Journalology

Who are WebmedCentral?

2011-01-31T22:23:00.003Z

"It is our effort to instill more rapidity, accountability, and transparency into biomedical publishing". WebmedCentral

It is essential in biomedical publishing to be transparent and accountable. Indeed, this is something with which the publishers of WebmedCentral agree. However, on their website they only say that "We are a group of medical and management professionals with no affiliation to any major biomedical publishing group." As posted on their YouTube video by Larry Weisenthal,

"Transparency begins at home. This is one of the most opaque, allegedly scientific web sites I've ever seen. Can you imagine submitting a serious scientific paper to a black hole, where it's impossible to learn the names of the publisher, editors, contributing editors, etc.?"

We know what WebmedCentral is, but who are they?

Their address is Suite 250, 162-168 Regent Street, London W1B 5TD, UK, but this is a P.O. Box set up by completeformations.co.uk. The whois details reveal nothing because the domain was registered by Luxembourgian company PrivacyProtect.org. More searching reveals their IP address, hosted by Liquid Web Inc. in Lansing, Michigan. WebmedCentral are on Twitter, but have only tweeted twice and give no more details. Messages were posted to newsgroups on behalf of WebmedCentral in August 2010 by a Michael Carr and a John Williams, but no contact details are given and searching for people by those names does not turn up any leads.

WebmedCentral advertised for freelancers on Elance, where they revealed in June 2009 that "We are a group of doctors based in Newcastle upon tyne." A small lead, but we can do better. Companies in the UK are registered with Companies House, and WebmedCentral is no exception. Their operating name is WEBMED LIMITED, aka WEBMED PVT LTD. and they have the registered number 07436770. This company gives the same address as given on the website, confirming that it is the correct organisation. Companies need to file certificates of incorporation and to name directors. Indeed, Webmed Ltd. was incorporated on 10 November 2010.

In the interest of transparency and accountability, I can reveal the names of the directors of Webmed Limited. These directors also run WebmedCentral, as confirmed by the contents of test manuscripts visible via Google. They are three NHS hospital doctors and a management consultant based in the North of England:

Kamal Mahawar, 36, Specialist Registrar, Sunderland Royal Hospital
Ajay Malviya, 37, Specialist Registrar in Orthopaedic Surgery, Wansbeck General Hospital, Ashington
Deepak Kejariwal, 37, Specialist Registrar, Department of Gastroenterology, University Hospital of North Durham (BMI Healthcare page, NHS page)
Manish Jain, 39, manager (probably this Manish Jain)

Publications and comments like Kumar G, Mahawar KK. The number of authors in articles published in three general medical journals. National Medical Journal of India 2007 Mar-Apr; 20(2): 101-2, Peer Review Practices in Biomedical Literature: A Time for Change?, Who publishes in leading general surgical journals? The divide between the developed and developing worlds, this reply to an article, and a letter to the Lancet show that they've obviously put a lot of thought into how to reform peer review and publishing.

Drs Mahawar, Malviya, Kejariwal, Mr Jain, you should be proud of launching a site that aims to reform biomedical publishing. Why hide away?

What is WebmedCentral?

2011-01-31T00:24:00.027Z

Loosely following the style of Jeffrey Beale's assessment in The Charleston Advisor of various OA startups, here is an assessment of WebmedCentral, a new post-publication review biomedical journal.

DESCRIPTION
WebmedCentral is a post-publication review biomedical web portal launched in July 2010. It aims to "eliminate bias, increase transparency, empower authors, improve speed and accountability, and encourage free exchange of ideas." There is no pre-publication screening, although the instructions for authors imply some oversight for issues such as patient consent. Authors may submit revised versions. Articles can be read for free on the website, where they may be reviewed both by reviewers solicited by the authors and by readers. There is a list of "Scholarly Reviewers" on the site. Readers may also rate articles. Biomedical videos are also published. The journal has ISSN 2046-1690, but articles do not appear to have DOIs. It is not indexed in PubMed, but the articles are indexed on Google Scholar. The site aims to host other open access, open peer reviewed journals.

SUMMARY
Content: Primary scientific research, case reports, and reviews make up the bulk of the articles, alongside opinion, hypotheses, and outright fringe science. None have been peer reviewed before publication.

Usability: The site has a category listing, browse by date, featured articles, popular articles, most reviewed articles, RSS feeds, basic and advanced search, latest reviews. The PDF is only available via a Javascript link.

Cost: Free to read and publish, unless the author pays the US$50 Premium Upload fee.

Licensing: Authors retain copyright. Personal non-commercial use, digital archiving and self-archiving are allowed, though no standard license is used and details are confusing

Contact:

Address: Suite 250, 162-168 Regent Street, London W1B 5TD, United Kingdom
Phone: None given
Fax: None given
Email: contact@webmedcentral.com or http://www.webmedcentral.com/Contact_Us
URL: http://www.webmedcentral.com

COST
Free to read and publish, the journal aims to receive income from advertising and sponsorship. They offer a "premium upload service" for $50 per article that allows authors to simply email their submission to the journal. Scholarly Reviewers who post three reviews can obtain a free "premium upload".

LICENSE
The simplest formulation is that "Authors keep copyright to the article but our readers will be freely able to read, copy, save, print and privately circulate the article." However, the details are less clear. At one point they say authors "are free to publish it elsewhere" but also say elsewhere that "we require ... an exclusive license". They also say that users have a "free, irrevocable, worldwide, perpetual right of access for personal non-commercial use, subject to proper attribution of authorship and ownership of rights" but then say users may "view or download a single copy of the material on this website solely for your personal, non-commercial use". But they allow self-archiving: "WebmedCentral allows the final version of all published research articles to be placed in any digital archive immediately on publication. Authors are free to archive articles themselves." The precise freedom all this gives to users to reproduce the text is unclear, but calling WebmedCentral "open access" would be misleading.

EVALUATION
The approach of WebmedCentral is reminiscent of Google Knol, which is where PLoS Currents is hosted, or of a preprint server, except there is an active post-publication peer review system.

Open peer review and community peer review are not new ideas. A similar approach to that of WebmedCentral was tried by Philica in recent years without great success; the site rapidly filled with crank publications. Another was 'E-Biomed', which was stifled and instead became PubMed Central. Although anticipated a decade ago, biomedical publishing has been wary of preprints and other proposals to remove or reduce pre-publication peer review. BioMed Central's Genome Biology had a preprint server, but it closed in January 2006. A humanities institute is experimenting with community review on Shakespeare Quarterly, though they are using a hybrid model rather than abandoning invited pre-publication review. More generally, MediaCommons argue for community peer review in their book "Planned Obsolescence". They are far from naïve, noting that

'Too many digital publishing experiments, like Philica, have lagged due to an assumption that might be summed up as "if you build it, they will come."'

Ethics:
The journal requires appropriate ethical approval for human and animal studies and will remove studies if they find that they fail to meet ethical standards. Articles may also be removed in cases of scientific misconduct or plagiarism. They suggest that authors use statistical advice, and ask authors to adhere to reporting standards such as CONSORT. They ask authors of clinical trials to adhere to the Good Publication Practice guidelines, but do not specifically mention trial registration. They endorse the ICMJE criteria for authorship and the use of medical writers should be declared. Funding and competing interests should be declared, though there is no definition of a competing interest. They ask authors to suggest at least three reviewers and to not only pick "friendly reviewers", and say they may invite further reviewers. How these policies are enforced and who enforces them is not clear.

Technical issues:
Previous versions of an article should be linked to, but this fails. The journal allows digital archiving and digital preservation by LOCKSS members. Some test articles can be found as Word documents that are not visible via the search, which raises questions about site security. The presentations of figures is in a sidebar and sometimes without even a thumbnail, though the pop-up view is user friendly. The referencing could be improved, with clearer formatting and hyperlinks down to the references. Some of the formatting of the reviews is poor, with changes in font and font size, and several reviews are double posted.

