $10k or something stupid.

I don’t think it’s that they don’t want to change. They can’t. They’ve ossified into 1990s companies running on 1990s software. It’s hard to steer a ship with a $2bn turnover, and impossible to replace the engines while still cruising.

Matt: I think it is probably a mistake to think that PeerJ will only encroach “upward”, onto the territory of more traditional journals (which is “all of them”). We’ve already talked about it taking business from arXiv (at least ours, although there is the large non-overlap in their respective subject domains–for now, anyway).

But my point is, the question, “Why wouldn’t I send this to PeerJ?” may not only kick in for papers that you might conceivably send elsewhere, but also for manuscripts that you might not conceivably send anywhere.

Mike: There are plenty of historical SV-POW! posts that could have been PeerJ articles on their own — for example, the shish-kebab post that ended up as part of Why Giraffes Have Short Necks.

Matt: Right. And if one is on the fence, shove it on the PeerJ preprint server and see what people have to say.

Mike: I think it’s the first megajournal to have an associated preprint server, and that may yet prove the most important of all its innovations.

Matt: It feels almost … struggling to find the right word, in part because it’s late and I need to go sleep. “Seditious” is not quite it, and neither is “seductive”.

At that point we started talking about something else, so I never did find out what word Matt was groping for. But what’s only gradually become clear to us is how much PeerJ is changing how we think about the academic publishing process. It’s shaking us out of mental ruts that we didn’t even know we were in. Exciting.

 

After the authors’ own work, the biggest contribution to a published paper is the reviews provided, gratis, by peers. When peer-review works as it’s supposed to, they add significant value to the final paper. But the actual reviews are never seen by anyone except the authors and the handling editor.

This is bad for several reasons.

First, good reviewers don’t get the credit they deserve. That’s unfair on those who do a good job — who generously invest a lot of time and effort in others’ work.

Second, bad reviewers don’t get the blame they deserve. That leaves them free to act in bad faith: blocking papers by people they don’t like, or whose work is critical of their own; or just doing a completely inadequate job. Because there are no negative consequences for doing a bad job, people have no external incentive to straighten up and fly right.

Third, the effort that goes into reviewing is largely wasted. Often the reviews themselves are significant pieces of work (that’s certainly true when I’m the one giving the review) and the wider community could benefit from seeing them. Frequently reviews contain extended discussion, not only of the paper’s subject matter but of scientific philosophy such as approaches to taxonomy or narrative structure.

Fourth, editors’ decisions remain unexplained. Most editors handle manucripts efficiently and fairly, but there are cases when this isn’t the case — as for example when I was one of three reviewers who wholeheartedly recommended acceptance but the editor rejected the paper. Even discussing that situation was difficult, because the reviews in question were not available for the world to read.

Fifth, and more general than any of the above, the reviewing process is opaque to the world. In times past, logistical reasons such as lack of space in printed journals meant that the sausage-machine approach to the review process was the only feasible one: no-one wants to see what goes into the machine or what goes on inside, we only want the final product. But we live in an increasingly open world, and consensus is that pretty much all processes benefit from openness.

There are various initiatives under way to change the legacy system of reviewing, including F1000 Research and the eLife decision-letter system. But at the moment only a small minority of papers are submitted to such venues.

What to do about the others?

And so I found myself wondering … what would happen if I just unilaterally posted the reviews I receive? I already make pages on this site for each of my published papers (example): it would be easy to extend those pages by also adding:

  • The submitted version of the manuscript
  • All the reviews I received
  • The editor’s decision letter
  • My response letter to the editor
  • The final published paper.

I know this is “not done”. My question is: why not? Is there an actual reason, other than inertia? Wouldn’t we all be better off if this was standard operating procedure?

[Note that this is orthogonal to reviewer anonymity. As it happens, I think that is also a bad thing, but it's independent of what I'm proposing here. I could post an unsigned review as-is, without revealing who wrote it even if I knew.]

