dodo-skeleton-flipped

Hey, remember this? Your bound-for-PeerJ manuscript is like our Mauritian friend here, and the March 1 deadline is approaching like a hungry sailor with a club. So if you still want a voucher, let me know ASAP.

Today (12th February) is the one-year anniversary of the first PeerJ papers! As Matt put it in an email this morning:

Hard to believe it’s been a year already. On the other hand, it’s also hard to believe that it’s only been a year. PeerJ is just such an established part of my worldview now.

That’s exactly right. PeerJ has so completely rewritten the rule-book (on price, speed and quality of service) that now when I’m thinking about new papers I’m going to write, the question I ask myself is no longer “Where shall I send this?” but “Is there any reason not to send it to PeerJ?”

dorsals-ab-composite

Dorsals A and B (probably D8 and D9) of NHM R5937, “The Archbishop”, a still-undescribed brachiosaurid sauropod from the Upper Jurassic Tendaguru Formation of Tanzania, which I will get done this year, and which is destined for PeerJ. Top row: dorsal view with anterior to the right. Bottom row, from left to right: left lateral, posterior, right lateral, anterior.

Yesterday in the comments of a post on The Scholarly Kitchen, Harvey Kane asked me “I am curious as to where you get the notion that publishing OA is less expensive and in some way “better” than the traditional model?” My reply was (in part):

My notion that OA publishing yields better results than traditional is rooted in the online-only nature of articles, which allows them to ignore arbitrary limits on word-count, number of figures, use of colour, etc., and to exploit online-only formats such as video, 3d models, CT-slice stacks, etc. In my own field of vertebrate palaeontology, it’s now routine to see in PLOS ONE descriptive articles that are many times more comprehensive than their equivalents in traditional journals — see for example the recent description of the frog Beelzebufo.

Of course there is nothing specific to open-access about this: there is no technical reason why an online-only subscription journal shouldn’t publish similarly detailed articles. But my experience so far has been that they don’t — perhaps because they are tied to the mindset that pages and illustrations are limited resources.

For Beelzebufo in PLOS ONE, read baby Parasaurolophus in PeerJ, which we described as “the world’s most open-access dinosaur“. This paper is 83 pages of technicolour goodness, plus all the 3d models you can eat. And the crazy thing is, this sort of detail in descriptive papers is not even exceptional any more — see for example the recent description of Canardia in PLOS ONE, or this analysis of croc respiration in PeerJ

Years ago, I said that in the Archbishop descriptions I wanted to raise the bar for quality of illustration. Well, I’ve taken so long over getting the Archbishop done that the bar has been raised, and now I’m scrambling to catch up. Certainly the illustrations even in our 2011 description of Brontomerus are starting to look a bit old-fashioned.

And of course, the truly astonishing thing about PeerJ is that it does this so very cheaply. Because I’m already a member (which cost me $99), the Archbishop description is going to be free to me to publish this year. (This year for sure!) If we also get our Barosaurus neck preprint published properly this year,then I’ll have to find $100 to upgrade my Basic membership to Enhanced. That’s cheap enough that it’s not even worth going through the hassle of trying to get Bristol to pay for me. And if I ever hit a year when I publish three or more papers, I’ll upgrade once more (for another $100) to the Investigator plan and then that’s it: I’m done paying PeerJ forever, however many papers I publish there. (Matt jumped straight to the all-you-can-eat plan, so he wouldn’t even have to think about it ever again.)

Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view. (Taylor and Wedel 2013b: figure 6)


Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view. (Taylor and Wedel 2013b: figure 6)

PeerJ’s pricing is making PLOS ONE’s $1350 APC look distinctly old-fashioned; and the $3000 charged by the legacy publishers (for a distinctly inferior product) is now frankly embarrassing. You might expect that as such low prices, PeerJ’s quality of service would suffer, but that’s not been our experience: editing, reviewing, typesetting and proofing for our neck-anatomy paper were all up there with the best we’ve received anywhere.

And it’s great to see that it’s not just minor researchers like Matt and me who are persuaded by PeerJ: they’ve now accumulated a frankly stellar list of 20 universities (so far) with institutional plans for researchers to publish there. When I say “stellar” I mean that the list includes Harvard, MIT, Cambridge, Berkeley, Stanford, Johns Hopkins, UCL, Carnegie Mellon, Duke … the list goes on.

We can only hope that the next year, and the next ten and twenty, are as successful for PeerJ as the first has been; and that other New Generation publishers will join it in pushing the field forward.

I leave the last word to Matt:

I’m getting Vicki a lifetime membership for Valentine’s Day. Because I’m a romantic.

She’s a lucky, lucky woman.