Publication volume:
There are 366 published articles as of 30/01/2011. Submission rates appear to have peaked following publicity in August, and have since declined (see figure).

Content:
There is currently no indication on the articles that they have received no pre-publication review. As might be expected given the lack of pre-publication review, some of the articles are fringe science: aliens, homeopathy, prayer, and telepathy are all represented. There is an account of chiropractic care of a patient with fibromyalgia, an opinion article on the evidence for homeopathy in acute upper respiratory tract infections by Peter Fisher and colleagues, a study linking 'emotional quotient' and telepathy that has the obligatory mention of quantum theory, an article on the hunt for alien life that takes in the Higgs Boson, the Bermuda Triangle, and alien implants , a virtually content-free account of acupuncture in rats, and an intercessory prayer study. The latter is, thankfully, a deliberate satire.

When you get this kind of opportunity of publishing without a filter, sex always seem to come to the fore: step forward, a hypothesis on why women don't sleep with the first man they see when they ovulate, two case reports of priapism, an institutional review of Peyronie's disease, and a case report of penile fracture. As pointed out by two reviewers, it contained the unfortunate typo in the title of the corpus callosum (in the brain) rather than the corpus cavernosum, hence it was republished (demonstrating that the article version system is not working).

Many of the articles are unpublishable in any biomedical journal: a rant about academic exploitation; a review of the biological activities of a herb that the author seems to have forgotten to write; an account of a trauma registry that is confused and sketchy; a review of oral health and inequality for which the recommendations section appears to be lifted verbatim from Nunn et al. 2008, who are not cited. How many more of the articles will contain plagiarism would be interesting to see.

On the more positive side, there are a series of interesting articles by three authors: Leonid Perlovsky has published a series of mainly hypothetical papers, e.g. on language and cognition; William Maloney, a New York dentist, has published a series of overviews and historical accounts, e.g. the medical legacy of Babe Ruth; Uner Tan has published a series of articles of his observations and theories of quadrapedal locomotion in humans, e.g. these two cases.

Other interesting reads are a survey of the role of hairdressers and bartenders as informal emotional support following the 9/11 attacks and their responses to this role, a study by Robert Dellavelle on how journals don't require ethics approval for meeting abstracts, and a series of witty anecdotes by an Israeli psychiatrist of cases of "curing demons" in his patients.

Around a quarter of the articles are case reports. The insatiable demand of hospital doctors to publish case reports has clashed with a reluctance of medical journals to publish what are often "me too" publications offering little generalisable insights, and which are often poorly presented and incomplete. The recent trend of open access case report journals - BMJ Case Reports, Cases Journal, Journal of Medical Case Reports, Clinical medicine insights. Case reports, Case Reports in Ophthalmology etc. from Karger, Case reports in Medicine from Hindawi and the American Journal of Case Reports (free, not OA) - doesn't appear to be matching demand.

There are also 58 reviews, 31 opinion articles, and at least 15 of the "original articles" are not research articles; less than half of the articles on WebmedCentral are primary research.

Reviews:
Some of the reviewers are published researchers, but they usually have only a handful of publications and they would be unlikely to be selected as peer reviewers by a mainstream biomedical journal editor – this could be seen as a positive or a negative. There are pages listing reviewer details, but the reviews by a single reviewer are not listed.

Relatively few articles have received an insightful review or comment. Around 55% (201 articles) have received a review of some kind, and the most any article has received is six reviews (see right hand panel of the figure). 138 reviews were unsolicited and 211 were solicited by the authors. The quality of the reviews is usually low. Just over half of both solicited and unsolicited reviews contain critical analysis, i.e. at least some mention of improvements the authors could make to their article, meaning that probably less than 25% of all articles receive any degree of critical analysis. Many reviews are sycophantic, for example one case report is said to be "the best ever article publishe[sic] so far". Many merely state what the articles is about - one author-invited reviewer spends 358 words reiterating what the article says and telling us that it is a "must read" - or give the views of the reviewer on the subject rather than the article - another reviewer devotes a mere 23 words of a 430 word review to even mentioning the paper. Most reviews are very short: the average is only ~115 words for both author-suggested and unsolicited reviewers; the longest is just over 1500 words (see left hand panel of the figure for the length distribution). Comments with critical analysis are much longer (~175 words) than those without (~50 words). If I were to see reviews like most of those on WebmedCentral during standard peer review, I would never use that reviewer again.

Some of the reviews include comments such as "this is suitable for publication" or "I hope it is accepted", which indicate a lack of awareness of the publishing model. One author has even reviewed his own paper. An article I consider unpublishable received the reviews, and I quote them in full, "good" and "No comment".

There are some examples where robust review has taken place. The concerns raised by the reviewers on this paper, including a lack of mention of ethics or consent, would lead most editors to reject such a paper – but WebmedCentral has no routine mechanism for doing this. Authors responded to reviews only on a handful of papers. A lively debate developed around a physician's self-case report, but this was a rare exception. I found one example of what appears to be functional peer review, with the authors revising their work and the reviewer stating that they are happy with the revisions.

In Bambi, Thumper's parents taught him that "If you can't say something nice... don't say nothing at all", but I think that the opposite applies in peer review. If you can't come up with critical comments about a paper, you're probably missing something: every paper has something wrong with it. The sycophantic nature of many of the reviews in WebmedCentral might be inherent to open (named) peer review, but in my experience and according to published studies, open peer review increases the length of reviews and makes them more polite, but has no effect on review quality. Another factor may be that many of the authors and reviewers of WebmedCentral are from India: R. A. Mashelkar argued in Science that "India must free itself from a traditional attitude that condemns irreverence", and Nikhil Kumar and Shirish Ranade argued in Current Science that "it is a preponderance of obsequious reverence and sycophancy that has placed the science in the country on a downhill slope." Are we seeing this unwillingness to criticise in action?

Overall assessment:
This is an interesting experiment in post-publication peer review, which both indicates the possibilities – instant publication, open community review – and the perils – unsound science, unbalanced opinion, and substandard writing being presented as part of the scientific literature.

Building a functioning publishing platform from scratch is no easy matter, and several hundred publications in seven months is an impressive figure. There has been a noticeable engagement from the community, with over 365 submissions and a total of nearly 350 reviews in seven months, 40% of them by reviewers not suggested by the authors. However, the submission rate is declining and the coverage and quality of reviews is not nearly high enough to functionally replace pre-publication review.

The onus is on the authors to obtain reviews: the journal states that it will obtain reviews, but this is not in evidence - just under half of the papers have no reviews, and 30% have only one review. More effort needs to be put into gaining reviews from qualified experts.

Reviews are essentially worthless if nobody pays any attention to them, be that an editor, the authors or the readers. Pre-publication peer review is not merely a filter, but it also acts to improve articles. On WebmedCentral there is no pressure for articles to be revised in accordance with any critical reviews, perhaps other than author embarrassment. As reviewers see a lack of response to their comments, they may lose enthusiasm.

Without a clear indication that reviewers have criticised an article and no indication that the articles are not peer reviewed, readers may view the work uncritically. If reviewers state for instance that the work is not sound, this should be clearly flagged up to readers near the top of the page, and articles should be sortable based on the answers given in the review from and the rating given by reviewers and readers. Another layer should be added, allowing articles to be promoted by agreement from their 'Scholarly Reviewers' to a "publication standard" level, giving authors an incentive to revise their work. "Featured articles" do exist, but the criteria used are not revealed. WebmedCentral are forming an "Advisory Board" of "eminent scientists"; perhaps this board will increase the rigour of the site.