We know that most academic journals and edited volumes ask authors to sign a copyright transfer agreement before proceeding with publication. When this is done, the publisher becomes the owner of the paper; the author may retain some rights according to the grace or otherwise of the publisher.

Plenty of authors have rightly railed against this land-grab, which publishers have been quite unable to justify. On occasion we’ve found ways to avoid the transfer, including the excellent structured approach that is the SPARC Author Addendum and my tactic of transferring copyright to my wife.

Works produced by the U.S. Federal Government are not protected by copyright. For example, papers written by Bill Parker as part of his work at Petrified Forest National Park are in the public domain.

Journals know this, and have clauses in their copyright transfer agreements to deal with it. For example, Elsevier’s template agreement has a box to check that says “I am a US Government employee and there is no copyright to transfer”, and the publishing agreement itself reads as follows (emphasis added):

Assignment of publishing rights
I hereby assign to <Copyright owner> the copyright in the manuscript identified above (government authors not electing to transfer agree to assign a non-exclusive licence) and any supplemental tables, illustrations or other information submitted therewith that are intended for publication as part of or as a supplement to the manuscript (the “Article”) in all forms and media (whether now known or hereafter developed), throughout the world, in all languages, for the full term of copyright, effective when and if the article is accepted for publication.

So journals and publishers are already set up to deal with public domain works that have no copyright. And that made me wonder why this option should be restricted to U.S. Federal employees.

What would happen if I just unilaterally place my manuscript in the public domain before submitting it? (This is easy to do: you can use the Creative Commons CC0 tool.)

Once I’d done that, I would be unable to sign a copyright transfer agreement. Not merely unwilling — I wouldn’t need to argue with publishers, “Oh, I don’t want to sign that”. It would be simpler than this. It’s would just be “There is no copyright to transfer”.

What would publishers say?

What could they say?

“We only publish public-domain works if they were written by U.S. federal employees”?

It’s an oddity to me that when publishers try to justify their existence with long lists of the valuable services they provide, they usually skip lightly over one of the few really big ones. For example, Kent Anderson’s exhausting 60-element list omitted it, and it had to be pointed out in a comment by Carol Anne Meyer:

One to add: Enhanced content linking, including CrossREF DOI reference linking, author name linking cited-by linking, related content linking, updates and corrections linking.

(Anderson’s list sidles up to this issue in his #28, “XML generation and DTD migration” and #29, “Tagging”, but doesn’t come right out and say it.)

Although there are a few journals whose PDFs just contain references formatted as in the manuscript — as we did for our arXiv PDF — nearly all mainstream publishers go through a more elaborate process that yields more information and enables the linking that Meyer is talking about. (This is true of the new kids on the block as well as the legacy publishers.)

The reference-formatting pipeline

When I submit a manuscript with formatted reference like:

Taylor, M.P., Hone, D.W.E., Wedel, M.J. and Naish, D. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285(2):150–161. doi:10.1111/j.1469-7998.2011.00824.x

(as indeed I did in that arXiv paper), the publisher will take that reference and break it down into structured data describing the specific paper I was referring to. It does this for various reasons: among them, it needs to provide this information for services like the Web Of Knowledge.

Once it has this structured representation of the reference, the publication process plays it out in whatever format the journal prefers: for example, had our paper appeared in JVP, Taylor and Francis’s publication pipeline would have rendered it:

Taylor, M. P., D. W. E. Hone, M. J. Wedel, and D. Naish. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285:150–161.

(With spaces between multiple initials, initials preceding surnames for all authors except the first, an “Oxford comma” before the last author, no italics for the journal name, no bold for the volume number, the issue number omitted altogether, and the DOI inexplicably removed.)

What’s needed in a submitted reference

Here’s the key point: so long as all the relevant information is included in some format (authors, year, article title, journal title, volume, page-range), it makes no difference how it’s formatted. Because the publication process involves breaking the reference down into its component fields, thus losing all the formatting, before reassembling it in the preferred format.

And this leads us the key question: why do journals insist that authors format their references in journal style at all? All the work that authors do to achieve this is thrown away anyway, when the reference is broken down into fields, so why do it?

