You know how every time you point out a problem to legacy publishers — like when they’re caught misrepresenting their open-access offerings they explain that it’s very complicated and will take months to fix?

Here’s how that should work:

To summarise: I found a bug in the PeerJ system; I reported it in two tweets (total word-count: 32); 27 hours later, they had fixed it, and our article was showing the end-pages in its bibliography.

Are you watching, Elsevier? 27 hours.

Of course, we do realise that it’s much harder for you. PeerJ have all that manpower, those thousands of people working on their system, while you only have one or two techies, who have all sorts of other duties as well as finding bug-reports on Twitter and immediately fixing them. It’s always tough for the little guy, isn’t it?

The SV-POW! journal finder

August 19, 2013

A while back, Elsevier launched its journal finder, tagged “Find the perfect journal for your article”.

Since our priorities in choosing a journal are a bit different from Elsevier, here is the SV-POW! journal finder.

(That’s version 2, by the way. Here’s the old version 1.)

Here’s a thing … Looks like the first ever mention of PeerJ on this blog was a year and nine days ago. All we said in that first post was “… the proliferation of other publishing experiments such as F1000 Research and PeerJ …” with no further comment.

That was just before the formal launch of PeerJ, which was on 12 June. A little more than two months later, Matt bought all-you-can-eat membership so he’d never have to think about it again. Three months on and we were enjoying the reference-formatting instructions (yes, really!) A few days after that — on 3rd December, the day it opened to submissions — we sent in what became our neck anatomy paper. They turned it around quickly enough to be in the first batch of articles on 12 February this year, for an impressive submission-to-publication time of two months and some silver.

Since then it’s cropped up all the time on SV-POW! — and for all the obvious reasons. Matt and I both see it as a game-changer, eating academic journals from “below”, and preprint servers and scholarly blogs from “above”. It’s certainly had an eventful year!

We wish it all the best in its second year. And its third, fourth and fifth years, and all the ones after that.

Schachner et al 2013 fig-13-full

Schachner et al. (2013: Figure 13): Diagrammatic representations of the crocodilian (A) and avian (B) lungs in left lateral view with colors identifying proposed homologous characters within the bronchial tree and air sac system of both groups. The image of the bird is modified from Duncker (1971). Abbreviations: AAS, abdominal air sac; CAS, cervical air sac; CRTS, cranial thoracic air sac; CSS, caudal sac-like structure; CTS, caudal thoracic air sac; d, dorsobronchi; GL, gas-exchanging lung; HS, horizontal septum; IAS, interclavicular air sac; L, laterobronchi; NGL, non-gas-exchanging lung; ObS, oblique septum; P, parabronchi; Pb, primary bronchus; Tr, trachea; v, ventrobronchi.

Gah! No time, no time. I am overdue on some things, so this is a short pointer post, not the thorough breakdown this paper deserves. The short, short version: Schachner et al. (2013) is out in PeerJ, describing airflow in the lungs of Nile crocs, and showing how surprisingly birdlike croc lungs actually are. If you’re reading this, you’re probably aware of the papers by Colleen Farmer and Kent Sanders a couple of years ago describing unidirectional airflow in alligator lungs. Hang on to your hat, because this new work is even more surprising.

I care about this not only because dinosaurian respiration is near and dear to my heart but also because I was a reviewer on this paper, and I am extremely happy to say that Schachner et al. elected to publish the review history alongside the finished paper. I am also pleasantly surprised, because as you’ll see when you read the reviews and responses, the process was a little…tense. But it all worked out well in the end, with a beautiful, solid paper by Schachner et al., and a totally transparent review process available for the world to see. Kudos to Emma, John, and Colleen on a fantastic, important paper, and for opting for maximal transparency in publishing!

UPDATE the next morning: Today’s PeerJ Blog post is an interview with lead author Emma Schachner, where it emerges that open review was one of the major selling points of PeerJ for her:

Once I was made aware of the transparent peer review process, along with the fact that the journal is both open access and very inexpensive to publish in, I was completely sold. […] The review process was fantastic. It was transparent and fast. The open review system allowed for direct communication between the authors and reviewers, generating a more refined final manuscript. I think that having open reviews is a great first step towards fixing the peer review system.

That post also links to this one, so now the link cycle is complete.


Schachner, E.R., Hutchinson, J.R., and Farmer, C.G. 2013. Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria. PeerJ 1:e60

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

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.

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

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

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

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

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

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

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

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

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.

In a comment on a recent Guardian piece (not mine, but a response to it), Peter Morgan asked:

A separate concern is whether the OA business model is sustainable in the long term of decades or even centuries. By contract, OA content has almost no commercial value, unless it is re-published in a for-profit volume. How confident can we be that the content of an OA journal that goes bankrupt will be preserved in an openly accessible way?

Don’t worry — you can be very confident. Reputable open-access journals arrange for their content to be archived in well-trusted third-party archives such as PubMed Central and CLOCKSS. See for example PeerJ’s blog about the arrangements they’re making or this statement from PLOS ONE.

A much more serious problem is this: what happens to the content of a non-OA journal when it goes bankrupt? In general, copyright for the content of such journals is owned by the publisher. This not only means that informal archive arrangements such as BioTorrents and The Disks Of Millions can’t be used — worse, it means that content archived in PubMed Central or CLOCKSS may never become available. If a failing publisher sells its assets, that will include the copyrights — and since literally any unethical corporation might sniff an asset-stripping opportunity, that could be disastrous.

In short, you can be much more confident that PLOS’s content will still be around in 10, 20 and 100 years than you can that Elsevier’s will.

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

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

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

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

The reference-formatting pipeline

When I submit a manuscript with formatted reference like:

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

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

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

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

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

What’s needed in a submitted reference

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

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

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

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

How far can we go?

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

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

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

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