Without the oversight of an editor choosing diverse reviewers and because most scientists are unaware of the site, it may become a closed community of the same authors positively reviewing each others' work – the precise opposite of the aim of the journal. Unless the process is reformed, WebmedCentral is likely to remain a "Cargo Cult science" journal, which in the main publishes articles that only superficially resemble the peer-reviewed literature, and that are reviewed in a manner that is only a pale imitation of pre-publication peer review.

Other commentary on WebmedCentral:

WebmedCentral and ginger pee on Pleion, a discussion on Ramy Aziz's FriendFeed, a blog review, a response to receiving an email from them, a brief welcome, a mention by Jenny Rohn in a Guardian comment thread, a comment by an author, an assessment in a sports science magazine, a mention in Lab Times, a critical appraisal of an article by PJ of Pyjamas in Bananas, a blog reaction in French, and a few Twitter comments.

But who runs this site?
"We are a group of medical and management professionals with no affiliation to any major biomedical publishing group" is all they say, but who runs the site shall be revealed in my next post: "Who are WebmedCentral?".

Editing Wikipedia - for scientists

2010-10-04T21:10:00.003Z

Wikipedia is now one of the most visited websites, and is probably the biggest source of fully free information. Wikipedia and Wikimedia in general fits well in the "open movement" alongside open source, open access, and open data. Many people, including scientists, find Wikipedia to be invaluable and read it on a daily basis, and some have even used it as a source, but you may find that the coverage is wrong or scanty. You can shrug and move on, or you can fix it yourself - and leave it better for the next reader.

If you're not contributing to Wikipedia already, as a scientist you're very well placed to do so as two of the main rules should be second nature - citing your sources and presenting the work of others neutrally. I could go into much more detail, but Darren Logan and his Cambridge colleagues have already written a brilliant guide in PLoS Computational Biology that is recommended reading for those who are as yet unfamiliar with the ins-and-outs of becoming a Wikipedian.

Joining PLoS ONE

2010-10-04T19:01:00.003Z

I'm excited to say I've just started as an Associate Editor with PLoS ONE at the Public Library of Science, after freelancing with them since the beginning of the year.

It's interesting timing in the wake of a surge in submissions post-Impact Factor and the recent brickbats hurled at the journal by PZ Myers and David Gorski, but I'm looking forward to helping the journal go from strength to strength.

Open access: the saviour for Chinese journals?

2010-09-17T18:43:00.003Z

Discussing the announcement that the Chinese government is going to crack down on poor quality journals, a Nature editorial puts forward the welcome view that moving towards open access might be the best approach for Chinese publishers:

"The best opportunity to revive Chinese publishing, whether in Chinese or English, probably lies in an open-access platform — increasingly popular in Western journals. Many Chinese journals already charge authors a publication fee, so should be able to make a smooth transition to the open-access model, in which they are supported by fees rather than by subscription revenues."

What is the scientific paper? 4: Access

2010-09-05T11:39:00.002Z

Completing the series exploring the question "what is the scientific paper?", reposted from my old blog, and originally written following Science Online 2009. As I reminded people at the time, these were just my own half-thought through ideas, not the policy or manifesto of anyone or anything I'm affiliated with.

A friend of mine once told me how much she hated "the proliferation of these bioinformatics papers." All these simulations and models of what happens in real life. All of it utterly useless -- since when was the stuff that comes out of a computer worth anything? None of it even remotely reflects anything that happens in real life. And the methodology papers -- the endless methodology papers. They're making yet another neural network and modifying a bayesian something-or-other, when they haven't even found where they left the markov models yet! How can you have so many of these methodology papers? Clearly they can be no more than incremental advances. (Of course, BLAST is an exception -- it's old enough to have been around and heard of when we were undergrads, and is therefore a perfectly legitimate and mainstream molecular biology tool.)

Similarly, some people still voice their skepticism about the need for open access. Access isn't really a problem, is it? These open access advocates are just making facile arguments about the how the people who pay for scientific research should have some kind of say regarding its dissemination.^[1] Come on, really, show me, who is in want of access? Everyone (everyone who matters) already has subscriptions, right? Access isn't a problem. And the open access "movement" isn't an ideology. It's just another business model.

And then, yesterday afternoon m'colleague shouted for advice handling an author of a scientific manuscript who was questioning the need to deposit her not inextensive collection of genomes in a database. I don't blame the author for wanting to get out of the chore—she had a lot of data, and depositing it will be a dull repetitive task. M'colleage was trying to write a letter and struggling to put into words the reason why we mandate deposition of sequence data, and why merely including them as supplementary MS Word files isn't good enough.

These attitudes, you will have noticed, have one particular thing in common: they all completely miss the fact that the biomedical sciences have moved on in the past quarter century. In almost every field (lets not wake the poor taxonomists) the science being done and the science being published today are not quite like that of 25 years ago. Even if the science of today were like that of 25 years ago the case for open data sharing would be strong enough; as it is, it's simply absurd to think that open sharing of data isn't worth doing.

Individual scientific papers -- the basic units of scientific research -- are rarely exciting; rarely even interesting. Where nerds get excited about science, it's where science offers a beautiful explanation for how the world works. And scientific papers don't do that. They offer some speculative interpretations of data on obscure problems in obscure systems. It is the literature as a whole -- hundreds of dull papers put together -- which tells a complete and exciting story. The sum is more than the parts -- the theory is more than the data.

In the field I know best -- cancer cell biology -- 99 in 100 papers published are tedious details, discovered with a science-by-numbers formula. The (anti-)proliferative effect of one abbreviation interacting with another abbreviation in three-letter-acronym-and-a-number cells, concluding with a suggestion that the authors' work might have implications for cancer treatment and a note that further work is necessary. Or even better, the complete lack of anything interesting at all happening when the first abbreviation interacts with the second. The abbreviations and their effects have been studied, in combination with others, in all of the most widely used three-letter-acronym-and-a-number cell-types, and somebody is scraping the barrel.

But the tedious details put together add up to an understanding of how the cell works and how it goes wrong. The details could be put together by a human, going through the thousands of papers on the topic, assembling the facts and finding the trends. Or, more plausibly, given the amount of tedious details out there, they could be assembled by a computer, with a database and a clever algorithm. Except that four in every five of those tedious details, discovered at great expense to taxpayers, will be inaccessible to that clever algorithm. They will be locked away in the basements of university libraries, hidden in human-readable prose that humans will never read. The results of billions of pounds of work searching for an understanding of cancer and a better chance at defeating it will be worthless, because they will never be amongst the parts that add up to the greater whole.

So I told m'colleague to explain to her author that unless she deposits her genome sequences, the last three years of her professional life will ultimately have been wasted. An average paper in a high-volume mid-tier journal that will be glanced at by a few colleagues when published. Another bullet point on a CV. They will never further science beyond that. They won't contribute any important discovery or real advance to the field. They will be forgotten. Nobody will seek them out when the time comes to make the leap forward.

That's just where biology is at these days: lots of tiny fragments of data, spread thin through the literature. The most interesting and important unanswered questions will require the synthesis of that work. The most interesting and important questions can't be answered without the heap of data that has already been produced, but which is locked away.

On machine readable data, Mike Ellis says, "at some point in the future, you'll want to do "something else" with your content. Right now you have no idea whatsoever what that something else might be." This is especially true in science: at some point in the future, tedious data obtained at great expensive, as part of the bigger picture, will finally be important and valuable. Right now, you can have no idea how important.

Publishers are allowed to get away with keeping science closed, holding it back, and wasting public money because there are still sufficient numbers of scientists who let them -- who have themselves failed to grasp that the world and science have changed.

