March 15, 2013
Today sees the publication of my big paper with Mike on neural spine bifurcation, which has been in the works since last April. It’s a free download here, and as usual we put the hi-res figures and other supporting info on a sidebar page.
Navel-gazing about the publication process
This paper is a departure for us, for several reasons.
For one thing, it’s a beast: a little over 13,000 words, not counting tables, figure captions, and the bibliography. I was all geared up to talk about how it’s my longest paper after the second Sauroposeidon paper (Wedel et al. 2000), but that’s not true. It’s my longest paper, period (13192 vs 12526 words), and the one with the most figures (25 vs 22).
It’s the first time we’ve written the paper in the open, on the blog, and then repackaged it for submission to a journal. I have several things to say about that. First, it was more work than I expected. It turns out that I definitely do have at least two “voices” as a writer, and the informal voice I used for the initial run of blog posts (linked here) was not going to cut it for formal publication. So although there is very little new material in the paper that was not in the blog posts, a lot of the prose is new because I had to rewrite almost the whole thing.
I have mixed feelings about this. On one hand, last May kinda sucked, because just about every minute that wasn’t spent eclipse chasing was spent rewriting the paper. On the other hand, as Mike has repeatedly pointed out to me, it was a pretty fast way to generate a big paper quickly, even with the rewriting. It was just over two months from the first post in the destined-to-become-a-paper series on April 5, to submission on June 14 (not June 24 as it says on the last page of the PDF), and if you leave out the 10 days in late May that I was galavanting around Arizona, the actual time spent working on the paper was a bit under two months. It would be nice to be that productive all the time (it helped that we were basically mining everything from previously published work; truly novel work usually needs more time to get up and going).
You may fairly wonder why, if almost all the content was already available on the blog, we went to the trouble of publishing it in a journal. Especially in light of sentiments like this. For my part, it’s down to two things. First, to paraphrase C.S. Lewis, what I wrote in that post was a yell, not a thought. I never intended to stop publishing in journals, I was just frustrated that traditional journals do so many stupid things that actually hurt science, like rejecting papers because of anticipated sexiness or for other BS reasons, not publishing peer reviews, etc. Happily, now there are better options.
Second, although in a sane world the quality of an argument or hypothesis would matter more than its mode of distribution, that’s not the world we live in. We’re happy enough to cite blog posts, etc. (they’re better than pers. comms., at least), but not everyone is, and the minimum bound of What Counts is controlled by people at the other end of the Overton window. So, bottom line, people are at least theoretically free to ignore stuff that is only published on blogs or other informal venues (DML, forums, etc.). If you want to force someone to engage with your ideas, you have to publish them in journals (for now). So we did.
Finally, ever since Darren’s azhdarchids-were-storks post got turned into a paper, it has bothered me that there is an icon for “Blogging on Peer-Reviewed Research” (from ResearchBlogging.org), but not one (that I know of) for “Blogging Into Peer-Reviewed Research”. If you have some graphic design chops and 10 minutes to kill, you could do the world a favor by creating one.
Hey, you! Want a project?
One of the few things in the paper that is not in any of the blog posts is the table summarizing the skeletal fusions in a bunch of famous sauropod specimens, to show how little consistency there is:
(Yes, we know that table legends typically go above, not below; this is just how they roll at PJVP.)
I want this to not get overlooked just because it’s in a long paper on neural spine bifurcation; as far as I’m concerned, it’s the most important part of the paper. I didn’t know that these potential ontogenetic indicators were all mutually contradictory across taxa before I started this project. Not only is the order of skeletal fusions inconsistent among taxa, but it might also be inconsistent among individuals or populations, or at least that’s what the variation among the different specimens of Apatosaurus suggests.
This problem cries out for more attention. As we say at the end of the paper:
To some extent the field of sauropod paleobiology suffers from ‘monograph tunnel vision’, in which our knowledge of most taxa is derived from a handful of specimens described decades ago (e.g. Diplodocus carnegii CM 84/94). Recent work by McIntosh (2005), Upchurch et al. (2005), and Harris (2006a, b, c, 2007) is a welcome antidote to this malady, but several of the taxa discussed herein are represented by many more specimens that have not been adequately described or assessed. A comprehensive program to document skeletal fusions and body size in all known specimens of, say, Camarasaurus, or Diplodocus, could be undertaken for relatively little cost (other than travel expenses, and even these could be offset through collaboration) and would add immeasurably to our knowledge of sauropod ontogeny.
So if you’re looking for a project on sauropod paleobiology and you can get around to a bunch of museums*, here’s work that needs doing. Also, you’ll probably make lots of other publishable observations along the way.
