A while back, I submitted evidence to the House of Lords’ inquiry into Open Access — pointlessly, as it turns out, since they were too busy listening to the whining of publishers, and of misinformed traditionalist academics who hadn’t taken the trouble to learn about OA before making public statements about it.

Today the Lords’ report [PDF version] is out, summarised here. And it’s a crushing disappointment. As I’d feared, this inquiry didn’t represent an opportunity to forge ahead, but a retreat. The RCUK’s excellent OA policy is to be emasculated by a more gradual implementation, the acceptance of longer embargoes and a toning down of the preference for Gold over Green. (While there is case for Green in the abstract, the form of Green required by the RCUK policy is much weaker that its form of Gold, in that it doesn’t require a liberal licence such as would enable text-mining, use in education, etc.)

On top of that, RCUK have been criticised for “lack of clarity”: quite unfair since their policy is pretty explicit and in any case has twice been clarified on their blog. This is not a hard resource to find: anyone honestly concerned about a perceived lack of clarity could find it in ten seconds of googling. RCUK also caught criticism for lack of consultation — also unfairly, as they made a call for comments which I also responded to.

RCUK has responded apologetically to all this — “Lessons have been learned and we will continue to actively engage with the academic and publishing sectors” as though the publishing sector has any right to a say. I would much rather RCUK had shown the balls to stick with the leadership they initially provided, but I assume they’re under political pressures and were left with no choice. Instead, venality from publishers, ignorance from certain academics and cowardice from the Lords has conspired to strip the UK of its leadership in OA, and reduce it to being a follower.

As Nature News editor Richard Van Noorden said, “In other words, RCUK in response promises nothing it wasn’t doing already”. And the reason was rather diplomatically stated by ICL researcher Stephen Curry:  “Not 100% convinced their lordships have mastered topic”. You can say that again.

Taking a step back — and a deep breath — the weakened RCUK policy is still A Good Thing — just a much less good thing than it could have been, and was on track to be. At a time when radical new journals like eLife and PeerJ are showing just how much better our publishing ecosystem can be, it’s desperately disappointing to see the Lords backing an approach to OA that will mean we

What I would like to see from RCUK now is a statement that, if the public that funds our research is to face yet longer embargoes before it can see that work, it must at least be allowed to use it when it gets it. RCUK must insist on CC BY for the Green arm of its policy.

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.

 

Comparison of mammalian dental patterns showing the differences in regionalization of tooth morphology. (A) Mus musculus (B) Sus scrofa (picture is of an immature pig with an unerupted M3) and (C) Stenella attenuata. Figure 1 from Armfield et al. 2013.

Comparison of mammalian dental patterns showing the differences in regionalization of tooth morphology. (A) Mus musculus (B) Sus scrofa (picture is of an immature pig with an unerupted M3) and (C) Stenella attenuata. Figure 1 from Armfield et al. 2013.

Hi folks, Matt here. This is a ridiculously busy week for me, for reasons that will become clear by the end of the post, so I’m bundling some news items.

First, my dissertation–which has been freely available online since 2007 anyway–is now on arXiv (link). Just in case the meteor takes out both me and WordPress but leaves arXiv unscathed, or possibly some outlet will let you cite arXived works but not “unpublished” ones. It was fast, easy, and free, and you should do the same with your (completed!) thesis or dissertation. Matt Cobley just posted his MS thesis, “The flexibility and musculature of the ostrich neck: Implications for the feeding ecology and reconstruction of the Sauropoda (Dinosauria:Saurischia)“, which is very timely and important work, and which you should go read right now. Mike and I cited both Matt’s thesis and my own diss. in our recent PeerJ paper, and the bibliographic entry for my diss. includes a link to the copy posted on my CV page, but arXiv links would have been simpler, faster, and probably more stable over the long run. Oddly enough, in the first proof the citation of my dissertation was removed, presumably by an automated process, since (a) PeerJ does allow citations of theses and dissertations–we checked, and (b) we suspected that already, because our citation of Matt Cobley’s work survived unscathed. Anyway, we just wrote back and asked them to add it back in, and they did–which has consistently been our experience as PeerJ members, and indeed as human beings: it’s often a pleasant surprise how much you can get just by asking nicely.

Speaking of PeerJ, the second batch of articles arrived today, 10 this time, including one on the evolution of whale teeth (see image at top). And, as I threatened to do last week, I used PeerJ in the classroom today, in talking with the MS students about how peer review works. Not only did it feel fantastic to be able to point the students to a whole bunch of published examples of peer review “in the wild”, but I got some good questions and comments after class. I don’t pretend to be nonpartisan about PeerJ. I think it’s the greatest thing since sliced bread. But frankly it didn’t take much selling. The interface is so intuitive and puts so much info at your fingertips that it feels very un-journal-like. What it feels like, in fact, is the first outlet (I almost said “journal”–how 2012 of me!) designed from the ground up to take full advantage of the web (feel free to quibble, PLOS fans, but I’m standing by that), and the students get that right away.