What is the scientific paper? 3: The metric

2010-09-02T20:09:00.004Z

Continuing the series exploring the question "what is the scientific paper?", reposted from my old blog, and originally written following Science Online 2009. The topic of this post was originally discussed on FriendFeed, here.

On my recent post, what is wrong with the scientific paper?, Steve Hitchcock said that the most important problem with the paper is access, and that when we solve the problem with access, everything else will follow. I agree that access is hugely important, I recognise that we haven't won everyone over yet, and I know we do have to continue working away at the access problem, so I will devote a future post to reviewing that topic. But having thought about it a little longer, I am more convinced than ever that it is not access that is the big problem which is holding back the paper and journal, and open access is not the solution from which all others follow and fall into place.

There is one big problem, a single great big problem from which all others follow. The great ultimate cause is not, as I said last week, the journal. It is more basic than that. It is the impact factor. The journal is the problem with disseminating science, but the reason it has become the problem, the reason people let the problem continue is the impact factor. The impact factor is a greater problem than the access problem, because the former stands in the way of solving the latter. The impact factor is a great big competition killer; by far the greatest barrier to innovation and development in the dissemination of science.

Scientists can look at all of the problems with disseminating science, and they can look at us proposing all of these creative and extravagant solutions. They might agree entirely with our assessment of the state of the scientific paper and of the journal, and they can get as excited as us at the possibilities the flow from new technologies. But blogs and wikis are mere hobbies, to be abandoned when real work starts piling up; databases a dull chore, hoops to jump through when preparing a paper. So long as academics can get credit for little else besides publishing in a journal — a journal with an impact factor — any solution to publishing science outside of the journal will never be anything more than a gimmick, a hobby that takes precious time away from career development.

In a worse position than blogs and wikis, where cheap easy products are openly available, are the wonderful but complicated ideas that would benefit from financial backing to implement — the databases, and open lab notebooks, and the like — but which are currently artificially rendered unviable because no scientist could ever afford to waste time and money on a product that isn't a journal with an impact factor. No scientist can try something new; no business can offer anything new. Even such an obviously good idea and such a tame and simple advance as open access to the scientific paper has taken over a decade to get as far as it has in part because it takes so long for start-up publishers with a novel business model to develop a portfolio of new journals with attractive impact factors.

I am not a research scientist. I don't have to play the publish-or-perish game. So I have no personal grudge; no career destroyed or grant lost by rejection from a top-tier journal. It doesn't bother me how much agony, absurdity, and arbitrary hoop-jumping research scientists have to go through in their assessments and applications. But it bothers me greatly that, by putting such weight on the publication record — not actual quantity and quality of science done, but a specific proprietary measure of the average impact of the journals (and journals alone) that it's published in — public institutions across the world are distorting markets, propping up big established publishers, and destroying innovation in the dissemination of science. End the malignant metric and everything else will follow.

What is the scientific paper? 2: What's wrong?

2010-08-30T21:19:00.002Z

Once again, this is a re-post of something I wrote on my old blog a year ago after the Science Online conference, looking at the future of the scientific paper. As I reminded people at the time, these were just my own half-thought through ideas, not the policy or manifesto of anyone or anything I'm affiliated with.

So in response to the Science Online conference, we've been thinking about the question, "what is the scientific paper?" I already gave my answer to that a couple of weeks ago, but promised to have a go at answering the more interesting question, "what is wrong with the scientific paper?"

I've been thinking through how to sum up the answer all week, and I'm afraid the simple answer is, "the journal". The journal is what's wrong with the scientific paper. Or rather, the journal is what is holding back the development of efficient modern methods of disseminating science. So I thought I'd spend this second post making some observations on what the scientific journal traditionally is and does; what I think the modern journal shouldn't be doing; and a couple of case studies of alternative technologies that disseminate certain kinds of scientific communications better than a journal ever could.

What is the (traditional) scientific journal?

The journal is a collection of scientific papers limited to some kind of theme coherent enough to make it worth ~~reading~~ buying.
The journal is led by a charismatic editor-in-chief and editorial board who attract people to publish in the journal.
The journal is printed on pages. It can do text, still pictures, graphs, and small tables.
The journal publishes a sufficiently large number of papers to make it worth printing several issues each year, but a sufficiently small number of papers to make each issue manageable.
The purpose of the journal is to be read and cited by other scientists.
The purpose of the journal is to be purchased by university libraries.
The journal provides a peer-review, copy-editing, marketing and media relations service to their scientists.
Publishing in a journal provides a way for scientists to be cited and credited for their work, based on the reputation of that journal.
The journal decentralises scientific publishing, allowing individual pockets of innovation within the publishing world, but making change overall very slow.

What should the modern journal (not) be doing?

It is perhaps rather foolish for somebody who works for a publisher of journals -- who works developing technologies for a publisher of journals -- to say that the problem with publishing science is the journal. It would be even more foolish for me to say that publishers perhaps shouldn't be trying to fix the problem with technology. Here are a couple of interesting technological advances that the more forward thinking journals have come up with lately.

At Sci Online, Theo Bloom demonstrated iSee, a structural biology visualisation applet for your "supplementary information". In the same category is J. Cell Biol's DataViewer, which is presented to us as a device for visualising raw microscopy data. Did you know that the results that come out of modern microscopes are not just pretty static pictures, but vast datasets full of hidden information? The JCB DataViewer unlocks that hidden information, by providing it and an interface to it as "supplementary information" with a paper.
PLoS Currents: all the constraints and benefits of a traditional journal, but without the peer-review. Solves the problem of delays in publication. Publishes items that look just like the traditional paper.

Should publishers and journals be doing these things? When you look more closely at JCB's DataViewer, you find that, useful though it may be, most of its power and potential is currently wasted. The DataViewer is presented to us as a device for visualising the supplementary information of a paper; in fact, it is a potentially important database of microscopy datasets with a handy graphical interface attached. Restricted to a single journal, the database functionality lays unused.

PLoS Currents? This is supposed to be a solution to the problem of delays in publishing special types of science deemed to be important and timely enough to need rapid communication to peers in the field. What have PLoS done? What makes PLoS Currents unique? How does it speed up intra-field communication of those important results? It drops one single aspect of the paper: peer review. In all other respects, PLoS Currents does all it can to make its papers look like the scientific paper, and its "journal" look like the scientific journal. Scientists are still asked to spend hours writing up these important timely results, with an abstract, introduction, methods, results, conclusions and references, with select figures and graphs and tables. Nobody has the imagination to go beyond the paper-journal-publisher model. We would sooner give up peer review than publish science in anything that doesn't look like papers have looked for a century.

Or how about Journal of Visualised Experiments? JOVE is, for some inexplicable reason, held up as a brilliant example of innovation in publishing science -- of making the most of the new technology provided by the web. Those who point out that, well, it's not really a "journal", is it?, are chastised for their own lack of imagination. But surely it's those who can't conceive of a publishing format branded as anything other than the "Journal of ..." who are lacking the imagination.

Final example: while thinking about this post, PLoS Computational Biology kindly came up with the absurd idea of being a software repository. NO! Software repositories already make perfectly good software repositories, and there are plenty of them. Trying to turn a journal into a software repository is a suboptimal solution to a problem that disappeared long ago -- long before scientific publishers could have imagined that the problem even existed.

Breaking out of the journal

The web makes all sorts of new methods of publishing, communicating, disseminating science possible. It also comes with all sorts of well developed and widely used solutions to the problems of disseminating science. The big old publishers haven't even realised the web has happened, let alone thought about what to do with it. The hip young publishers know what's possible, and they want to be the ones to realise the possibilities. Good on the hip young publishers. But with each new possibility, scientists should be asking whether publishers, even the hip young ones, are really right for the job. Sometimes they are. Sometimes not.

