Long-time SV-POW! readers will remember that three years ago, full of enthusiasm after speaking about Barosaurus at the Edinburgh SVPCA, Matt and I got that talk written up in double-quick time and had it published as a PeerJ Preprint in less than three weeks. Very quickly, the preprint attracted substantive, helpful reviews: three within the first 24 hours, and several more in the next few days.

This was great: it gave us the opportunity to handle those review comments and get the manuscript turned around into an already-reviewed formal journal submission in less then a month from the original talk.

So of course what we did instead was: nothing. For three years.

I can’t excuse that. I can’t even explain it. It’s not as though we’ve spent those three years churning out a torrent of other awesome papers. We’ve both just been … a bit lame.

Anyway, here’s a story that will be hauntingly familiar. A month ago, full of enthusiasm after speaking about Barosaurus at the Liverpool SVPCA, Matt and I found ourselves keen to write up that talk in double-quick time. It’s an exciting tale of new specimens, reinterpretation of an important old specimen, and a neck eight times as long as that 0f a world-record giraffe.

But it would be crazy to write the new Barosaurus paper without first having dealt with the old Barosaurus paper. So now, finally, three years on, we’ve done that. Version 2 of the preprint is now available (Taylor and Wedel 2016), incorporating all the fine suggestions of the people who reviewed the first version — and with a slightly spiffed-up title. What’s more, the new version has also been submitted for formal peer-review. (In retrospect, I can’t think why we didn’t do that when we put the first preprint up.)

Taylor and Wedel 2016: Figure 3. Barosaurus lentus holotype YPM 429, vertebra R, C?15. Top row: dorsal view; middle row, left to right: posterior, right lateral and anterior views; bottom row: ventral view, from Lull (1919: plate II). Note the apparently very low, undivided neural spine at the intersection of the PRSLs and POSLs, forward-shifted neural arch, broad prezygapophyses, broad, wing-like prezygadiapophyseal laminae, and great width across the diapophyses and across the parapophyses. Abbreviations: dia, diapophysis; para, parapophysis; prz, prezygapophysis; prdl, prezygadiapophyseal lamina; spol, spinopostzygapophyseal lamina; sprl, spinoprezygapophyseal lamina. Scale bar = 500 mm.

Taylor and Wedel 2016: Figure 3. Barosaurus lentus holotype YPM 429, vertebra R, C?15. Top row: dorsal view; middle row: posterior, right lateral and anterior views; bottom row: ventral view, from Lull (1919: plate II). Note the apparently very low, undivided neural spine at the intersection of the SPRLs and SPOLs, forward-shifted neural arch, broad prezygapophyses, broad, wing-like prezygadiapophyseal laminae, and great width across the diapophyses and across the parapophyses. Abbreviations: dia, diapophysis; para, parapophysis; prz, prezygapophysis; prdl, prezygadiapophyseal lamina; spol, spinopostzygapophyseal lamina; sprl, spinoprezygapophyseal lamina. Scale bar = 500 mm.

A big part of the purpose of this post is to thank Emanuel Tschopp, Mark Robinson, Andy Farke, John Foster and Mickey Mortimer for their reviews back in 2013. I know it’s overdue, but they are at least all acknowledged in the new version of the manuscript.

Now we cross our fingers, and hope that the formally solicited reviews for the new version of the manuscript are as helpful and constructive as the reviews in that first round. Once those reviews are in, we should be able to move quickly and painlessly to a formally published version of this paper. (I know, I know — I shouldn’t offer such a hostage to fortune.)

Meanwhile, I will finally be working on handling the reviews of this other PeerJ submission, which I received back in October last year. Yes, I have been lax; but I am back in the saddle now.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2016. The neck of Barosaurus: longer, wider and weirder than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v2 doi:10.7287/peerj.preprints.67v2

As explained in careful detail over at Stupid Patent of the Month, Elsevier has applied for, and been granted, a patent for online peer-review. The special sauce that persuaded the US Patent Office that this is a new invention is cascading peer review — an idea so obvious and so well-established that even The Scholarly Kitchen was writing about it as a commonplace in 2010.

Apparently this is from the actual patent. I can't verify that at the moment, as the site hosting it seems to be down.

Apparently this is from the actual patent. I can’t verify that at the moment, as the site hosting it seems to be down.

