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

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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.

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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.)

Here at SV-POW!, we are an equal-opportunity criticiser of publishers: SpringerPLOS, Elsevier, the Royal Society, Nature, we don’t care. We call problems as we see them, where we see them. Here is one that has lingered for far too long. PLOS ONE’s journal information page says:

Too often a journal’s decision to publish a paper is dominated by what the Editor/s think is interesting and will gain greater readership — both of which are subjective judgments and lead to decisions which are frustrating and delay the publication of your work. PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound.

Which is as we would expect it to be. But their reviewer guidelines page gives more detail as follows (emphasis added):

[Academic Editors] can employ a variety of methods, alone or in combination, to reach a decision in which they are confident:

  • They can conduct the peer review themselves, based on their own knowledge and experience
  • They can take further advice through discussion with other members of the editorial board
  • They can solicit reports from further referees

As has been noted in comments on this blog, this first form, in which the editor makes the decision alone, is “unlike any other first-tier academic journal”. When I submitted my own manuscript to PLOS ONE a few weeks ago, I did it in the expectation that it would be reviewed in the usual way, by two experts chosen by the editor, who would then use those reviews in conjunction with her own expertise to make a decision. I’d hate to think it would go down the easier track, and so not be accorded the recognition that a properly peer-reviewed article gets. (Merely discussing with other editors would also not constitute proper peer-review in many people’s eyes, so only the third track is really the whole deal.)

The problem here is not a widespread one. Back when we first discussed this in any detail, about 13% of PLOS ONE papers slipped through on the editor-only inside lane. But more recent figures (based on the 1,837 manuscripts that received a decision between 1st July and 30th September 2010) say that only 4.2% of articles take this track. Evidently the process was by then in decline; it’s a shame we don’t have more recent numbers.

But the real issue here is lack of transparency. Four and half years ago, Matt said “I really wish they’d just state the review track for each article–i.e., solo editor approved, multiple editor approved, or externally reviewed [...] I also hope that authors are allowed to preferentially request ‘tougher’ review tracks”.

It seems that still isn’t done. Looking at this article, which at the time of writing is the most recent one published by PLOS ONE, there is a little “PEER REVIEWED” logo up at the top, but no detail of which track was taken. PLOS themselves evidently take the line that all three tracks constitute peer-review, as “Academic Editors are not employees [...] they are external peer reviewers“.

So I call on PLOS ONE to either:

A. eliminate the non-traditional peer-review tracks, or

B1. Allow submitting authors to specify they want the traditional track, and

B2. Specify explicitly on each published paper which track was taken.

Because I am preparing this paper from PLOS ONE, with its stupid numbered-references system, I am finally getting to grips with a reference-management system. Specifically, Zotero, which is both free and open source, which means it can’t be taken over by Elsevier.

As a complete Zotero n00b, I’ve run into a few issues that more experienced users will no doubt find laughable. Here are two of them. I need to cite Greg Paul’s classic 1988 paper on the skeletal reconstruction of Giraffatitan:

Paul, Gregory S. 1988. The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2(3):1-14.

When I render this using Zotero’s PLOS ONE style, it comes out as:

Paul GS (1988) The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs. Hunteria 2: 1–14.

So the first problem is, how can I get Giraffatitan to be set in italics?

And the second one, which is arguably more important, is how can I get the issue number included? I undertsand that PLOS ONE referencing style omits the issue-numbers by preference, since they are often redundant, with the pages of each volume being numbered consecutively across volumes. But Hunteria is one of those journals (PaleoBios is another) that resets page-numbers at the start of each issue. As a result, Hunteria volume 2 had at least three page 14s, one in each of its issues, so that issue number is a crucial part of the reference.

Help me, SV-POW! readers — you’re my only hope.

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