* The more the better, but for Morrison taxa I would say minimally: Yale, AMNH, Carnegie, Cleveland Museum of Natural History, Field Museum, Dinosaur National Monument, BYU, University of Utah, and University of Wyoming, plus Smithsonian, University of Kansas, OMNH, Denver Museum, Wyoming Dinosaur Center, and a few others if you can swing it. Oh, and Diplodocus hayi down in Houston. Check John Foster’s and Jack McIntosh’s publications for lists of specimens–there are a LOT more out there than most people are familiar with.
- Wedel, M.J., R.L. Cifelli and R.K. Sanders. 2000. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4): 343-388.
- Wedel, M.J., and Taylor, M.P. 2013. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. Palarch’s Journal of Vertebrate Palaeontology 10(1): 1-34.
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.
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.
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.
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.
September 26, 2012
Today sees the publication, on arXiv (more on that choice in a separate post), of Mike and Matt’s new paper on sauropod neck anatomy. In this paper, we try to figure out why it is that sauropods evolved necks six times longer than that of the world-record giraffe — as shown in Figure 3 from the paper (with a small version of Figure 1 included as a cameo to the same scale):
This paper started life as a late-night discussion over a couple of beers, while Matt was over in England for SVPCA back in (I think) 2008. It was originally going to be a short note in PaleoBios, just noting some of the oddities of sauropod cervical architecture — such as the way that cervical ribs, ventral to the centra, elongate posteriorly but their dorsal counterparts the epipophyses do not.
As so often, the tale grew in the telling, so that a paper we’d initially imagined as a two-or-three-page note became Chapter 5 of my dissertation under the sober title of “Vertebral morphology and the evolution of long necks in sauropod dinosaurs”, weighing in at 41 1.5-spaced pages. By now the manuscript had metastatised into a comparison between the necks of sauropods and other animals and an analysis of the factors that enabled sauropods to achieve so much more than mammals, birds, other theropods and pterosaurs.
(At this point we had one of our less satisfactory reviewing experiences. We sent the manuscript to a respected journal, where it wasn’t even sent out to reviewers until more than a month had passed. We then had to repeatedly prod the editor before anything else happened. Eventually, two reviews came back: one of them careful and detailed; but the other, which we’d waited five months for, dismissed our 53-page manuscript in 108 words. So two words per page, or about 2/3 of a word per day of review time. But let’s not dwell on that.)
This work made its next appearance as my talk at SVPCA 2010 in Cambridge, under the title Why giraffes have such short necks. For the talk, I radically restructured the material into a form that had a stronger narrative – a process that involved a lot of back and forth with Matt, dry-running the talk, and workshopping the order in which ideas were presented. The talk seemed to go down well, and we liked the new structure so much more than the old that we reworked the manuscript into a form that more closely resembled the talk.
That’s the version of the manuscript that we perfected in New York when we should have been at all-you-can-eat sushi places. It’s the version that we submitted on the train from New York to New Haven as we went to visit the collections of the Yale Peabody Museum. And it’s the version that was cursorily rejected from mid-to-low ranked palaeo journal because a reviewer said “The manuscript reads as a long “story” instead of a scientific manuscript” — which was of course precisely what we’d intended.
Needless to say, it was deeply disheartening to have had what we were convinced was a good paper rejected twice from journals, at a cost of three years’ delay, on the basis of these reviews. One option would have been to put the manuscript back into the conventional “scientific paper” straitjacket for the second journal’s benefit. But no. We were not going to invest more work to make the paper less good. We decided to keep it in its current, more readable, form and to find a journal that likes it on that basis.
At the moment, the plan is to send it to PeerJ when that opens to submissions. (Both Matt and I are already members.) But that three-years-and-rolling delay really rankles, and we both felt that it wasn’t serving science to keep the paper locked up until it finally makes it into a journal — hence the deposition in arXiv which we plan to talk about more next time.
In the paper, we review seven characteristics of sauropod anatomy that facilitated the evolution of long necks: absolutely large body size; quadrupedal stance; proportionally small, light head; large number of cervical vertebrae; elongation of cervical vertebrae; air-sac system; and vertebral pneumaticity. And we show that giraffes have only two of these seven features. (Ostriches do the next best, with five, but they are defeated by their feeble absolute size.)
The paper incorporates some material from SV-POW! posts, including Sauropods were corn-on-the-cob, not shish kebabs. In fact, come to think of it, we should have cited that post as a source. Oh well. We do cite one SV-POW! post: Darren’s Invading the postzyg, which at the time of writing is the only published-in-any-sense source for pneumaticity invading cervical postzygapogyses from the medial surface.
As for the non-extended epipophyses that kicked the whole project off: we did illustrate how they could look, and discussed why they would seem to make mechanical sense:
But we found and explained some good reasons why this apparently appealing arrangement would not work. You’ll need to read the paper for details.
