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.


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.


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:


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

Open peer-review at PeerJ

February 14, 2013

There are a lot of things to love about PeerJ, which of course is why we sent our neck-anatomy paper there. I’ll discuss another time how its pricing scheme changes everything for Gold OA in the sciences, and maybe another time write about how well its papers display on mobile devices, or about the quick turnaround or 21st-century graphical design of the PDFs.

But among the most interesting things about PeerJ is its use of open peer review: reviewers are encouraged (though not required) to disclose their identity, and authors are encouraged (but also not required) to make the review history publicly available along with the final papers.

Uptake of open peer-review

Uptake of this option on the initial batch of 30 papers has been OK: 12 papers (40%) have had reviews posted:

# Title Reviews
1 How long is a piece of loop? Reviews
2 Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome Reviews
3 The roles of STP and LTP in synaptic encoding Reviews
5 Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences Reviews
6 Soil carbon determination by thermogravimetrics
7 Mutations changing tropomodulin affinity for tropomyosin alter neurite formation and extension
8 Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing Reviews
9 The effects of fixation target size and luminance on microsaccades and square-wave jerks
10 Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
11 Assessing insect responses to climate change: What are we testing for? Where should we be heading? Reviews
12 Novel control of lactate dehydrogenase from the freeze tolerant wood frog: role of posttranslational modifications
13 Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning
14 Simultaneous recordings of ocular microtremor and microsaccades with a piezoelectric sensor and a video-oculography system
15 Fluorescent protein tagging confirms the presence of ribosomal proteins at Drosophila polytene chromosomes Reviews
16 Na+/Ca2+ selectivity in the bacterial voltage-gated sodium channel NavAb Reviews
17 Timing of molt of barn swallows is delayed in a rare Clock genotype
19 Perceptual elements in Penn & Teller’s “Cups and Balls” magic trick Reviews
21 Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerant marine mollusc, Littorina littorea
22 Poorer verbal working memory for a second language selectively impacts academic achievement in university medical students Reviews
25 Repeated hands-and-knees positioning during labour: a randomized pilot study
26 Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model
27 Novel enzyme-polymer conjugates for biotechnological applications
28 Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice
29 Anti-apoptotic signaling as a cytoprotective mechanism in mammalian hibernation
30 A practical implementation of de-Pake-ing via weighted Fourier transformation
31 Analysis of innate and acquired resistance to anti-CD20 antibodies in malignant and nonmalignant B cells
33 A perfusion study of the handling of urea and urea analogues by the gills of the dogfish shark (Squalus acanthias)
34 Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by nonhost bacterial pathogens Reviews
36 Why sauropods had long necks; and why giraffes have short necks Reviews
37 Pain assessment in children undergoing venipuncture: the Wong-Baker faces scale versus skin conductance fluctuations

(Articles 4, 18, 20, 23, 24, 32 and 35 do not exist — presumably they didn’t make it through review, typesetting and proofing in time for the launch. Or maybe they were rejected after having been assigned numbers.)

It’s interesting to see that most of the earliest papers did elect to publish reviews, but few of the later ones. This may reflect that the “early adopters” — the people who were quickest to get their submissions in after PeerJ opened its doors — also tend to be the more open-oriented people in other respects. It would be great if the authors of some of those other 18 papers were to make their reviews open, too: I’m sure it’s not too late.

What’s the value of open peer-review?

First, it improves transparency. In standard peer-review, three people (and editor and two reviewers) make a decision on behalf of the entire community, and no-one else can see what was done or why. In our case, John Hutchinson was our handling editor. We’ve often said on this blog how much we like and respect him, and it would be easy for someone on the outside to suspect that he’d been tempted to give us an easy ride. Anyone who reads the review history can see for themselves that he didn’t.

Second, it gives credit where it’s due. Reviewers who do a good job often plough in many hours of time that they could be spending on their own work, and it’s right that they should be recognised. In this case, Heinrich Mallison did a careful line-by-line critique of the whole 50-page manuscript and sent up a marked-up copy which was invaluable in making revisions. That sort of work should be acknowledged. [At the moment, that marked-up manuscript is not on the PeerJ review-history page. I’ve been told they’re going to fix that.]

