Journalology roundup #11

Publishing and Values. "At first glance, the decision of a scholarly society to move its journals from one publisher to another might seem like inside baseball for the publishing industry. But the news that the American Anthropological Association is moving all of its journals from the University of California Press to Wiley-Blackwell is being viewed by scholars, librarians and publishing industry officials — including many who have nothing to do with anthropology or the publishers involved — as significant and potentially worrisome".

Questioned findings confirmed. "The results of three papers by University of Wisconsin researcher appear valid, but possible grant fraud unresolved".

The effect of open access and downloads ('hits') on citation impact: a bibliography of studies. "a continually updated bibliography on the relationship between open access and impact/citations"

Peer usage versus peer review. "It is often asserted that peer review is the essence of scientific evaluation, but this is incorrect. Peer review is not specific to science but is employed by all academic subjects from English literature to theology. Neither is it necessary to science. Until a few decades ago—and during the scientific golden age of the mid-20th century—there was very little peer review in the modern sense. So peer review is neither necessary nor sufficient for scientific progress. The truly definitive scientific evaluation is in fact "peer usage," which entails testing facts and theories not by opinion but in actual practice. This means that, even when published in the best journals, new science should never be regarded as valid until its predictions have been retrospectively validated by use in further relevant research by competent scientific peers".
That's all well and good, but this article is a puff piece by Bruce Charlton, Editor-in-Chief of Medical Hypotheses. The journal isn't peer reviewed; articles are 'editorially selected', and it charges a publication fee with no peer review. It has been accused of being a vanity publication for pseudo-scientists. I'd take what he thinks about peer review with a large pinch of salt.

The Rosiglitazone Story - Lessons from an FDA Advisory Committee Meeting. "The basic plot of the rosiglitazone story quickly became obvious to the advisory committee: a new "wonder drug," approved prematurely and for the wrong reasons by a weakened and underfunded government agency subjected to pressure from industry, had caused undue harm to patients..."

How Quickly Do Systematic Reviews Go Out of Date? A Survival Analysis.
Systematic Reviews: Time to Address Clinical and Policy Relevance As Well As Methodological Rigor."We urgently need a new type of review. It would combine the scientific rigor of systematic reviews with the clinically nuanced contextualization and opinion of traditional review articles while clearly distinguishing between evidence and opinion".

The Bytes Behind Biology. "Performing 21 trillion calculations per second, a supercomputer in Pittsburgh provided the first atomic-level look at the inner workings of the nuclear pore complex. That's just one of its accomplishments". Like, wow.

Should PLoS ONE count as peer-reviewed? "According to their journal information page, an important part of their peer review process is community review. Indeed, the journal only requires review by a single editor before publication. One commenter on Zivkovic’s blog post about the process suggests that this is an inadequate level of peer review: "My current view is that with PLoS ONE, if you have $1250, you have a published paper". Zivkovic’s response is that all articles are fully reviewed, that reviewers don’t know whether the publication fee has been waived, and that half of all submissions are rejected, while many are revised several times before publication. While that may be true, PLoS ONE would not qualify as peer-reviewed under the standards I’ve proposed for BPR3 (a minimum of two reviewers in addition to the journal editor prior to publication)".

Scientist accuses OA policies of being unclear. "Scientist Peter Murray-Rust has blasted publishers for “a systemic failure to embrace open access”. He warns that anyone who purchases author-pays Open Access content may end up paying a lot of money for something not labelled as Open Access". This isn't referring to pure OA journals. It is referrring to "open choice" journals, in which authors can opt to pay to have their article OA in an otherwise subscription journal.

Resignation from Editorial Boards. Tom Wilson, founder of the Elsevier journal, the International Journal of Information Management: "I suggested, last week, that academics should resign from editorial boards of journals published by the supporters of PRISM. Clearly, then, I had to do so myself ... Given that one of the claims of the PRISM Website is that the publishers spend significant amounts of money on supporting the peer review process, and given that, in common with other academic referees, I have never benefited from that spending, I shall in future refuse to undertake unpaid refereeing work for any journal which is not an open access publication".

The Perils of Industrialization. "How the industrialization of academic science has ruined research, and what we can do about it ... science is driven by customer demand, because society funds basic research only to satisfy well-defined interests - for example, the discovery of new therapies. To meet this demand, scientists must function as efficient machines that convert grant money into publications. Scientists therefore must give up academic freedom and work only on projects for which they can obtain grants".

Selling Systems Biology. "Can this still-unproven (and much-hyped) field revolutionize drug discovery?"

Research ethics: Hyperactivity in children: the Gillberg affair. "What drove members of a highly respected psychiatric research group to defy the Swedish courts and destroy 15 years' worth of irreplaceable data? A decade after the Gillberg affair began, Jonathan Gornall examines the facts"

Medical education research remains the poor relation. "Research into medical education is stagnating and urgently needs the resources to become more rigorous and relevant. The requirement that clinical practice should be based on the best available evidence has been paralleled by calls for medical education to become more evidence based. This has resulted, among other initiatives, in the establishment of the Best Evidence for Medical Education (BEME) Collaboration and the Campbell Collaboration, an off-shoot of the Cochrane Collaboration. The BEME initiative includes dissemination of best evidence to support medical education and the encouragement of a culture capable of nurturing more rigorous and better funded research. Evidence from the United States suggests such nurturing is much needed. In 2004, Carline analysed reports of medical education research in two major North American journals (Academic Medicine and Teaching and Learning in Medicine) and found that only a minority of studies were supported by external research grants. She was critical about the quality, rigour, and generalisability of most of these studies. Her concerns were echoed last year by Chen and colleagues, who advocated moving the focus of medical education research from learners to patient oriented clinical outcomes, thus increasing the relevance and its likely attractiveness to funders".
I can't disagree. The standard of medical education research that I have seen submitted to our journals has been quite low.