Sadly, we were not able to include this slide from the talk illustrating the consequences:
Anyway, go and read the paper! It’s freely available, of course, like all arXiv depositions, and in particular uses the permissive Creative Commons Attribution (CC BY) licence. We have assembled related information over on this page, including full-resolution versions of all the figures.
In the fields of maths, physics and computer science, where deposition in arXiv is ubiquitous, standard practice is to go right ahead and cite works in arXiv as soon as they’re available, rather than waiting for them to appear in journals. We will be happy for the same to happen with our paper: if it contains information that’s of value to you, then feel free to cite the arXiv version.
April 17, 2012
Item 1: With his new piece at the Guardian, “Persistent myths about open access scientific publishing”, Mike continues to be a thorn in the side of exploitative commercial publishers, who just can’t seem to keep their facts straight. This time Mike unravels some choice bits of nonsense that keep getting circulated about open access publishing: that OA publishing must necessarily cost as much as barrier-based publishing, that the peer review process is expensive for publishers, and that authors who can’t pay OA publication fees will be left out in the cold. It’s cleanly and compellingly argued–go read for yourself.
Item 2: The Yates et al. prosauropod pneumaticity paper is officially published in the latest issue of Acta Palaeontologica Polonica, and I have updated the citation and links accordingly. This may not seem like big news, in that the accepted manuscript has been available online for 13 months, and the final published version does not differ materially from that version other than being pretty. But it’s an opportunity to talk about something that we haven’t really addressed here before, which is the potential for prompt publication to accelerate research.
A bit of background: standard practice at APP is to post accepted manuscripts as soon as they’re, well, accepted, unless the authors ask otherwise (for example, because the paper contains taxonomic acts and the first public version needs to be the version of record). Not everyone likes this policy–I know Darren objects, and I’m sure there are others. The chief complaint is that it muddies the waters around when the paper is published. Is a paper published when a manuscript is posted to a preprint server like arXiv, or when the accepted manuscript is made freely available by a journal, or when the official, formatted version is published online, or when it arrives in printed hardcopy?
Now, this is an interesting question to ponder, but I think it’s only interesting from the standpoint of rules (e.g., codes governing nomenclature) and how we’re going to decide what counts. From the standpoint of moving science forward, the paper is published as soon as it is available for other researchers to use openly–i.e., not just to use in private in their own research, but also to cite. And since that’s the axis I care most about, I prefer to see accepted manuscripts made widely available as soon as possible, and I support APP’s policy. In the case of Yates et al. (2012), having the accepted manuscript online for the past year meant that it was available for Butler et al. (2012) to use, and cite, in their broad reassessment of pneumaticity in Triassic archosaurs. If our manuscript has not been published, that might not have been the case; Adam gave a talk on our project at the 2009 SVP in Bristol, but Butler et al. might have been loathe to cite an abstract, and some journals explicitly forbid it.
So I say bring it on. Let’s really accelerate research, by letting people see the content as early as possible. Making other researchers wait just so they can see a prettier version of the same information seems to me to be a triumph of style over science.
- Butler, R.J., Barrett, P.M., and Gower, D.J. 2012. Reassessment of the evidence for postcranial skeletal pneumaticity in Triassic archosaurs, and the early evolution of the avian respiratory system. PLoS ONE 7(3): e34094. doi:10.1371/journal.pone.0034094
- Yates, A.M., Wedel, M.J., and Bonnan, M.F. 2012. The early evolution of postcranial skeletal pneumaticity in sauropodomorph dinosaurs. Acta Palaeontologica Polonica 57(1):85-100. doi: http://dx.doi.org/10.4202/app.2010.0075
April 2, 2012
The story so far …
Nature Precedings is, or was, a preprint server, somewhat in the spirit of an arXiv for biology. It describes, or described, itself as “a permanent, citable archive for pre-publication research and preliminary findings”.
This is a very useful thing. In our recentish paper on how sauropod necks were not sexually selected (Taylor et al. 2011), we wanted to mention in passing (as part of a much more involved argument about sauropod feeding ecology) that the DinoMorph results should not be taken as face value because “assumptions about the mobility of intervertebral joints are probably incorrect”. The obvious thing to cite for this is an old SV-POW! post (Taylor 2009) and so we did. (It’s gratifying to see an SV-POW! post sitting cheerfully in the bibliography of a conventionally published paper. There have been a few of these now.)
But what happens if SV-POW! goes away? What if Matt, Darren and I are all simultaneously run over by buses, and WordPress cancel the blog after a period of inactivity? For that matter, what if WordPress goes bust and shuts down its servers, or starts charging for hosting so that we decided to go elsewhere? Anyone trying to follow the reference in our necks-for-sex paper would by stymied. It seemed to me that the professional thing to do was to post a copy somewhere more permanent.