Well. What can this mean?

A cynic might think that this is the first step an untrustworthy company would take preparatory to filing a lot of time-wasting and resource-sapping nuisance lawsuits on its smaller, faster-moving competitors. They certainly have previous in the courts: remember that they have brought legal action their own customers as well as threatening Academia.edu and of course trying to take Sci-Hub down.

Elsevier representatives are talking this down: Tom Reller has tweeted “There is no need for concern regarding the patent. It’s simply meant to protect our own proprietary waterfall system from being copied” — which would be fine, had their proprietary waterfall system not been itself copied from the ample prior art. Similarly, Alicia Wise has said on a public mailing list “People appear to be suggesting that we patented online peer review in an attempt to own it.  No, we just patented our own novel systems.” Well. Let’s hope.

But Cathy Wojewodzki, on the same list, asked the key question:

I guess our real question is Why did you patent this? What is it you hope to market or control?

We await a meaningful answer.

Long time readers may remember the stupid contortions I had to go through in order to avoid giving the Geological Society copyright in my 2010 paper about the history of sauropod research, and how the Geol. Soc. nevertheless included a fraudulent claim of copyright ownership in the published version.

The way I left it back in 2010, my wife, Fiona, was the copyright holder. I should have fixed this a while back, but I now note for the record that she has this morning assigned copyright back to me:

From: Fiona Taylor <REDACTED>
To: Mike Taylor <mike@indexdata.com>
Date: 15 August 2016 at 11:03
Subject: Transfer

I, Fiona J. Taylor of Oakleigh Farm House, Crooked End, Ruardean, GL17 9XF, England, hereby transfer to you, Michael P. Taylor of Oakleigh Farm House, Crooked End, Ruardean, GL17 9XF, England, the copyright of your article “Sauropod dinosaur research: a historical review”. This email constitutes a legally binding transfer.

Sorry to post something so boring, after so long a gap (nearly a month!) Hopefully we’ll have some more interesting things to say — and some time to say them — soon!

As predicted, the popular and useful Social Sciences repository SSRN, having been acquired by Elsevier, is now being destroyed. Papers are being quietly vanished from SSRN, without their authors even being notified. This is happening even in cases when the copyright is held by the authors (who posted them, giving implicit permission for them to be redistributed), and even more astonishingly when papers are under Creative Commons licences. Details at PrawfsBlawg.

These are not the actions of a publisher acting in good faith.

6a00d8341c4eab53ef01bb09011389970d-800wi

As James Grimmelmann comments:

There’s no longer a point in deterring SSRN. Its new owners at Elsevier have made their true colors clear, and we as a community canot afford to centralize our scholarly communications in the hands of for-profit publishers.

It is time to depublish all of our articles from SSRN and walk away completely. It doesn’t matter if they reverse course now. We can’t trust them in the long run. It’s time to walk away from SSRN.

And as Tony Ross Hellaur puts in, an another comment on the same post (emphasis mine):

Anybody who bought Elsevier’s line that “both existing and future SSRN content will be largely unaffected” following the sell-off should now wake up. Elsevier is aggressive in enforcing copyright, and have the resources and scale to be able to make extreme judgements on what constitutes copyright violation and then to put the burden of proof on individual researchers to show otherwise.

The good news: Brandon Butler points out in the comments that there is a new and open alternative to SSRN: Announcing the development of SocArXiv, an open social science archive. SocArXiv has some very good people behind it. I hope it takes off, and that the zombie SSRN is rapidly defleshed.

A few months ago I got an email from Nathan Myers, who asked me:

Do you have advice for someone who wants to spin up a new OA journal? Is there automation for the boring parts? Is someone you know well versed in what to do?

In many ways, I’m the wrong person to ask: I’ve never started a journal, OA or otherwise, nor even served on an editorial board.

But, hey, I’m not one to let something like that stop me. So here’s what I told Nathan. I’m sure I missed a lot of important possibilities: please point them out in this comments. I’ll try to keep this post updated as the landscape changes.


There are several good options at this point.

The simplest and cheapest is probably to use Annotum, a WordPress plugin that helps with the review workflow. I’ve not used it myself, but I know it’s what PLOS Currents uses, so it’s obvious battle-ready. I’m not sure but I think you can use it as a theme in a wordpress.com-hosted free blog.

