16 Dec 2007

Funding for publication ethics research

The Committee on Publication Ethics (COPE) has established a Grant Scheme to fund research in the field of publication ethics. The Scheme is designed to provide financial support to any member of COPE for a defined research project that is in the broad area of the organisation’s interests, and specifically in the area of ethical standards and practice in biomedical publishing.

The project should have a specific goal and be intended to form the kernel of a future publication.
A maximum sum of £5000 will be allocated to any one project, but applications for smaller sums are welcomed.

The terms and conditions of the Grant are as follows:

1. At least one of the applicants must be a member of COPE.

2. Calls for applications will be made twice a year with closing dates of 1 December and 1 June. An electronic version of the application form must be sent to the Administrator no later than 12 pm (noon GMT) on the closing date for consideration by COPE Council.

3. The application must contain a lay summary of the project, a definition of the question to be posed, sufficient methodological detail to allow assessment of the viability of the project, a clear timeline and a definition of the likely deliverables. A full justification for the sum requested must accompany the application.

4. A report on the progress of the research should be presented within one year of the award and at the end of the project. The grant must be used within two years from the date of award, and balance sheets must be forwarded annually. These should be sent to the Administrator. Any remaining funds after two years must be returned.

5. It is anticipated that the work stemming from the project will be presented at one of COPE’s annual seminar meetings within 2–3 years of the award. Such data may also be published in peer-reviewed journals. Any publications or related presentations at meetings by the recipient emanating in part or whole from COPE’s support should be duly acknowledged and copies sent to the Administrator.

Applications are reviewed by a COPE sub-committee. Applicants will be advised of a decision as soon as practicable after the deadline date.

An application form can be obtained by contacting Linda Gough, COPE administrator, at LGough@bmj.com or 020 7383 6602.


The closing date for receipt of applications is 1 June 2008.

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And who made that banner ad? Yours truly.

17 Nov 2007

Journalology roundup #13 - plagiarism special

Policing plagiarism. "The internet has made both copying other people's work and detecting plagiarism much easier. Michael Cross looks at some of the tools used to tackle plagiarism".

Plagiarism and punishment. "Plagiarism is one of the three high crimes of research fraud. The US Office for Research Integrity (ORI) puts it up there with the big boys, fabrication and falsification, in its definition of research misconduct (http://ori.dhhs.gov). Some have argued that the definition should extend to lesser crimes such as undeclared conflict of interest and duplicate publication, but to my knowledge no one has questioned that theft of another person's work is fraud".

Plagiarism? No, we're just borrowing better English
. "The accusations made by arXiv that my colleagues and I have plagiarized the works of others, reported in your News story 'Turkish physicists face accusations of plagiarism' (Nature 449, 8; doi:10.1038/449008b 2007) are upsetting and unfair. It's inappropriate to single out my colleagues and myself on this issue. For those of us whose mother tongue is not English, using beautiful sentences from other studies on the same subject in our introductions is not unusual".

University drops case against Croatian academic accused of plagiarism. "A senior Croatian academic and obstetrician has escaped punishment over allegations of plagiarism in his published work by Zagreb University's "court of honour" because the alleged offences took place some years ago and he retired in August. The allegations against Asim Kurjak were originally made in the BMJ by Iain Chalmers of the James Lind Library in Oxford last year".

Is There an Effective Approach to Deterring Students from Plagiarizing?
"The students from 2004/2005 were warned that their essays would be examined by plagiarism detection software and that those who had plagiarized would be penalized. Students from 2004/2005 plagiarized significantly less of their essays than students from the previous two groups".

What authorship really means



The wonderful Piled Higher and Deeper comic.

1 Nov 2007

This Is The Truth

- A WEB EXPERIMENT -

(In no particular order)

1. Cigarettes are bad for you.

2. Men and Women are equal.

3. Global Warming is real, and (by the way) it’s all our fault.*

4. It’s not all relative.

5. Gin is better than Whiskey. Whiskey is better than Gin.

6. Intelligent Design is wrong.

7. Overconsumption is a serious problem.

8. The Millennium Development Goals are worthy*.

9. Wilco is good, sometimes exceptional, but often inconsequential.
(I don't understand this one...)

10. Shit happens (ditto for sex and death).

11. Creationism is silly. (also, see 6)

12. SUVs are just stupid.

13. The truth is worth more than an iPod*.

14. On the whole, disorder increases.

15. Science, for better or for worse, is all around.

- - -
If you agree with the above statements, please link to this page: http://www.scq.ubc.ca/?p=677 by tagging the word “truth” (yes, just like that),and spread the word.


This is a Google bomb from The Science Creative Quarterly.