The answer is, or was, Nature Precedings. So a couple of months ago I made up an PDF containing the same text and images as the blog post, and submitted it to Precedings, where it can be found now (Taylor 2012). Matt and I were talking about doing the same for all the SV-POW! posts we know of that have been cited in formal literature, and perhaps getting into the habit of repositing PDFs of all such articles whenever we want to cite them, and then citing the Precedings version instead.
Not so fast!
I got an email three days ago from Precedings:
Subject: Nature Precedings change in service
As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.
Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.
Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community. Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication. While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.
Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area. We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.
Nature Publishing Group
Well, let’s pick this apart.
- “Change in service” means “end of service”. A really pointless and insulting euphemism. Come on, NPG, give it to us straight! We can take it!
- We have a promise that “the archive will be maintained by NPG, while all hosted content will remain freely accessible to all”.
- The reason given for shutting down is that “technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived”. I can’t start to understand what, if anything, that means.
- What to make of “we plan to introduce new services in this area”? What kind of new service can there be in this area that isn’t a preprint server?
Now I don’t want to be too harsh here, just because NPG have withdrawn a service that was free in the first place. They were under no obligation to keep providing it, of course. And the most important thing is that the papers already reposited there will live on.
But it’s just sad that this is going away. We need it, or something like it.
The number one question is, will the archived documents really stay around? I want to trust that they will, but it’s harder to keep trusting a no-longer-live system than one that has blood circulating. It would be ironic indeed if the original SV-POW! post turns out to be more durable than the Precedings version!
But going forward, the question is where to reposit future citation-worthy SV-POW! posts? What are the alternative services to Precedings?
It’s at times like these that we biologists suffer from Physics envy. They have arXiv, which does this right and has been doing it right since forever. We really need an arXiv for biology. Or better still, we need arXiv to expand to cover our field.
Taylor, Michael P. 2009. Range of motion in intervertebral joints: why we don’t trust DinoMorph. Sauropod Vertebra Picture of the Week, 30 May 2009. Available at http://svpow.wordpress.com/2009/05/30/range-of-motion-in-intervertebral-joints-why-we-dont-trust-dinomorph/
Taylor, Michael P., David W. E. Hone, Mathew J. Wedel and Darren Naish. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285:150-161. doi:10.1111/j.1469-7998.2011.00824.x
December 14, 2011
This year, I missed The Paleo Paper Challenge over on Archosaur Musings — it was one of hundreds of blog posts I missed while I was in Cancun with my day-job and then in Bonn for the 2nd International Workshop on Sauropod Biology and Gigantism. That means I missed out on my annual tradition of promising to get the looong-overdue Archbishop description done by the end of the year.
But this year, Matt and I are going to have our own private Palaeo Paper Challenge. And to make sure we heap on maximum pressure to get the work done, we’re announcing it here.
Here’s the deal. We have two manuscripts — one of them Taylor and Wedel, the other Wedel and Taylor — which have been sitting in limbo for a stupidly long time. Both are complete, and have in fact been submitted once and gone through review. We just need to get them sorted out, turned around, and resubmitted.
(The Taylor and Wedel one is on the anatomy of sauropod cervicals and the evolution of their long necks. It’s based on the last remaining unpublished chapter of my dissertation, and turned up in a modified form as my SVPCA 2010 talk, Why Giraffes Have Such Short Necks. The Wedel and Taylor one is on the occurrence and implications of intermittent pneumaticity in the tails of sauropods, and turned up as his SVPCA 2010 talk, Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.)
We’re going to be realistic: we both have far too much going in (incuding, you know, families) to get these done by the end of 2011. But we have relatively clear Januaries, so our commitment is that we will submit by the end of January 2012. If either of us fails, you all have permission to be ruthlessly derisive of that person.
… and in other news …
Some time while we were all in Bonn, the SV-POW! hit-counter rolled over the One Million mark. Thanks to all of your for reading!
October 31, 2011
Back when Darren and I did the Xenoposeidon description, we were young and foolish, and only illustrated the holotype vertebra NHM R2095 in four aspects: left and right lateral,anterior and posterior. No dorsal or ventral views.
Also, because the figure was intended for Palaeontology, which prints only in greyscale, I stupidly prepared the figure in greyscale, rather than preparing it in colour and then flattening it down at the last moment. (Happily I’d learned that lesson by the time we did our neck-posture paper: although it was destined for Acta Palaeontologia Polonica, which also prints in greyscale, and though the PDF uses greyscale figures, the online full-resolution figures are in colour.)
As if that wasn’t dumb enough, I also composited the four featured views such that the two lateral views were adjacent, and above the anterior and posterior views — so it wasn’t easy to match up features on the sides and front/back between the views. Since then, I have landed on a better way of presenting multi-view figures, as in my much-admire’d turkey cervical and pig skull images.