And the answer of course is “there is no good reason”. Which is why several journals, including PeerJ, eLifePLOS ONE and certain Elsevier journals have abandoned the requirement completely. (At the other end of the scale, JVP has been known to reject papers without review for such offences as using the wrong kind of dash in a page-range.)

Like so much of how we do things in scholarly publishing, requiring journal-style formatting at the submission stage is a relic of how things used to be done and makes no sense whatsoever in 2012. Before we had citation databases, the publication pipeline was much more straight-through, and the author’s references could be used “as is” in the final publication. Not any more.

How far can we go?

All of this leads me to wonder how far we can go in cutting down the author burden of referencing. Do we actually need to give all the author/title/etc. information for each reference?

In the case of references that have a DOI, I think not (though I’ve not yet discussed this with any publishers). I think that it suffices to give only the DOI. Because once you have a DOI, you can look up all the reference data. Go try it yourself: go to http://www.crossref.org/guestquery/ and paste my DOI “10.1111/j.1469-7998.2011.00824.x” into the DOI Query box at the bottom of the page. Select the “unixref” radio button and hit the Search button. Scroll down to the bottom of the results page, and voila! — an XML document containing everything you could wish to know about the referenced paper.

And the data in that structured document is of course what the publication process uses to render out the reference in the journal’s preferred style.

Am I missing something? Or is this really all we need?

I just saw this tweet from palaeohistologist Sarah Werning, and it summed up what science is all about so well that I wanted to give it wider and more permanent coverage:

This is exactly right. Kudos to Sarah for saying it so beautifully.

(Sarah’s work can most recently be seen in Nesbitt et al.’s (2012) paper on a newly recognised ancient dinosaur or near dinosaur relative, and especially in the high-resolution supplementary images that she deposited at MorphoBank.)


[backup image]

I think I figured out what the core, immutable quality of science is. It’s not formal publication, it’s not peer-review, it’s not “the scientific method” (whatever that means). It’s not replicability, it’s not properly citing sources, it’s not Popperian falsification. Underlying all those things is something more fundamental.

Humility.

We all know that it’s good to be able to admit when you’ve been wrong about something. We all like to see that quality in others. We all like to think that we possess it ourselves — although, needless to say, in our case it never comes up. And it’s that last part that’s the rub. It goes so, so strongly against the grain for us to admit the possibility of error in our own work.

If science was just a matter of increasing the sum of human knowledge, it would suffice for us all to note our thoughts in blogs and have done. But because we’re not humble by nature — because we need to have humility formally imposed on us — we need the scaffolding of all those other things I mentioned:

  • Formal publication is important so that there’s a permanent record of what we claimed to have found. We can’t weasel out of an earlier mistake by claiming never to have made it.
  • Peer-review helps to prevent us from making mistakes in those formal publications. (That applies to informal pre-submission reviews as well as gatekeeper reviews.)
  • Whatever the scientific method means in detail, it’s a way to keep hypothesis, experiment, result and conclusion separate, so other scientists can clearly see what has been done, what is fact and what is opinion.
  • Replicability is providing enough information to enable others to determine on their own whether we’ve made mistakes.
  • Properly citing sources allows others to check that our assumptions are well supported.
  • Popperian falsification helps prevent us from having too much faith in our own ideas, by leaving them for the community to test.

All these standard parts of how science is done are about helping us to spot our own mistakes, giving opportunity for others to spot them, and providing a means for them to be corrected. (Of course, they have other benefits, too: for example, citing sources is important as a way of giving credit.)

We may not be humble people; but doing science forces us to act humbly.

Counting beans

October 10, 2012

The reason most of my work is in the form of journal articles is that I didn’t know there were other ways to communicate. Now that I know that there are other and in some ways demonstrably better ways (arXiv, etc.), my enthusiasm for sending stuff to journals is flagging. Whereas before I was happy to do it and the tenure beans were a happy side-effect, now I can see that the tenure beans are in fact shackles preventing me from taking a better path.

