29 Oct 2007

Journalology roundup #12

Dealing with scientific misconduct. "Europe needs policies for good scientific practice and for investigating misconduct allegations".

That Dezenhall briefing in full! Anti-OA briefing exposed!

Achievement index climbs the ranks. "Hirsch measure can predict future success of researchers".

It's Time to Free the Dark Data of Failed Scientific Experiments. "In 1981, the New England Journal of Medicine published a Harvard study that showed an unexpected link between drinking coffee and pancreatic cancer. As it happened, researchers were anticipating a connection between alcohol or tobacco and cancer. But according to the survey of several hundred patients, booze and cigarettes didn't seem to increase your risk. Then came a surprise: An incidental survey question suggested that coffee did increase the chances of pancreatic cancer. So that's what got published. Those positive results, alas, were entirely anomalous; 20 years of follow-up research showed the coffee-cancer connection to be bunk. Nonetheless, it's a textbook example of so-called publication bias, where science gets skewed because only positive correlations see the light of day. After all, the surprising findings are what makes the news (and careers)".
We agree with this at BioMed Central! We already publish the Journal of Negative Results in Biomedicine, and we have another project addressing this issue on the way - watch this space.

A method of knocking out genes in mice needs more discrimination than many have recognized. "No technology is without caveats, and there will always be a degree of uncertainty with which researchers have to live. But in the interest of best scientific practice, everyone involved would be wise not to neglect the dangers and subtleties at play even in routine experiments".

Calling all charlatans. A group of researchers puts companies making scientific claims on the spot. "One day in early July, a customer service representative for a company called Crystalite Salt received a phone call from Jennifer Lardge, a physicist. Lardge was curious about the science behind one of their products: lumps of salt, called lamps, that are meant to improve your health when they are heated. "I was looking at your Web site and I was just wondering about how salt lamps actually work"".

Open Society Institute awards grant to support Open Access Documentary Project. "The Open Society Institute has awarded a grant to support the production and distribution of the Open Access Documentary Project, a collection of online videos celebrating the benefits of open access to scientific and medical research. Intelligent Television and BioMed Central are co-producers of the Project".

When Is Open Access Not Open Access? "Since 2003, when PLoS Biology was launched, there has been a spectacular growth in “open-access” journals. The Directory of Open Access Journals (http://www.doaj.org/), hosted by Lund University Libraries, lists 2,816 open-access journals as this article goes to press (and probably more by the time you read this). Authors also have various “open-access” options within existing subscription journals offered by traditional publishers (e.g., Blackwell, Springer, Oxford University Press, and many others). In return for a fee to the publisher, an author's individual article is made freely available and (sometimes) deposited in PubMed Central (PMC). But, as open access grows in prominence, so too has confusion about what open access means, particularly with regard to unrestricted use of content-which true open access allows. This confusion is being promulgated by journal publishers at the expense of authors and funding agencies wanting to support open access".

The Basement Interviews: Peter Suber. Read this! Another great interview by Richard Poynder. "Philosopher, jurist, and one-time stand-up comic, Peter Suber is widely viewed as the de facto leader of the open access (OA) movement".

Self-archiving and permissions barriers. Peter Suber and Peter Murray-Rust are trying in vain to persuade Stevan Harnad that Green OA/self-archiving does not solve the problem of permission barriers.

The Journal of Electronic Publishing - latest issue. Lots of interesting things!
University Publishing in a Digital Age; What Happened to the E-book Revolution?; The Google Story and Google and the Myth of Universal Knowledge; Electronic Publishing as a Course Context for a Capstone Project on Protein Design; New (Social) Structures for New (Networked) Texts; The Prevalence of Additional Electronic Features in Pure E-Journals; Blogs as a Student Content Management System; Redefining Scholarly Publishing as a Service Industry; Market Formation for E-Books: Diffusion, Confusion or Delusion?