Finally, I’m giving a couple of talks here on campus later this week, and if you’re in the area and not already bored to tears by my yammering on about inflated dinosaurs, you should come by. First up, Thursday at 5:30 at WesternU’s Pumerantz Library is my family-friendly, “Flip-top heads, air-filled bones, and teenage pregnancy: how the largest dinosaurs got so big”. Then on Friday in Compatriots’ Hall in the Health Sciences Center (HSC–southwest corner of Palomares and 2nd St. in Pomona) is my more-technical-but-hopefully-not-forbiddingly-so college seminar talk, “Pneumatic bones and giant dinosaurs: an update on 5 more years of research”, or as I call it, “Thanks for giving me a job in 2008, here’s how I’ve been earning my keep”.

That’s all for now–gotta go polish those talks!

UPDATE a few hours later:

How to get to my talks, if you’re not familiar with the WU campus. Red arrows show you on what sides of these giant square buildings to find the entrances. For the library  talk, walk through the front doors and BAM! you’re there. For Friday’s talk, go left around the staircase and into the nice conference room just past the atrium. Be warned, almost all the lots you can see in the satellite view require university permits during business hours, and street parking may be hard to scare up on Friday.

WU campus satellite

If you’ll forgive me a rather self-indulgent post, the neck-anatomy paper that I and Matt recently had published in PeerJ is important to me for three reasons beyond the usual satisfaction of getting a piece of work out in a good journal.

fig4

Taylor and Wedel (1023:figure 4). Extent of soft tissue on ostrich and sauropod necks. 1, ostrich neck in cross section from Wedel (2003, figure 2). Bone is white, air-spaces are black, and soft tissue is grey. 2, hypothetical sauropod neck with similarly proportioned soft-tissue. (Diplodocus vertebra silhouette modified from Paul 1997, figure 4A). The extent of soft tissue depicted greatly exceeds that shown in any published life restoration of a sauropod, and is unrealistic. 3, More realistic sauropod neck. It is not that the soft-tissue is reduced but that the vertebra within is enlarged, and mass is reduced by extensive pneumaticity in both the bone and the soft-tissue.

Three milestones

First, it brings a drought to an end. For one reason and another, I didn’t get a single paper published in 2012 — my last hit was the neck sexual-selection paper in September 2011, and I’d started to feel that I was drifting off into the distance a bit. Good to be back on the horse.

Second, amazing though it may seem, it’s the first Taylor/Wedel paper (in either order). Matt and I have been collaborating in one form or another for more than thirteen years now (even if the first couple of years of that were just me asking dumb questions and him telling me interesting things). Along the way, we’ve shared the authorship of a few papers with other authors (Taylor, Wedel and Naish 2009 on habitual neck posture; Taylor, Wedel and Cifelli 2011 on Brontomerus; and Taylor, Hone, Wedel and Naish 2011 on sexual selection) but of all the many Mike-‘n’-Matt projects we’ve started, this is the first to make it out into the world.

(As it happens — and at the risk of leaving the stadium before the fat lady sings — we should be adding to that tally of one Real Soon Now. Further bulletins as events warrant.)

Third, and most important, it means that my entire Ph.D is now published. Chapter 1 (the sauropod-history review) was in the Geological Society dinosaur-history volume;  chapter 2 (the Brachiosaurus revision) was in JVP; chapter 3 (the Xenoposeidon description) was in Palaeontology; chapter 4 (the Brontomerus description) was in Acta Palaeontologica Polonica, and now chapter 5 (neck anatomy) is in PeerJ. I’m pretty happy with the selection of venues there: I’m pleased to have had papers in JVP and Palaeontology even though I won’t be going back to either until they’re open access.

Figure 1. Necks of long-necked non-sauropods, to scale. The giraffe and Paraceratherium are the longest necked mammals; the ostrich is the longest necked extant bird; Therizinosaurus and Gigantoraptor are the largest representatives of two long-necked theropod clades; Arambourgiania is the longest necked pterosaur; and Tanystropheus has a uniquely long neck relative to torso length. Human head modified from Gray’s Anatomy (1918 edition, fig. 602). Giraffe modified from photograph by Kevin Ryder (CC BY, http://flic.kr/p/cRvCcQ). Ostrich modified from photograph by “kei51” (CC BY, http://flic.kr/p/cowoYW). Paraceratherium modified from Osborn (1923, figure 1). Therizinosaurus modified from Nothronychus reconstruction by Scott Hartman. Gigantoraptor modified from Heyuannia reconstruction by Scott Hartman. Arambourgiania modified from Zhejiangopterus reconstruction by Witton & Naish (2008, figure 1). Tanystropheus modified from reconstruction by David Peters. Alternating blue and pink bars are 1 m tall.