Posting palaeo papers on arXiv

September 28, 2012

Over on Facebook, where Darren posted a note about our new paper, most of the discussion has not been about its content but about where it was published. We’re not too surprised by that, even though we’d love to be talking about the science. We did choose arXiv with our eyes open, knowing that there’s no tradition of palaeontology being published there, and wanting to start a new tradition of palaeontology being routinely published there. Having now made the step for the first time, I see no reason ever to not post a paper on arXiv, as soon as it’s ready, before — or maybe even instead of — submitting it to a journal.

(Instead of? Maybe. We’ll discuss that below.)

The key issue is this: science isn’t really science until it’s out there where it can be used. We wrote the bulk of the neck-anatomy paper back in 2008 — the year that we first submitted it to a journal. In the four years since then, all the observations and deductions that it contains have been unavailable to the world. And that is stupid. The work might just as well never have been done. Now that it’s on arXiv, that’s over. I was delighted to get an email less than 24 hours after the paper was published, from an author working on a related issue, thanking us for posting the paper, saying that he will now revise his own in-prep manucript in light of its findings, and cite our paper. Which of course is the whole point: to get our science out there where it can do some damage.

Because the alternative is horrible, really. Horribly wasteful, horribly dispiriting, horribly retarding for science. For example, a couple of weeks ago in his SVPCA talk, David Norman was lamenting again that he never got around to publishing the iguanodont systematic work that was in his dissertation, I-don’t-know-how-many-years-ago. The result of that interminable delay is that others have done other, conflicting iguanodont systematic work, and Norman is now trying belatedly to undo that and bring his own perspective. A terrible an unnecessary slowing of ornithopod science, and a waste of duplicated effort. (Thankfully it’s only ornithopods.)

And of course David Norman is very far from being alone. Pretty much any palaeontologist you talk to will tell you of a handful of papers — many more in some cases — that were finished many years previously but have never seen the light of day. (I still have a couple myself, but there is no point in resurrecting them now because progress has overtaken them.) I wonder what proportion of all Ph.D work ever sees the light of day? Half? Less? It’s crazy.

Figure 8. Sauropod cervical vertebrae showing anteriorly and posteriorly directed spurs projecting from neurapophyses. 1, cervical 5 of Sauroposeidon holotype OMNH 53062 in right lateral view, photograph by MJW. 2, cervical 9 of Mamenchisaurus hochuanensis holotype CCG V 20401 in left lateral view, reversed, from photograph by MPT. 3, cervical 7 or 8 of Omeisaurus junghsiensisYoung, 1939 holotype in right lateral view, after Young (1939, figure 2). (No specimen number was assigned to this material, which has since been lost. D. W. E. Hone personal communication, 2008.)

Publish now, publish later

So, please folks: we all need to be posting our work on preprint servers as soon as we consider it finished. It doesn’t mean that the posted versions can’t subsequently be obsoleted by improved versions that have gone through peer-review and been published in conventional journals. But it does mean that the world can know about the work, and build on it, and get the benefit of it, as soon as it’s done.

You see, we have a very fundamental problem in academia: publishing fulfils two completely separate roles. Its primary role (or at least the role that should be primary) is to make work available to the community; the secondary role is to provide a means of keeping score — something that can be used when making decisions about who to appoint to jobs, when to promote, who gets grants, who gets tenure and so on. I am not going to argue that the latter shouldn’t happen at all — clearly a functioning community needs some way to infer the standing of its participants. But I do think it’s ridiculous when the bean-counting function of publication trumps the actual publication role of publication. Yet we’ve all been in a position where we have essentially complete work that could easily go on a blog, or in the PalAss newsletter, or in a minor journal, or somewhere — but we hang onto it because we want to get it into a Big Journal.

