I'm now somebody. I'm in PubMed.
I mentioned before that I'd co-authored an editorial on authorship, and the article is now available online. I've also just published an editorial with Penny about BMC Systems Biology.
Isn't it exciting? Of course, neither article was peer-reviewed...
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?"
Multiple Stab Wounds May Be Harmful To Monkeys. Repeatedly stabbing monkeys with sharpened objects may have an adverse effect on their health, according to a new study.
In other news, four CIA agents are trapped in a dating mining disaster.
An average of 25 people a day have viewed this blog since I started posting back in January, from all over the world. As well as Western Europe, the US, Canada and Japan, there are readers in Argentina, India, China, Russia, Iran and Saudi Arabia, to name but a few countries. 
A mere 7 months since I first registered my blog with Technorati, they've finally got around to recognising it!
I've built up a bit of a backlog with these snippets. Lord knows how some bloggers manage daily updates!
Should medical journals carry drug advertising?
Yes: Richard Smith (former-Editor of the BMJ). "Major journals like the BMJ have multiple sources of income-subscriptions, classified advertising, non-pharmaceutical advertising, reprints, and sales of articles to other publications. These multiple sources bring independence from each, but at least one is, I believe, much more pernicious than advertising-and that is reprints (sales of large numbers of copies of individual articles)".
No: Gareth Williams. "Editors set high standards for their publications, and contributors who fall short on evidence, honesty, clarity of writing, and professionalism can expect to face the full wrath of peer review. How peculiar that the journals feel able to relax their principles and print, alongside the research papers, material that would not look out of place in a glossy tabloid and that often raises two fingers to evidence based medicine".
Richard Smith's description of the BMJ as an 'open access journal' is slightly inaccurate, given that BMJ Unlocked doesn't allow redistribution and reuse...
The conflict vitae: a CV for the new millennium. "I propose that the International Committee of Medical Journal Editors, the American Academy of Continuing Medical Education, and other interested parties endorse a single document with a single set of definitions for disclosure of financial conflicts of interest. This conflict vitae would not be revised for specific presentations or papers, but would simply be updated like an academic curriculum vitae and submitted in its entirety when requested.....Importantly, it would be easy to configure the standardised elements of the conflict vitae into a searchable online database maintained by an independent organisation such as ClinicalTrials.gov. This would facilitate an exciting and novel body of meta-research linking studies and conflicts."
There's a blog post on the topic here.
Going all the way: how Hindawi became an open access publisher. "As the Hindawi Publishing Corporation approaches its tenth anniversary, the author looks back at the history of Hindawi and examines a number of challenges that the company has faced over the past decade. These challenges include the rapid expansion of the company's workforce, the establishment of a standard editorial system for its journals, and the conversion of Hindawi's entire operation to an open access publication model. Although some of Hindawi's characteristics may not be common among other publishers, many of the challenges that Hindawi has faced are the result of recent developments within the scholarly publishing market that have implications for the entire industry".
Preston McAfee Shakes Things Up in Academic Publishing. "Journal time to publication lags have become embarrassing…. The system is broken. Consequently, Economic Inquiry is starting an experiment. In this experiment, an author can submit under a “no revisions” policy... I (or the co-editor) will either accept or reject. What will not happen is a request for a revision… Authors who receive an acceptance would have the option of publishing without changes. If a referee noticed a minor problem and put it in the report, self-respecting authors would fix the problem. But such fixes would not be a condition of publication".
My tuppence-worth - this sounds a bit like Biology Direct, but retaining the option to reject if flawed - this system should stop the endless cycling that can occur in a review process. It might also make authors tighten up their work before submitting. I wonder though how many authors would subsequently resubmit quite quickly once they'd fixed the problems? Is this to be banned under this system? i.e. is it literally 'one strike and you're out' as far as that journal is concerned? Part of the blame for endless rounds of revision is the authors not knowing when to cut their losses. Any author could instigate this rule by themselves, and some do in order to try to 'game' the peer review process - if they get comments they don't like, they withdraw the manuscript, and try elsewhere in the hope of coming across more lenient reviewers.
