Let there be no mistake: I value the Open Access (OA )model of publication, for both moral and practical reasons that have been elaborated upon in many other places. Briefly: 1) OA is the right thing to do, as the results of publicly funded research should be available to the public and 2) it is the practical thing to, as the broadest sharing of knowledge possible is fundamental to educational and scientific advances.

This post deals with the difficulty  that still exists on the ground. I see the current author-pays model of OA publishing as still somewhat problematic, with the result of driving many of my colleagues away from OA. One supporting argument for OA is that small universities and four-year colleges, and institutes in developing countries can ill-afford to subscribe to a large number of close-access publications. this places researchers and students at a disadvantage. Therefore, the OA model of publishing does them a favor by reducing subscription fees, granting broader access to publications.

On the the flip side , it is in those very same institutes that researchers have less “disposable income” to pay for publications.  $2500, a typical OA fee, for a lab funded by an R15  (small NIH grants given to less research-intensive institutes) or a small NSF grant is a larger chunk of change than $2500 for a lab holding a couple of R01s (the larger NIH “workhorse” grant). Knowing the limit on these grants, a researcher squeezed for funding would rather budget for an extra month for a graduate student than for OA publication fees.  In way, OA fees are something of a regressive tax: it hurts those with less disposable income more. The OA advocates would say that the money saved by the institute from the reduction of library fees can be rolled into subsidizing publications. Some institutions do that by subscribing to OA journals, thus reducing the publication fees their authors are required to pay. However, many do not, and 10% of $2500 still leaves $2250 to pay.

Yes, PLoS grants “hardship” fee waivers, but many other publishers do not. However, requesting waivers in many cases is something of a dilemma: Prof. SmallU may have the $2500, but using those towards publication would mean running out of lab materials earlier than needed, or letting a graduate student off for the summer. In many cases it is not that the money is not there (after all, Prof. SmallU did manage to fund the research!) but facing this tough choice is problematic, and many people would be reluctant to ask for a subsidy or a waiver. Also, there is hardly any reward in small universities  for publishing in OA. Publishing OA, by itself, figures very little, if at all in promotion & tenure  decisions.

Therefore, when publishing those journals which have both options, OA and closed access, there is very little incentive to shell out the $2500 (usually more in the “two option” journals)  once the paper is accepted. OA-only journals are often shunned altogether.

So what would be the solution? I agree with FakeElsevier that it has to come from the funding agencies. But maybe, instead of OA being a flat-fee, and hence regressive, it can be turned, with the help of the granting agencies, into a progressive fee. After all, those same agencies know how much funding a lab has anyhow, as this must be provided with every grant request, award, and progress report. If a lab is able to demonstrate a “publication hardship”, perhaps an extra subsidy can be given once a paper is accepted, provided it is used towards an OA publication. Knowing that this extra money is there may help nudge Prof. SmallU in the direction of publishing in OA. Also, the subsidy can be contingent upon the university subscribing to the OA journal, thus sharing the burden and creating and incentive for departmental library committees to pressure administrators to allocate funds towards OA access.

As it stands now, the motivation for low-budget labs, the supposed best beneficiaries of OA publishing, is not to publish OA. Unless stronger incentives are given, those labs will continue to get their reading material via those journals their library subscribes to, and through emailed electronic copies. Incidentally, a practice that the scientific publishing industry is starting to notice and is even attempting to stop.

The Scientist is one of my favorite go-to destinations for keeping up with current biomedical research. That’s why I was rather sad when it was recently announced that The Scientist will be closing down. However, it seems like The Scientist will continue to be published after all:

NEW YORK, NY–(Marketwire – Oct 14, 2011) – Sciencenow Inc., a member of The Science Navigation Group, and LabX Media Group are pleased to announce that they have signed a nonbinding Letter of Intent specifying terms for the acquisition of The Scientist by LabX Media Group. The parties hope to close a transaction by the end of October.

Sande Giaccone, Sales and Marketing Director of The Scientist, said, “We are delighted that, following the decision to cease publication of The Scientist, LabX Media Group has stepped in to save The Scientist and keep the majority of its existing team together. We hope to return to our normal high service level for all our readers, contributors, and advertisers in the next few weeks. We sincerely appreciate the support of our advertisers in the past and hope to regain their confidence going forward. The Scientist is complementary to LabX Media’s existing stable of products and, subject to closing of a transaction, we look forward to working with them in the future.”