Let me say again that I do realise how unusual and privileged my own position is: that a lot of my colleagues do need to play the Publication Prestige game for career reasons (though it terrifies my how much time some colleagues waste squeezing their papers into two-and-a-half-page format in the futile hope of rolling three sixes on the Science ‘n’ Nature 3D6). Let’s admit right now that most palaeontologists do need to try to get their work into Proc B, or Paleobiology, or what have you. Fair enough. They should feel free. But the crucial point is this: that is no reason not to post pre-prints so we can all get on with actually benefitting from your work in the mean time.

Actually, I feel pretty stupid that it’s taken me this long to realise that all my work should go up on arXiv.

Figure 11. Archosaur cervical vertebrae in posterior view, Showing muscle attachment points in phylogenetic context. Blue arrows indicate epaxial muscles attaching to neural spines, red arrows indicate epaxial muscles attaching to epipophyses, and green arrows indicate hypaxial muscles attaching to cervical ribs. While hypaxial musculature anchors consistently on the cervical ribs, the principle epaxial muscle migrate from the neural spine in crocodilians to the epipophyses in non-avial theropods and modern birds, with either or both sets of muscles being significant in sauropods. 1, fifth cervical vertebra of Alligator mississippiensis, MCZ 81457, traced from 3D scans by Leon Claessens, courtesy of MCZ. Epipophyses are absent. 2, eighth cervical vertebra ofGiraffatitan brancai paralectotype HMN SII, traced from Janensch (1950, figures 43 and 46). 3, eleventh cervical vertebra of Camarasaurus supremus, reconstruction within AMNH 5761/X, “cervical series I”, modified from Osborn and Mook (1921, plate LXVII). 4, fifth cervical vertebra of the abelisaurid theropod Majungasaurus crenatissimus,UA 8678, traced from O’Connor (2007, figures 8 and 20). 5, seventh cervical vertebra of a turkey, Meleagris gallopavo, traced from photographs by MPT.

Exceptions?

So are there any special cases? Any kinds of papers that we should keep dry until they make it into actual journals? I can think of two classes that you could argue for — one of them convincingly, the other not.

First, the unconvincing one. When I discussed this with Matt (and half the fun of doing that is that usually neither of us really knows what we think about this stuff until we’re done arguing it through), he suggested to me that we couldn’t have put the Brontomerus paper on arXiv, because that would have leaked the name, creating a nomen nudum. My initial reaction was to agree with him that this is an exception. But when I thought about it a bit more, I realised there’s actually no compelling reason not to post such a paper on arXiv. So you create a nomen nudum? So what? Really: what is the negative consequence of that? I can’t think of one. OK, the name will appear on Wikipedia and mailing lists before the ICZN recognises it — but who does that hurt? No-one that I can think of. The only real argument against posting is that it could invite scooping. But is that a real threat? I doubt it. I can’t think of anyone who would be barefaced enough to scoop a taxon that had already been published on arXiv — and if they did, the whole world would know unambiguously exactly what had happened.

So what is the one real reason not to post a preprint? I think that might be a legitimate choice when publicity needs to be co-ordinated. So while nomenclatural issues should not have stopped us from arXiving the Brontomerus paper, publicity should. In preparation for that paper’s publication day, we did a lot of careful work with the UCL publicity team: writing non-specialist summaries, press-releases and FAQs, soliciting and preparing illustrations and videos, circulating materials under embargo, and so on. In general, mainsteam media are only interested in a story if it’s news, and that means you need to make sure it’s new when they first hear about it. Posting the article in advance on a publicly accessible archive would mess that up, and probably damage the work’s coverage in the press, TV and radio.

Publication venues are a continuum

It’s become apparent to us only gradually that there’s really no clear cut-off where a paper becomes “properly published”. There’s a continuum that runs from least to most formal and exclusive:

SV-POW! — arXiv — PLOS ONE — JVP — Nature

1. On SV-POW!, we write what we want and publish it when we want. We can promise you that it won’t go away, but you only have our word for it. But some of what we write here is still science, and has been cited in papers published in more formal venues — though, as far as I know, only by Matt and me so far.

