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2012 January 30

F1000 Research—yet another open-access publisher

Filed under: Uncategorized — gasstationwithoutpumps @ 21:38
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F1000, who publish the extremely pricey “Faculty of 1000″ reviews of scientific literature are now throwing their hat in the open-access publication ring with F1000 Research.

They are planning to do post-publication review,which is the current darling of the open-access advocates, as it pretty much guarantees that anything someone wants to publish will appear—the only barrier being the price the author has to pay to get it published. F1000 has been doing post-publication review (of work from any scientific journal) for years, so they have some ideas about how that should go.

I’ve written some Faculty of 1000 reviews, and I found their editorial constraints rather limiting.  They never wanted any negative comments about a paper, just superlatives.  Even the very good papers I read generally had a few flaws, and they kept wanting to remove mention of those parts from my reviews.  I’ve pretty much given up doing reviews for Faculty of 1000 for several reasons:

  • Their subscription prices are so high that the University of California Library has come close to unsubscribing a couple of times, and I don’t want to be providing free content to a company then charging so much for the content.
  • Their editorial policy of “superlatives only” does not match my more balanced (or perhaps just more negative) reviewing style.
  • I’ve lost interest in the field for which the originally recruited me. I find it very difficult these days to read most papers on protein structure prediction and related fields.  Mostly people are rehashing ideas that have been around for a decade or more, rarely improving on them.  There are probably only a handful of good papers a year in the field, and I don’t have the patience to find them.  (That is the job of F1000 reviewers, and if I were eagerly reading dozens of papers I’d be glad to share the occasional gem, but I’m not eagerly reading papers, so I almost never encounter the good ones.)

Given F1000′s history, I’m worried that the new F1000 Research will be very expensive and will quickly become a repository for trash papers. In a standard open-access journal that problem can be avoided with strong editorial control (PLoS Computational Biology generally publishes decent papers, for example), but with only post-publication review, the venue is likely to get clogged with stuff too bad to be published elsewhere.

Who is going to want to do post-publication review of a stream of junk?  It is hard enough reading the mediocre papers that have already been through peer review already—reading the ones that even the authors think would fail peer review would be excruciating.  If no one competent is reading and critiquing the papers, then the junk will not be filtered out and the whole process will degrade into a vanity press.  There are already dozens of vanity open-access journals that will print any sort of s**t if the author pays the fee (even going through a pretense of peer reviewing), and I did not see anything in the F1000 Research announcement that suggested that they would avoid this trap.

Note that what F1000 is proposing is very different from the open access in arXiv, the (mostly) pre-publication archive heavily used by the physics community. “Open access to 731,853 e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics.”  The arXiv site does not provide discussion forums, but many researchers put papers into arXiv for pre-publication discussion before submitting them to peer-reviewed journals.  There are enough respected scientists doing this that people do regularly look through arXiv for interesting material in their field. Because depositing a paper in arXiv gets it read by a few people, but does not count as publication for promotion and tenure, there is little incentive to clog arXiv with junk.

People do sometimes stick papers in there to establish that they got an idea first, even if the paper needs some work still before it is publishable, and sometimes the early drafts of a paper have flaws that are revealed before publication, but most of the papers in arXiv are published in peer-reviewed journals eventually.

Also, note that the fields most rife with sloppy research and outright fraud are not covered by arXiv (medical research seems to have the lion’s share of scientific fraud, probably because of the amount of money involved). Although there are some crackpot papers in arXiv, for the most part it is real science. I believe that F1000 wants to cover a wider swath, including fields in which fraud and crackpot theorists are a more common problem.  Relying on post-publication review seems a risky endeavor.