Mary Beth Aberlin, Editor in Chief of The Scientist, said, “Naturally, we were all saddened by the decision to cease publication of The Scientist, and grateful to our readers and contributors for all their kind words concerning the magazine. The editorial team and I are delighted that LabX Media Group has been able to agree on terms with Sciencenow, Inc. with such dispatch. Our dedicated editorial team will remain intact and continue to produce a magazine that maintains our editorial standards.

Bob Kafato, President of LabX Media Group, said, “The quality life science content that The Scientist produces is second to none and we are happy to be adding this to our portfolio of media products for lab professionals.”

Kudos to LabX. You have rescued a fine journal. Thanks to Linda Kosta for calling my attention to this fortunate turn of events.

After WWII, Pacific islands occupied by the US military were regularly receiving goods via air. Once the military evacuated , the goods stopped arriving. Some inhabitants of those islands mistakenly thought that receiving the cargo was due to some divine intervention that required rituals they saw American servicemen performing. This eventually led them to performing activities like making their own airfields, waving in non-existent planes while wearing coconut headphones, etc, all in the hopes that material would magically come from the sky. These attempts were called cargo cults. Since then, “cargo cult” has been used metaphorically to describe an attempt to recreate successful outcomes by replicating conditions associated with those outcomes, even though those conditions are either effects and not causes of those outcomes.[Wikipedia]

Science culture is not void of its own cargo-cult, despite the fact that science is supposed to be the ultimate cargo-cult dispeller.  I have written before about solicitations for author-pays publications whose quality, shall we say, is less than assured. Actually, it seems like some of these publications will print anything as long as you pay them.  Here is what my inbox brought in today, all bold-faced typing is mine:

____ is a peer-reviewed journal that includes an international board of accomplished editors and researchers in their fields. There will be submissions on subjects such as cheminformatics, computational drug discovery, experimental medicine and analysis tools, personalized medicines, cancer informatics, hematology, diagnostic imaging, medical imaging and methods and gene therapy, among other latest breathtaking topics.

Indeed, breathtaking. This journal seems to have a strong focus on, um, whatever. But what really takes your breath away is that you really have to work hard to  qualify for publication. Specifically, self-plagiarism is rigorously weeded out:

If you (sic) paper has been published in any other platform, a new version of your paper for ___ (Vol 1 No 1) must reflect at least 25% difference in content from the one published in any conference proceeding or any other journal.

So I have to justify a “25% difference” between my submission to this journal and my previous manuscript? Do I change every fourth word from a previously published paper? And how do I measure this “25% difference”? Use the cosine measure for similarity of text?  Extended Jaccard similarity? Something else?

Each published paper in the ___ is subject to a publication fee of USD 300 for a maximum of 6 pages. A complimentary copy (print version) of the ___ (Vol 1 No 1) issue that carries your reviewed paper will be mailed to your mailing address.

I guess we all saw that coming.

These actually work. Click for description

The new top-tier competitor to Science and Nature proposed by three leading funders of scientific research last week is a great idea, but I think runs a risk of opening the scientific process to a potentially damaging slander by opponents of science.

As practising academic scientists we’re all concerned, and intimately entangled, with the scientific publication process. We are authors, reviewers, editors, sometimes journal chiefs and, in a very real sense, our entire careers may hang upon whether and where our work is published. Impact factors, journal reputations, author counts and ordering, and other actuarial metrics are foremost in our minds every time a promotion case or job application is submitted. The cost of publishing work raises its head every time we have to dip into consumables to fund a colour figure. Each time we submit to peer review we set sail anew, all paranoid, on the Sea of Judgement by Anonymous Colleagues and Competitors. We are, as a group, highly sensitive to changes in the scientific publishing ecosystem. So it’s no surprise that the scientific world and its experimental dog have opinions on this potential competitor to Science, Nature and Cell.

And, at first glance, the new journal could be a beautiful thing.

The journal is planned to be fully Open Access, underwritten at least initially by the funding bodies, so there will be no, or reduced, author charges. Author charges can be a problem where projects lack money allocated to publication costs. I’ve usually been lucky enough to obtain support for Open Access publication, but this still adds a level of political and financial consideration when deciding where to submit work. Where funding bodies require OA publication (and this is increasingly a condition of funding) I think it is only right that they support this route financially, and the Howard Hughes Medical Institute, Wellcome Trust, and the Max Planck Society are to be congratulated for taking this stand.