Third, it gives blame where it’s due. Some reviewers who are excessively critical, or criticise in a non-constructive way that can’t be addressed in a revision; others are positive about the manuscript but make no real contribution to improve it. It’s right that reviewers who don’t do their job properly should be called out on that. (Of course anonymity can go some way towards shielding bad reviewers, but even then it’s often quite obvious who’s responsible for a given review.)

Fourth, it encourages good behaviour from reviewers. When they know their good work will receive credit and their bad work will reflect on them, they will have more incentive to do their best. Too often, reviews are seen as a tax on researchers’ time. Making them visible helps to bring them into the mainstream.

Fifth, it avoids wasted effort. Sometimes a review is a serious piece of work in its own right — Matt tells me that for one manuscript we was refereeing, he wrote a detailed critical review that was longer than the  manuscript itself. Of course, no-one ever saw that work but the original author and his handling editor, which is a terrible waste. Publishing reviews fixes that.

Sixth, and this is crucial, open peer-review is a fantastic teaching tool. Matt has already explained how showing his Western students real reviews in a real process is going to help them much more than made up ones.

What are the drawbacks of open peer-review?

Search me. I sure as heck can’t think of any.

Changing peer-review culture

PeerJ didn’t invent open peer-review — far from it. It’s been around for a while, practiced by some BMC journals and also adopted more recently by eLIFE — another of the new breed of born-digital open-access journals. Another new publishing initiative, F1000 Research, is built entirely on the concept of open review.

The importance of PeerJ doing the same is that it helps to bring open peer-review into the mainstream. PeerJ’s going to be a big journal — its explicit goal is to be a PLOS ONE-scale megajournal. One of the many things it can achieve is to help shift the default reviewing culture to open.

In our PeerJ neck-anatomy paper, we speculated on how long individual cervical vertebrae might have grown. Here is the relevant section:

Mere isometric scaling would of course suffice for larger animals to have longer necks, but Parrish (2006, p. 213) found a stronger result: that neck length is positively allometric with respect to body size in sauropods, varying with torso length to the power 1.35. This suggests that the necks of super-giant sauropods may have been even longer than imagined: Carpenter (2006, p. 133) estimated the neck length of the apocryphal giant Amphicoelias fragillimus Cope, 1878 as 16.75 m, 2.21 times the length of 7.5 m used for Diplodocus, but if Parrish’s allometric curve pertained then the true value would have been 2.21^1.35 = 2.92 times as long as the neck of Diplodocus, or 21.9 m; and the longest single vertebra would have been 187 cm long.

Now this speculation is shot through with uncertainty. As we’ve discussed before, at length, all estimates of Amphicoelias fragillimus length and mass are wildly speculative; and Parrish’s allometry result was extrapolated from an unconvincingly small data set. But still, these numbers are probably the best we can do with what we have.

In Diplodocus carnegii, C14 is the longest individual vertebra at 642 mm long (Hatcher 1901, p. 38). The Amphicoelias:Diplodocus size ratio of 2.21 from Carpenter and the neck allometry constant of 1.35 from Parrish suggest that the corresponding vertebra in the big boy would have been 2.92 times as long as that 642 mm, hence the 187 cm that we reported.

So what does a 187-cm long cervical vertebra look like? Scaling up from the Diplodocus carnegii C14 in Hatcher (1901: plate III) and using my good self as a scalebar, here it is:


I find that just a little bit frightening. In more ways than one.


  • Carpenter, Kenneth. 2006 Biggest of the big: a critical re-evaluation of the mega-sauropod Amphicoelias fragillimus (Cope, 1878). New Mexico Museum of Natural History and Science Bulletin 36:131.
  • Cope, Edward D. 1878. Geology and paleontology: a new species of Amphicoelias. The American Naturalist 12:563.
  • Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
  • Parrish, J. Michael. 2006. The origins of high browsing and the effects of phylogeny and scaling on neck length in sauropodomorphs. pp 201-224 in: Amniote paleobiology, University of Chicago Press, Chicago.
Apatosaurus lousiae 1/12 scale skeleton, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Apatosaurus lousiae 1/12 scale skeleton in left antero-lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Today our paper on sauropod neck anatomy is formally published in PeerJ.