The effect of Web 2.0 on the future of medical practice and education: Darwikinian evolution or folksonomic revolution? "[Few] clinicians will probably know about or have used health-related podcasts, blogs or wikis. Even fewer will know about collabularies, folksonomies, and mashups. In short, most will not be aware of the emergence of “Web 2.0”... The term Web 2.0 does not refer to new technical standards, but to new ways of using the Internet as a platform for interactive applications. A distinguishing characteristic of Web 2.0 is the concept of online social networking — the use of Internet technologies to create value through mass user participation. These technologies are characterised by constant development and enrichment (evolution) as a result of user interaction (the so-called perpetual beta). Those who use these services assist with their development and are part of the “collective intelligence” which is harnessed to make the services better and more responsive. Web 2.0 phenomena that are particularly relevant to the dissemination of medical information include blogs, wikis and podcasts (or their visual equivalent, vodcasts)".
Thomas Stossel argues in two articles against the current obsession with COI disclosure:
Conflicts of Interest in Dermatology: More than Skin Deep? The monies that industry contributes to education and research mean more of these activities take place. If dermatologists cannot sort out promotion from substance, it is the fault of their character, their training programs, or both—not of companies.
Divergent Views on Managing Clinical Conflicts of Interest. "Lacking data—the essence of rigor and evidence-based medicine—commentators turn to conjecture and taste. Commercial involvement “might” detract from patient care (which is always possible), for which reason such involvement is inherently distasteful, and therefore its mere “appearance” deserves censure and prohibition. Rules based on the possibility of harm are fine as long as the rules themselves are not harmful. But these rules are harmful, and proposing to preserve rigor and evidence-based medicine by regulating subjective appearances violates that which is to be preserved".
And here are two replies to him:
Full Disclosure—Nothing Less Will Do. "The question remains as to whether COI is a problem in dermatology. I cannot think of any logical reason why those of us in dermatology should be exempt from human nature. Money makes the world go round, and the sums of money involved in drug-company research are vast".
Divergent Views on Managing Clinical Conflicts of Interest—Reply. "Dr Stossel’s recent statement in an article in The Wall Street Journal resonates with us too: “If a physician can be influenced into prescribing certain drugs just because he had pizza with a pharmaceutical guy, then it’s the fault of his training and not the drug company.” However, there is a fundamental and strategic difference between Dr Stossel’s approach and the one reached by broad consensus at Mayo Clinic. Dr Stossel favors empowering staff and students to report un-warranted claims in marketing, to interrogate offending companies, and to inflict severe punishments for severe misbehavior. Mayo Clinic has adopted a more proactive approach, developing policies that encourage recognition and management of COIs in leadership, research, purchasing, and clinical practice activities, thereby avoiding the need for punitive consequences which by definition occur after the damage is done".
Human-subjects research: Trial and error. "The ethics committees that oversee research done in humans have been attacked from all sides. Heidi Ledford recounts the struggle to come up with alternatives".
WHO database to include drug trials in China and India. "Researchers, funders, and patients will soon be able to find out which clinical trials are being held in China and India, the World Health Organization announced".
Compete, collaborate, compel. "Procedures for microattribution need to be established by journals and databases so that data producers have an overwhelming incentive to deposit their results in public databases and thereby to receive quantitative credit for the use of every published data accession"
Post-publication review could aid skills and quality. Journals could institute periodic post-publication review, in which the journal would solicit formal review of the article, focusing on how well its methods and results have held up, given the research that has been published in the intervening period... Young scientists participating in journal clubs could be asked to derive and post a consensus comment on the article under discussion.
Former UPenn postdoc faked images. "A University of Pennsylvania postdoc extensively manipulated data in three published papers according to an Office of Research Integrity (ORI) announcement released last month".
Yale and BioMed Central. Yale have not renewed their BMC membership. Their reasoning is that the costs to the library of article processing charges for Yale authors have risen, and thus our business model is allegedly unsustainable.
Two quick points:
1. Costs of article-processing charges scale with the number of articles published, which will scale with research funding. This is inherently sustainable!
2. Traditional publishing costs have also risen - they really are unsustainable.
Here are some links about this story:
Yale announcement.
Matt Cockerill's response on the BMC blog.
The Scientist's story (ouch).
Bill Hooker's blog (thanks Bill!).
Academic accused of living on borrowed lines. "A shockwave could be about to hit the normally tranquil waters of social science. A German economist, specializing in environmental science and technology, has allegedly committed serial plagiarism and invented academic affiliations going back decades. The case should act as a warning sign to editors about how widespread plagiarism and deception may be".
Why review? Good reviewers underpin the quality of a journal. At Nature Medicine, what do we seek in our reviewers? And how do we retain the best in the face of the plethora of requests from an increasing number of journals?
Selling the self-evident. 'press releases about self-evident findings, and the news stories they engender, can be comforting to the public, since they give people faith in their knowledge of the world. "You think the whole point of news is that it's supposed to be something new or exciting, but the obvious findings remove the alien and difficult side of science that people often see."'