Michael Eisen points out that the new journal is a triumph for Open Access, and I think he’s right, there. Even in the short 15 or so years that I’ve been an active researcher, the internet has transformed me from a troll at the library copy machine into a blasé, and heavy, consumer of online PDFs. As befits one of the driving personalities behind PLoS, he says a great many sensible and worthwhile things about the new journal in his blog article. But I do think he overstates the potential impact on peer review. In his article, Eisen identifies three key areas of peer review that this new journal wants to shake up:

1) Rapid review and turnover: I think there’s a realistic chance, particularly with a financial incentive, of encouraging scientists to prioritise reviews for this journal, reducing turnaround time. And if there’s a flat payment to the reviewer per manuscript reviewed, then there’s no perverse incentive to cycle through rounds of revision. I think this will work, but I do share Eisen’s worry that uncompensated review requests from other bodies could come somewhat down the list of Things To Do Today, as a result.

2) Fewer demands for changes and additional experiments: The press release from the funding bodies states their desire to limit reviewers’ calls for more work. But really, if a piece of work is unconvincing because it lacks a key experiment, then that’s the fault of the work and not the fault of the review process. A competent peer review process would bounce the manuscript until the supporting evidence is provided. All that an editorial policy of fewer requests for changes and experiments can do is either accept a manuscript with insufficient support and so dilute journal quality, or reject at an earlier stage in the process.

3) Arbitrary editorial decisions on the grounds of sexiness: The new journal will have an editorial team of experienced, active scientists, rather than “junior scientists who are no longer active researchers”. This is quite obviously a pointed comment about the editorial composition of publications such as Science and Nature, rather than fair comment about scientific publication on the whole. Most journals I deal with have editorial and review boards comprising active researchers, and I believe that outside the usual extremely high-impact suspects, it is the norm to have an editorial panel of experienced, active scientists. I don’t see this policy being particularly ground-shaking.

Where I think that the new journal will shake up peer review is in its intent to publish reviewers’ comments publicly, but anonymously. This cuts both ways: authors will no longer be able to “get away with” ignoring potentially serious criticisms from a minority reviewer, unnoticed, after publication; But nor will poor or unreasonable reviewers be able to hide behind the opaqueness of the current review process. If readers can comment on or rate the quality of reviews, as well as papers, honest and insightful reviewers could be rewarded at the expense of the half-hearted and overly pedantic.

But I do have one serious criticism, which comes not from being a scientist, but instead thinking about how the public sees science.

In recent times, public trust, or rather the lack of it, in science as a human endeavour has been exemplified by the events of ClimateGate, and European attitudes towards genetic modification. Popular media presentation of difficult ethical issues in science is, well, difficult, and it’s useful in the face of criticism to be able to fall back on demonstrable claims of the independence of results from financial inducements, and the anonymity and stringency of peer review in journals that are disinterested in the outcome of our work. And that is where I think the new journal risks offering an easy target to those who would seek to undermine public confidence in science.

In 2009, it was revealed that the publisher Elsevier had been paid by the pharmaceutical company Merck, Sharp and Dohme to “produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles–most of which presented data favourable to Merck products” : The Australasian Journal of Bone and Joint Medicine. Intuitively, suspicions of vested interests can be expected to arise where there is no obvious and transparent independence in the chain that links the funder of research to the lab that carries out that research, and to the journal that publishes it. Even PLoS Medicine‘s policy on research funded by tobacco companies perpetuates this common perception that, unless the source of funding can be decoupled in some way from the outcome of research, and ‘review’ for publication, then publication amounts to little more than advertising.

When a piece of work is carried out by scientists funded by body X, reviewed by scientists funded by body X (who are even paid to review the paper by body X), and published in a journal bankrolled by body X, this intuitively looks like self-publication or advertising by body X. Where ‘body X’ is “Big Tobacco”, or “Big Pharma”, the conflict of interest is so self-evident that it has become a cliché. When ‘body X’ is “HHMI/Wellcome/MPS”, as a scientist I recoil at the potential association of such respected investors in science with cheap and shady practices. I don’t have any doubt that, as the journal’s press release states, the “editorial team will be editorially independent of the funders”, and that all published manuscripts will be competently assessed and of the highest quality. But from the point of view of those outside the circle of science, there is always an option to suggest sleight of hand, however ethically clean the journal is. Without independence and transparency in the cycle of funding and publication, we risk delivering an opportunity for slander into the hands of those who would undermine science for political goals.