There’s not much new to say about the paper, since we posted it to arXiv last year and told the world about it then (post 1, post 2, post 3). Although a lot more attractive in form, this version is almost identical in content, modulo some changes requested by the PeerJ reviewers, and some changes to the figures to make sure every part of every figure was CC BY or otherwise in the public domain. Many thanks to everyone who gave us permission to use their images, especially Scott Hartman, who is rapidly getting to be the go-to person for this sort of thing just by doing good work and being a nice guy.

The big news, of course, is not the paper but the outlet. We’re excited about PeerJ because it promises to be a game-changer, for lots of reasons. Mike has a nice article in the Guardian today about the thing that is getting the most attention, which is the cost to publish. I blogged about it last fall, when I bought the max bling lifetime membership–for about one-tenth of the OA publication fee for a single article from one of the big barrier-based publishers.

Apatosaurus lousiae 1/12 scale skeleton, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Apatosaurus lousiae 1/12 scale skeleton in left lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Then there’s turnaround time: for our paper, a mere 72 days, including both submission day (Dec. 3) and publication day (Feb. 12). My fastest turnaround before this was 73 days for my sauropod nerve paper, but that was from submission to posting of the accepted manuscript, not publication of the final version of record. Prior to that I’d had a couple of papers published within six months of submission, but that was definitely the exception rather than the rule. And sadly, I’ve had several situations now where a paper  languished in peer review for six months.

And that brings me to peer review–the real “peer” in PeerJ. When you sign up a lifetime membership, you agree to review one paper a year for them to keep your membership active. Certainly not a crushing amount of work, especially since I’ve been averaging 5 or 6 reviews a year for much less congenial outlets.

I’ve seen this from both sides now, since I was tapped to review a manuscript for PeerJ back in December. The first thing I liked is that they asked for the review back within 10 days. That’s just about right. I can see a thorough review taking three days (not working straight through, obviously, but taking time to carefully read, digest, look stuff up, and compose the review), and a busy academic maybe needing a week to find that kind of time. If one is too busy to get it done within 10 days, better to just be honest, say that, and decline the review. There is certainly no reason to let reviewers have manuscripts for four to six weeks, let alone the three to four months that was standard when I got into this business.

Apatosaurus lousiae 1/12 scale skeleton in dorsal view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Apatosaurus lousiae 1/12 scale skeleton in dorsal view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

The second thing I liked is that they gave me the option to sign the review (which is almost always implicitly present, whether reviewers take advantage of it or not), and they gave the authors of the manuscript the option to publish my review alongside the paper. I love that. It means that, for the first time ever*, maybe the time and effort I put into the review will not disappear without a trace after I send it off. (It is astonishingly wasteful that we write these detailed technical critiques and then consign them to never be seen by any but a handful of people.) And it had a salutary effect on my reviewing. I always strive to be thoughtful and constructive in my reviews, but the knowledge that this review might be published for the world to see made me a lot more careful, both in what I said and how I said it. Hopefully, the authors I reviewed for will opt to publish my review, so you will be able to judge for yourself whether I succeeded–I’ll keep you posted on that. UPDATE: Hooray! The paper is out, and it’s a beaut, and the authors did publish the review history, which is excellent. The paper is Schachner et al. (2013), “Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria”, the reviews by Pat O’Connor and myself and the author responses and the editor’s letters are all available by clicking the “Peer review history” link on the sidebar, and you should go read all of it right now.

* There are a bare handful of other outlets that publish reviews alongside papers, but I’ve never been tapped to review for them, so this was my first experience with a peer review that might be published.

Naturally Mike and I took the maximum openness option and had our reviews and all the rest of the paper trail published alongside our paper, and I intend to do this every time from here on out. As far as I’m concerned, the benefits of open peer review massively outweigh those from anonymous peer review. There will always be a few jackasses in the world, and if openness itself doesn’t force better behavior out of them, at least they’ll be easier to identify and route around in an open world. Anyway, to see our reviews, expand ‘Author and article information’ at the top of this page, and click the link in the green box that says, “The authors have chosen to make the review history of this article public.”

One happy result of this will manifest in just a few weeks. Bunny-wrangler and sometime elephant-tracker Brian Kraatz and I co-teach a research capstone course for the MS students at WesternU, and one of the things we cover is peer review. Last year I had to dig up a couple of my reviews that were sufficiently old and anonymous that no harm could come from sharing them with the students, but even so, they only got half the story, because I no longer had the manuscripts and couldn’t have shared them if I had. This year I’ll be able to point the students at PeerJ and say, “Go look. There’s the back-and-forth. That’s how we do this. Now you know.”

