3 Aug 2008

Journalology round-ups return!

My, doesn't time fly, etc. etc.

Open access

Gaining impact, readers and authors through fee-less-free dissemination: an experiment with open access. "Most journals in India and other developing countries face the challenges of shortage of quality articles, poor international recognition, maintaining publication schedule and managing the finances. Many of these problems are inter-linked and are related to the journal’s visibility. Most of these journals have limited circulation beyond their own country. The limited visibility and accessibility of the journals leads to poor citation and impact factor, which in turn repel the authors and subscribers. Free online access to the journal’s content has to potential to solve this long standing problem of journals from the developing world".

Hidden cost of open access
. An stunningly ill-informed commentary on open access. "Disseminating research via the web is appealing, but it lacks journals' peer-review quality filter, says Philip Altbach. The Harvard Faculty of Arts and Sciences recently joined the "open-access" movement, urging its professors to post their research on a freely accessible website. In so doing, it aligned itself with those critics of the traditional journal publishing system who assert that knowledge should be free to everyone and not the preserve of increasingly monopolistic and predatory multinational journal publishers. For Harvard University, the decision is relatively cost free. Its institutional prestige and the prominence of many of its faculty will ensure that scholars gravitate to its website. But in most cases, open access simply places material on the internet to join the exponentially expanding universe of information. The problem is one of selection. How does a user of research select the best and most relevant material from the vast array of information available?"

Open Access 2.0: Access to Scholarly Publications Moves to a New Phase. "What publishing does well-traditional publishing, that is, where you pay for what you read, whether in print or online-is command attention. This is not a trivial matter in a world that seemingly generates more and more information effortlessly, but still has the poor reader stuck with something close to the Biblical lifespan of three score and ten and a clock that stubbornly insists that a day is 24 hours and no more. Attention is the scarce commodity; any service that makes those 24 hours more productive is welcome. A service that winnows through the huge outpouring of information and says (with authority), Pay attention to this; pay less attention to that; and as for that other thing, ignore it entirely-such a service is well worth paying for. The name of that service is publishing".

Get More from Your Academic Research. "In the age of the Internet, the ways you share and use academic research results are changing - rapidly, fundamentally, irreversibly. There’s great potential in change. After all, faster and wider sharing of journal articles, research data, simulations, syntheses, analyses, and other findings fuels the advance of knowledge. It’s a two-way street - sharing research benefits you and others. But will the promise of digital scholarship be fully realized? How will yesterday’s norms adapt to tomorrow’s possibilities? This website will help you understand the changing landscape and how it affects you and your research. It also offers practical ways to look out for your own interests as a researcher. A scholarly revolution is underway. It enables you to get a greater return from your research. All you have to do is share it".

Is apathy the main barrier to Open Access? "Why is the adoption of Open Access not proceeding even faster than its already heady pace? Perhaps from my side of the fence, where all things Open Access appear logical and highly desirable, I simply can’t comprehend why others might not agree. Part of me wonders, though, if apathy doesn’t play a part".

Open Access: Doing the numbersrs. "One question that has been repeatedly (and heatedly) debated since 1994 - when Open Access (OA) advocate Stevan Harnad first posted his "Subversive Proposal" - is the questions of costs. That is, what are the essential costs of publishing a scholarly paper? To date no one appears to have come up with an adequate answer".

Also see Scholarly Publishing Re-invented: Real Costs and Real Freedoms.

New YouTube channel for Open Access

Science Dissemination using Open Access
. A compendium of selected literature on Open Access (a 200+ page PDF book!).

Open access myths
. There are real issues and controversies related to open access--but there are also myths, arguments that have been refuted but that keep showing up time and time again.

Open Science recommendations from Science Commons

Open Access cards from SPARC. "Eye-catching and inexpensive to distribute, our new Open Access teaser cards are designed to grab student attention where they roam. Order copies or print your own, tear apart, and place this guerrilla piece strategically around campus - in library carrels, around the coffee shop, or around the department. Phrases like “The article you couldn’t read might have earned your paper an A+, but you’ll never know” point readers directly to the problem of research access and invite them to check the righttoresearch.org web site to learn more".