GenBank, the database of gene sequences and genome projects, had to happen. Journals simply can't publish the raw results from a whole genome sequencing project. (Thought I don't suppose they gave up without trying.) And GenBank comes with dozens of benefits that papers, when spread across a decentralised system of journals, just can't have. Yes, I know that databases aren't the optimal solution for every variety of data, but they are suitable -- desirable; even required -- for more of them than you might think. The microscopy data in JCB dataviewer (or the structural data in iSee) would, I suspect, be of much greater value were it branded as a standalone public database with a fancy front-end, than as a fancy visualisation applet for some scattered and hidden supplementary files, restricted to a single journal.

Like it or not, science increasingly depends on data being published in public machine readable formats. Those who spend their days looking one-at-a-time at the elements of a single cell signalling pathway in every tumour cell line available to them are wasting our money if they bury their data in a fragmented and closed publication record. Nobody reads those papers, and the individual fragments of data don't tell us anything. Journal publishers think they can ensure that data is correctly published, but so far their only great successes are with the likes of GenBank and MIAME, where journals have ensured that data be deposited in public databases outside of the journal format.

ArXiV. Does this need any explanation? What does PLoS Currents offer that isn't already solved better by pre-print servers? Just a brand name that makes it look as though it's a journal. If you require rapid dissemination of important timely results and you want to go to the effort of writing a full traditional scientific paper, put it on a pre-print server while it's going through peer review in a real journal. Don't just abandon peer review while making it look like you've just published a real paper in a real journal.

Better yet, don't write a proper traditional paper. If you need rapid communication of important timely results, why waste time with all of the irrelevant trimmings of a scientific paper? The in-depth background and discussion and that list of a hundred references. Put these critical results on a blog with a few lines of explanation, and later submit the full paper for peer review in a real journal.

Credit where it's due

All the real scientists reading -- the ones looking for jobs and grants and promotion and tenure -- have spotted the one great big flaw in all these suggestions: credit. At least a paper in PLoS Currents can be listed in a CV. Nobody even reads blogs, let alone cites them. How can you get a grant on the back of a blog post? Am I suggesting you should be able to get a grant on the back of a blog post?

Maybe. I don't know. I don't think so. At the moment, publishing papers in journals is pretty much all a researcher can get any credit for. Asking researchers to go beyond the paper-in-journal format is going to create problems of assigning credit, and I don't know exactly what the solution to that problem might be. Simply, I haven't put much effort into considering solutions. I'm a consumer rather than creator of science, so that particular problem doesn't keep me awake at night. But there surely are solutions -- plenty of them.

Fact is, it's quite obvious to anyone in or observing science that the current method of ensuring that scientists are credited for their hard work is really quite broken. Trying to cram every new kind of "stuff" into that broken system is hardly helping.

Business models

Meanwhile, the publishers will be asking how we see the business models for these non-journal based methods of publishing working. Frankly, I'm not really interested. But then, JOVE is hardly the beacon of business success anyway. If publishers want science publishing to be a business, they need to find the new business models that work without strangling science. Otherwise, they're liable to find out that, on the web, some institutions and individual scientists can do a better job of disseminating science than the professionals can, and out of their own pocket.

The paper of the future

I don't necessarily think that anybody should stop writing papers -- perhaps not even the ones that nobody reads. The paper solves several problems better than any other proposed solution. A peer reviewed scientific paper, in a journal if you like, is as good a way as any to provide a permanent record of a unit of science done, and of a research group's interpretation of the significance of that unit of science. And it needn't change all that much. Making them shorter and a lot less waffley would be to my taste -- there's no need to put that much effort into words that won't be read. And give them semantic markup, animations, and comment threads, if you like. But don't pretend that those things are anything more than incremental advances. The real revolutions in the dissemination of science can only occur beyond the shackles of the traditional paper and journal. Every new Journal of Stuff is another step back.

Updates for 2010

Peter Murray Rust has been saying interesting things about domain-specific data repositories, which I am sure are worth paying more attention to than I have yet had time to.

When I originally posted this, I was challenged for not mentioning the problem of closed-access journals at all; that problem is addressed in the subsequent posts.

What is the scientific paper? 1: Observations

2010-08-17T22:57:00.004Z

Last year, after Science Online, I wrote a series of posts inspired by Ian Mulvany's question, what is the scientific paper? Those were originally posted on my old blog; now, with SoLo approaching once again, seems like a good time to revisit them, while migrating them over to Journalology.

Science Online charged us with answering the question, what is the scientific paper? Here is the answer. It comes from the perspective of somebody who has been middle author on just two, but who has spent a little bit of time working with them and with people who think a lot about them.

What does the scientific paper look like?

It's a few thousand words -- probably between 4 and 15 pages long (but can be <1 >100 pages).
It's mostly prose text, with a little bit of graphs, tables, and pictures.
It has a set matter-of-fact style and structure.
It's written in (American) English.¹

What is in the scientific paper?

Who did the science.
Why the science was done.
How the science was done.
Data!
The authors' interpretation of what was achieved by doing the science.
Pointers to the other bits of science mentioned.

Where is the scientific paper?

It is in a journal, available in one or both of:

printed on 4-15 sheets of dead trees, between a pair of glossy (or not so glossy) covers in the basement of a library.
a journal website, possibly with technology deliberately designed to make it difficult and expensive to get to, probably only available in a clunky and poorly designed PDF file.

It might also be in-part or in-full in a searchable database, like PubMed.
If you're really lucky, it is available as HTML and XML.

What is the scientific paper for?

It aims to be a complete, objective, reliable, and permanent record of a unit of science done.
It's a way of telling your field what you've done.
It's a way of telling your field what you've found.
It's a way of giving data and resources to your field.
It's a (the?) way of proving to your (potential) employer/funder that you have done something worthwhile.
It's a way of making money for publishers

How is the scientific paper made?

The authors are given some money and lab space on the condition that they use it to do some science and write a paper about it.²
The authors do some science and write a paper about it.
They give it to a journal. The journal thinks about it.
Peer review! Months of scrutiny, discussion, and revisions.
Production! The words are turned into PDFs and printed pages.

What is the scientific paper not?

Part of a conversation.
Quick and efficient.
Diverse and flexible.
Possible to edit after acceptance by the journal (except in extreme circumstances, and via slow and unsatisfactory mechanisms).
Possible to edit by anybody except "the authors".
A way of making your data and resources reusable.
A way of telling the layperson what you've done and found.

Wait, that wasn't really what the question meant, you say? Well, indeed. But before we get to the real questions -- "what's wrong with the scientific paper?" and "what do you suppose we do about that?" -- it's good to define some terms and lay out the basics. Do you think I've got any of my observations wrong, or think I've overlooked some important property of the scientific paper? Do say -- it would be good to try to agree on what the paper is before going any further.

Footnotes

Thanks to Hannah who added this point in the comments on the old blog
Thanks to Cameron Neylon, ditto

Incentivising academic fraud

2010-08-17T21:06:00.004Z

Catching up with the newsfeeds after a week working in Beijing (where citizens are saved from reading such subversive content as Journalology -- as they are all Blogspot blogs), I notice the Economist discussing academic fraud in China.

Being the Economist, it attempts to explain China's fraud epidemic focus on incentives:

China may be susceptible, suggests Dr Cong Cao, a specialist on the sociology of science in China at the State University of New York, because academics expect to advance according to the number, not the quality, of their published works. Thus reward can come without academic rigour. Nor do senior scientists, who are rarely punished for fraud, set a decent example to their juniors.