Science, process and product alike, out in the open, freely available to the world: that’s why I’m proud to be a member of PeerJ.

(And I haven’t even mentioned the preprint server, or all the thought the PeerJ team put into the graphic design of the papers themselves, or how responsive the production team was in helping us get the finished product just right, or….)

Apatosaurus lousiae 1/12 scale skeleton in left postero-lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

Apatosaurus lousiae 1/12 scale skeleton in left postero-lateral view, modelled by Phil Platt, assembled and photographed by Brant Bassam. Image courtesy of BrantWorks.com.

The pictures in this post have nothing to do with our paper, other than showing off one of the beautiful products of the factors we discuss therein. The images are all borrowed from Brant Bassam’s amazing BrantWorks, which we will definitely be discussing more in the future. Explicit permission to reproduce the images with credit can be found on this page. Thanks, Brant!

UPDATE: Bonus Figure

This special version of Figure 3 from our new paper goes out to Dean, who inspired it with this comment. As Tony Stark said, “It’s like Christmas, only with more…me.” Click to enWedelate.

Matt Wedel (6'2" or 1.88m tall) with various long-necked amniotes for scale.

A selection of Matt Wedels (6’2″ or 1.88m tall) with various long-necked amniotes for scale.

What is a viral licence?

February 8, 2013

Earlier today, Richard Van Noorden pointed out on Twitter that in this video, at about 5:40, the speaker says that “CC BY is essentially a viral licence”. I was surprised to say the least that the speaker — Sue Joshua, Director of Legal Affairs at John Wiley & Sons — would make such a basic mistake. I’d have expected a copyright lawyer to know what the term “viral licence” means.

Hence this post.

A viral licence is one that imposes the same terms on derived works. If you don’t believe me, here’s the Wikipedia entry, and if you don’t believe that here’s Princeton University’s definition.

This is the meaning of the term “viral licence”. It doesn’t mean “a licence that has suddenly become popular, i.e. ‘gone viral'”. It refers specifically to a licence that (by design) infects numerous works by transmitting itself to from one work to others.

The classic example of a viral licence is the GNU General Public Licence, which is used for much of the world’s most important free software including the Linux kernel. [Disclosure: in my day-job, some of the software we release is under the GPL: YAZ Proxy, Metaproxy, pazpar2, Zebra, IRSpy, MKDru.]

The other best-known viral licence is Creative Commons Attribute-ShareAlike (CC BY-SA). Specifically, this is differentiated from the more common non-viral CC BY licence by the addition of the ShareAlike clause, which says:

Share Alike — If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one.

The reason that CC BY is the most widely used licence for open-access publications is precisely that it is not viral — its non-viral nature means that work licenced using it can be deployed in the widest possible range of circumstances, which is generally what funders want in exchange for their money.

Why am I making such a big deal about this? Because we need to communicate! The term “viral licence” has one meaning, which makes it very easy and unambiguous to talk about. But if we allow Sue Joshua’s confusion to spread, the term will soon become debased just as “open access” has. I was surprised to see in today’s Twitter stream that a couple of people who I expected to know this term seemed unclear on it, so it’s worth clearing up.

[In this post I am not interested in arguing about whether viral licences are a good or a bad thing; just in establishing what they are.]

Hot on the heels of the UK House of Lords’ inquiry into Open Access, the Business, Innovation and Skills Committee of the House of Commons has begun its own inquiry. This morning I submitted my own evidence. Here it is.

[It’s not too late to make your own submission. It doesn’t have to be as long as this: just let the government know your attitude regarding the parts of the question that concern you most. Again, details are here. Get writing!]

Business, Innovation and Skills Committee

Inquiry into the Government’s Open Access Policy

Dr. Michael P. Taylor

7th February 2013

I am an honorary research associate in the Department of Earth Sciences at the University of Bristol. A computer programmer by profession, I completed a Ph.D in my spare time in 2009, and continue to publish research in vertebrate palaeontology. Although my Bristol affiliation gives me reasonable access to paywalled literature, the mechanics of access are cumbersome as I work exclusively off-campus. My unusual circumstances give me a perspective from both inside and outside academia.