Open Access Doesn’t Drive Citations
. "Davis and colleagues at Cornell University have just published in BMJ a very interesting and well-designed study addressing the question of whether open access drives citations".

ORLY? Gunther Eysenbach and Stevan Harnad point out flaws in the study, including the killer fact that the follow-up was only 1 year, while citations don't accrue until after a year...

PLoS ONE: Take Two. "Declan Butler's article about PLoS financials in this week's Nature has provoked a predictable - and many ways understandable - backlash from open access fans". My opinion - the Nature piece was a clumsy hatchet job, deliberately smearing PLoS and PLoS ONE and seeking out OA opponents for sound bites. Declan should be ashamed of himself, and he should write an apology for doing such shoddy reporting.

Publication ethics

Men still hold the power in biomedical publishing. "Between 1970 and 2005, 16 of the most influential medical journals had 118 editors in chief. A study of sex equality in biomedical publishing found that only eight of them were women. The same journals had 3237 editorial board members, 371 of whom were women. Equality has improved over the years-16% of editorial board members were female in 2005 up from 1.4% in 1970-but men still hold the lion’s share of the power. Eleven of the 16 journals studied, including the BMJ, had no female editors during the 35 year study period. The authors found that general medical journals from the UK and Canada appointed significantly more women to their editorial boards (29/107; 27%) than similar journals from the US (6/50; 12%), although these figures are just a snapshot of five journals in the year 2000, so they should be treated with caution. Does it matter if senior positions at biomedical journals are top heavy with men? At least one prominent female editor thinks so. Sex biased editorial boards means sex biased journal content, she writes in a linked editorial, and a skewed influence on the wider community. Journals should start by encouraging women reviewers and making sure they are considered alongside men for a place on the editorial board. Alison Tonk, BMJ. Arch Intern Med 2008;168:544-8". BioMed Central is clearly bucking this trend with our in-house staff - for example, all four of the editors who work on Journal of Biology are female! We still have some work to do on our editorial boards, and we are definitely working on it.

GMC suspends Raj Persaud for plagiarism. "The celebrity psychiatrist Raj Persaud was suspended from practising for three months today for passing off other scholars' work as his own".

A tale of two articles. An interesting 'history of science' tale of competing research and publishing in genetics. "In 1974, two articles regarding meiotic recombination in fungi were submitted for publication: one to the proceedings of a meeting held in Gatlinburg, Tennessee (Mortimer and Fogel 1974), and the other, which remained unpublished for 4 years, to (Kitani 1978). The two articles dealt with relationships among gene conversion, crossing over, and crossover interference, and they appeared to flatly contradict each other. Mortimer and Fogel claimed that crossovers accompanied by conversion interfered with additional, nearby crossing over; Kitani claimed that such crossovers did not interfere. Mortimer and Fogel's (1974) article was based on data from the ARG4 and HIS1 loci of yeast (Saccharomyces cerevisiae); Kitani's was based on data from the g locus of Sordaria fimicola. Was one of them wrong, or is recombination in Sordaria truly so different from that in yeast? And why did it take 4 years to move Kitani's article through the GeneticsGenetics editorial process?".

Caution needed in using plagiarism detection software
. "From this brief exercise, it is clear that although Errami and Garner have made progress in a worthwhile cause, their efforts have not achieved their intended purpose, and despite their words of caution regarding the utility of their database, the surprisingly high number of false positives is alarming. Although the availability of such a database could act as a deterrent to undesirable and unethical behavior, the misuse and misinterpretation of information from Déjà vu could have damaging consequences to the reputations and careers of honest scientists. Incorrect entries in the Déjà vu database could lead to false accusations of scientific misconduct. Our exercise shows that a large number of authors may have to defend themselves to free their names from such unfounded allegations. There is no doubt that Errami and Garner’s undertaking is challenging and daunting, but one cannot help but wonder whether the publication of "A Tale of Two Citations" was premature. Safeguarding the integrity of biomedical research is essential, but one must also remember that the first rule in medicine is, "First, do no harm.""

Bias in the Design, Interpretation, and Publication of Industry-Sponsored Clinical Research. "Physicians have an obligation to be skeptical consumers of research, especially as they make care decisions based on the findings".

