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.

Matt’s post yesterday was one of several posts on this blog that have alluded to Clay Shirky’s now-classic article How We Will Read [archived copy]. Here is the key passage that we keep coming back to:

Publishing is not evolving. Publishing is going away. Because the word “publishing” means a cadre of professionals who are taking on the incredible difficulty and complexity and expense of making something public. That’s not a job anymore. That’s a button. There’s a button that says “publish,” and when you press it, it’s done.

In ye olden times of 1997, it was difficult and expensive to make things public, and it was easy and cheap to keep things private. Privacy was the default setting. We had a class of people called publishers because it took special professional skill to make words and images visible to the public. Now it doesn’t take professional skills. It doesn’t take any skills. It takes a WordPress install.

… and of course as SV-POW! itself demonstrates, it doesn’t even need a WordPress install — you can just use the free online service.

This passage has made a lot of people very excited; and a lot other people very unhappy and even angry. There are several reasons for the widely differing responses, but I think one of the important ones is a pun on the word “publish”.

When Shirky uses the word, he is talking  about making something public, available to the world. Which after all is its actual meaning.

But when academics use the word “publish” they usually mean something quite different — they mean the whole process that a research paper goes through between submission and a PDF appearing in a stable location (and in some cases, copies being printed). That process involves many other aspects besides actual publishing — something that in fact Shirky goes straight on to acknowledge:

The question isn’t what happens to publishing — the entire category has been evacuated. The question is, what are the parent professions needed around writing? Publishing isn’t one of them. Editing, we need, desperately. Fact-checking, we need. For some kinds of long-form texts, we need designers.

And this is dead on target. Many writers need editors[*], to varying degrees. Fact-checking could be equated with peer-review, which we pretty much all agree is still very important. Most academic publishers do a certain amount of design (although I suspect that in the great majority of cases this is 99% automatic, and probably involves human judgement only in respect of where to position the illustrations).

But due to the historical accident that it used to be difficult and costly to make and distribute copies, all those other tasks — relatively inexpensive ones, back in the days when distribution was the expensive thing — have become bundled with the actual publishing. With hilarious consequences, as they say. You know, “hilarious” in the sense of “tragic, and breathtakingly frustrating”.

funny-sad-truck-head-down

That’s why we’re stuck in an idiot world where, when we need someone to peer-review our manuscript, we usually trade away our copyright in exchange (and not even to the people who provide the expert review). If you stop and think about that for a moment, it makes absolutely no sense. When I recently wrote a book about Doctor Who, I had several people proofread it, but I didn’t hand over copyright to any of them. My ability to distribute copies was not hobbled by having had independent eyes look it over. There is no reason why it should have, and there is no reason why our ability to distribute copies of our academic works should be limited, either.

What we need is the ability to pay a reasonable fee for the services we need —  peer-review, layout design, reference linking — and have the work published freely.

Well, wouldja lookit that. Looks like I just invented Gold Open Access.

Is publishing just a button? Yes. Making things public is now trivial to do, and in fact much of what so-called publishers now do is labouring to prevent things from being public. But we do need other things apart from actual publishing — things that publishers have historically provided, for reasons that used to make sense but no longer do.

Exactly what those things are, and how extensive and important they are, is a discussion for another day, but they do exist.

 

[*] Note: the whole issue of academic publishing is further confused by another pun, this one on the word “editor”. When Shirky refers to editors, he means people who sharpen up an author’s prose — cutting passages, changing word choices, etc. Academic editors very rarely do that, and would be resented if they did. In our world, an “editor” is usually the nominally independent third party who solicits and evaluates peer-reviews, and makes the accept/reject decision. Do we need editors, in this academic sense? We’ll discuss that properly another time, but I’ll say now that I am inclined to think we do.

At the end of October, we published a short piece called CC-By documents cannot be re-enclosed if their publisher is acquired. In an interesting discussion in the comments, moominoid asked:

Isn’t this what happened when DeGruyter acquired BEPress?

And subsequently expanded:

This is the announcement of the acquisition. If you visit the journals now, they are behind paywalls, when they were OA before the acquisition.

Having previously read (and commented favourably on) an interview with bepress CEO Jean-Gabriel Bankier,  I was disappointed to think this might be true. I emailed him to ask for clarification, and he passed my message on to Irene Kamotsky, bepress’s Director of Strategic Initiatives. A little later, she send a helpful a detailed response, which I now reproduce with her permission.