So, putting it all together, here is how we should have illustrated illustrated Xenoposeidon back in 2007 (click through for high resolution):
(Top row: dorsal view, with anterior facing left; middle row, from left to right: anterior, left lateral, posterior, right lateral; bottom row, ventral view, with anterior facing left. As always with images of NHM-owned material, this is copyright the NHM.)
Of course, if we’d published in PLoS ONE, then this high-resolution (4775 x 4095), full colour image could have been the published one rather than an afterthought on a blog somewhere. But we didn’t: back then, we weren’t so aware of the opportunities available to us now that we live in the Shiny Digital Future.
In other news, the boys and I all registered Xbox Live accounts a few days ago. I chose the name “Xenoposeidon”, only to find to my amazement that someone else had already registered it. But “Brontomerus” was free, so I used that instead.
September 23, 2011
With our baby’s appearance in National Geographic this week, she’s now been in four mainstream magazines:
That’s National Geographic at top left, Macleans next to it; The Scientist at bottom left, and National Geographic Kids next to that. (The articles in the first three of these are available online here, here and here, but I can’t find anything on the NG Kids web-site.)
There is a point to this post, beyond
gloating celebrating Brontomerus: it’s that diligent preparation improves a study’s chance of getting good coverage. A few people have asked us to write a bit about what we did, so at the risk of sounding self-congratulatory, here it is.
Most of Brontomerus‘s visibility is due to the hard work of the UCL Publicity team, and especially the excellent and widely-reproduced video that they made in the Grant Museum. But we made it easy for UCL to take an interest by preparing a bunch of materials ahead of time, before they even knew that there was a paper coming out. We called it the Brontomerus press pack, and made sure it contained everything anyone could need for writing and illustrating stories about our animal:
- The basic story
- Background on what a sauropod is
- Two variations of a life restoration
- A video of a rotating 3d model of the animal
- A photo of all the bones; detailed photo of the important ilium
- A skeletal reconstruction
- A photo of the three co-authors with the material
- Explicit credits, copyrights and permissions for the images and video
- Link to the proof PDF of the paper itself
- A fact sheet, noting common errors to avoid
In short, we tried to give journalists, and radio and TV researchers, everything they needed to put together a story aimed at their own audience. More than that — we tried to make it easy for them. They have plenty going on, after all: Brontomerus came out on the day that the Libyan protests really took off, so it’s not as though news editors were short of material to fill their slots. I suspect that if we’d not got all the ducks in such a neat row, Brontomerus would have disappeared from the news schedule in double-quick time.
Another important thing you can do to make news editors’ jobs easier: make sure that the images you provide are in high resolution, so they don’t pixellate when they’re blown up to fill a screen; and be explicit about image/video credit, copyright and permissions. Let them know what they can use and under what conditions. If you make them hunt for that information, or even chase you for it, they’ll probably lose interest and do a different piece instead. And we really wanted the artist who’d done the Brontomerus work to be credited: Paco Gasco did a fantastic job, and deserved to be known for it.
Equally important, by getting as much material as possible ready before even contacting the university publicity people, we made their job easier. Once they were on board, we were able to extend the page with extras like an official press release and the video, but the framework was all in place ahead of time.
In short, there is a whole load that you can do to prepare a study for media coverage. Not much of it is rocket-science. It’s basically just about getting the work done. And it is work, plenty of it.
Still. It’s worth it.
And another thing …
You should all get across to Heinrich Mallison’s new blog and check it out. Lots of excellent palaeo-photography, even if today’s post is about a stinkin’ mammal.
Addendum (from Matt)
First, some credit where it’s due. We didn’t figure all of this out on our own. For Brontomerus in particular, we took a lot of cues from the fact sheet that Irmis et al. put together for their 2007 “rise of dinosaurs” paper that made the cover of Science.
Second, we did figure some of it out on our own, but not all at once. If you look at Mike’s unofficial online press packs for Xenoposeidon (2007), our neck posture paper (2009), and Brontomerus (2011), you’ll see that each one is better than the one before.
Finally, you may be saying to yourself, “Okay, I understand that I’m supposed to make things easy for journalists and have a bunch of stuff queued up for them. But where do I put it?”
Well, online, obviously. If you don’t already have a blog, WordPress and Blogger and probably a zillion other services give them out for free, and you can make an ad hoc, one-shot blog for every press-release-worthy paper, as Mark Witton and Darren did for their azhdarchid paleobiology paper in PLoS ONE.
But let me wax preachy for a minute. If you’re a young researcher and you’re trying to make an impact, why aren’t you blogging? It’s not an intolerable commitment. Sure, regular posting brings more readers, but irregular posting brings more readers than not having a blog at all.