Taylor and Wedel (2013:figure 1). Necks of long-necked non-sauropods, to scale. The giraffe and Paraceratherium are the longest necked mammals; the ostrich is the longest necked extant bird; Therizinosaurus and Gigantoraptor are the largest representatives of two long-necked theropod clades; Arambourgiania is the longest necked pterosaur; and Tanystropheus has a uniquely long neck relative to torso length. Human head modified from Gray’s Anatomy (1918 edition, fig. 602). Giraffe modified from photograph by Kevin Ryder (CC BY, http://flic.kr/p/cRvCcQ). Ostrich modified from photograph by “kei51” (CC BY, http://flic.kr/p/cowoYW). Paraceratherium modified from Osborn (1923, figure 1). Therizinosaurus modified from Nothronychus reconstruction by Scott Hartman. Gigantoraptor modified from Heyuannia reconstruction by Scott Hartman. Arambourgiania modified from Zhejiangopterus reconstruction by Witton & Naish (2008, figure 1). Tanystropheus modified from reconstruction by David Peters. Alternating blue and pink bars are 1 m tall.

Dissertation thoughts

Actually I have strangely conflicted feelings about my Ph.D all being published now. I like the feeling of closure, but I also feel a bit sad that the dissertation itself — by far the most substantial single piece of work I’ve produced in any field — is now wholly obsolete. Really, the only reason anyone would possibly want to read it now would be for the acknowledgements or the laughably incorrect predictions of what I’d be working on next. Happily, I don’t have to lament time wasted on the dissertation: all five chapters were originally written to be papers, and the versions in the dissertation are all formatted as for the journals they were initially submitted to. (Three of them ended up in different venues, having initially been rejected, but that’s another story.)

An oddity of my Ph.D is that all five chapters were side-projects. They’re all things that I worked on when I was supposed to be working on a core project to do with the Archbishop and the mechanics of neck support. Every one of them I thought would be a quick job that I could push out before returning to my main work. And every one of them “grew in the telling” until it was substantial enough to function as a chapter. I am sure there’s a moral to this story, but heck if I can figure out what it is.

For reasons that seemed to make sense to me at the time, I did not post my dissertation on the Internet when it was accepted. I feared scooping myself on the as-yet unpublished material (Brontomerus and neck anatomy). Honestly, I don’t know what I was thinking. If I was doing it today I would certainly make it available from the moment it was okayed. As of just a couple of days ago it is now available — just in time to be of no interest to anyone.

xx

Taylor and Wedel (2013:figure 2). Full skeletal reconstructions of selected long-necked non-sauropods, to scale. 1, Paraceratherium. 2, Therizinosaurus. 3, Gigantoraptor. 4, Elasmosaurus. 5, Tanystropheus. Elasmosaurus modified from Cope (1870, plate II, figure 1). Other image sources as for Fig. 1. Scale bar = 2 m.

Co-authoring dissertation chapters

A final thing worth mentioning: as noted above, three of the chapters of my dissertation (Xenoposeidon, Brontomerus, neck anatomy) were co-authored. I think this is not particularly common, so it’s probably worth commenting on.

How does it work? For one of the papers, the Brontomerus description, I just excised Matt’s and Rich’s contributions, which were quite separate from the core of the paper, and used a sole-authored version as the chapter. For the other two, I put an explicit statement in the front-matter saying who did what:

Chapter 3 (description of Xenoposeidon): I was responsible for the anatomical part of the introduction, the systematic palaeontology section, description, comparisons and interpretation, phylogenetic analysis, length and mass calculations, diversity discussion, references, figures with their captions except figure 2, and both tables. Darren Naish of the University of Portsmouth was responsible for the geological and historical part of the introduction, the historical taxonomy section, and figure 2.

Chapter 5 (evolution of long necks): this chapter was written by me as a consequence of a series of discussions with Mathew J. Wedel. Dr. Wedel also contributed figure 5.

My sense was that the examiners were perfectly happy with this. Arguably it’s a good preparation for functioning as a researcher, since so many papers are co-authored. It’s not really realistic practice to sole-author all your work. That said, I doubt papers where I wasn’t lead author would have been welcomed.

I mention this because co-authoring may be a more widely available option than is recognised. My advice would be simple: check with your own supervisor first!

If you found the hypothetical Amphicoelias fragillimus cervical in a recent post a bit too much to swallow, I won’t blame you. But how big do we know Morrison diplodocoid cervicals got?

The longest centrum of any specimen of anything, anywhere, is that of the cervical vertebra BYU 9024 that’s part of the Supersaurus vivianae holotype. It’s 138 cm long, which means that composited at scale with an MTSRSU, it looks like this:

latin-love-god-with-supersaurus

This is not hypothetical. It’s an actual fossil.