Disclaimer: as an unfunded researcher, I have mixed feelings about open-access publication. I like getting papers for free, and I like the idea of distributing scientific papers as freely and cheaply as possible. But most of the business models call for the author to pay for publication, which is fine for those who have grants that can pay publication charges, but deadly for those of us without funding.  Open-access publishing may, in fact, restrict publishing to a smaller group of authors than the traditional publication model—those with money.  Requiring those with grants to publish in open-access venues makes some sense to me as a taxpayer, but if it results in the loss of subscriber-pays journals, many researchers will be excluded from publication, and everyone will need to spend even more time writing grant proposals instead of doing research.

What I’d like to see are more things like arXiv, which provide free access funded neither by the authors nor the readers, but by organizations with an interest in free distribution of scientific literature (granting agencies, governments, and research libraries, for example).  I doubt that F1000, as a for-profit company, plans anything like that.

2011 November 15

New NSF program without peer review

Filed under: Uncategorized — gasstationwithoutpumps @ 00:11
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In an attempt to be more nimble and interdisciplinary, NSF has instituted a new program that will consume up to 2% of NSF’s budget without peer review, just on a couple of program officers’ say-so. The official announcement, CREATIV: Creative Research Awards for Transformative Interdisciplinary Ventures, says that grants up to $1 million (spread over 5 years) can be funded this way.

The goals are to

  • Create new interdisciplinary opportunities that are not perceived to exist presently.
  • Attract unusually creative high-risk / high-reward interdisciplinary proposals.
  • Provide substantial funding, not limited to the exploratory stage of the pursuit of novel ideas.
  • Designate no favored topics; be open to all NSF-supported areas of science, engineering, and education research.


A CREATIV award must be substantially co-funded by at least two intellectually distinct NSF divisions or programs (this criterion is elaborated in the FAQ page. The maximum total award is $800,000 for two co-funding programs, and $1,000,000 for three or more co-funding programs. All awards are subject to the availability of funds.


Before writing and submitting a CREATIV proposal, it is the principal investigator’s responsibility to obtain written authorization to submit a CREATIV proposal by NSF program directors from at least two intellectually distinct divisions or programs.

This program looks like it may be accessible by bioinformatics researchers, but I fear that it removes some of NSF’s credibility, since it seems to fund things on a who-you-know basis, rather than on relying on peer review.  (Of course, ever since NSF copied NIH and started doing panel reviews rather than independent individual reviews of proposals, they have been sadly subject to groupthink, with the corresponding risk-averse selection of proposals.)

Hat-tip to ScienceInsider, whose article New NSF Program Sidesteps External Peer Review alerted me to this program.

2011 July 13

Yet another open access journal

Filed under: Uncategorized — gasstationwithoutpumps @ 09:31
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With hundreds of journals and journal publishers starting up open-access journals, why would I bother picking out one to write about?

As a researcher without funding, I can’t afford to pay $3000 for every paper I want to or ought to publish, and the University is not likely to provide funds for that (they have all those administrators to pay outsize salaries to and all that bonded debt to start paying down, after all), so the author-pays model for publishing does not work well for me, though I appreciate the value of free access to scientific literature.

I’ve blogged before about  an AAUP article on open-access publicationISCB open-access policies, and IEEE open-access publishing, as well as passing on an announcement of an advertiser-pays open-access journal.

There is a new journal coming out (name still undecided, so far as I can tell), that is trying a different model: direct subsidy of the journal by funding agencies.  A press release from HHMI announced that Randy Schekman, a cell biologist and HHMI investigator at the University of California, Berkeley will be the senior editor and gave a few details about the publication:

… their fundamental goals: publication of highly significant research; an independent editorial team comprised of active, practicing scientists; and a rapid and transparent peer review.

Expected to launch in about a year, the journal will be online and open access. Schekman says he does not expect the journal to hold the copyright to the literature, but to utilize Creative Commons licenses so that the data can be widely shared.

Schekman reports that editors will be appropriately compensated, noting for example that senior editors will be expected to devote 20 percent of their time to the journal and would be paid accordingly.