We started SV-POW! as a joke, and continued it during the actually-posting-weekly-about-sauropod-vertebrae phase (which lasted for 2.5 years) because it was fun and challenging, and maintain it now because it’s fun, we enjoy the wacky discussions that get going from time to time in the comments, and, frankly, we’re addicted to having a soapbox where we can say pretty much whatever we want. We didn’t explicitly plan it as a way to funnel readers to our scientific work, but that has been one of its great exaptive benefits. I’d be shocked if the same isn’t true for other researchers who blog.
So, moral of the story: if you’re a researcher and you’re not blogging, you’re missing out. Your work is reaching fewer people than it might. Come out and play. Join the conversation. Interact. Your future self will thank you.
July 6, 2011
Matt recently told us how to get ideas for papers, but if you’ve not previously published, you may be wondering how you get from idea to actual manuscript. I’ve written about twenty palaeontology papers now, not counting trivial ones like encyclopaedia entries and corrections (plus a few in computer science). So while there are plenty of people out there with much bigger CVs than mine, I’ve accumulated enough different experiences over the last six or seven years that hopefully I can shed a bit of light on the process. DISCLAIMER: this means I am going to be citing myself like crazy, and will look like a complete egomaniac. That really is not the point of this exercise.
Before I plough in, a digression: you may legitimately wonder why, if I’ve written 20 papers, my publications page lists only fourteen. A couple are in press but not yet out: my work on those is done, I just have to wait for the wheels to grind exceeding fine. A few more are in review. Others, though once completed, are now in the process of being revised, either in response to reviewers’ comments or because they were rejected outright and need retooling for submission to another journal. Maybe the most interesting category, though, is that I have two or three papers that I think are dead: they’ve been submitted and rejected, and I think I will probably never resubmit them. In two cases — dinosaur diversity surveys — the manuscripts have aged badly, because the rapid rate of new dinosaurs being named is rendering them more and more obsolete. To bring these up to publishable standard again would involve rebuilding the database and redoing the stats, and I just can’t summon up enthusiasm for that work when I have other projects going on that are so much more fun.
Anyway, we’re not here to talk about how to abandon finished manuscripts — we’re here to talk about how to get them finished in the first place.
In my projects, I have used three broad approaches. Let’s look at them in turn.
Approach 1. Gather notes first
If you take this approach, you’ll begin by gathering all your thoughts on the subject of the manuscript-to-be into one place — these days, most likely a single file or folder on your computer, but in the old days it might well have been a physical notebook. Don’t think about the structure of the manuscript, or about narrative flow, at this stage. Don’t worry about what to include and what to exclude: just gather everything you can, pour it into a pot, and stir it. You can think about the other stuff later.
The idea here is to separate “left-brain” and “right-brain” activity, so you can concentrate on one of them at a time. During the gathering phase, you’re being creative, an artist playing with ideas. When you’re done, you switch into engineer mode, and your task becomes to synthesise some or all those ideas into a coherent argument. It’s easier to think about one of these things at a time than both at once, so the theory goes.
Handy household hint: you don’t have to put all your ideas into a single paper. Find a set of thoughts that fit together into a narrative, and build the paper around that. The other ideas will find homes in subsequent papers, they’re not lost.
The right-brain-then-left-brain approach sounds good; but in practice, I’ve found this doesn’t work well for me. In fact, looking back over my submissions, it looks like I’ve only done it twice, and both times it’s resulted in a huge amount of work. Those two papers are the Taylor et al. (2009) paper on habitual sauropod neck posture and Taylor et al. (2011) on sexual selection of sauropod necks. These were three- and four-way collaborations between myself, Matt, Darren, and for the latter David Hone. And for such short papers (eight and twelve pages respectively) they took an amazingly long time to put together. They went through long sequence of revisions and rewrites before reaching their final forms, and lead authorship swapped hands many times along the way — we all held it at one time or another on both papers.
So what was the problem? Only this: that “synthesise all those ideas into a coherent argument” sounds like a straightforward mechanical process, but it’s not. It’s an art in itself — it requires taste, judgement, and most of all a lot of hard work. (And of course, this is especially true when working with the team, when everyone has different ideas.) When you start the composition process using a big ol’ bucket full of observations, it’s hard to tie them all together in a sequence that makes sense; and sure enough, we didn’t. Early “complete” drafts of the neck-posture paper contained all the same information as the published version, but they were incoherent and repetitive. One moment you’d be reading about some assertion that Stevens and Parrish had made about ONP being habitual, then next you’d be reading something about semi-circular canal orientation, then it would be be some observation on extant animal behaviour, then it would be back to DinoMorph, and so on. Reading it felt like being batted around inside a pinball machine.