Triceratops-dorsal-full

As 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 other folks to publish in PeerJ for free, as long as the papers are submitted by March 1, 2014. Here’s the scoop, straight from the monkey’s mouth:

If you have colleagues who would like to publish at PeerJ, then we want to give them the opportunity to try us out for free. Therefore, as a Published PeerJ Author, we are providing you with 5 unique ‘Referral Codes’ (which expire on March 1st) to distribute to your colleagues. Each code entitles the recipient to an entirely FREE PeerJ publication. They simply need to quote your referral code in the “Notes to Staff” field, when they submit to PeerJ, and as a result they will be able to publish that article for free (assuming it passes peer-review). Please disseminate these codes to colleagues who you feel will use them, but please make sure that they realize that this code is only valid for submissions made before March 1st, 2014.

Note that this is alongside the current promo wherein, if you post a preprint to PeerJ PrePrints (which is a smashing way of getting fast feedback, or at least it was for us), that manuscript can be published in PeerJ for free, as long as it is formally submitted before January 1, 2014. So if you can get the lead out before the end of the year and don’t have an allergy to fast feedback, you don’t actually need one of these codes.

Trex-dorsal-full

So. If you’re not a PeerJ member but you have a manuscript that you’d like to send to PeerJ before the first of next March, let us know and we’ll hook you up with a referral code. If you’re fairly sure you will use one but aren’t ready to ship yet, let me know and I’ll set one aside for you, with the proviso that I can give it away if we’re getting close to the deadline and you’re not realistically going to make it.

If we get more takers than codes, we’ll figure out some fair way of choosing who gets a code, probably randomly. I will be strongly biased toward people without big paychecks* or institutional support, like grad students and postdocs. (If you’re an undergrad, you can already publish in PeerJ for free, at least for the duration of the pilot program.) So if you’re a grad student or postdoc with a serious plan to get published, speak up and you’ll go to the head of the line. So if you let us know why getting a code would benefit you, you’re more likely to get one.

* I know in academia none of us think we have big paychecks, but compared to most grad students and postdocs, those of us with steady full-time employment are living the dream. I’m trying to reach the folks for whom the $99 lifetime membership fee would be a genuine impediment.

Smilodon-Nelson-Maniscalco-TOP-full

As is apparently the usual thing now when I’m writing about PeerJ and don’t have any images of my own queued up, I’ve borrowed images from Brant Bassam’s astoundingly cool BrantWorks.com to spice up this post. Explicit permission to reproduce the images with credit can be found on this page, which is coincidentally where these images themselves are from. Get on over there and prepare to lose some time looking at sweet stuff.

Update! Five more Golden Tickets available!

As noted in the comment below, Heinrich Mallison also has five PeerJ vouchers to distribute to deserving causes. So if Matt and I run out, the options are still open. Feel free to contact Heinrich directly or to go through us if you prefer.

 

It shouldn’t come as a huge surprise to regular readers that PeerJ is Matt’s and my favourite journal. Reasons include its super-fast turnaround, beautiful formatting that doesn’t look like a facsimile of 1980s printed journals, and its responsiveness to authors and readers. But the top reason is undoubtedly its openness: not only are the article open access, but the peer-review process is also (optionally) open, and of course PeerJ preprints are inherently open science.

During open access week, PeerJ now publishes this paper (Farke et al. 2013), describing the most open-access dinosaur in the world.

FarkeEtAl2013-parasaurolophus-fig4

It’s a baby Parasaurolophus, but despite being a stinkin’ ornithopod it’s a fascinating specimen for a lot of reasons. For one thing, it’s the most complete known Parasaurolophus. For another, its young age enables new insights into hadrosaur ontogeny. It’s really nicely preserved, with soft-tissue preservation of both the skin and the beak. The most important aspect of the preservation may be that C-scanning shows the cranial airways clearly:

FarkeEtAl2013-parasaurolophus-fig9

This makes it possible for the new specimen to show us the ontogenetic trajectory of Parasaurolophus – specifically to see how its distinctive tubular crest grew.

FarkeEtAl2013-parasaurolophus-fig11

But none of this goodness is the reason that we at SV-POW! Towers are excited about this paper. The special sauce is the ground-breaking degree of openness in how the specimen is presented. Not only is the paper itself open access (and the 28 beautiful illustrations correspondingly open, and available in high-resolution versions). But best of all, CT scan data, surface models and segmentation data are freely available on FigShare. That’s all the 3d data that the team produced: everything they used in writing the paper is free for us all. We can use it to verify or falsify their conclusions; we can use it to make new mechanical models; we can use it to make replicas of the bones on 3d printers. In short: we can do science on this specimen, to a degree that’s never been possible with any previously published dinosaur.

This is great, and it shows a generosity of spirit from Andy Farke and his co-authors.