Todai researchers lied in medical articles. "University of Tokyo researchers lied about gaining the approval of an ethics review board and conducted studies without donors' consent for several articles published in medical journals, officials admitted Friday".

Research reporting

The EQUATOR Network launch meeting. Achieving Transparency in Reporting Health Research.

Publication bias was not a good reason to discourage trials with low power. "The objective was to investigate whether it is justified to discourage trials with less than 80% power. Trials with low power are unlikely to produce conclusive results, but their findings can be used by pooling then in a meta-analysis. However, such an analysis may be biased, because trials with low power are likely to have a nonsignificant result and are less likely to be published than trials with a statistically significant outcome... The impact of publication bias does not warrant the exclusion of trials with 50% power".

Graphical presentation of diagnostic information. "Graphical displays of results allow researchers to summarise and communicate the key findings of their study. Diagnostic information should be presented in an easily interpretable way, which conveys both test characteristics (diagnostic accuracy) and the potential for use in clinical practice (predictive value)... Graphical displays are currently underused in primary diagnostic accuracy studies and systematic reviews of such studies. Work is required to improve graphical displays, to better communicate the utility of a test in clinical practice and the implications of test results for individual patients".

The Fixing Proteomics Campaign
is bringing together the people in proteomics who want to tackle the growing frustration and unfair perception that proteomics hasn't delivered.

In the media, science is about absolute truth statements from arbitrary authority figures in white coats. "Even academics are influenced by media coverage: a seminal paper from the New England Journal of Medicine in 1991 said that if a study was covered by The New York Times it was significantly more likely to be cited by other academic papers. But for three months large parts of the NYT went on strike. The journalists wrote stories about academic research which never saw the light of day. The research saw no increase in citations. People read newspapers. Despite everything we think we know, their contents seep in, we believe them to be true, and we act upon them".

Free Microsoft tools for scholarly communication
. The following tools are freely available now:
* Add-ins. The Article Authoring Add-in for Word 2007 enables metadata to be captured at the authoring stage to preserve document structure and semantic information throughout the publishing process, which is essential for enabling search, discovery and analysis in subsequent stages of the life cycle. The Creative Commons Add-in for Office 2007 allows authors to embed Creative Commons licenses directly into an Office document (Word, Excel or PowerPoint) by linking to the Creative Commons site via a Web service.
* The Microsoft e-Journal Service [alpha version]. This offering provides a hosted, full-service solution that facilitates easy self-publishing of online-only journals to facilitate the availability of conference proceedings and small and medium-sized journals.
* Research Output Repository Platform [slides, forum, about]. This platform helps capture and leverage semantic relationships among academic objects - such as papers, lectures, presentations and video - to greatly facilitate access to these items in exciting new ways.
* The Research Information Centre [forthcoming]. In close partnership with the British Library, this collaborative workspace will be hosted via Microsoft Office SharePoint Server 2007 and will allow researchers to collaborate throughout the entire research project workflow, from seeking research funding to searching and collecting information, as well as managing data, papers and other research objects throughout the research process....

Peer review

Big bucks for peer review? "The NIH's $1 billion plan to improve peer review also includes compensation for reviewers: Grant reviewers will be compensated $250,000 for six years of service, if they qualify, The Chronicle of Higher Education reported. This surpasses the current $200 per day compensation".

The effectiveness of the peer review process
: inter-referee agreement and predictive validity of manuscript refereeing at Angewandte Chemie.

Sample Size and Precision in NIH Peer Review
. NIH should adjust their peer review system to account for the number of reviewers needed to provide adequate precision in their evaluations.

Evaluative Criteria for Qualitative Research in Health Care: Controversies and Recommendations. Seven criteria for good qualitative research emerged: (1) carrying out ethical research; (2) importance of the research; (3) clarity and coherence of the research report; (4) use of appropriate and rigorous methods; (5) importance of reflexivity or attending to researcher bias; (6) importance of establishing validity or credibility; and (7) importance of verification or reliability.

