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.

I had an email out of the blue this morning, from someone I’d not previously corresponded with, asking me an important question about PeerJ. I thought it was worth sharing the question, and its answer, more generally. So here it is.

Do you have any insight into the PeerJ business model? When I try to persuade people to publish in PeerJ, a very common response is that the journal can’t possibly last because the numbers don’t add up.

And indeed PeerJ’s financial model does seem too good to be true: rather than charging an APC of $1350 (as PLOS ONE does) or $3000 (as the legacy publishers do for their not-really-open hybrid articles), PeerJ charges just $99 per author — which buys not just the right to publish one article, but one per year for life. (Or you can pay $300 for the right to publish any number of papers forever.)

PeerJ is a privately owned company and does not disclose its internal financial details. Since I have no connection with PeerJ (other than being a very satisfied customer), I know nothing of the financials.

But here is what we do know.

1. PeerJ is run by Pete Binfield, who has more experience of running open-access megajournals than anyone alive, and he’s confident enough in the financial model to have staked his own livelihood on it.

2. The principal outside investor in PeerJ is Tim O’Reilly, who has more experience of making money from free-to-read content than anyone alive, and he’s confident enough in the financial model to have staked a seven-figure sum on it.

3. Most importantly, the content in PeerJ is safe forever, because it’s fully, properly, BOAI-compliant open access, licenced using CC By, and archived at PubMed Central. So even if the worst happened, if PeerJ went bankrupt, everything published in it would live on.

4. Since CC-By documents cannot be re-enclosed if their publisher is acquired, even if PeerJ were acquired by a predatory barrier-based publisher such as Elsevier, the articles would remain safe.

5. We have got into the habit of paying far too much for publishing. On average paywalled papers cost the world more than $5000 each. Legacy publishers typically charge APCs of $3000 or so. Yet born-digital publishers such as Ubiquity Press need charge only $500, and show the breakdown of that cost. (And note that $80 of that is set aside to cover waivered articles for which no fee is paid.) Against that analysis, PeerJ’s fees don’t look crazy. The truth is that, as well as their 35% profit-margins, legacy publishers’ costs are sky-high because they are dragging around the carcass of print-based publishing.

6. Numerous universities are confident enough of the PeerJ model that they have signed up for institutional plans. You know, little universities like Cambridge, UCL and Bristol (UK), and Harvard, MIT and Cornell (USA).

Putting it all together, we see that the PeerJ financial model is roughly in alignment with other new-model publishers, that the details are persuasive enough to convince the world-leading experts who know about them, that the open-access papers published in PeerJ will be freely available to the world forever, whatever happens — which is more than we can say for articles “published” behind paywalls, and that the world’s leading universities are on board.

In short, there is no rational reason not to publish in PeerJ (unless you’re statistically illiterate enough to think that its lack of an impact factor is of any scientific significance).

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.

 

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.

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.

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

Folks,

I am preparing 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 like:

Juvenile sauropods have proportionally short cervicals (Wedel et al. 200: 368–369, Fig. 14, and Table 4)

And reformatting them as:

Juvenile sauropods have proportionally short cervicals [31]: 368–369, Fig. 14, and Table 4.

Which doesn’t look right at all.

My question: how, when using numbered references, can I properly refer to page-range and figure number? Because there has to be a way — doesn’t there?

Surely it can’t be the case that in the culture of numbered-reference journals, you just don’t bother to specify with any more precision than pointing at a 46-page paper? I know Science ‘n’ Nature don’t care much about science or nature, but they can’t be that sloppy, can they? And if they are, I’d be horrified to find that the PLOS journals are so infected with me-too that they’re prepared to copy such poor practice?

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

fig4

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

Three milestones

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

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

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

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

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

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

Dissertation thoughts

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

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

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

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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!

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:

amphicoelias-fragillimus-c14-whiteBG

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

References

  • 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.