Date: 10 November 2014 14:27
From: Irene Kamotsky
To: Mike Taylor
Cc: Jean-Gabriel Bankier
Subject: Re: Previous OA journals enclosed behind paywalls?

Dear Mike,

I apologize for sitting on this for so long — thank you so much for following up, and for clarifying what was, indeed, always a bit confusing about the bepress-published journals that are now with deGruyter.

To answer your question, the bepress journals were not open access in the formal (Budapest) definition of the term, and they never used a CC license. The copyright was traditional publisher-owned copyright, with permission to authors to post their articles on their websites and university IRs.

The bepress journals did have an unusual access policy: we made all articles available to readers for free, as a way to demonstrate demand and urge libraries to subscribe. Basically, if a guest filled out a short form we would grant them access to the article. We would tally those forms by institution and then call the library and ask them to subscribe. There’s an article in Learned Publishing that describes the model in more detail. It wasn’t open access but it was a good balance for many years. Unfortunately, libraries facing strong budget pressures stopped subscribing. They said “we can’t justify paying for a title that our authors can get for free. We have to spend the money on titles that are otherwise unavailable.”

At the same time, we had already developed our institutional repository and publishing platform called Digital Commons. This platform allowed libraries to host and publish their own faculty’s and students’ journals (among all the other digital scholarly content produced on campus), and this has turned out to be an extremely successful approach. There are now nearly 800 journals published by libraries using Digital Commons, the vast majority of which are open access (and none charge author article fees). You can see a brief overview of this new model in a recent report.

I’d be happy to talk more about the new direction in library-led publishing; I know this is a growing interest among UK libraries. Is this something you’re seeing as well?

Thanks again for getting in touch, and clarifying this point.

All best,
Irene

In a comment on the last post, Mark Robinson asked an important question:

You linked to the preprint of your The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines submission – does this mean that it has not yet been formally published?

As so often in these discussions, it depends what we mean by our terms. The Barosaurus paper, like this one on neck cartilage, is “published” in the sense that it’s been released to the public, and has a stable home at a well known location maintained by a reputable journal. It’s open for public comment, and can be cited in other publications. (I notice that it’s been cited in Wikipedia). It’s been made public, which after all is the root meaning of the term “publish”.

On the other hand, it’s not yet “published” in the sense of having been through a pre-publication peer-review process, and perhaps more importantly it’s not yet been made available via other channels such as PubMed Central — so, unlike say our previous PeerJ paper on sauropod neck anatomy, it would in some sense go away if PeerJ folded or were acquired by a hostile entity. But then the practical truth is of course that we’d just make it directly available here on SV-POW!, where any search would find it.

In short, the definition of what it means for a paper to be “published” is rather fluid, and is presently in the process of drifting. More than that, conventions vary hugely between fields. In maths and astronomy, posting a preprint on arXiv (their equivalent of PeerJ Preprints, roughly) pretty much is publication. No-one in those fields would dream of not citing a paper that had been published in that way, and reputations in those fields are made on the basis of arXiv preprints. [Note: I was mistaken about this, or at least oversimplified. See David Roberts’ and Michael Richmond’s comments below.]

Maybe the most practical question to ask about the published-ness or otherwise of a paper is, how does it affect the author’s job prospects? When it comes to evaluation by a job-search panel, or a promotion committee, or a tenure board, what counts? And that is a very hard question to answer, as it depends largely on the institution in question, the individuals on the committee, and the particular academic field. My gut feeling is that if I were looking for a job in palaeo, the Barosaurus preprint and this cartilage paper would both count for very little, if anything. But, candidly, I consider that a bug in evaluation methods, not a problem with pre-printing per se. But then again, it’s very easy for me to say that, as I’m in the privileged position of not needing to look for a job in palaeo.

For Matt and me, at least as things stand right now, we do feel that we have unfinished business with these papers. In their present state, they represent real work and a real (if small) advance in the field; but we don’t feel that our work here is done. That’s why I submitted the cartilage paper for peer-review at the same time as posting it as a preprint (it’s great that PeerJ lets you do both together); and it’s why one of Matt’s jobs in the very near future will be getting the Barosaurus revised in accordance with the very helpful reviews that we received, and then also submitted for peer-review. We do still want that “we went through review” badge on our work (without believing it means more than it really does) and the archiving in PubMed Central and CLOCKSS, and the removal of any reason for anyone to be unsure whether those papers “really count”.

But I don’t know whether in ten years, or even five, our attitude will be the same. After all, it changed long ago in maths and astronomy, where — glory be! — papers are judged primarily on their content rather than on where they end up published.