Statistically significant papers in psychiatry were cited more often than others. Authors cite studies based on their P-value rather than intrinsic scientific merit. This practice skews the research evidence.
OReFiL: an online resource finder for life sciences. "We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page". This is cool! Enter search terms, and it finds software tools and databases that match those terms!
Authors' financial interests should be made known to manuscript reviewers. Yup. We do this on our medical journals, and we'll be doing it on the biology ones too.
Words, words, words. "Wilcken et al. refer to two observations on the use of tamoxifen changing clinical practice, “and thousands of lives were potentially saved”. Are we fooling ourselves? Surely it is more accurate to say, in the situation of breast cancer in lives already well advanced, that thousands of deaths were postponed? ... Could we leave “lives saved” to the populist sensationalist media, and only use it in medicine for interventions in trauma, and possibly infection, in young people whose life expectancy is otherwise so good that their life has been truly “saved”?"
Neuroscientist censured for misconduct. "Researcher falsified data while a postdoc at Dartmouth, according to ORI".
Scientific publishing stagnates in the US. "US scientists and engineers have not increased the rate at which they publish papers in peer-reviewed journals since the 1990s despite rising research and development funding, reports the National Scientific Foundation (NSF). Meanwhile, the total number of papers published across Asian nations and the European Union has increased".
The Coming Revolution in Scholarly Communications & Cyberinfrastructure. "That's the title for the collection of essays in the most recent CTWatch Quarterly v3i3. There's an incredible array of essays on the future of scholarly publishing, all of them very interesting and worthwhile (I've not read all of the essays yet, but I will). Authors include such notables as Clifford Lynch, Paul Ginsparg, Timo Hannay, Stevan Harnad, Peter Suber and others. This is must-read stuff for everybody in science and libraries as changes to the way scholarship is published will affect virtually everything we do".
Web sites and publishers plan video offerings, but will researchers embrace the new medium? Ten months after the launch of the first life sciences video journal, scientists are cautiously embracing online video to provide detailed demonstrations of experimental protocols or explanations of results. But so far, Web sites offering such videos get few visitors compared to journals and other online resources.
And finally...
The first article from JORASS. An Investigation Into Whether The Prices Charged for the Same Item by the Staff at the University Refectory Fluctuate More Wildly Than The Stock Market. It has been noticed by many that the prices charged for like items on a day to day basis at the university refectory can fluctuate dramatically. This study investigates those pricing fluctuations and compares them over a one week period to the variation displayed in the stock markets of the UK, Japan and the United States.
Sample Cover Letter for Journal Manuscript Resubmissions. Enclosed is our latest version of Ms # 85-02-22-RRRRR, that is, the re-re-re-revised revision of our paper. Choke on it. We have again rewritten the entire manuscript from start to finish. We even changed the goddamn running head! Hopefully we have suffered enough by now to satisfy even you and your bloodthirsty reviewers.
The Partnership for Research Integrity in Science & Medicine (PRISM) are scum.
Their arguments against open access are stupid, tired and old, and have been dealt with before.
Rather than dealing with this tripe all over again, instead here are some links to the explosion of reaction on the blogosphere.
The Partnership for Integrity in Science Dissemination (PISD) are also in on the act, arguing that if open access were to come to fruition "civilization would suddenly collapse. Cities would rust, industries would implode, dinosaurs would once again rule the Earth".
A Blog Around the Clock has the definitive run-down on the reactions.
Of course, Peter Suber!
Bryan Vickery has posted BioMed Central's response.
The Scientific Activist: Now that is one ugly PRISM.
Peter Murray-Rust: Analysis and letters to OUP and CUP.
Bill Hooker has a lot to say.
Jonathan Eisen calls for a boycott of the AAP.
open... Through a PRISM darkly.
The Daily Transcript.
Boing Boing points out PRISM's copyright infringement.
putting down a marker.
Caveat Lector pulls no punches!
Confessions of a Science Librarian: "a sad, pathetic story".
Living the Scientific Life.
Bayblab.
Open Access Stole Christmas.
Adventures in Science and Ethics.
Heather Morrison.
Women's Bioethics Project.
Wired: Astroturf spreads to science journals.
PRISM bullshit and hypocrisy.
Stevan Harnad.
And finally... separated at birth?
Eric Dezenhall, anti-OA lobbier.
Dr Evil.
Comparison and images taken from the post Evil is his one and only name on Science After Sunclipse.