Max Planck Society Dumps Springer Deal Over Pricing. "The Max Planck Society (MPS), a major German research organization, issued a strongly worded statement this week to announce it was cancelling access to Springer's online collection of journals over pricing. The cancellation will take effect as of December 31, 2007. MPS Vice President Kurt Mehlhorn said negotiations to extend the deal failed because, according to an MPS evaluation based on factors including usage and comparisons with other publishers, Springer was intent on charging "approximately double the price" the organization regarded as "reasonable.""

Institutional Academic Industry Relationships. "Almost two-thirds (60%) of department chairs had some form of personal relationship with industry, including serving as a consultant (27%), a member of a scientific advisory board (27%), a paid speaker (14%), an officer (7%), a founder (9%), or a member of the board of directors (11%)... Overall, institutional academic-industry relationships are highly prevalent and underscore the need for their active disclosure and management".

Open Clinical Trials
. "The FDA Revitalization Act sets a precedent in mandating the reporting of trial results in a public database... With this legislation, clinical trials in the United States will be played out in the public arena. Research volunteers will know that their participation is part of an unbiased public record. We think that fully open clinical trials will lead to more effective and safer treatments for patients... Open for all to see, future clinical trials can lead to new treatments that will make a difference in safely combating disease".

Do trialists endorse clinical trial registration? "Although disagreement was apparent on certain issues, our findings illustrate that trial registration is gradually becoming part of the current research paradigm internationally. Our results also suggest that researchers require more knowledge to inform their decision to comply with the International standards at this early stage of voluntary trial registration."

Publication bias for CAM trials. Non-US CAM trialists are more likely to publish positive results. "All CAM clinical trials published in the four highest impact factor general medicine journals between 1965 and 2004 were abstracted using Medline... CAM trials published in the European journals were significantly more likely to be positive compared to those published in the U.S. journals (76% vs. 50%, odds ratio [OR]=3.15, P<0.0001).>

How to cite a blog.

Conflicts of interest in the open access debate

I can accept that some society publishers are concerned that open access may make it harder for them to fund their activities. I can accept that some people are confused about the implications of open access.

What I find very difficult to accept is that executives at the American Chemical Society appear to be raising spurious arguments against open access, such as calling it 'Socialized Science', and that they have clear, undeclared conflicts of interest in this debate, namely that they are paid bonuses depending on the profits of the publishing division of the ACS.

Just as we now expect medics to declare their competing interests in journal publications, anyone involved in the open access debate should declare their own competing interests. My own financial competing interest is a fixed salary received from BioMed Central. Let's see some more transparency from all concerned.

Don't reinvent the wheel - jump on the bandwagon!

In A modest (billion-dollar) proposal, Alexandre Linhares suggests that "papers published online should be freely accessible to all, no login, no paywall, nothing in the way. Copyright should remain in the hands of authors".

I was surprised to read this, as I thought this was what we were doing already with the open access movement. I posted this in reply:

I completely agree. Stevan Harnad proposed something quite similar in his "Subversive Proposal" way back in 1994; he calls electronic publishing that is free of the tyranny of paper the "Post-Gutenberg World".

The Internet truly has allowed the beginnings of a revolution in scientific publishing. Vitek Tracz (my employer) launched BioMed Central in 1999, and Mike Eisen and Harold Varmus launched the Public Library of Science in 2000 (originally an advocacy organisation, now a publisher). BioMed Central and PLoS are the two biggest players in open access publishing. All our peer-reviewed research is immediately available online at no charge and with no access barriers. Copyright is retained by the authors. Under the Creative Commons license, anyone can copy and reproduce the articles: all anyone needs to do is properly attribute the source.

Some people thought that Vitek had lost it when he launched BioMed Central. Well, BioMed Central has seen our submissions double every 14-18 months, and PLoS has seen a similar rapid growth. Smaller open access publishers like JMIR, Hindawi, Libertas Academica are thriving. The impact on the world of publishing is clear – over the last two or three years, virtually every large biomedical publisher has begun to offer authors an option of publishing open access, and in physics CERN has even promised not to publish with any journal not offering an open access option.