The trouble with this explanation is that these same incentives apply in many -- most -- other countries also. Science everywhere is plagued by the publish-or-perish game and the incentives it generates. Academic careers stand and fall on the basis of publication counts. Some countries at least try to judge quality of output in addition to quantity, but most methods are no more sophisticated than that used by China -- and every method has its incentives for fraud.

Nor does a lack of disincentives in China explain why they stand out. Fraud is rarely satisfactorily punished anywhere. If it is even discovered at all, the photoshopped figures and made-up numbers become an accident; the original data was lost sometime after that project was completed; the grad student who handled that particular experiment has moved on, and can no longer be contacted. A researcher getting fired for fraud is big news, not because fraud is rare, but because failing to weasel out of an allegation is rare.

It is my fear that China is perceived as having a higher rate of fraud compared to other countries not because it does, but because Chinese researchers aren't very good at it yet. Their fiddled figures are crude and easily spotted; their fictitious facts are amateur inventions that can not be believed. The worrying thing about these rough and unrefined fabrications is not that they themselves, easily found out and struck from the record, exist. The worrying fact is that they must be the tip of a great iceberg; 99% of the fakes are unseen, produced by forgers skilled enough to mask their work in convincing disguises and cover their tracks perfectly. As science in China matures, and the student to supervisor ratio falls and natural selection picks the cleverest conmen, the epidemic of clumsy and primitive fraud will end. That's when China joins the ranks of countries experiencing advanced and undetectable fraud epidemics.

Discussing fraud as a symptom of a Chinese problem -- of a failure of Chinese academic administration or a flaw in the Chinese culture and psyche -- is a nice distraction from the uncomfortable fact that fraud is a symptom of a global problem -- of failing academic administration everywhere. The Chinese copied the publish-or-perish game from the west. Soon they'll get good at it.

New word - evoluating

2010-08-10T11:35:00.004Z

"Evoluating". It's probably an attempt to use the French "évoluer" in English, I think it means "evolving".

The Scientist has an attack of CNS disease

2010-08-06T11:46:00.005Z

The Scientist this week tells us that

"Peer review isn’t perfect [who knew?]— meet 5 high-impact papers that should have ended up in bigger journals."

Wait, what? These high-impact papers got those citations despite ending up in "second tier" journals, so I doubt the authors have been crying into their beer about this "injustice". This is an example of CNS Disease, a term coined by Harold Varmus to characterise the obsession with Cell, Nature and Science. Not all high-impact papers must published in one of these journals, and not all papers published in these journals will be high impact. Biomedical publishing is not just a game in which editors sort articles by predicted future impact - at least, I hope it's not.

Authors chose their publication venue for all sorts of reasons, and it's hard to predict which new work will set the world on fire. Take BLAST - it was a "quick and dirty" algorithm that gave similar results to the Smith and Waterman algorithm only much faster, and the gain in speed came at a loss of accuracy. Only use by scientists in practice could decide whether this was a good approach. Focussing on the umpteen thousand citations to BLAST is missing the point: the important thing about BLAST is the millions or billions of hours of computer time saved by using it. As Joe, the other denizen of Journalology Towers, said recently:

"Lord protect us from the idea that an academic publication might have any value beyond its ability to accumulate citations."

The stuff we didn't have time to blog about in July

2010-07-31T14:46:00.005Z

Some old fashioned publishers are still claiming that open-access mandates -- by forcing the publishers to acknowledge that the internet has happened and that this event makes the status quo business model that they cling to wasteful and unsustainable -- will "stifle innovation". In other news, war has been found to be peace and it was discovered that freedom is slavery.

An unexpected and not entirely welcome development in open science: the Information Commissioner -- charged with enforcing the UK's freedom of information act -- has ruled that data collected by a Queen's University Belfast researcher falls under the remit of the act, and the data must now be released. This seems to be something of an accidental victory for open science, though rather unfortunate that it should come about as the result of a stunt by a climate change denier, and not as part of a planned, consensual, and multilateral shift in academic culture. I've yet to see much written on the repercussions of the decision (though I am a little behind on reading).

WikiReviews? A potentially interesting project for collaborating on "living" review articles, initially on cancer, introduced by George Lundberg.

Scientists who end up in industry could inadvertently find themselves in trouble when the natural tendency of the scientist to share information for the benefit of mankind conflicts with the natural tendency of big companies to jealously and zealously guard everything they have. In the US, researchers innocently publishing a scientific paper can face (at least, the threat of) decades in prison for industrial espionage if they're not very careful.

Elsevier experiments with peer review

2010-07-05T16:28:00.007Z

Well I never. I've been advocating the adoption of open peer review and community peer review for a while now; I didn't expect one of the pioneers of community peer review to be Elsevier, but they've surprised me.

On 21 June, they announced a three-month trial of what they are calling PeerChoice on Chemical Physics Letters, which allows potential reviewers to volunteer to review papers. As Ida Sim points out, this doesn't open up peer review in the sense of making it more transparent, but it should help speed up peer review and it might avoid the bias caused by editors selecting from a limited pool of the same 'usual suspect' reviewers.

The devil is in the details: who gets to be in the pool of potential reviewers; how will you motivate reviewers to volunteer, when getting reviewers to agree when directly inviting them can be hard enough; will volunteers be vetted for suitability for that article; is this alongside or instead of editorial selection? These question aside, let's hope it's a success.

---
Edit: There's some answers on the hidden-away page about PeerChoice - PeerChoice is supplementary to editor-invited reviewers. Registered reviewers will see titles and abstracts and be allowed to download the manuscript if they agree to provide a "timely review." There doesn't appear to be a vetting/vetoing system, but the editor still makes the decision. The trial is on nanostructures and materials; the results might not be applicable outside that very narrow field as scholars in different fields react in very different ways to variations in the peer review process.

Green is no goal

2010-06-09T15:07:00.006Z

To achieve a sufficiently large but distant win, it is worth sacrificing a much smaller but nearer win if it stands in the way or distracts and delays the larger achievement. To achieve a small but near win, it is not worth sacrificing a much larger but more distant win. But the difference in magnitude must be sufficiently large, and the difference in distance sufficiently small, to make delaying the gratification really pay off. Speculation and argument over the sizes and distances and relative probabilities of success and incompatibilities of the competing achievements fuel many a political argument.

Like "green" open access.

Green open access is simple: for every scientific journal paper, at least one of the authors must take action to ensure that the paper is freely available to the world online, somehow. They can deposit the text in PubMed central, or put a crude PDF of a draft version on their website. The increasingly preferred method for many advocates of green OA, though, is the institutional repository: each university library manages its own database of affiliated researchers' papers. This will solve the problem: the inability of people to read a paper that they want to read.

A heresy for you: access is not an interesting problem. The stubborn toll access publishers are correct when they say that most people can read most of the papers that they want to read. Yes, it takes emails to the authors, piracy amongst friends, and borrowed passwords, and yes it is a real problem, and no, the toll access publishers do not have any excuse to do nothing about it. But it's not an interesting problem any more. Letting us read a paper for free, without having to log-in or pester the author, once the paper reaches twelve months old, is not a revolution.

There are other similarly dull problems in science and publishing that green OA doesn't address. Like how to save university libraries from the parasitic subscription access publishers that are slowly killing their helpless hosts. Green OA tells parasitic publishers that they can continue draining libraries of their budgets with subscription bundles to poor quality journals that few people want to read, so long as they open access to the papers after twelve months. Now, as libraries face their greatest budget squeezes of the recession, is the perfect time for them to get some guts, speak up, say 'no', and shake off these parasites once and for all, before somebody comes along and hides them behind a bigger and stickier sticking plaster. Students should be rioting at the news that they are expected to do without textbooks and computers because their library has chosen instead to spend the several tens of thousands of pounds on a package of obscure and substandard journals. Instead, we're distracted by green OA, told that it is the one thing that academia desperately needs.

