Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Today sees the description of Aquilops americanus (“American eagle face”), a new basal neoceratopsian from the Cloverly Formation of Montana, by Andy Farke, Rich Cifelli, Des Maxwell, and myself, with life restorations by Brian Engh. The paper, which has just been published in PLOS ONE, is open access, so you can download it, read it, share it, repost it, remix it, and in general do any of the vast scope of activities allowed under a CC-BY license, as long as we’re credited. Here’s the link – have fun.

Obviously ceratopsians are much more Andy’s bailiwick than mine, and you should go read his intro post here. In fact, you may well be wondering what the heck a guy who normally works on huge sauropod vertebrae is doing on a paper about a tiny ceratopsian skull. The short, short version is that I’m here because I know people.

OMNH 34557, the holotype of Aquilops

OMNH 34557, the holotype of Aquilops

The slightly longer version is that OMNH 34557, the holotype partial skull of Aquilops, was discovered by Scott Madsen back in 1999, on one of the joint Cloverly expeditions that Rich and Des had going on at the time. That the OMNH had gotten a good ceratopsian skull out of Cloverly has been one of the worst-kept secrets in paleo. But for various complicated reasons, it was still unpublished when I got to Claremont in 2008. Meanwhile, Andy Farke was starting to really rock out on ceratopsians at around that time.

For the record, the light bulb did not immediately go off over my head. In fact, it took a little over a year for me to realize, “Hey, I know two people with a ceratopsian that needs describing, and I also know someone who would really like to head that up. I should put these folks together.” So I proposed it to Rich, Des, and Andy in the spring of 2010, and here we are. My role on the paper was basically social glue and go-fer. And I drew the skull reconstruction – more on that in the next post.

One of the world's smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale.

One of the world’s smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale. Copyright Leah Vanderburg, courtesy of the Sam Noble Oklahoma Museum of Natural History.

Anyway, it’s not my meager contribution that you should care about. I am fairly certain that, just as Brontomerus coasted to global fame on the strength of Paco Gasco’s dynamite life restoration, whatever attention Aquilops gets will be due in large part to Brian Engh’s detailed and thoughtful work in bringing it to life – Brian has a nice post about that here. I am very happy to report that the three pieces Brian did for us – the fleshed-out head that appears at the top of this post and as Figure 6C in the paper, the Cloverly environment scene with the marauding Gobiconodon, and the sketch of the woman holding an Aquilops - are also available to world under the CC-BY license. So have fun with those, too.

Finally, I need to thank a couple of people. Steve Henriksen, our Vice President for Research here at Western University of Health Sciences, provided funds to commission the art from Brian. And Gary Wisser in our scientific visualization center used his sweet optical scanner to generate the hi-res 3D model of the skull. That model is also freely available online, as supplementary information with the paper. So if you have access to a 3D printer, you can print your own Aquilops – for research, for teaching, or just for fun.

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Next time: Aquilöps gets röck döts.

Reference

Farke, A.A., Maxwell, W.D., Cifelli, R.L., and Wedel, M.J. 2014. A ceratopsian dinosaur from the Lower Cretaceous of Western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055

Despite the flagrant trolling of its title, Nature‘s recent opinion-piece Open access is tiring out peer reviewers is mostly pretty good. But the implication that the rise of open-access journals has increased the aggregate burden of peer-review is flatly wrong, so I felt obliged to leave a comment explaining why. Here is that comment, promoted to a post of its own (with minor edits for clarity):


 

Much of what is said here is correct and important. Although it would be nice if Nature could make a bit more of an effort to avoid the obvious conflict-of-interest issues that lead it to title the piece so misleadingly as an attack on open access. I am glad that so many of the other commenters on this piece saw straight through that rather snide piece of propaganda.

Only one important error of interpretation here, I think. I quote:

The rise of the open-access (OA) movement compounds this effect [i.e. the increasing number of articles needing peer-review.] The business case for online OA journals, to which authors pay submission fees, works best at high volume. And for many of these journals, submitted work is published as long as it is methodologically sound. It does not have to demonstrate, for example, the novelty or societal relevance that some traditional journals demand.

The implication is that journals of this kind (PLOS ONE, PeerJ, the various Frontiers journals) increase the total peer-review burden. In fact, the exact opposite is the case. They greatly reduce the the total amount of peer reviewing.