DISCLAIMER: L.P. adds that the views represented here are his own, and do not reflect those of his employer, or those of any other of his professional affiliations.

The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers’ comments will be published anonymously.

Nice. The journal will be online-only and open access too, and they promise  ”an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation.” I especially like the “limited need for modifications or additional experiments”, especially since even Nature has recently published a scathing opinion piece about reviewers’ almost reflexive demands for additional experiments.

With these three giants behind the journal, it’s a safe bet this journal will be up there with PLoS Biology, Nature and Science.

For now, Byte Size Biology readers are welcome to suggest a name for this new journal. Maybe you can strike a deal with the yet-to-be-named editor-in-chief: a lifetime  publication fee waiver if your name gets chosen.

Of course, I have no affiliation with this new journal, so don’t bet on it happening.

The National Academies Press are offering all their books in PDF format for free. The announcement yesterday created a serious traffic surge on their site. But the books are still there, and are still free. Got to buy that new 5Tb external disk now….

Well, their accents don’t exactly fit the population in the NLM….

Click for larger image

The next email in my inbox was this:

OK, that’s taking things a bit too far. Random solicitation of editors (did I mention that was not my field?) does not lend credibility to the publisher.

Which brings us to a nice post by Kevin Karplus about the not-so-savory side of open access publishing, or the “author-pays” model. First, a clarification of terms:  Open Access means access to research publications by the general public without needing to pay for access through a personal or institutional subscription. Author-pays would mean that publication fees are covered by the author. The two are not necessarily cojoined. There are plenty of closed-access publications whose page and figure charges run as high or even higher than Open Access publications. But in the case of Open Access, the revenue does not come from subscriptions. The only other sources are advertisements and author fees. Since many Open access publications are web-only and are quite specialized, advertisements are not a practical source of revenue. This leaves us with author fees. So to publish open access you pretty much need to have money. If you happen to fall on hard times and you lose some funding, or need to skimp for a while, author-pays publishing is becomes less of an option, despite supposed hardship fee waivers. Since more journals are adopting the Open-Access model,  many publications venues are being closed off to poorly funded researchers.

But I would like to address a point that was minor in Kevin’s post, yet is quite important: the wrongly perceived association of Open-Access with the cheapening of scientific publication. And by “cheapening” I do not mean the lowering of costs, although publication costs for web-only publications are considerably lower than those for print. I meant cheapening in the figurative sense: the attrition of scientific quality. Since the barrier for getting a scientific publication up & running is  not lower: you still need staff, good editorial board, good editors, etc, etc. This all costs money, even if you do away withe  the substantial expense of paper printing.  But the barrier is considerably lower if you are willing to do away with credibility, and just set up what is essentially a web-based manuscript clearinghouse. Since many of those journals (like the one above) profess to be Open Access, some misinformed souls may associate Open Access ~= Bad Science. Especially if they are inundated by these emails like I am. From several publishers at that.

I worry that widespread adoption of the new policy could result in dominance of author-pays models for publication, which would squeeze out unfunded researchers from publication, and lead to a further dilution of peer review, as the journal publishers would no longer care as much about quality (no subscribers to please) as about quantity (maximizing author fees).

– Gas station without pumps, December 15, 2010

Now, bad journals, bad papers and fraud have been around for ever. In early 2009 it was revealed that Elsevier published a journal that was almost entirely ghost-written by Merck to promote Vioxx. The Elsevier fake journal and  ghost writing scandal had nothing to do with Open Access. Other examples of marginal or even fraudulent publications in closed-access forums are not hard to find. Especially funny is the 2005 case of  SCIgen, a program that generates random Computer Science research papers, including graphs, figures, and citations. One randomly generated paper was accepted to WMSCI 2005. (See the whole story on the scigen blog, you’ll need to page back to the beginning. This makes for a fascinating, surreal and somewhat disturbing read.)