More interesting than these little problems are the opportunities that are currently presented to us: the real revolutions. Open, structured, reusable data has already demonstrated its revolutionary credentials in the field of genomics. Genome data that can be searched and mined by powerful computers and clever algorithms has enabled cheap and easy high-throughput hypothesis testing, and even hypothesis generation: it has led to countless discoveries that weren't on anybody's mind when they set out to collect the data, because the database as a whole is worth far more than the sum of the individual data gathering experiments. There are vast quantities of data in the literature: from microscopy to biogeography, epidemiological trends to drug toxicity. There are great and important discoveries waiting to be made in that data. But they're not being made, because unlike with genomics, no organisation has made the effort to build the database; no campaign group has achieved a mandate that the data be made open and reusable. Instead, the data, where it is available at all, is locked away in non-standard tables within unstructured PDF files, distributed across largely subscription access journals that reserve all rights to reuse.Gold open-access at least, by making literature mining possible, doesn't stifle these new open data opportunities, even if it's not the full solution; green open-access, by focussing on the need for access to human readable literature, distracts us from these possibilities entirely.

Or open notebook science: a model that, by getting scientists to discuss their ideas and publish their experiments in the open in real time, would force a revolution in the way that scientists work, the way that groups compete and collaborate, and the way that careers are evaluated and achievement rewarded; a revolution to the whole rhythm and pace of scientific discovery and the individual scientist's working life. A revolution that rather makes the whole issue of access to journal papers go away altogether.

Green OA advocates argue that open science, open data, and ONS are vague and fantastical distractions from the pressing matter of human access to journal articles; the we shouldn't waste time thinking about the former until we have solved the latter. I believe that green OA is a mundane and increasingly irrelevant distraction from the real problems and opportunities that are available for science to solve and grasp, but for a limited time only. The long-term achievements are too big to risk for the sake of such a small one.

Why spend time designing a better horse shoe when you could be inventing the railway train?

(Apologies for the unpolished post - this was made from my phone on the side of a Welsh mountain.)

Literature hacks: PubMed searches by RSS

2010-06-01T20:48:00.003Z

There are all sorts of ways you could find out about new articles that you might want to read. There's that big room across campus that's full of old writings on paper, but that's too far away and they have some silly rule about not eating your lunch near their writings on paper, and anyway you're not sure you still have the card that lets you in. You can't trust your colleagues to point out an article that isn't crushingly mediocre, unless it's because it concerns a species or a disease whose name sounds mildly amusingly puerile, but those ones are never actually remotely related to your work. You subscribe to electronic tables of contents, but these days everyone's publishing in PLoS ONE, and you're not wading through their contents every week in the hope of finding the occasional thing that's relevant. You could regularly search PubMed, but that means typing in keywords over and over, and wading through the results asking yourself, "have I seen this paper already, or do I just feel like I've seen this paper already?"

So you could subscribe to email alerts for your PubMed searches, but my god, man, what the hell do you think you're doing? What, you haven't got enough email already? Make you feel special, having your phone stop you every five minutes with unimportant impersonal notifications? If it's not private, not time-critical, and does not require a reply, it should not be pestering you with an email. That article has taken ten years to get from concept to publication, it can wait a little longer for you to read it -- not that you even read more than one in every twenty of the articles you're alerted to.

Which is why it should be obvious to any of our readers why they should be using ~~HubMed's~~ RSS feeds of PubMed searches, with their Google Reader, to keep up with the literature. New articles will accumulate and be available to scroll through in the sophisticated and cleanly laid out environs of the Google Reader, when it's convenient for you to read them. Reader will tick off items that you've seen and present to you items that you haven't yet seen, without ever screaming "look at me, look at me right now!"

Update: Since I originally wrote this, PubMed released their major update, introducing their own implementation of RSS saved searches, which looks at least as good as that of HubMed, and takes less effort to set up -- just click the RSS button next to the search box on the search results page.

"Predatory" open access publishers

2010-05-19T14:20:00.009Z

The Charleston Adviser has published an interesting analysis of some of the recent open access 'upstarts', titled "“Predatory” Open-Access Scholarly Publishers". They include some that I've noted before such as Bentham Open and Scientific Journals International.

As I would have expected, Libertas Academica and its sister publisher Dove Press do better than the others included in this review, but they are still far from passing with flying colours. The reviewer, Jeffrey Beall of Auraria Library, University of Colorado Denver, places a very clear "author beware" sign on:

Academic Journals
Academic Journals
ANSINetswork
Bentham Open
Insight Knowledge
Knowledgia Review
Science Publications
Scientific Journals International

Beall's summary is worth repeating:

"These publishers are predatory because their mission is not to promote, preserve, and make available scholarship; instead, their mission is to exploit the author-pays, Open-Access model for their own profit.
They work by spamming scholarly e-mail lists, with calls for papers and invitations to serve on nominal editorial boards. If you subscribe to any professional e-mail lists, you likely have received some of these solicitations. Also, these publishers typically provide little or no peer-review. In fact, in most cases, their peer review process is a façade.
None of these publishers mentions digital preservation. Indeed, any of these publishers could disappear at a moment’s notice, resulting in the loss of its content."

I'd not touch any of them with a bargepole.

Why you can't copy abstracts into Wikipedia

2010-05-13T15:47:00.003Z

This is an archival repost of something first published elsewhere a year ago.

I am not a lawyer, but I do have six years experience of Wikipedia, was once a very prolific Wikipedian, and, despite my lack of activity there in more recent years, am apparently still an "admin" on the English language Wikipedia. This, coupled with working for an open-access publisher, means that I have also picked up a little knowledge of (mostly US & UK) copyright over the years. Since I can't boil all that down to just 250 characters (or whatever the limit is), this post serves to answer this question, raised at FriendFeed: 'Does an article in pubmed belong to the "legal public domain", can I copy and paste it in wikipedia?'

The answer is 'no'. I don't endorse this position, and I'm not trying to be a killjoy, but it is the correct answer nonetheless. Since there appears to be some confusion over why the answer is 'no', let me explain. First I'll define some terms, then the copyright status of journal abstracts, and finally why the policy of Wikipedia must be to exclude abstracts.

First the definitions. Don't quote me on these. Like I say, IANAL. These are all just definitions that I have picked up over the years in the context of Wikipedia and open-access. In order of increasing protection of rights:

Public domain: completely exempt from all rights given by copyright law. Anyone can reprint it, remix it, and make money selling it, with no obligations.
Public/copyleft licensed, e.g. GFDL, CC-BY: the producer of the work has asserted their ownership and claim their rights, but have voluntarily given everyone in the world permission to do certain things with the work without having to ask first. There are actually several tiers of these licenses.
Copyright: you're not allowed to do anything with the work, unless the copyright owner has said you can.

Public domain is not a synonym for "publicly available". Something is not "in the public domain" just because it is on the internet -- indeed, most of the internet is not public domain, it falls in that third category. There is no presumption that you are allowed copy and paste material all over the internets. Perhaps there are corners of the internet where that is de facto the case, and perhaps it would be great if everything was public domain or copyleft, but it's not. Napster was a place where music was de facto public domain, before the recording industry reminded them that the law doesn't work that way. However, there is a fourth area to copyright: fair use.

Fair use is not a fourth category, like the categories above. Fair use is just a set of exemptions to copyright protections. It allows you to make use of copyrighted material without the owner's permission to do so. However, it is very limited: you may only use a limited amount of the copyright material, and you can only do a limited range of things with it. If you want to use something copyrighted and say that you are doing so under fair use provisions, you have to make the case for your specific creation being fair use of the material. Getting away with claiming fair use for an abstract in PubMed does not mean that you will get away with it for Wikipedia, or some other creation. And the copyright owner is always within their rights to object to your fair use claim.