I speak only for myself, not for the University of Bristol.

Executive summary

  1. The UK currently leads the world in Open Access, and as a result enjoys a significant citation advantage; the rest of the world is following.
  2. The purpose of funding research is to benefit society as a whole. When publishers’ interests conflict with those of broader society, the government must serve society.
  3. The inclusion of publishers on the Finch Committee represents a conflict of interest. Some recommendations of the Finch Report were compromised by this conflict of interest.
  4. Gold OA has a real advantages over Green OA in that it presents a single Version Of Record. But the Finch Report does not give proper weight to Green OA.
  5. The form of Green OA mandated by the RCUK policy is badly compromised in allowing restrictive licences and delayed access that reduce the value of the research.
  6. There is no evidence that Green OA negatively affects subscription revenue.
  7. CC BY allows commercial re-use by design, in order to obtain the best return on research investment. It explicitly prohibits plagiarism. It does not infringe author’s rights, in fact allowing authors to retain more rights than the prevailing copyright-transfer regime.
  8. The use of CC BY means that research does not merely allow us to know more, but to do more. It is not anti-commercial, it is anti-monopoly (and so facilitates an efficient market).
  9. Gold OA APCs vary greatly between publishers: traditional publishers are far more expensive than new OA-only publishers. Much lower APCs than the £1500–£2000 quoted by the Finch Report are achievable with no loss of publication quality. Government funding should cover only a base APC of perhaps £1000 to encourage downward pressure on prices.
  10. The government must make decisions on the basis of what benefits the UK as a whole, not what benefits any single industry. The government should allow both Gold and Green OA; should require the CC BY licence, whichever route is taken; should tolerate no embargo on Green OA; and should not fully fund exploitatively high APCs.


1. First, I enthusiastically welcome the government’s clearly stated commitment to Open Access (OA). There is no question that the free availability of research outputs will have a significant positive effect – not only by accelerating further research, but also in the form of practical improvements in health, education and industry.

2. I am also delighted to see the UK leading the world in Open Access. RCUK’s pre-Finch OA policy was one of the world’s earliest and most significant; the Finch Report established a clarity of vision not previously seen in any national OA policy; and BIS’s public commitment to OA in all government-funded work was a world first. As noted below, there are strong pragmatic reasons for the UK to maintain a position of leadership. But even leaving these aside, the symbolic value of leadership in open access can hardly be overstated.

3. Equally, it has been hugely encouraging to see the world following the UK’s lead. In the days after the announcement of the UK policy, similar declarations followed from several European countries; and most importantly, the €80M “Horizon 2020” programme of the European Commission also announced an Open Access policy. [Note added 18 May 2015: Eek! I only just noticed my error here: Horizon 2020 is a €80 billion program, so I dropped three orders of magnitude.] Global research is not a zero-sum game: the UK’s gain is not other countries’ loss or vice versa. As more countries open up their research outputs, the whole world benefits.

4. Against this backdrop, implementation issues must be discussed with a simple but important principle in mind: who is publicly-funded research for? When the question is stated explicitly, the answer is immediately obvious: it is for the public that funds it – for the citizens whose health, education and economic prospects are all improved by Open Access.

5. Unfortunately, the implementation strategies recommended by the Finch Report are not those that would most benefit the public, but are slanted towards the interests of academic publishers. This is because, as noted on page 113 of the Finch Report, three of the fourteen working members of the group represent publishers. The involvement of publishers in deciding the UK’s publishing policy is mystifying, as it represents a clear conflict of interest.

6. There is no question that in the process of research, publishers provide important services; but so do the providers of IT infrastructure and manufacturers of laboratory equipment, and their input was not sought in formulating policy. Neither should publishers have been consulted. The proper approach would have been for researchers, librarians, university administrators, funders, medics, educators and businesses to have worked out what policy and what strategy would best serve them in their goal of performing, disseminating and exploiting research; and then to negotiate with publishers (as with IT service providers and lab-equipment manufacturers) to obtain the necessary services at the best prices.

7. It is because of publisher involvement in the Finch Committee that the recommendations of the Report are skewed towards the interests of that one small group at the expense of citizens. All of the flaws in the recommendations in the report are directly attributable to this.