But emails such as those above (and I get them weekly from many sources despite –or maybe because– repeated requests to unsubscribe), do show that some publishers all but say that they will publish for cash, and they obviously couldn’t care less who provides editorial and review services as long as they go through the motions of supposed peer-review. They justify the author-pays publication costs by providing Open Access — the icing on top a rather rancid cake. Unfortunately, spam such as this may cause some people to associate anything Open Access with the publication of marginal and low quality research.

Well, but if my Thunderbird email client can tell the difference between good and bad science, maybe we can educate humans about the non-association of Open Access with bad science. I jut hope that the term Open Access is not one of the parameters in my Thunderbird’s spam filter. Does anyone know how to check that?

Credit: xkcd.com

But now the science in the article itself is coming under fire. Several blog posts by notable microbiologists and biochemists  have questioned the claims made in the paper. To sum those up: yes, the microbes contain arsenate, the can grow on arsenic-rich media but there is no convincing evidence that arsenic gets incorporated into DNA, much less other molecules that use phosphate. Because this research is so much in the spotlight, the comments on it are in the spotlight too. I believe we will see some very interesting correspondence on the website and in the upcoming issues of Science.

Which brings me to the point of this post: is the peer-review publication culture undergoing a reform?  The arsenate bacteria article itself went through the peer-review mill, which means that at least three scientists which are credited as experts in the field have looked at it and given it a clean bill of health. But once it got published, hundreds of microbiologists and biochemists had a look, and many were less than convinced of some of its claims.  So which is better for the process of peer-review: three anonymous referees before publication, or 100 after? Or maybe we should use both?

A personal example: I recently  published a paper  in PLoS Computational Biology, which went through two pre-publication review cycles making it much better. However, even after those revisions an error (minor, fortunately) slipped through. A reader emailed me about it, and I immediately went to PLoS-CB‘s site and addressed that error as an inline comment in the paper. This mechanism provided by PLoS is laudable: I wish it were used more, and that other journals could provide it.

So, post-publication peer-review seems to be a good thing: it quickly identifies issues with the science, and helps to fix them.  So why is it not done more? Well, for one, there is the lack of anonymity. Post-publication commentators do not have the luxury of the official peer-reviewers of hiding their identity. Another is lack of credit: while some credit is given for pre-publication review, which is recognized as service rendered to the community, none is given yet for post-publication review. But why not? It is scientists like Rosie Redfield, Larry Moran, Jim Hu and others who did a great public service by taking the time to carefully read and then publicly critique the paper.  And in case there are still doubters of the value of science blogging, please read this piece by Larry Moran and for blogging as a career enhancer in science, “10 benefits for my career of blogging/ tweeting etc.) #fb” by Jonathan Eisen.

Where am I going with this? I’m not sure. But it seems like the fallout from the arsenate bacteria paper brings to light a new kind of science culture, in which post-publication critiques in expert science blogs are given. Perhaps all this energy could be harnessed to provide a better publication environment for research papers.  This has been going on for some time, as many science bloggers emphasize paper critique. But high profile incidents like the arsenate bacteria bring the value of post-publication review to light. To paraphrase a quote by Carl Sagan which was mentioned at the press conference held when the paper was published: “extraordinary claims attract extraordinary blogging”.

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

JSUR Call for Participation

Submit your short (2-4page) and full length manuscripts to the Journal
of Serendipitous and Unexpected Results.

Over the past month we’ve received a great amount of press and
publicity for the Journal of Serendipitous and Unexpected Results
(JSUR). Thanks to everyone who helped spread the word, please keep it
up!

In Richard Feynman’s 1966 Nobel Lecture, he said, “We have a habit in
writing articles published in scientific journals to make the work as
finished as possible, to cover up all the tracks, to not worry about
the blind alleys or describe how you had the wrong idea first, and so
on. So there isn’t any place to publish, in a dignified manner, what
you actually did in order to do the work.”

We’re writing to invite you to solicit short (2-4page) and full length
submissions to JSUR.  Why not prepare a 2-4 page writeup discussing
side-investigations, alleyways, or false-starts in your latest
published or unpublished research? Papers of this length place a
minimal burden on the authors, while providing extremely valuable
research insights to a broad audience.

Journal website: http://www.jsur.org

Sincerely,
The JSUR Editorial Board