UK science head backs ethics code. "The British government's chief scientific advisor has set out a universal ethical code for scientists. Professor Sir David King has outlined seven principles aimed at building trust between scientists and society. Described as the scientific equivalent of doctors' Hippocratic Oath, the code includes clauses on corruption, public consultation and the environment".

THE CODE
* Act with skill and care, keep skills up to date
* Prevent corrupt practice and declare conflicts of interest
* Respect and acknowledge the work of other scientists
* Ensure that research is justified and lawful
* Minimise impacts on people, animals and the environment
* Discuss issues science raises for society
* Do not mislead; present evidence honestly

I think I can endorse that!

Does tenure need to change? "We asked, our readers answered. Here's what you would do to improve how academia evaluates scientists - and whether you think tenure should lose its own... well, tenure".

NIH genetic database "a good start". "New rules for sharing genome-wide association data will spur collaboration, but may complicate publication and subject consent, researchers say".

Office of Research Integrity Newsletter. "plagiarism is defined as “the appropriation of another person’s ideas, processes, results, or words without giving appropriate credit.” ORI interpreted its definition of plagiarism to apply to the theft or misappropriation of intellectual property and/or the substantial unattributed textual copying of another’s work. ORI’s interpretation does not include authorship or credit disputes or “self-plagiarism” of one’s work from one paper to another or from a paper to a grant application".

Association Between Funding and Quality of Published Medical Education Research. "The quality of published medical education research is associated with study funding."

Medicine Residents' Understanding of the Biostatistics and Results in the Medical Literature. Most residents in this study lacked the knowledge in biostatistics needed to interpret many of the results in published clinical research. Residency programs should include more effective biostatistics training in their curricula to successfully prepare residents for this important lifelong learning skill.

Journalists: anything to declare? "There are real dangers in being too close to PR people: lovely though they may be, their trade is, by definition, manipulation". Yeah, watch out, our Charlie's a sneaky one.

Use and Abuse of the Controlled Clinical Trial. "The majority of RCTs published in our best scientific journals, at first glance, would seem to satisfy the requirements of an RCT as a scientific endeavor. Randomization, blindness, placebo, power calculation, and scrutiny for statistical significance are present. On the other hand, a closer look can bring inherent problems to the surface".

Be Openly Accessible - or Be Obscure. Now that the Canadian Institutes for Health Research's Open Access to Research Outputs Policy Announcement has been released, it is high time to celebrate the Chair of the CIHR Advisory Committee on Access to Research Outputs, one of Canada's most noteworthy open access advocates, Dr. Jim Till. Formerly a member of the Open Access News team when it was a group blog, Jim is now the author of one of the most thoughtful and thought-provoking blogs on open access on the web: Be Openly Accessible or Be Obscure.

A conversation with three open access publishers about the challenges of sustainability.
Alma Swan, Director, Key Perspectives Ltd, Mark Patterson, Director of Publishing, Public Library of Science, Bryan Vickery, Deputy Publisher, BioMed Central and Editorial Director, Chemistry Central and Paul Peters, Head of Business Development, Hindawi Publishing Corporation.

University-Press Leader Quit Publishers' Panel Over Anti-Open-Access Campaign. "James D. Jordan, president and director of Columbia University Press... tendered his resignation from the Executive Council of the AAP’s Professional and Scholarly Publishing division on August 28, five days after Prism was announced. A task force of the Executive Council put the campaign together. “I resigned from the Executive Council because I did not feel that serving at this time was the best use of my time or Columbia resources, and because I had vocally opposed the launch of the Prism Web site and did not subscribe to arguments supporting it and opposing the NIH’s public-access proposals.”"

Reed Elsevier launches open access web portal. "The publishing giant has just launched a web portal called OncologySTAT. The service is aimed at physicians, who will be required to register their personal information at the site in order to gain immediate and free access to research papers from 100 of Reed Elsevier's journals. Elsevier plans to finance the service with revenue generated by advertising and sponsorship from pharmaceutical companies".
More here, here and here.

Uninformed consent? The US should revamp rules on informed consent to ensure that people have all of the information and support they need before deciding to enroll in clinical trials.

Patents and scientific peer review. "There is an interesting complement to the patent system in the domain of assigning credit to ideas, which is the academic peer-review system. The inventor of the idea in the case of academia is the author. The equivalent to the patent office is the editorial board of the academic journal that the author submits to. There is an idiosyncratic historical connection between the two systems too. Einstein famously worked as a patent clerk in Bern, Switzerland, before becoming a published academic. At the time that Einstein was working the volume of patent applications was probably on a par with the submission rate of academic papers to peer reviewed journals, though I have no figures to back this up. In both cases an idea was submitted, examined by experts for originality and either accepted, granting the creator rights, or rejected, sending them back to the drawing board. Fast forward to today and it seems that on the whole the two systems, work in almost the completely opposite manner from one another".

Open Data for Global Science

And finally:
Malaria treatments: fish or DDT? "Two new studies have found that a species of edible fish (BioMed Central) or the pesticide DDT (PloS One) can control malaria. Hmm, which to choose?"