PeerJ launches today! (and we’re in it!)

February 12, 2013

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.

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18 Responses to “PeerJ launches today! (and we’re in it!)”


  1. Thanks Mike – we are very pleased you enjoyed your experience and we look forward to publishing more extinct megaflora from this community!

  2. Mike Taylor Says:

    “Megaflora”?! I can only assume you’re referring to the alleged Bruhathkayosaurus tibia :-)

  3. Dean Says:

    I love that revised sauropod neck scale…the size didn’t really sink in until I threw in a human for scale!

  4. M.E. Says:

    Small question – why did you bother publishing in PeerJ if the article was already available through arXiv?

  5. Matt Wedel Says:

    Small question – why did you bother publishing in PeerJ if the article was already available through arXiv?

    Good question!

    There are several reasons. One is that, rightly or wrongly, the imprimatur of formal publication still matters–even to us, apparently.

    Let me unpack that a bit. Personally I am happy to read, learn from, and cite stuff based on its internal solidity (are the observations documented, do the inferences follow, were the tests conducted rigorously) regardless of where it appears. But there are a couple of buts. The first is that not everyone is–indeed, when we posted the pre-publication version of this paper to arXiv, we caught hell on Facebook from someone who thinks that nothing outside of journal articles and books should be cited. The second is that I am happy to judge that “internal solidity” in fields I know well, but outside my bailiwick I need some help separating the wheat from the chaff. Peer review is a notoriously inefficient filter at catching bad science (and, IMHO, an overly effective roadblock for slowing or stopping good science), and the same goes for journal publication. Nevertheless, if something in another field is formally published in a peer-reviewed outlet, then I know that at least a couple of other people who theoretically know that field decided it was non-BS, and that’s more than I can say for stuff in unfamiliar fields that is not so published. (Plus, if it’s more than a few months old I can chase the paper trail and see what the reaction was.)

    Ultimately, and as Mike has said, I think the major value of peer review is that it shows that the authors were sufficiently serious to deliberately subject their work to close scrutiny. And that may be why we all tolerate it even though it is so clearly broken: ironically, the worse the peer review system is, the better it functions as an honest signal, because if you’re willing to put up with it you must really be serious.

    Savor that, because it’s the most spirited defense of peer review I’m ever going to mount.

    (Guerrilla point that I just thought of: now that they both exist, we can point to the similarity of the PeerJ version and the arXiv version–the actual data didn’t change at all–as evidence that not citing archived preprints is just silly.)

    Another factor, at least for me, is simply bling. Sure, we could have made a prettier-looking document than the one we submitted to arXiv, but nothing nearly as nice as the formatted PDF we got from PeerJ.

    A much less superficial motivator: this isn’t just any journal, this is PeerJ. They’re doing a LOT of revolutionary stuff, and we support pretty much all of it, and we want to be part of it.

    But in the end it comes down to an assumption inherent in your question. Why bother publishing in PeerJ? Because it was hardly any bother at all. The cost/benefit table titled massively in our favor. We think a lot of other researchers will find the same.


  6. Matt Wedel writes:
    (Guerrilla point that I just thought of: now that they both exist, we can point to the similarity of the PeerJ version and the arXiv version–the actual data didn’t change at all–as evidence that not citing archived preprints is just silly.)

    I intend to save each version of my current MS (subject: pterosaurs) as it moves through submission to review to acceptance to publication. I will then provide these versions of the MS for inspection. I want to see each version in comparison, including data points added, removed, etc. But my understanding is that each of these versions CAN differ in some degree. And now that I have the PeerJ version of your work, I do NOT need to cite the arXiv version. Indeed, as long as there is a “more formal” venue for the MS, that one is always going to the better version, with ANY form of revisions and thus more recent in content. That’s why we don’t try to cite pre-review MSS, and really shouldn’t.


  7. [...] our PeerJ neck-anatomy paper, we speculated on how long individual cervical vertebrae might have grown. Here is the relevant [...]

  8. Vertebrat Says:

    No, Puertasaurus, don’t swallow Matt like that! He should be facing the other way, so he can examine your cervicals on the way down.

    as long as there is a “more formal” venue for the MS, that one is always going to the better version, with ANY form of revisions and thus more recent in content. That’s why we don’t try to cite pre-review MSS, and really shouldn’t.

    Doesn’t this boil down to “use the latest version”? (Except when the latest version has been cut down to fit a page limit or otherwise isn’t as good for whatever reason.) Telling people that it’s bad to cite pre-review content may perpetuate the view they’re not allowed to cite anything that hasn’t been filtered.

  9. Mark Robinson Says:

    Fantabulous stuff! I agree with Matt – even if it was a bit bothersome to submit to PeerJ, it is such an important (and good for everyone, everyone that counts anyway) initiative that if you believe that to be so, you should be supporting it to the max to reduce the chances of sneering negative ninnies being able to smugly say “I told you so” in 5 or whenever year’s time.


  10. [...] 12-2-2013: PeerJ launches today! (and we’re in it!) [...]


  11. [...] 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 [...]


  12. [...] 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 [...]


  13. [...] a manuscript for PLOS ONE, which uses numbered references rather than author+date citations like sane journals. And I am hating it. I am taking perfectly good statements [...]


  14. [...] Long-time readers might remember that when I’m not programming, I am a palaeontologist specialising in the sauropod dinosaurs.  (I got my Ph.D from the University of Portsmouth in 2009, and I’m currently an honorary research associate at UCL).  One of the reasons I’ve not been writing The Reinvigorated Programmer much in recent weeks is that I have — finally — got around to working on resubmission of a couple of pretty substantial papers.  (One is the description of a new genus; the other is about the anatomy and mechanics of sauropod necks.) [...]


  15. […] 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 […]


  16. […] everything PLOS ONE does at a fraction of the cost, and further includes a preprint service and open peer-review. Ditto for F1000 Research, which in addition offers unlimited revisions (a topic close to my heart […]


  17. […] a nice little perk–presumably for being early adopters and users of PeerJ–Mike and I each have been given a small number of referral codes, which will allow […]


  18. […] (12th February) is the one-year anniversary of the first PeerJ papers! As Matt put it in an email this […]


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