Specific issues

The Government’s acceptance of the recommendations of the Finch Group Report ‘Accessibility, sustainability, excellence: how to expand access to research publications’, including its preference for the ‘gold’ over the ‘green’ open access model

8. There are good and legitimate reasons to prefer Gold over Green. Most importantly, there is no possibility of confusion over which is the version of record under the Gold model. However, the Finch Report goes much further than expressing a preference for Gold, by almost entirely omitting Green from its discussion. (The word “green” appears only three times in the 140 pages of the report and one of these is a reference to the HM Treasury Green Book.)

9. Perhaps as a result of this, the Green OA provisions of the revised RCUK policy are much weaker than its Gold OA provisions. In particular, while RCUK-funded work that is published as Gold OA must use the very permissive Creative Commons Attribution licence (CC BY), whereas work published as Green OA may have restrictive non-commercial clauses inserted. The inclusion of non-commercial clauses greatly diminishes the value of work, as discussed in the next section.

10. The Finch Report also allows embargoes – i.e. delays in availability – when research is published as Green OA, and the RCUK policy follows this (although it shortens the delays). Allowing such delays necessarily entails delaying all the benefits of Open Access, and thereby retards the progress of research, medicine, education and industry. There is no justification for these delays: even if they benefit publishers by enabling them to avoid subscription cancellations, the interests of publishers must be outweighed by those of all the other stakeholders.

11. In any case, counter-intuitively there is no evidence that Green OA hurts subscription revenue at all. The JISC/European-funded PEER project1, after nearly four years’ work, concluded that “there is no evidence that self-archiving has harmful effects on journal viability”. This is the only large-scale analysis of this issue to have been undertaken, and the only solid data we have to go on: publishers’ statements about effects of Green OA on subscription revenue are guesses, not informed by data.

12. In conclusion, the full benefit of Green OA will be realised only if Green articles are licenced using CC BY and if they are made available from the date of publication rather than after an embargo. If these changes have a negative effect on publishers (which all the evidence says they will not), then that is regrettable; but it would not be a reason to delay access to, and reduce the utility of, publicly funded research.

Rights of use and re-use in relation to open access research publications, including the implications of Creative Commons ‘CC-BY’ licences

13. The CC BY licence embodies the original definition of the term “Open Access” by the Budapest Open Access Initiative (BOAI)2, and has been widely adopted as the open-access licence of choice by respected OA publishers such as BioMed Central (BMC) and the Public Library of Science (PLOS). It ensures that the published works can be used by the widest spectrum of organisations – not only to facilitate further pure research, but also to be used in education and to catalyse innovation in industry

14. Recently some regrettable misunderstandings of the CC BY licence have been promulgated, notably in an anti-Finch letter from editors of 21 history journals3. This claimed that the use of CC BY “means that commercial re-use, plagiarism, and republication of an author’s work will be possible, subject to the author being ‘credited’ (but it is not clear in what way they would be credited). We believe that this is a serious infringement of intellectual property rights and we do not want our authors to have to sign away their rights in order to publish with us.” I will address these misunderstandings in turn.

15. commercial re-use: yes, by design the CC BY licence makes this possible. Contrary to the assumption of the history-journal editors, this is not a bug but a feature. The goal of the UK government policy is to benefit the UK in general, including its many commercial concerns.

16. plagiarism: it is flatly wrong to say that CC BY encourages plagiarism. Plagiarism is the use of another person’s work without acknowledgement; but the CC BY licence explicitly does require acknowledgement. It is not possible to plagiarise and be within the terms of this licence.

17. republication of an author’s work: yes, the CC BY licence does allow this. So do the agreements currently in use by most publishers, which allow the publisher to anthologise and otherwise reuse author’s works with or without their consent. Again, this is a good thing: it enables the full value of the work to be realised, whether in an educational or commercial setting.

18. it is not clear in what way they would be credited: on the contrary, the text of the CC BY licence4 plainly states “You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work)”.

19. serious infringement of intellectual property rights: quite the reverse: the CC BY licence codifies the standard scholarly practice whereby authors’ works are used in various ways with full attribution but without further financial compensation. (After all, scholars have already been paid for their work.)

