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.

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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.

Just like the last time I tried to post a comment on Richard Van Noorden’s piece on open-access economics, the comment I posted has been rejected with a fatuous “This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service” message.

SERIOUSLY, NATURE PUBLISHING GROUP. HOW HARD CAN IT BE?

You will notice that neither WordPress-hosted blogs such as SV-POW!, nor Blogger-hosted blogs such as Mark Witton’s offering — nor indeed PLOS-hosted blogs such as The Integrative Paleontologists — consistently throws away perfectly good comments.

It’s 2013. There is no excuse for running a non-functional blog. None. If you aspire to be a hub of meaningful discussion, you have to make your software work right. It’s not good blowing it off with a snort and a giggle, “Oh, yeah, that happens all the time, ha ha”. It’s contemptible — worse, it’s comtemptuous of your readers and of the people who spend time and effort to provide you with free content.

Sort it out.

For anyone who cares, here is the actual comment that I tried to post:

My thanks to Richard Van Noorden and David Crotty for useful criticisms of my simple calculations.

If both sets of figures are correct — that average profit-margins for the Big Four are 36% but the average across the industry is “only” 20-30% then it’s clear that the great majority of the parasitism that currently infests academia can be laid at the doors of the Big Four.

Is the Big-Four number correct? All we have to go on is the figures that those corporations themselves publish — and those are what I used in the linked blog post. If Wiley have now changed what they report, then we can use their new number instead. What we can’t legitimately do is look at what they say they make, then use a different number of our own choosing.

And here is where we reach the real problem: the appalling lack of transparency. David Crotty rightly points out “the assumption that the entirety of the $9.4 billion brought in by the publishing industry comes from subscriptions”. But I have tried very hard to get a number for what proportion of income is indeed from subscriptions, and not been able to get answers from Big-Four publishers. One of them explicitly told me to stop even asking. In the face of such obscurity, all we can do is work with what numbers we do have.

If any of the Big Four would like to reveal the true numbers, I would be delighted to hear them, and to revise my calculations accordingly.

Meanwhile here is my least bad re-calculation. If industry average profit margins are 20-30%, we’ll use the middle of the range, 25%. That means that 1/4 of the annual $9.4 billion revenue is profit — 2.35 billion. By coincidence, this is almost exactly equal to the price of publishing the year’s 1.8 million articles as Gold OA at a PLOS ONE price-point of $1350, namely $2.43 billion. Remember, this is not saying that what we spend on subscriptions would fund 100% Gold OA. It’s saying that what we throw away as sheer profit for publishers would fund it.

If that doesn’t make anyone absolutely furious, then that person’s outrage-meter is badly in need of recalibration. We’re supposed to be doing science here, not enriching shareholders with public money.

Thanks for listening.

My thanks for Richard Van Noorden for drawing my attention to his new piece Open access: The true cost of science publishing in Nature. I wrote a detailed comment on this article, but when I went to post it, I was told “This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service”:

banned-from-nature

This news to me. No-one at Nature thought to tell me, or anything. Their system said nothing about when I logged in, nor when I started entering my comment. Just waited till I’d finished, then trashed it.

I have no idea why I am banned. How can I have, when I’ve never received any notification? I can only assume it’s for posting opinions that are at odds with what NPG would prefer we all thought — at least, in the absence of any actual data, that’s the best hypothesis I can come up with. Update 40 minutes later: turns out it was a glitch in the spam-filter. Richard got it fixed, and my comment is now up on the article.

Listen up, Nature Publishing Group: you will never get meaningful dialogue in your comments if you silently ban everyone who expresses a non-party-line opinion random people for no discernable reason. You should be aspiring to be a hub of civilised discourse on these important issues, not an echo-chamber. (If you want that, you can just go and read The Scholarly Kitchen.)

Anyway: I am paranoid enough that I copied my comment before submitting it — I’ve been screwed in too many ways by too many commenting systems to trust anything but my own. So here is that comment, stripped of its context but still IMHO important. Perhaps someone who has not been banned from commenting at Nature could post it for me?

Thanks for this useful post, Richard. I am provoked by this statement:

“Analysts estimate profit margins at 20–30% for the industry.”

Where do such low numbers come from? As is by now well known, the profit margins for the Big Four publishers (Elsevier, Springer, Wiley and Informa) are between 32.4 and 42 percent — not one of them has a margin as low as the highest end of the range you cite. Not only that, but commercial academic publishers’ profit margins continue to rise year on year.

The average profit margin among the Big Four is 36%, which means that of the $9.4 billion spent on subscriptions in 2011, $3.39 billion was simply poured down the academic drain. Note that this profit alone would be enough to pay APCs for 2.5 million PLOS ONE articles, 40% more than the world actually produced in that year.