 

Last night, I submitted a paper for publication — for the first time since April 2013. I’d almost forgotten what it felt like. But, because we’re living in the Shiny Digital Future, you don’t have to wait till it’s been through review and formal publication to read it. I submitted to PeerJ, and at the same time, made it available as a preprint (Taylor 2014).

It’s called “Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs”, and frankly the results are weird. Here’s a taste:

Taylor (2014:figure 3). Effect of adding cartilage to the neutral pose of the neck of Apatosaurus louisae CM 3018. Images of vertebra from Gilmore (1936:plate XXIV). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 1. If the slightly sub-horizontal osteological neutral pose of Stevens and Parrish (1999) is correct, then the cartilaginous neutral pose would be correspondingly slightly lower than depicted here, but still much closer to the elevated posture than to horizontal. (Note that the posture shown here would not have been the habitual posture in life: see discussion.)

Taylor (2014:figure 3). Effect of adding cartilage to the neutral pose of the neck of Apatosaurus louisae CM 3018. Images of vertebra from Gilmore (1936:plate XXIV). At the bottom, the vertebrae are composed in a horizontal posture. Superimposed, the same vertebrae are shown inclined by the additional extension angles indicated in Table 1. If the slightly sub-horizontal osteological neutral pose of Stevens and Parrish (1999) is correct, then the cartilaginous neutral pose would be correspondingly slightly lower than depicted here, but still much closer to the elevated posture than to horizontal. (Note that the posture shown here would not have been the habitual posture in life: see discussion.)

A year back, as I was composing a blog-post about our neck-cartilage paper in PLOS ONE (Taylor and Wedel 2013c), I found myself writing down the rather trivial formula for the additional angle of extension at an intervertebral joint once the cartilage is taken into account. In that post, I finished with the promise “I guess that will have to go in a followup now”. Amazingly it’s taken me a year to get that one-pager written and submitted. (Although in the usual way of things, the manuscript ended up being 13 pages long.)

To summarise the main point of the paper: when you insert cartilage of thickness t between two vertebrae whose zygapophyses articulate at height h above the centra, the more anterior vertebra is forced upwards by t/h radians. Our best guess for how much cartilage is between the adjacent vertebrae in an Apatosaurus neck is about 10% of centrum length: the image above shows the effect of inserting that much cartilage at each joint.

And yes, it’s weird. But it’s where the data leads me, so I think it would be dishonest not to publish it.

I’ll be interested to see what the reviewers make of this. You are all of course welcome to leave comments on the preprint itself; but because this is going through conventional peer-review straight away (unlike our Barosaurus preprint), there’s no need to offer the kind of detailed and comprehensive comment that several people did with the previous one. Of course feel free if you wish, but I’m not depending on it.

References

Gilmore Charles W. 1936. Osteology of Apatosaurus, with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175–300 and plates XXI–XXXIV.

Stevens, Kent A., and J. Michael Parrish. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284(5415):798–800. doi:10.1126/science.284.5415.798

Taylor, Michael P. 2014. Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs. PeerJ PrePrints 2:e588v1 doi:10.7287/peerj.preprints.588v1

Taylor, Michael P., and Mathew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10):e78214. 17 pages. doi:10.1371/journal.pone.0078214

Just a quick post today, to refute an incorrect idea about open access that has unfortunately been propagated from time to time. That is the idea that if (say) PLOS were acquired by a barrier-based publisher such as Taylor and Francis, then its papers could be hidden behind paywalls and effectively lost to the world. For example, in Glyn Moody’s article The Open Access Schism, Heather Morrison is quoted as follows:

A major concern about the current move towards CC-BY is that it might allow re-enclosure by companies […] This is a scenario suggested by assistant professor in the School of Information Studies at the University of Ottawa Heather Morrison. As she explains, “There is nothing in the CC BY license that would stop a business from taking all of the works, with attribution, and selling them under a more restrictive license—not only a more restrictive CC-type license (STM’s license is a good indication of what could happen here), but even behind a paywall, then buying out the OA publisher and taking down the OA content.”

This is flatly incorrect.

Reputable open-access publishers not only publish papers on their own sites but also place them in third-party archives, precisely to guard against doomsday scenarios. If (say) PeerJ were made an offer they couldn’t refuse by Elsevier, then the new owners could certainly shut down the PeerJ site; but there’s nothing the could do about the copies of PeerJ articles on PubMed Central, in CLOCKSS and elsewhere. And of course everyone who already has copies of the articles would always be free to distribute them in any way, including posting complete archives on their own websites.