20. we do not want our authors to have to sign away their rights in order to publish with us: this statement betrays a surprising ignorance of standard journal requirements, including those of many of the journals whose editors signed the letter. These journals require the author to sign copyright over to the publisher, a far greater violation of intellectual property rights than in the open-access model.

21. The goal of the CC BY licence is to allow the full value of a work to be realised. By contrast, the non-commercial (NC) clause that the current RCUK policy allows in the case of Green OA outright prohibits use of the work in many important situations – e.g. in health, education and commercial enterprises. Worse still, the uncertainty introduced by a non-commercial clause has a chilling effect, stifling uses that might be allowed but which the innovator does not want to risk having to defend in court. There is no justification for a ban on commercial use of research publications. We fund research not only in order to know more, but in order to do more.

22. A particularly important application of Open Access articles is that massive numbers of articles can be “mined” by computer programs far more efficiently than any human can read them. Such techniques are already in use in a limited way and proving their value: for example, in discovering and synthesising new chemical formulae5. However, such work is greatly impeded by the difficulty of obtaining permission from publishers, and assurances that they will not claim ownership of the results. The use of a permissive licence such as CC BY disposes of such concerns and encourages innovative uses of research data that we cannot yet envisage.

23. Eric Kansa, of the University of California at Berkeley, summed up the misunderstandings and realities of fully open licences such as CC BY very efficiently: “While Open Access is not anti-commercial, it is anti-monopoly”. Monopolies lead to inefficient markets and poor economic utilisation. Permissive licences on publicly-funded work fix that.

24. In conclusion: for the benefit of the country as a whole, the government should renew its commitment to the use of the CC BY licence on all the Gold OA research that it funds, and extend this to Green OA publications as well.

The costs of article processing charges (APCs) and the implications for research funding and for the taxpayer

25. Simple calculations6 conservatively estimate the overall cost to the worldwide academic community of an average paywalled article at £3307 (£4.96 billion total paywall revenue each year for 1.5 million articles). Naively, an APC needs only be cheaper than this to achieve a net economic improvement. In practice, APCs need to be significantly cheaper because of the difficulty of making a transition to Gold OA while subscriptions are still being paid.

26. At present, APCs for Gold OA are under strong price pressure. I will review some key data points as they were one year ago, then consider recent developments.

  • Typical APCs from traditional publishers (Elsevier “sponsored article”, Springer Open Choice) are in the region of $3000 (about £1950)
  • The open-access megajournal PLOS ONE charges $1350 (about £862)
  • The broad survey of Solomon and Björk (2012) found an average Gold OA fee of $906 (about £579).

27. In the last year, significant developments have changed the landscape. In roughly chronological order:

  • The new high-impact journal eLife, sponsored by the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust, is initially waiving all APCs.
  • The new for-profit open-access megajournal PeerJ introduces a new model where each author pays $99 (about £63) for a lifetime membership, which covers one publication each year at no further charge. (A $299 (~£189) lifetime membership covers unlimited publications.)
  • The new Forum of Mathematics journals will waive all APCs for the first three years, after which they may charge £500 or may find a different revenue stream and retain a zero APC.
  • The open-access humanities megajournal SAGE Open recently dropped its APC to $99.

28. Other new open-access ventures continue to emerge, including the Episciences initiative to create overlay journals for arXiv, and the Open Library of Humanities.

29. As low as these prices are, a surprising finding by Stuart Shieber of Harvard is that 70% of all open-access journals charge no APC at all7. Others have independently found similar results.

30. In the light of all this, it is surprising that the Finch Report suggests a typical APC of “£1500-£2000”. The only explanation for this is that the bulk of the APCs in the sample that this range was calculated from was biased by many high-priced papers in traditional publishers’ journals. If this is so, then a cultural change is required in researchers. There is no reason why the majority of papers should not be published in outlets with much lower APCs. (In most cases the new journals also offer other benefits, such as unlimited colour figures and supplementary information, and the ability to include audio and video in the published work.)

31. A shift away from traditional journals to newer “born open-access” journals is likely to be accelerated if there is some pressure on researchers to overcome their innate conservatism and choose venues accordingly. Researchers may find it more convenient to keep submitting to the same journals they have used previously, publishing their work as Gold OA with the APCs covered by funders. But this convenience, while attractive in the short term, will inhibit long-term change.