(Just for the record: C8 of the Sauroposeidon holotype OMNH 53062 is slightly longer overall, at 140 cm. But that includes overhanging prezygapophyses. Its centrum is “only” 125 cm long.)

Publishers versus libraries

February 16, 2013

A couple of years ago, Matt wrote about the conflict between authors and publishers. Yesterday, two offical statements about the FASTR bill showed us with devastating clarity that publishers are opposed to libraries, too.

FASTR, the Fair Access to Science and Technology Research act, wants to extend the NIH’s open-access policy to all other US Government departments with research budgets exceeding $100M, and to reduce the embargo period on new papers to six months, down from the current twelve.

I won’t insult the intelligence of long-time readers by explaining yet again why this would be a good thing for research, medicine, engineering, industry, education, and indeed everyone and everything except barrier-based publishers. Because for the purposes of this particular post it doesn’t matter what’s actually in the act.

All you need to know is in the two statements: one issued by the Association of American Publishers (AAP), and one from the Association of College and Research Libraries (ACRL). AAP is against the FASTR bill, and ACRL is for it. For our present purposes, it doesn’t matter what their various reasons are. All we need to know is that publishers want the opposite of what libraries want.

It’s time to abandon the comforting but laughable fiction that barrier-based publishers are our friends, our colleagues or our partners. They’re not. They’re our enemies. Hard words, but true ones. In the immortal words of Tom Holtz, “Sorry if that makes some people feel bad, but I’m not in the ‘make people feel good business’; I’m a scientist.”

“But Mike”, you say. “Not all the publishers that are members of the AAP agree with its stance.” That is good news, Fictional Interlocutor. I greatly look forward to seeing them break ranks, one by one, to repudiate the AAP’s antediluvian and anti-science stance. Bring it on, Good Guy Publishers. I will be delighted to give credit just as soon as some is due.

Update (later the same day)

Great to see this letter in support of FASTR signed by ten important organisations: The American Library Association, Association of Academic Health Sciences Libraries, Association of College & Research Libraries, Association of Research Libraries, Creative Commons, Electronic Frontier Foundation, Greater Western Library Alliance, Public Knowledge, Public Library of Science and SPARC.

 

Wire skull

Big news yesterday. Identical bills were introduced into the US House of Representatives and Senate that, if passed, will make federally-funded research freely available within six months of publication. Here’s the exact wording, from the press release on Mike Doyle’s (D-PA) website:

The Fair Access to Science and Technology Research Act (FASTR) would require federal agencies with annual extramural research budgets of $100 million or more to provide the public with online access to research manuscripts stemming from funded research no later than six months after publication in a peer-reviewed journal.

As Peter Suber explains here and here, FASTR is a stronger version of FRPAA, the Federal Research Public Access Act, which has been introduced in Congress three times before (2006, 2009, and 2012) but never come up for a vote. However, momentum for open access is gathering, both on the supply side with progressive new outlets like eLife and PeerJ, and on the demand side of, well, citizens demanding access to the research they’ve already paid for, and legislators increasingly agreeing with them. So FASTR  has a real shot at getting to a vote, and if voted on, could well pass. Which would be awesome, because we all need access.

Raptor skull in cardboard

I am especially happy that FASTR has bipartisan sponsorship in both houses of Congress. The sponsoring representatives in the House are Mike Doyle (D-PA), Kevin Yoder (R-KS), and Zoe Lofgren (D-CA). The identical Senate bill was introduced by John Cornyn (R-TX) and Ron Wyden (D-OR). So we’ve got Democrats from deeply blue states and Republicans from deeply red states, which is awesome and totally appropriate, because this issue really does cut across party lines. And, hell, last year Elsevier managed to hire bipartisan sponsorship for their toxic–in more ways than one–and rapidly-killed Research Works Act, so it’s nicely symmetrical that politicians from both sides of the aisle have come together to sponsor that bill’s near-opposite.

What can you do? If you live in the US, contact your legislators and tell them to support FASTR! It takes almost no time at all and it makes a big difference. This afternoon I called all five of the sponsoring legislators to thank them, and I called my representative and both California senators to encourage them to support the bill, and all told it took just a little over half an hour. If you skipped the thank yous and just got in touch with the legislators who represent you, it could be done in 15 minutes, and you’ve probably wasted more time than that today daydreaming about dinosaurs. Here’s what you’ll need.

Encourage your legislators:

Thank the bills’ sponsors:

This is big. This matters. Send an email, pick up the phone, make a difference.

Rexy skeleton

I didn’t have any really motivational “contact your legislators!” artwork so the photos in this post are of papier mache dinosaurs–all stinkin’ theropods, I’m afraid–that I’m building with my son. More to come on that soon, but in the meantime, check this out and give it a whirl–after you contact your legislators!

The Three Machesketeers