We probably could have submitted it in that form, and found a venue for it. But we didn’t, because we wanted our paper not just to contain a bunch of relevant facts, but to lay our an argument, a connected sequence of observations and deductions, that would tell a story, make a compelling case. We wanted our paper to convince. And doing that is an art — hence the many, many, revisions and rewrites. We got there in the end, and all three of us are happy with how the paper came out, but it was a real hack to get there, and it left me wondering whether we’d gone about it the wrong way.
On the other hand, what other way is there to write a genuinely three- or four-cornered collaborative paper? Most of the other collaborative papers I’ve been involved with have had a very clear lead author who contributed the bulk of the prose, with the remaining authors contributing specific passages of text – and of course other input, just as important, such as the discussions that gave rise to the project in the first place. The genesis of the neck-posture project was that we each contributed a stack of notes — some about what has previously been written on the subject, some about the flaws in those assertions, some about the behaviour of extant animals — and I just don’t see a significantly better way of melding all those into a coherent narrative than the multiple-pass approach that we adopted.
So anyway, what I’ve mostly done instead is:
Approach 2. Just write a manuscript
There is something enormously empowering about firing up OpenOffice (or MS-Word, if you must), choosing File -> New, looking at that brand new white page, and typing a title. Once you’ve done that, you’re up and running. You’re really doing it. It gets much harder to procrastinate. Even if you end up changing that title half a dozen times, and rejigging the order of the manuscript, and rewriting the conclusions, and retaking the photos and doing the figures again, and reworking the statistical analysis because new data has come in, none of that changes the fact that once you’ve started a manuscript, you’ve started. It doesn’t matter if it gets three new heads and five new shafts along the way, it’s still the axe the George Washington used to chop down the cherry tree.
So with this approach, the idea is that after accumulating information and internalising it, you just sit down and start writing — telling the story in an order that makes sense and draws the reader in. The liberating thing is not trying to use any of the actual wording of your notes, not feeling obliged to work them all into the manuscript, just writing.
A technique that people often recommend at this stage — and one that in theory at least I endorse — is not to bother with your citations and references at this stage, or even with boring typographical details like italicising your genus and species names. You don’t want to let yourself get sucked into any of that detailed clerical work — it will break the flow of your thoughts, and prevent you from getting them all down in a sequence that makes sense. You want to be writing in the same spirit that you would explain the ideas to an intelligent friend in a pub, after maybe the second pint, waving your hands wildly to get you through the difficult bits, but not worrying about that because the point is to get your idea across — or rather, your sequence of ideas, that gets the listener from A to B. You can go back in fill in the references later.
Like I said, in theory I endorse this technique. In practice, I don’t seem to be able to do it: when I start to write, the citations just thrust themselves into my mind and I’m not able to write a perfectly simple sentence like “the humeri of brachiosaurids are the longest known in any sauropods, exceeding 2 m in length” without shoving in a “(Janensch 1961)”, and nine times out of ten going and re-checking that paper so I can specifically cite the table on page 187. Whether this is a good or a bad thing, I couldn’t say — maybe if I could discipline myself not to do this, I’d save myself the pain later in the writing process of having to shuffle the text to get it into an order that tells the right story.
A digression on story-telling
I’ve used the metaphor of story-telling a couple of times, and I think it’s absolutely central here. You want to draw your reader through the paper.
Of course, what we mean by “story” is very different from one paper to another. For example, in my short paper surveying dinosaur diversity (Taylor 2006), the story could hardly have been different from how it turns out: here’s where the data was from, here’s what I did with it, here are the results, and then end with some discussion. By contrast, there were lots of different ways I could have structured my plea to the ICZN to recognise electronic publication (Taylor 2009b), but I went for an approach where the section headings outlined the core argument even if you didn’t read the actual text: 1. Background: the availability of the name Darwinius masillae; 2. The Code is in danger of becoming an irrelevance; 3. Paper journals are going away; 4. The time to act is now; 5. Electronic documents are different from electronic media; 6. We must come to terms with the ubiquity of PDF; 7. The current rules are too hard to get right (and finally a Conclusion).
For a fairly hardcore descriptive paper like the Xenoposeidon description (Taylor and Naish 2007, natch), you’re more limited in how much of a story you can tell, and pretty much constrained by the usual Introduction, Systematic Palaeontology, Description, Systematics, Discussion structure. But even there, we laid out what I think is a fairly compelling story by splitting the “description” section into two parts: one that was purely descriptive, and a subsequent one containing all the comparisons. Only after those two sections did we progress to the phylogenetic analysis that weakly corroborated our inferences.
For my Brachiosaurus/Giraffatitan paper (Taylor 2009a), though, I subverted the usual structure by postponing the Systematic Palaeontology until after I’d done all the necessary descriptive work to support the generic separation, rather than presenting the systematic conclusion up front and then going back and justifying it. I also gave that paper a very, very short introduction (116 words incuding citations and taxonomic authorities), pushing the rest of what would normally be considered introductory material back into a separate Historical Background section. Why? Because that way I could put the end-of-introduction subsections on Anatomical Nomenclature, Anatomical Abbreviations and Institutional Abbreviations up front on the first page where they belong, rather than buried on the sixth page as they would otherwise have been.