Let’s not accept this kind of scaremongering.

 

It’s nearly two years since Alexander Brown wrote Open access: why academic publishers still add value for the Guardian, in which he listed ways that he feels publishers make a contribution. I wrote a lengthy comment in response — long enough that it got truncated at 5000 characters and I had to post a second comment with the tail end. At the time, I intended to turn that comment into an SV-POW! post, but for some reason I never did. Belatedly, here it is.

I’m a bit nonplussed by this article, in which a publisher lists a lot of important services that they claim to provide, nearly all of which turn out to be either not important at all (if not actively harmful) or provided for free by academics. Let’s go through them one by one, and see how they measure up against the average cost to academia of $5333 per paywalled academic paper.

strong, skilled editors to ensure that research can be universally understood

It is authors who make their work understood. As the author of a dozen published papers myself, I’ve certainly never received any help from an editor to make my work more comprehensible. But even if I had, this would have been done by a handling editor, who is a volunteer academic.

to recognise emerging fields and create new journals

Publisher don’t recognise emerging fields, researchers do. The last thing we need is more journals — there are already far more than anyone can keep track of. The more fruitful trend is the consolidation into a smaller number of more generalist journals, with tools for finding papers relevant to each individual researcher’s interest. (PLOS ONE exemplifies this.)

to build and maintain the brands and reputations of journals.

Journal brands are actively harmful to science. Please stop building and maintaining them.

recruitment and management of editorial review boards

Yes — this, at last, is a real cost in return for a real benefit.

coordination of peer review to ensure the integrity of the scholarly record

This is done by volunteer academics at no cost to the publisher.

Yes, editorial board members and reviewers are by and large unpaid. However there are still scores of people whose full time jobs are managing this process for a growing body of scientific literature.

This seems more like confession of inefficiency than a claim of achievement. No doubt Google could double the number of managers they have to look after their engineers; but that would hardly result in doubling their output. The real question here should be why traditional publishers feel they need so many staff to do so little.

helping customers learn how best to find what they need

How does this happen? I have never had a publisher help me to find anything.

rigorous efforts to acquire content

This means sending spam emails inviting researchers to submit to journals. Like everyone else I know, I bin these on receipt. Researchers know what journals they want to publish in, and when they discover new journals it’s by word of mouth from trusted colleagues.

publicise the brilliance of our authors

Please. This never happens. Authors need to publicise their own work, with or without the help of their institutions, but certainly without significant help from publishers. Often the publisher’s most significant contribution to the publicity process is to release a paper prematurely, thus destroying any attempt at co-ordinating press embargoes.

Developing systems and platforms that can cost well into the tens of millions of dollars/pounds/euros

Again, the fact that a publisher spends this much only shows how inefficient they are. There are several free journal-management systems, including Annotum (used by PLOS Currents) and Open Journal Systems (used by 11,500 journals). If publishers don’t use these tools, that’s no reason to charge researchers more.

with the advent of mobile technology, the job becomes exponentially more difficult as we add “whenever they want it” to the list of our customers’ needs

I have no idea what this means. Any open-access journal’s article are always free “whenever they want it”, whatever device someone is reading on.

While the dissemination of research may not require ink and paper like it used to, distribution remains a very real cost

Yes. To pick a well-known large-scale example, it costs arXiv about $7 per paper to accept, host, archive and serve each of its papers indefinitely. A bit less than $5333, admittedly.

Also included in these activities are archive projects like the Springer Book Archives, a massive undertaking to digitise more than 150 years of previously unavailable titles

This is indeed a valuable programme. But it has nothing to do with ongoing publishing, and is a red herring in the current discussion.

for OA authors Springer deposits a researcher’s work into the institutional repositories these scientists are often required to use, helping to provide further access to scholarly works.

This is good. It saves the author a good fifteen minutes. £5333 well spent!

It is hard to imagine how anyone with an internet connection could do this with the speed, efficiency and added value with which publishers operate

On the contrary: it’s hard to understand how publishers manage to do it so inefficiently.

I just find all this baffling. Any researcher who has actually been through the process of publication knows that it is researchers who do all the significiant work: not only the research, but the writing, the preparation of illustrations, the editorial process, the peer-reviewing, the copy-editing, and increasingly even the typesetting. Hosting, archiving and replication can be done for $7 per paper. So I still don’t see where the publishers are adding any value that is of value to the academy.

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