So to spell it out, subscription profits alone would be enough to fund OA publication of ALL research, with just under a billion dollars left over to fund additional research. It’s not just idiotic that we keep paying this ludicrously inflated subscriptions, it’s iniquitous.

How disruptive is PeerJ?

February 21, 2013

Matt and I were discussing “portable peer-review” services like Rubriq, and the conversation quickly wandered to the subject of PeerJ. Then I realised that that seems to be happening with all our conversations lately. Here’s a partial transcript.

Mike: I don’t see portable peer-review catching on. Who’s going to pay for it unless journals give an equal discount from APCs? And what journal is going to do that when they get the peer-review done for free anyway? If I was Elsevier, I wouldn’t say “OK, we’ll accept your external review and give you a $700 discount”, I’d charge the full $3000 and get two more free reviews done.

Plus, you know, I can get all the peer-review I want, free of charge, at PeerJ.

Matt: Yeah, that was pretty much my take. Even as I was sending that I thought about adding, “I wonder if this is one more thing that PeerJ will kill.” Only ‘abort’ is more the verb I want, in that I don’t see this ever getting off the ground anyway.

Mike: I think the world at large has yet to realise what a black hole PeerJ is, in the sense that it’s warping all the space near it. Pretty much every time I have any thought at all about scholarly publishing now, that thought it swiftly followed by “… or, wait, I should just use PeerJ for that.”

Matt: Exactly. It makes me think that we may be discovering the contours of that space-warping effect for some time, in that we’re used to one model, and that, among all the other things PeerJ does, it quacks something like that old model so we tend to think of it as a very cool duck, and not the freakin’ tyrannosaur that is going to eat scholarly publishing.

Also makes me think of that Paul Graham thing about noticing that the door is open, and there being a lag between the freedom to do something and the adoption of that newly facilitated action or behavior.

Interesting times.

New thought: assuming PeerJ does not implode, will the established powers try to start PeerJ-alikes, and if so, what will they charge (amount), and what will they charge for (lifetime membership? decadal? annual? per 1000 pages published?).

Mike: Sweet metaphor. It’s true. It’s qualitatively different from other journals in two respects.

First, the APC is literally an order of magnitude less — and at that point, a quantitative difference becomes qualitative. Someone like [NAME REDACTED] would worry about paying $1350 to PLOS ONE, but didn’t even stop and think before saying, yeah, I’ll do that.

Second, the lifetime membership changes the game for all subsequent submissions. Now when you have a manuscript ready to go, your question isn’t going to be “where shall I send this?”, it’s going to be “is there are compelling reason not to send this to PeerJ?”

Legacy publishers won’t start PeerJ-alikes because they can’t. As noted in many SV-POW! posts, Elsevier takes about $5000 for each article they put behind a paywall. Slice away the 40% profit and you get $3000 which not coincidentally is what they charge as an APC. They have old, slow, encumbered systems and processes and top-heavy organisation. At $3000 they are only breaking even. They can’t compete at a PLOS-like $1350 level and they can’t even think about competing at PeerJ levels. If they offered a lifetime membership they’d have to ask $10k or something stupid.

I don’t think it’s that they don’t want to change. They can’t. They’ve ossified into 1990s companies running on 1990s software. It’s hard to steer a ship with a $2bn turnover, and impossible to replace the engines while still cruising.

Matt: I think it is probably a mistake to think that PeerJ will only encroach “upward”, onto the territory of more traditional journals (which is “all of them”). We’ve already talked about it taking business from arXiv (at least ours, although there is the large non-overlap in their respective subject domains–for now, anyway).

But my point is, the question, “Why wouldn’t I send this to PeerJ?” may not only kick in for papers that you might conceivably send elsewhere, but also for manuscripts that you might not conceivably send anywhere.

Mike: There are plenty of historical SV-POW! posts that could have been PeerJ articles on their own — for example, the shish-kebab post that ended up as part of Why Giraffes Have Short Necks.

Matt: Right. And if one is on the fence, shove it on the PeerJ preprint server and see what people have to say.

Mike: I think it’s the first megajournal to have an associated preprint server, and that may yet prove the most important of all its innovations.

Matt: It feels almost … struggling to find the right word, in part because it’s late and I need to go sleep. “Seditious” is not quite it, and neither is “seductive”.

At that point we started talking about something else, so I never did find out what word Matt was groping for. But what’s only gradually become clear to us is how much PeerJ is changing how we think about the academic publishing process. It’s shaking us out of mental ruts that we didn’t even know we were in. Exciting.

 

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