Well, it seems that I have have drifted a bit from what I intended to talk about, and got onto the subject of how to structure a paper; but since that’s sort of relevant, I won’t let it spoil my day.
Anyway, the two approaches I’ve discussed so far really bracket the range of ways to put a manuscript together, and most projects will fall somewhere on the continuum between them. But every now and then an opportunity comes up to use a third way:
Approach 3. Convert from another medium
I already mentioned my paper on electronic publication (Taylor 2009b), but long-time SV-POW! readers will remember that much of the material in this paper was cannibalised from a sequence of SV-POW! posts (notably Non-Open Academic Publishing Is Dead) as well as a few comments that I’d left on relevant posts on other people’s blogs. On paper, you’d say this is a lot like approach 1, in that while I had much of material to hand, it needed sorting, integrating and rewriting. In fact, it went much more smoothly than the neck-posture paper’s editing process, perhaps because all the the source material was my own rather than having come from several different authors; and perhaps because the posts and comments were already in a chronological order which reflected the way my thoughts had arrived at the position where they eventually landed.
But a more interesting example of this route is the survey of the history of sauropod studies (Taylor 2010). This started life as a slideshow, the accompaniment for my talk the the conference Dinosaurs: A Historical Perspective. (Yes, the very same talk which Fiona fell asleep in, when I rehearsed it on her.) To put together a talk, you already have to have your story together — the sequence in which things happen, the sections that you chop it all up into, the references forward to things you’re going to say, and back to things you’ve said. So transcribing that all down into a manuscript is surprisingly straightforward — at least, it was for me, for this project. It really was, almost literally, as case of taking each slide in turn, writing a little essay about what it depicted, and moving on.
So I kind of recommend that. In fact, I’d go further: do not ever give a conference talk without immediately transcribing your slides into a manuscript. If you do, you’re throwing away a super-easy publication: you’ve already done all the hard work.
(I didn’t know I was going to say that, just as I didn’t know I was going to digress onto story-telling earlier. Turns out that this is an essay in the literal French sense of “an attempt”, something that you only figure out as you’re writing it. Now that I’ve said you should always turn your slideshows into papers, I find myself wondering whether I’ve taken my own advice … Hmm, quick check of the old publications list and I see that, hmm, I have roughly three sets of unconverted slides. So that gives me something to do in the evenings, then.)
I only have two things to say about this, and they have both been said better by other people (computer scientists, as it happens):
Say what you mean, simply and directly.
– Brian W. Kernighan and P. J. Plauger
Present to inform, not to impress; if you inform, you will impress.
– Frederick P. Brooks
In short, do not write “the taxon under consideration exhibits a tendency towards velocitous aerial locomotion” when you could write “it flies fast”.
A final thought
All I’ve done here is list and discuss what’s worked for me (and some of the things that haven’t). If these things don’t work for you, don’t do them. If you find a way that works better, then by all means use that.
But if you’re struggling to find a way to get started, then follow Approach 2 above. Just start writing, and keep going until you’re finished.
Hope that’s helpful.
[Once more, I'm sorry that the reference list is so me-centric, but I had to use my own papers as examples because I don't know the genesis of anyone else's.]
- Taylor, Michael P. 2006. Dinosaur diversity analysed by clade, age, place and year of description. pp. 134-138 in Paul M. Barrett and Susan E. Evans (eds.), Ninth international symposium on Mesozoic terrestrial ecosystems and biota, Manchester, UK. Cambridge Publications. Natural History Museum, London, UK. 187 pp.
- Taylor, Michael P. 2009a. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrae Paleontology 29(3):787-806.
- Taylor, Michael P. 2009b. Electronic publication of nomenclatural acts is inevitable, and will be accepted by the taxonomic community with or without the endorsement of the Code. Bulletin of Zoological Nomenclature 66(3):205-214.
- Taylor, Michael P. 2010. Sauropod dinosaur research: a historical review. pp. 361-386 in: Richard T. J. Moody, Eric Buffetaut, Darren Naish and David M. Martill (eds.), Dinosaurs and Other Extinct Saurians: a Historical Perspective. Geological Society of London, Special Publication 343. doi: 10.1144/SP343.22
- Taylor, Michael P., and Darren Naish. 2007. An unusual new neosauropod dinosaur from the Lower Cretaceous Hastings Beds Group of East Sussex, England. Palaeontology 50(6):1547-1564. doi: 10.1111/j.1475-4983.2007.00728.x
- Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2):213-230.