But more than that: I think it’s a great career move. Not so long ago, I might have answered the question “should we release our data?” with a snarky answer: “it depends on why you have a science career: to advance science, or to advance your career”. I don’t see it that way any more. By giving away their data, Farke’s team are certainly not precluding using it themselves as the basis for more papers — and if others use it in their work, then Farke et al. will get cited more. Everyone wins.

Open it up, folks. Do work worthy of giants, and then let others stand freely on your shoulders. They won’t weigh you down; if anything, they’ll lift you up.

References

Farke, Andrew A., Derek J. Chok, Annisa Herrero, Brandon Scolieri, and Sarah Werning. 2013. Ontogeny in the tube-crested dinosaur Parasaurolophus (Hadrosauridae) and heterochrony in hadrosaurids. PeerJ 1:e182. http://dx.doi.org/10.7717/peerj.182

Yesterday I announced that our new paper on Barosaurus was up as a PeerJ preprint and invited feedback.

I woke up this morning to find its third substantial review waiting for me.

That means that this paper has now accumulated as much useful feedback in the twenty-seven hours since I submitted it as any previous submission I’ve ever made.

xx

Taylor and Wedel (2013b: figure 7). Barosaurus lentus holotype YPM 429, Vertebra S (C?12). Left column from top to bottom: dorsal, right lateral and ventral views; right column: anterior view. Inset shows displaced fragment of broken prezygapophysis. Note the narrow span across the parapophyses in ventral view, and the lack of damage to the ventral surface of the centrum which would indicate transverse crushing.

It’s worth reviewing the timeline here:

  • Monday 23rd September, 1:19 am: I completed the submission process.
  • 7:03 am: the preprint was published. It took less than six hours.
  • 10:52 am: received a careful, detailed review from Emanuel Tschopp. It took less than four hours from publication, and so of course less than ten from submission.
  • About 5:00 pm: received a second review, this one from Mark Robinson. (I don’t know the exact time because PeerJ’s page doesn’t show an actual timestamp, just “21 hours ago”.)
  • Tuesday 24th September, about 4:00 am: received a third review, this from ceratopsian-jockey and open-science guru Andy Farke.

Total time from submission to receiving three substantial reviews: about 27 hours.

It’s worth contrasting that with the times taken to get from submission to the receipt of reviews — usually only two of them — when going through the traditional journal route. Here are a few of mine:

  • Diplodocoid phylogenetic nomenclature at the Journal of Paleontology, 2004-5 (the first reviews I ever received): three months and 14 days.
  • Revised version of the same paper at PaleoBios, 2005 (my first published paper): one month and 10 days.
  • Xenoposeidon description at Palaeontology, 2006: three months and 19 days, although that included a delay as the handling editor sent it to a third, tie-breaking, reviewer.
  • Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2008: one month and 11 days.
  • Sauropod neck anatomy (eventually to be published in a very different form in PeerJ) at Paleobiologyfive months and two days.
  • Trivial correction to the Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2010: five months and 11 days, bizarrely for a half-page paper.

Despite the wide variations in submission-to-review time at these journals, it’s clear that you can expect to wait at least a month before getting any feedback at all on your submission at traditional journals. Even PeerJ took 19 days to get the reviews of our neck-anatomy paper back to us.

So I am now pretty such sold on the pre-printing route. As well as getting this early version of the paper out there early so that other palaeontologists can benefit from it (and so that we can’t be pre-emptively plagiarised), issuing a preprint has meant that we’ve got really useful feedback very quickly.

I highly recommend this route.

By the way, in case anyone’s wondering, PeerJ Preprints is not only for manuscripts that are destined for PeerJ proper. They’re perfectly happy for you to use their service as a place to gather feedback for your work before submitting it elsewhere. So even if your work is destined for, say, JVP, there’s a lot to be gained by preprinting it first.

I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!

Figure6-vertebra-q-composite

Taylor and Wedel (2013b: figure 6). Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view.

I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:

Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.

Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.

If the PrePrint successfully passes these checks, it will be made public.

You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.

Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).

Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.

And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.

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Taylor and Wedel (2013b: Figure 9). Partial reconstruction of the Barosaurus lentus holotype YPM 429, cervical vertebra R, approximating its undamaged state by allowing for dorsoventral crushing, shearing and loss of some extremities. Anterior and posterior views scaled to 125% of uncorrected width and 80% of uncorrected height. Dorsal view scaled to 80% of uncorrected height; condyle moved forward and cotyle scaled to 50% of uncorrected width to allow for shearing. Lateral view scaled to 125% of uncorrected height, and sheared backwards 15 degrees. Metapophyses and postzygapophyses drawn in multiple views based on vertebrae Q and S and AMNH 6341 material.

I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.

Now here’s what we’d like:

We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.

So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.

Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
  • Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1

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.

Reference

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 http://dx.doi.org/10.7717/peerj.60

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