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.

21 Sep 2007

Published at last!

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...

20 Sep 2007

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?"

Facebook - science meets social networking

In my recent look at Web 2.0 I noted that "Facebook is more for play than for work". I underestimated it. Facebook has exploded in popularity since they removed the need to belong to a recognised school or university, and the addition of applications in May has given it an extra boost. BioMed Central has now jumped onto the Web 2.0 bandwagon, with the new functionality of including links to social network sites - including Facebook - on each article, which has been well received. Facebook has a plethora of groups, allowing people to easily discuss any number of topics, and has a growing number of applications, some useful, some fun (like Scrabulous, the Scrabble app), some totally pointless (like Zombies). There are now a host of science-related groups and a handful of applications, and I'm going to list just a few that I've come across, some of which I use myself.


Facebook 'friends' tend to be people you've actually met in real life (LinkedIn is the real professional networking site), but I do have two 'friends' who I've only 'met' electronically, and one of them is Bora Zivkovic, of Blog Around the Clock fame and lately PLoS ONE. However, I may meet Bora if I make it to the 2008 North Carolina Science Blogging Conference, for which I received an invite through... Facebook.

I have almost certainly missed your favourite group or application - if so, why not leave a comment? I might even accept a Facebook friend request.


General sciency stuff

Science and Technology in Society
Bioinformatics
Epigenetics
Neuroscience and Brain Studies
Cognitive Science
Support Stem Cell Research
ScienceHack Science Videos
Folding@Home Protein Researcher
American Association for the Advancement of Science
Integrative Medicine International
National Center for Science Education
British Research Funding E-petition
Pro-Test Cancer/Medical Research
All groups with Common Interest: Science


Open access

Librarians for open access
Creative Commons fan club
Access to Research Now!
SPARC
Help make NIH-funded research findings freely available to everyone!


Journals

Nurture by Nature
PLoS
New Scientist
SEED Magazine
Library Student Journal
Open Medicine
HighWire Press appreciation society
NEJM Fan Club
Student BMJ readers ...!
RCSI Student Medical Journal
Elsevier


Science blogging

Science Bloggers
Science Writers
Adventures in Science and Ethics
ScienceBlogs fan club
Stranger Fruit
A Blog Around The Clock
Order of the Science Scouts of Exemplary Repute and Above Average Physique
Hard Bloggin' Scientists
The DNA Network
Pharyngula
nodalpoint
Savage Minds
Flog Blog, to add blog posts to your Facebook profile.


Anti-woo

The James Randi Educational Foundation
badscience
Church of the Flying Spaghetti Monster (my religion is 'Pastafarian' on Facebook)
Church of the Invisible Pink Unicorn
Homeopathy is Pseudoscience
"The Great Global Warming Swindle" is a swindle
Charles Darwin Has a Posse
Prof. Steve Steve is my Hero


Just for fun

Null Hypothesis - The Journal of Unlikely Science (and an application, The Prof's Weird Fact Box)
The Official PHD Comics Group (Piled Higher and Deeper also has an application giving a feed of the comic to your profile)
Grad Students: they're Not Bad People, they Just Made Terrible Life Choices
You know you've worked too long in a lab when
We look so sexy in our labcoats, we need safety goggles... for protection
We're scientists AND we're sexy!
Argh, the lab fairy has screwed up my experiments again!

Two groups close to my heart

The Lomas Lab (I'm also supporting alpha-1-antitrypsin deficiency awareness, as it was what my research was on)
Oxford Biologists Reunite!

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p.s. After posting this, I discovered a Facebook campaign that I should share. Nothing to do with science, but my hippy, liberal nature means I've got to flag this up:

8 Sep 2007

Multiple Stab Wounds May Be Harmful To Monkeys

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.



2 Sep 2007

Journalology blog statistics

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.

It seems that you're reading Journalology as part of your dedicated "social notworking": page views plummet by 40% at the weekends, and it appears that Wednesdays are the most boring work days, as daily readership tips 30 on average on those days.

The most read posts have been Tools to search the literature, Peer review lite at PLoS ONE? (my ever first post), My favourite Firefox add-ons (by virtue of it appearing second in a Google search for "favourite Firefox add-ons") and Mashups, mining, mirrors and open access. I was pleasantly surprised to discover that one of my posts is among the top 10 Google results for the phrase "Political correctness gone mad". The most viewed tag has been Impact Factor, another indication of the unfortunate domination of this metric.

Thanks for reading!

Tracked by Technorati!

A mere 7 months since I first registered my blog with Technorati, they've finally got around to recognising it!

Journalology roundup #10

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.

PRISM are scum

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.