2. On arXiv, there is a bit more of a barrier to clear: you have to get an existing arXiv user to endorse your membership application, and each article you submit is given a cursory check by staff to ensure that it really is a piece of scientific research rather than a diary entry, movie review or spam. Once it’s posted, the paper is guaranteed to remain at the same URL, unchanged, so long as arXiv endures (and it’s supported by Cornell). Crucially, the maths, physics and computer science communities that use arXiv uncontroversially consider this degree of filtering and permanence sufficient to constitute a published, citeable source.

3. At PLOS ONE, your paper only gets published if it’s been through peer-review — but the reviewing criteria pertain only to scientific soundness and do not attempt to evaluate likely impact or importance.

4. At JVP and other conventional journals, your paper has to make it through a two-pronged peer-review process: it has to be judged both sound scientifically (as at PLOS ONE) and also sufficiently on-topic and important to merit appearing in the journal.

5. Finally, at Nature and Science, your paper has to be sound and be judged sexy — someone has to guess that it’s going to prove important and popular.

Where along this continuum does the formal scientific record begin? We could make a case that all of it counts, provided that measures are taken to make the SV-POW! posts permanent and immutable. (This can be done submitting them to WebCite or to a service such as Nature Precedings used to provide.) But whether or not you accept that, it seems clear that arXiv and upwards is permanent, scientific and citeable.

This raises an interesting question: do we actually need to go ahead and publish our neck-anatomy paper in a more conventional venue? I’m honestly not sure at the moment, and I’d be interested to hear arguments in either direction. In terms of the progress of science, probably not: our actual work is out there, now, for the world to use as it sees fit. But from a career perspective, it’s probably still worth our while to get it into a journal, just so it can sit more neatly on our publication lists and help Matt’s tenure case more. And yet I don’t honestly expect any eventual journal-published version to be better in any meaningful way than the one on arXiv. After all, it’s already benefitted from two rounds of peer-review, three if you count the comments of my dissertation examiners. More likely, a journal will be less useful, as we have to cut length, eliminate illustrations, and so on.

So it seems to me that we have a hard choice ahead of us now. Call that paper done and more onto making more science? Or spend more time and effort on re-publishing it in exchange for prestige? I really don’t know.

For what it’s worth, it seems that standard practice in maths, physics and computer science is to republish arXiv articles in journals. But there are some scientists who routinely do not do this, instead allowing the arXiv version to stand as the only version of record. Perhaps that is a route best left to tenured greybeards rather than bright young things like Matt.

Figure 5. Simplified myology of that sauropod neck, in left lateral view, based primarily on homology with birds, modified from Wedel and Sanders (2002, figure 2). Dashed arrows indicate muscle passing medially behind bone. A, B. Muscles inserting on the epipophyses, shown in red. C, D, E. Muscles inserting on the cervical ribs, shown in green. F, G. Muscles inserting on the neural spine, shown in blue. H. Muscles inserting on the ansa costotransversaria (“cervical rib loop”), shown in brown. Specifically: A. M. longus colli dorsalis. B. M. cervicalis ascendens. C. M. flexor colli lateralis. D. M. flexor colli medialis. E. M. longus colli ventralis. In birds, this muscle originates from the processes carotici, which are absent in the vertebrae of sauropods. F. Mm. intercristales. G. Mm. interspinales. H. Mm. intertransversarii. Vertebrae modified from Gilmore (1936, plate 24).

Citing papers in arXiv

Finally, a practicality: since it’ll likely be a year or more before any journal-published version of our neck-anatomy paper comes out, people wanting to use it in their own work will need to know how to cite a paper in arXiv. Standard procedure seems to be just to use authors, year, title and arXiv ID. But in a conventional-journal citation, I like the way that the page-range gives you a sense of how long the paper is. So I think it’s worth appending page-count to the citations. And while you’re at it, you may as well throw in the figure and table counts, too, yielding the version that we’ve been using:

  • Taylor, Michael P., and Mathew J. Wedel. 2012. Why sauropods had long necks; and why giraffes have short necks. arXiv:1209.5439. 39 pages, 11 figures, 3 tables.
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