Tackling peer review bias. "New statistical analyses of the National Institutes of Health's peer review process suggest that the current system may be missing the mark on funding the right proposals. Reviews of as many as 25% of all proposals are biased, according to a study led by Valen Johnson, from MD Anderson Cancer Center published July 29 in Proceedings of the National Academy of Sciences".

Post-publication paper assessment
. "There has been an interesting discussion going on at the message board for editors of PLoS One".

Knol - thinking about authority. "A knol is an authoritative article about a specific topic.
So by its own assertion, right at the top of the Knol page, Knols are about authority. But they've made an interesting choice, which is to attach authority to authorship. This is a model that we understand quite well, since it is the classic Britannica model. So if you want to organise knowledge this way, it's quite easy, you get Learned Persons to write articles in their areas of expertise. There are, however, multiple problems with this approach... So Google has created an odd hybrid system. It's seeded with some articles mostly from medicine, but it's open to anyone. A system that claims authoritativeness, with no mechanism to verify this, other than a weak name-verification procedure".


The use and misuse of bibliometric indices in evaluating scholarly performance. "Quantifying the relative performance of individual scholars, groups of scholars, departments, institutions, provinces/states/regions and countries has become an integral part of decision-making over research policy, funding allocations, awarding of grants, faculty hirings, and claims for promotion and tenure. Bibliometric indices (based mainly upon citation counts), such as the h-index and the journal impact factor, are heavily relied upon in such assessments. There is a growing consensus, and a deep concern, that these indices - more-and-more often used as a replacement for the informed judgement of peers - are misunderstood and are, therefore, often misinterpreted and misused. The articles in this ESEP Theme Section present a range of perspectives on these issues. Alternative approaches, tools and metrics that will hopefully lead to a more balanced role for these instruments are presented".

Citation Statistics. A report from the International Mathematical Union. "The idea that research assessment must be done using "simple and objective" methods is increasingly prevalent today. The "simple and objective" methods are broadly interpreted as bibliometrics, that is, citation data and the statistics derived from them. There is a belief that citation statistics are inherently more accurate because they substitute simple numbers for complex judgments, and hence overcome the possible subjectivity of peer review. But this belief is unfounded".

Standard identifier could mobilize data and free time
. "The rise of bioinformatics has focused attention on the growing depth and scope of database content. However, it is difficult or impossible given the existing citation metrics system to identify who originally created or added value to a datum. Without a system to reward, we shall continue to rely on the good will or spare time of researchers to mobilize data into the public domain".

More articles, fewer citations
. "As more journal articles go online, only more recent articles tend to be cited, according to a study published in Science. In addition, only a small group of journals and articles are being cited, the study found".

And finally....

No sh*t, Sherlock. "editors value an original, rigorously designed manuscript with valid methodology and appropriate conclusions".

It is alive. "They're at it again. Armed with another new idea from the Discovery Institute, that bastion of ignorance, right-wing political ideology, and pseudo-scientific claptrap, the creationist movement has mounted yet another assault on science. This time it comes in two flavors: propaganda and legislative".

In search of cases of "falling in love"
. Richard Smith sends an unusual call for papers! "We are very interested at Cases Journal with problems that may be severe but which people don't usually take to doctors. partly for that reason but mainly because it's fascinating we are looking for cases of "falling in love." Have you fallen in love yourself recently enough to remember the experience? Did your pulse rate rise? Did you stop sleeping well and obsess all the time about the person you loved? Did you stop eating well and perhaps start smoking? Was your thinking deranged? Could you work well? Was your case perhaps complicated by jealousy? Did you suffer long term consequences? Please find us cases".

Having an impact (factor)
. The entrance to The Pearly Gates. There are fluffy clouds everywhere. In the center is a podium with an enormous open book. A tall figure in white robes with white hair and beard stands at the podium. Approaching is a thin, middle-aged man with glasses and a bewildered expression. He is the soul of a recently deceased genome biologist.
GB: Hey, I'm not worried. I was a good scientist, a good citizen, a good family man, I think, too. I never...
St Peter: Yes, yes, I'm sure, but you see, none of that matters. The only thing that matters is your IF.
St Peter: Your impact factor. That's all we use now. If your IF is above 10, then you enter here. If it's lower, well...

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