Scholastica offers very low-cost support for running an overlay journal, as for example the recently launched Discrete Analysis: see Tim Gowers’ blog-post about the new journal.

Open Journals Systems is a widely used software package for running open-access journals — IIRC they have more that 10,000 running installations worldwide. I’ve not used it, but it evidently has what it takes.

If you have some funding to cover production charges, or are able to charge an APC, you can use a full-service option from a low-cost OA publisher such as Ubiquity Press.

PeerJ’s system is widely liked — very easy for authors and reviewers to use. Its software is all on GitHub, though I think some work would be needed to tie it all together. If you have the software engineering chops, this may be the best option for performance/price ratio.

What else?

Back in mid-April, when I (Mike) was at the OSI2016 conference, I was involved in the “Moral Dimensions of Open” group. (It was in preparation for this that wrote the Moral Dimensions series of posts here on SV-POW!.)

Like all the other groups, ours was tasked with making a presentation to the plenary session, taking questions and feedback, and presenting a version 2 on the final day. Here’s the title page that I contributed.

morality-report

Each group was also asked to write a short paper summarising their discussions and conclusions, with all the papers to be published openly. The resulting papers are now available: sixteen of them in all. And among them is Ansolabehere et al. (2016), “The Moral Dimensions of Open”, of which I am one of nine authors. (There were ten authors of the presentation: for some reason, Ryan Merkley is not on the paper.)

As you can imagine in a group that contained open-access advocates, human rights activists, representatives of both old-school and new-wave publishers, agriculturalists and more, consensus was far from unanimous, and it was quite a rocky road to arriving at a form of the paper that we could all live with. In this case, the standard note that was added to all the papers is very appropriate:

This document reflects the combined input of the authors listed here (in alphabetical order by last name) as well as contributions from other OSI2016 delegates. The findings and recommendations expressed herein do not necessarily reflect the opinions of the individual authors listed here, nor their agencies, trustees, officers, or staff.

Is this the moral-dimensions paper I would have written? No, it’s not. Being a nine-way collaboration, it pulls in too many directions to have as clear a through-line as I’d like; and it’s arguably a bit mealy-mouthed in places. But over all, I am pretty happy with it. I think it makes some important points, and makes them reasonably well given the sometimes clumsy prose that you always get when something is written by committee.

Anyway, I think it’s worth a read.

By the way, I’d like to place on record my thanks to Cheryl Ball of West Virginia University, who did the bulk of the heavy lifting in putting together both the presentation and the paper. While everyone in the group contributed ideas and many contributed prose, Cheryl dug in and did the actual work. Really, she deserves to be lead author on this paper — and would be, but for the alphabetical-order convention.

References

 

In discussions of open access, it’s pretty common for us biologists to suffer from arXiv envy: the sense that mathematicians and physicists have the access problem solved, because they all put their work on arXiv.

That’s a widespread idea, which is why we see tweets like this one, which floated past in my stream today:

Turns out, not so much. A preprint by Larivière et al. (2013) looked at various aspects of the relationship between papers on arXiv and their corresponding versions in journals, as indexed by the Web of Science. they were interested in several other things (like the average delay between arXiv publication and journal publication) but the aspect of their work that struck me was this:

LariviereEtAl2013-fig2

Even in mathematics, the field that is most committed to arXiv, only a feeble 21.5% of published papers are also available on arXiv! In physics, it’s 20%, and “Earth and Space” it’s a smidge under 12%. For everything else, it’s virtually nothing.

Does that come as a shock to anyone else? I’ve not seen figures before, but I always thought the numbers were more like 90-95% in maths, physics and astronomy.

Even within the most arXiv-aware subfields, the numbers are disappointing:

LariviereEtAl2013-fig3

Even the very best subfield manages to get only about 72% of its publications into arXiv. After the second best (69%), no other subfield does better than a frankly abject 31%.

So unless I am badly misunderstanding this study, it seems the old idea that you don’t need open-access journals in maths and physics because everything’s on arXiv is way off base.

How very disappointing.

References

  • Larivière, Vincent, Cassidy R. Sugimoto, Benoit Macaluso, Staša Milojević, Blaise Cronin, Mike Thelwall. 2013. arXiv e-prints and the journal of record: An analysis of roles and relationships. arXiv 1306.3261.