32. For this reason, I would support a cap on the APCs that will be paid by funders: for example, RCUK could elect to fund the first £1000 of each APC, leaving authors who insist on using more expensive journals to top up the fee from their own grants. The resulting downward pressure on prices would ensure that a true market in Gold OA provision emerges.

33. In some quarters, such a scheme might be described as a curtailment of academic freedom. It is not. The phrase “academic freedom” refers to the freedom to choose what to study and what opinions to express – not what venues to publish the results in. A researcher who freely elects what to work on is just as free, whatever journal his paper appears in.

34. In conclusion, government funding should cover the costs of modest APCs; but there is no need for them to continue to support very expensive journals as far cheaper alternatives are now becoming available at no loss of quality.

The level of ‘gold’ open access uptake in the rest of the world versus the UK, and the ability of UK higher education institutions to remain competitive.

35. Some critics of the Finch Report and RCUK’s updated OA policy have complained that by making British-funded research outputs Open Access, these policies will put the UK’s researchers at a competitive disadvantage with the rest of the world, because our research grants will have to bear the cost of APCs while those of others do not.

36. This complaint is true, but misleading. In the first place, all the signs are that the world as a whole is moving towards universal Open Access, so any period of Britain alone paying APCs will likely be short.

37. But more importantly, by making their work Open Access, British researchers place themselves at a huge advantage in terms of the visibility of their work. Numerous studies have now been performed on the Open-Access Citation Advantage. A good summary is found in the meta-analysis of Swan (2010)8. Swan surveyed 31 studies of the OACA, showing that 27 of them found an advantage of between 45% and 600%. I analysed the final table of that report, averaging the citation advantages given for each of ten academic fields (using the midpoints of ranges when given), and found that on average open-access articles are cited 2.76 times as often as non-open.

38. In conclusion, having made a bold beginning, the UK government should push vigorously on with its open-access plans, yielding benefits for medicine, education and industry, and giving its academics a competitive advantage over the rest of the world.


39. We must remember that what is best for the country as a whole will not necessarily be best for each group that is affected. In this case, it is clear that the UK will benefit from Open Access that is immediate and uses permissive licences, whether achieved by the Gold or Green route. It is likely that publishers will (rightly or wrongly) fear some damage to their business as this change is made. But the interests of one small group – publishers – must not be allowed to compromise decisions made on behalf of all other stakeholders. In particular, the government of the UK is beholden to its citizens, not to the publishing industry. The government must make decisions that promote the welfare of citizens rather than decisions that suit any one business.

40. Note that publishers who find the revised Green-OA terms unacceptable will be at liberty to decline offers of manuscripts resulting from Government-funded research. (In practice, this is unlikely to happen: rather than forego the opportunity to publish publicly funded research, publishers will simply accept the loss of their government-granted monopoly on the commercial exploitation of this research.)

41. It is not the job of government to concern itself with challenges faced by the publishing community at the expense of other stakeholders. This assertion does not arise from hostility to publishers, but from a simple recognition of who the government serves.


1. PEER Project: http://www.peerproject.eu/

3. Statement on position in relation to open access: http://www.history.ac.uk/news/2012-12-10/statement-position-relation-open-access

4. Creative Commons Attribution 3.0 Unported: http://creativecommons.org/licenses/by/3.0/

6. What does it cost to publish a paywalled paper with anyone?: https://svpow.com/2012/07/18/what-does-it-cost-to-publish-a-paywalled-paper-with-anyone/

8. Swan, Alma (2010) The Open Access citation advantage: Studies and results to date. http://eprints.soton.ac.uk/268516/2/Citation_advantage_paper.pdf

Other response to this call:

Here are cervical vertebrae 2-15 of Diplodocus carnegii in right lateral view, from Hatcher (1901: plate 3). Click to embiggen, and then just gaze in wonder for a while.


Wouldn’t that look smashing, printed, framed, and hanging on the wall?

I wonder if I will ever stop finding new interesting things to think about in this image. I doubt it.

(For a bit o’ fair-and-balanced, remember that this neck may not be complete, and that some of the neural spines are sculptures.)

Thanks to Mike for the scan.


Hatcher, John Bell. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.