The difference to your proposal is that we're not reliant on internet advertising, although we do make some income in this way. Being reliant on advertising risks making a journal answerable to its advertisers, as if they see something they don't like they can pull the plug - a similar state of affairs to that you claim that IBM Systems Journal is in. Because we don't charge readers, we've turned the funding model on its head. As publishing is in effect the final part of the research process, it makes sense to ask authors to fund the publication process, and we do this by charging authors (or more usually their institution or grant funding body) an article processing charge. This funding model scales perfectly with the amount of research conducted. PLoS has been quite reliant on philanthropic grants, but they are weaning themselves off these grants now that their high-volume journal PLoS ONE has been launched. There are several others way to fund open access journals, including society support; Peter Suber's blog is the best source of information on this.

The suggestion of only allowing searching on the journal website would leave a journal stillborn. The key to success is to have as many readers find and read the work as is possible – this is the whole point of open access! We are indexed and tracked by as many services as we can find, and we are mirrored by PubMed Central and on several other international websites. Authors want visibility, and that is what we give them.

Google have already made their first move into scientific publishing with Google Scholar, which is to my mind one of the most powerful ways to find scientific research. The full text of all of our articles is fully searchable by Google Scholar. Google's area of expertise is the organisation of information, and Google Scholar fits perfectly into this program. Microsoft is also moving in this direction – they have built their own literature search engine (Windows Live Academic Search), and Microsoft Research are sponsoring BioMed Central's latest research awards.

BioMed Central has its own publishing platform – we built it in-house, and we handle our own submissions, peer review and web publishing. We like to think that it is user friendly, we've certainly received positive feedback. We have an independent journals program that allows researchers and societies to launch new journals using our platform, or to transfer across existing journals. PLoS have their own platform and are working on an open source platform called Topaz, and an open source platform called Open Journal Systems is already being used by several small open access journals.

Our published articles already easily integrate figures and movies. Annotation of manuscripts and integration of figures and movies during peer review would be a boon, and several publishers included BioMed Central are looking into this, but it is hardly a 'killer app'. We can already handle LaTex (familiar to many mathematicians and computer scientists) and Wolfram’s Publicon, both easy for typesetting, and we have little trouble with MS Word or PDFs.

Google or Adobe don't need to reinvent the wheel, but they could certainly jump onto the open access bandwagon. It's already rolling at quite a pace.

Conversion to open access

Stevan Harnad is arguing again that conversion of journals to open access is a distraction to self-archiving, which he believes will more quickly and broadly deliver open access.

He suggests that publishers face a 'Prisoner's Dilemma' in converting from toll access to open access. The prisoner's dilemma is when two prisoners are being interrogated. If both stay quiet and refuse to implicate each other, they may get a short sentence. This is an example of 'honour among thieves'. If one implicates the other, they will get let free and the other will be punished. But if each implicates the other, both get severely punished. While I can see how Game Theory in general is worth invoking in this debate, I cannot see how the Prisoner's Dilemma translates to journal publishing strategies. Maybe I'm just being slow.

I don't believe that open choice options bring the major conflicts that Stevan describes. While I much prefer full open access journals, a transition to open access via open choice means that journals maintain a stable source of income. The alternative of shifting to open access only by mandating self-archiving creates an unstable situation in which journals may face widespread cancellations from libraries, without having set in place the alternative models needed once you cannot charge your readers (article processing charges, advertising, volunteerism or grants). Peter Suber, as ever, has written on this extensively, so I won't repeat all of this in depth.

Among publishers who are converting to open access, Oxford Journals deserve being singled out for praise. Not only do they already have several fully open access journals, but their Oxford Open scheme is transparent and well advertised. What is more, they are actively adjusting the subscription charges on their online journals based on the income they are receiving from the Oxford Open option. They are an excellent example of the way that publishers can adjust to the open access revolution.