For the first three to four years, to help establish the journal, no fees will be charged to authors. Once the journal is established, it is anticipated that authors will be charged an article processing fee to cover some of the ongoing costs of publication.

So they almost got it right.  They’ll have direct funding of the journal for 3 or 4 years, but after that they switch to author-pays.  I’d rather see less “appropriate compensation” for editors and a promise to directly fund publication for longer.  I suspect that Schekman’s experience at PNAS (where he pushed a little in the direction of better science, but did not eliminate the old-boys’ network submission policies) will lead him to gold-plate the new journal and run through the funding agency money without leaving a lasting legacy of free-for-authors, free-for-readers journal.

I think that part of the reviewer and editor fatigue that makes it hard to recruit reviewers is not that they aren’t paid, but that there is a huge revenue stream which they are not part of.  People don’t mind doing volunteer work, but they hate someone else making money off their volunteer work.  I don’t like reviewing for the journals owned by the publishers who are making millions ripping-off libraries, and I’m reluctant to support a “vanity press” where the reviewers’ comments to reject are ignored in the quest for more author fees.  I would be much more willing to do volunteer reviewing work for a subsidized journal which made no money and had no expensive paid editors.

This new journal had the potential to be a low-cost, high-quality journal, but I think it just misses the mark, and by paying editors “appropriately” and paying referees a retainer, they’ll end up being too expensive to continue.  Funding agencies are in the habit of starting things, then killing them off a few years later by discontinuing funding.  Planning to switch to an author-pays model after a few years is essentially setting this up to be just like other open-access journals, but with much higher costs, and so higher author fees. If this high-cost model is followed, then it will end up being a colossal waste of money, when for about the same amount of funding, the journal could have been set up as a free-for-authors, free-for-readers journal for at least a decade.

2010 December 26

Snarky comments from reviewers

Filed under: Uncategorized — gasstationwithoutpumps @ 19:26
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Environmental Microbiology recently published a fun, free article “Referees’ quotes – 2010” (DOI: 10.1111/j.1462-2920.2010.02394.x). The article consists of quotes from referee comments in the preceding year, many of them quite snarky.  For example, there is the rejection “This paper is desperate. Please reject it completely and then block the author’s email ID so they can’t use the online system in future” and the rather depressing comment  “It is sad to see so much enthusiasm and effort go into analyzing a dataset that is just not big enough.

Read the whole set and be reassured that most of the comments you’ve gotten on your papers in the past year have been more positive.

2010 November 5

Peer review reviewed

Filed under: Uncategorized — gasstationwithoutpumps @ 00:05
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The Scientist, published by F1000, recently ran a couple of articles (Peer Review and the Age of Aquarius and I Hate Your Paper) claiming that peer review is badly broken and needs to be replaced by some other mechanism. This is a recurring theme for them, as they published a similar polemic (Is Peer Review Broken?) in 2006.

While I agree that peer review as currently implemented has some problems (see Corrupted peer review), I do think it rather self-serving of F1000 to be pushing so hard for a post-publication review system.  After all, they make their livings collecting free post-publication reviews from scientists like me, and selling them at very high prices to academic libraries.  I know that the University of California librarians have been pondering canceling their subscription to Faculty of 1000, because it is so very expensive per use.

Quite frankly, I don’t think that post-publication review has a snowball’s chance in hell of working as the primary quality-control system in scientific publishing.  No one has enough time to look at more than a tiny fraction of the carefully filtered papers of the current peer-review system.  Who is going to have time to do post-publication review of the 5–10 times larger pool of mostly crappy papers that would be produced under a publish-first, evaluate-later model? Certainly not the people who have expertise in the field.

Disclaimer: I am a reviewer for F1000 Biology.  In “payment” for the 11 reviews I have done so far, they have sent me a coffee mug and will be sending me a biography of Sydney Brenner, which I will donate to a library somewhere (probably the local high school or city library, depending on the reading level and how interesting it seems to be).

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