It’s an open secret that nearly every paper eventually gets published somewhere. Under the old regime, the usual approach is to “work down the ladder”, submitting the same paper repeatedly to progressively less prestigious journals until it reached one that was prepared to publish work of the supplied level of sexiness. As a result, many papers go through four, five or more rounds of peer-review before finally finding a home. Instead, such papers when submitted to a review-for-soundness-only venue such as PLOS ONE require only a single round of review. (Assuming of course that they are indeed methodologically sound!)

The rise of review-for-soundness-only journals (“megajournals”) is an unequivocal improvement in the scientific publishing landscape, and should be welcomed by all parties: authors, who no longer have to submit to the monumental waste of time and effort that is the work-down-the-ladder system; readers, who get access to new research much more quickly; and editors and reviewers who no longer have to burn hours re-reviewing and re-re-reviewing perfectly good papers that have already been repeatedly rejected for a perceived lack of glamour.

A few bits and pieces about the PLOS Collection on sauropod gigantism that launched yesterday.

2013-10-29-SauropodEbook1-thumb

First, there’s a nice write-up of one of our papers (Wedel and Taylor 2013b on pneumaticity in sauropod tails) in the Huffington Post today. It’s the work of PLOS blogger Brad Balukjian, a former student of Matt’s from Berkeley days. The introduction added by the PLOS blogs manager is one of those where you keep wanting to interrupt, “Well, actually it’s not quite like that …” but the post itself, once it kicks in, is good. Go read it.

Brad also has a guest-post on Discover magazine’s Crux blog: How Brachiosaurus (and Brethren) Became So Gigantic. He gives an overview of the sauropod gigantism collection as a whole. Well worth a read to get your bearings on the issue of sauropod gigantism in general, and the new collection in particular.

PLOS’s own community blog EveryONE also has its own brief introduction to the collection.

And PLOS and PeerJ editor Andy Farke, recently in these pages because of his sensational juvenile Parasaurolophus paper, contributes his own overview of the collection, How Big? How Tall? And…How Did It Happen?

Finally, if you’re at SVP, go and pick up your free copy of the collection. Matt was somehow under the impression that the PLOS USB drives with the sauropod gigantism collection would be distributed with the conference packet when people registered. In fact, people have to go by the PLOS table in the exhibitor area (booth 4 in the San Diego ballroom) to pick them up. There are plenty of them, but apparently a lot of people don’t know that they can get them.

References

This is an exciting day: the new PLOS Collection on sauropod gigantism is published to coincide with the start of this year’s SVP meeting! Like all PLOS papers, the contents are free to the world: free to read and to re-use.  (What is a Collection? It’s like an edited volume, but free online instead of printed on paper.)

There are fourteen papers in the new Collection, encompassing neck posture (yay!), nutrition (finally putting to bed the Nourishing Vomit Of Eucamerotus hypothesis), locomotion, physiology and evolutionary ecology. Lots every sauropod-lover to enjoy.

x

Taylor and Wedel (2013c: Figure 12). CT slices from fifth cervical vertebrae of Sauroposeidon. X-ray scout image and three posterior-view CT slices through the C5/C6 intervertebral joint in Sauroposeidon OMNH 53062. In the bottom half of figure, structures from C6 are traced in red and those from C5 are traced in blue. Note that the condyle of C6 is centered in the cotyle of C5 and that the right zygapophyses are in articulation.

Matt and I are particularly excited that we have two papers in this collection: Taylor and Wedel (2013c) on intervertebral cartilage in necks, and Wedel and Taylor (2013b) on pneumaticity in the tails of (particularly) Giraffatitan and Apatosaurus. So we have both ends of the animal covered. It also represents a long-overdue notch on our bed-post: for all our pro-PLOS rhetoric, this is the first time either of has had a paper published in a PLOS journal.

Wedel and Taylor (2013b: Figure 4). Giraffatitan brancai tail MB.R.5000 (‘Fund no’) in right lateral view. Dark blue vertebrae have pneumatic fossae on both sides, light blue vertebrae have pneumatic fossae only on the right side, and white vertebrae have no pneumatic fossae on either side. The first caudal vertebra (hatched) was not recovered and is reconstructed in plaster.

It’s a bit of a statistical anomaly that after a decade of collaboration in which there was never a Taylor & Wedel or Wedel & Taylor paper, suddenly we have five of them out in a single year (including the Barosaurus preprint, which we expect to eventually wind up as Taylor and Wedel 2014). Sorry about the alphabet soup.

Since Matt is away at SVP this week, I’ll be blogging mostly about the Taylor and Wedel paper this week. When Matt returns to civilian life, the stage should be clear for him to blog about pneumatic caudals.

Happy days!

References

I just read Mick Watson’s post Why I resigned as PLOS ONE academic editor on his blog opiniomics. Turns out his frustration with PLOS ONE is not to do with his editorial work but with the long silences he faced as an author at that journal when trying to get a bad decision appealed.

I can totally identify with that, though my most frustrating experiences along these lines have been with other journals. (yes, Paleobiology, I’m looking at you.) So here’s what I wrote in response (lightly edited from the version that appeared as a comment on the original blog).

There’s one thing that PLOS ONE could and should do to mitigate this kind of frustration: communicate. And so should all other journals.

At every step in the appeal process — and indeed the initial review process — an automated email should be sent to the author. So for the initial submission:

  1. “Your paper has been assigned an academic editor.”
  2. “Your paper has been sent out to a reviewer.”
  3. “An invited reviewer has declined to review; we will try another.”
  4. “An invited reviewer failed to accept or decline within two weeks; we will try another.”
  5. “A review has been submitted.”
  6. “A reviewer has failed to submit his report within four weeks; we are making contact again to ask for a quick response.”
  7. “A reviewer has failed to submit his report within six weeks; we have dropped that reviewer from this process and will try another.”
  8. “All reviews are in; the editor is considering the decision.”
  9. Decision letter.

And for the appeal:

  1. “Your appeal has been noted and is under consideration.”
  2. “We have contacted the original handling editor.”
  3. “The original handling editor has responded.”
  4. “The original handling editor has failed to respond after four weeks; we are escalating to a senior editor.”
  5. [perhaps] go back into some of all of the submission process.
  6. Decision letter.

Most if not all of these stages in the process already have workflow logic in the manuscript-handing system. There is no reason not to send the poor author emails when they happen — it’s no extra work for the editor or reviewers.

Speaking as the veteran of plenty of long-drawn-out silences from journals that I’ve submitted to, I know that getting these messages would have made a big difference to me.

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.)

Christopher W. Schadt tells a distasteful story over on his blog, about how a PLOS ONE paper that he was a co-author on was republished as part of a non-PLOS printed volume that retails for $100. The editors and publishers of this volume neither asked the authors’ permission to do this (which is fair enough, it was published as CC By), nor even took the elementary courtesy of informing them. Worse, the reprinted copy in the book doesn’t have a reference to the original version in PLOS ONE.

It’s clear the editors of this book have (to put it mildly) been rather rude here. But what they’ve done is possibly legal and in accordance with the terms under which the article was originally published. The CC By licence requires attribution, and sure enough the work is attributed to the correct authors.

But does CC By require that the original publication also be credited? Not exactly. The terms of the licence say that the work can be reused subject to this condition:

Attribution — You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).

So the author could specify (and PLOS should probably specify in the published form of their articles) that the manner in which the work should be attributed requires not only authorship to be recognised but also the original publication in PLOS to be cited.

But the current PLOS wording on this is unfortunately a mess. Schadt’s article, like all PLOS ONE articles, says:

Copyright: © 2010 Reganold et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

This is probably intended to say that attribution must mention both author and source (i.e. citation of original publication). But what this wording actually does, wrongly, is state that this is what the CC BY licence intrinsically requires.

So PLOS have a bit of work to do to tidy this up. And they are not alone in this. PeerJ uses the exact same form of words, and BMC says something a bit different (“… provided the original work is properly cited”) which us also open to misinterpretation.

All three of these publishers, and probably many others using CC By, need to tighten their wording so that they don’t claim that CC By requires a full citation, but stipulate that in their use of CC By, providing a citation is part of what constitutes proper attribution.

Had PLOS ONE done that, then the reprinted version of the Reganold et al. paper would have been clearly not covered by the CC By licencing option, and so would have constituted copyright violation plain and simple. As it is, they’re clearly guilty but have some wiggle-room. (To be fair, representatives of the production company and publisher have been quick to apologise on Schadt’s blog.)

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