The copyright status of journal abstracts. Copyright to most journal abstracts will be owned by the journal's publisher (or society). Copyright to others will be owned by the authors. For open-access papers, the copyright is usually owned by the authors, but the journal has made sure that they have released it under a copyleft license, allowing you to do lots of things with their work. Papers written by employees of US federal agencies in the course of their employment will be public domain, as will very old papers.

It is true that there is a culture amongst scientists of free movement of published ideas. Copyright is worthless to a scientist, who actively wants his ideas to spread, so long as he is cited and acknowledged. Scientists freely share and reprint things like abstracts.

Scientists assume that publishers feel the same about all use of "their" material. Note the fierce and desperate opposition some of the traditional publishers raise against the open-access movement, though. Ideas mean different things to a scientist and to a (traditional) publisher. You shouldn't presume that publishers will react in the same laid-back way as scientists do when the words that "belong" to them are used in novel ways.

Note that PubMed carefully argues the case that its use of abstracts falls under fair use provisions. It doesn't just say "yeah, whatever, everyone freely reproduces abstracts, no one cares."

Why you can't turn abstracts into Wikipedia articles. Wikipedia can't be laid back about copyright any more than PubMed can. Wikipedia is now, what, a top-ten website by most metrics? People notice things that are put on Wikipedia. If you start putting abstracts on it, somewhere a publisher will notice, not like it, and have the material removed. You could claim fair use, but (and remember, IANAL), I very much doubt you would be successful: an encyclopedia is very different to an index, and in Wikipedia you are remixing the material. Well, whatever. One page gets deleted. No lasting harm done. End of story?

Not exactly. Wikipedia is GFDL. What you put on Wikipedia gets copied to hundreds of mirrors and put in paper versions. People use it for whatever commercial purposes they want, and it gets remixed to death. It's difficult to undo what goes into Wikipedia. That is why, when you write in Wikipedia, you must declare either that the words are your own, or that they are already released under a compatible copyleft license. You are not just giving permission for your words to be used on Wikipedia, you are giving permission for your words to be reused and remixed for virtually any purpose. This is why Wikipedia has to be pretty careful not to let copyright violations through.

This is also why Wikipedia does not actually allow any text to be contributed as fair use (except when marked as quotations): the permissions granted by Wikipedia are just too great for the fair use claim to be defensible.

But can't Wikipedia make an exception for abstracts? Theoretically, perhaps it could be done, but sadly, the reality is 'no'. Wikipedia is too big, too old, too well known, too bureaucratic. Wikipedia's policy on copyrights is well established; it must be generalist, covering all fields and all nations, and it can't afford to be lax. To come up with exceptions to the policy would be too difficult for such a generalist site with such a tiny legal team. The Wikipedians would have to establish beyond doubt that publishers were happy for their abstracts to be used not just on the encyclopedia, but by anyone, anywhere, for virtually any purpose, reprinted and remixed. And that sounds like the open-access movement to me.

Conclusions. You can't put (non-open access) abstracts on Wikipedia. It would be nice if the gentlemen's agreement whereby publishers overlooked reuse of their material by scientists extended to all spheres, but that ain't necessarily so. Of course, it would great if it were so, and the story is just one of thousands which emphasise the need for a more rational and restricted copyright system.

Amusing typo of the day

2010-05-13T11:10:00.003Z

The authors of a manuscript say their work has been approved by an "intuitional review board". I suppose it just knows when a study is ethical.

Medical Hypotheses' editor is sacked

2010-05-12T17:00:00.003Z

So Bruce Charlton's editorship at Medical Hypotheses comes to an end, and I must raise a small cheer. Schadenfreude is an ugly thing, but this journal was a boon to fringe 'scientists' everywhere, giving them the apparent legitimacy of publishing in a 'proper journal' (owned by Elsevier, indexed in PubMed) without the pesky hurdle of peer review. It was no surprise that it favoured kooks, having been set up by David Horrobin, a pusher of evening primose oil.

The final straw was allowing AIDS denialists a platform, and the subsequent outcry from scientists and Charlton's inability to see what he did wrong led Elsevier to pull the plug. Charlton thinks that as an editor he has a perfect right to publish whatever papers he wishes, but unaccountable editorial control is no way to run a journal. Poor editorial decisions should have consequences, and the lack of any peer review or other quality control on Medical Hypotheses (the only criterion being that a paper was 'interesting') always doomed it to be derided by serious scientists and medics.

Will the new (and improved?) Medical Hypotheses see any more gems like too much sex causing RSI, kissing evolving to spread germs, cancer being caused by stopping smoking, masturbation being good for relieving a bunged up nose, or the origin of belly button fluff?

Peer review in the dock

2010-03-18T22:02:00.002Z

Academic publishing, and peer review in particular, was headline news in February -- from stem cell researchers claiming that their work was being sabotaged by reviewers with conflicts of interest, to mainstream news noticing the absurdity of the impact factor situation. BBC Radio 4 must have decided that now was a good time to air an unedited repeat of 2008's documentary Peer Review in the Dock. So now certainly seems like a good time to post an unedited repeat of my comments from the time.

--

A few thoughts on Peer Review In The Dock (this evening, Radio 4).

Nobody has ever questioned whether peer review is really needed: wrong. A lot of people have questioned this, and many experiments have been tried. The most prominent recent example is probably PLoS ONE (no reference to this in the programme). They very rapidly discovered that, yes, a minimum standard is peer review is required when running a journal. But perhaps moving to a non-review model is like communism: you need to have world revolution for it to have any chance of working; going it alone will just lead to your own collapse.
Peer-reviewers aren't trained: somewhat misleading. Reviewers, at least in the publishing model that I am familiar with, are actively publishing research scientists of at least medium seniority. Most will, while pursuing their doctorates, have participated in "journal clubs" (where the grad students get together to shred a published paper), and many will also have co-reviewed manuscripts alongside their supervisors (not strictly allowed, but very widespread). What all students certainly are trained to do, even at undergraduate level, is not to take the truth of published work for granted, and to watch for potential flaws. To teach science is to teach scepticism. Which brings me on to the next point...
Reviewers aren't all that great at spotting errors: so what? Academics and publishers know this. The system is designed this way. Review is supposed to be a basic filter for sanity and competence; it is only journalists who hear "peer-reviewed" and think it is the definitive stamp of authenticity. Like democracy and trial-by-jury, it is not used because it works, but because it fails less disastrously than the alternatives. (Incidentally, their example of introducing deliberate errors to a paper and seeing who notices them is not entirely fair: most papers are not only reviewed by the journals reviewers, but by the authors' colleagues before they submit the manuscript, and by editors before review.)
The last part of the programme was devoted to publication bias. Publication bias is a big problem. But it has little, if anything, to do with peer-review, and everything to do with publisher policies and author dishonesty. The only conceivable connection it has with peer-review is that some people still mistakenly believe that negative results aren't worth publishing at all -- something that journals like BMC Research Notes and PLoS ONE, and initiatives like trial registration are explicitly tackling.

The programme explored what is an interesting issue in academic publishing at the moment (there are more interesting issues, of course), but, I think, from the wrong perspective. While it discussed many very real problems with the system, these problems are all well known and acknowledged; for decades people have explored solutions, and there are many interesting current developments. The makers of the programme seemed mostly unaware of these.

This is, of course, the limitation of having a half-hour national radio programme about a topic like academic publishing.

Peter Suber's open access word contest

2010-03-03T21:08:00.005Z

Peter Suber, the guru of open access, has challenged readers of the SPARC Open Access Newsletter to come up with a new word.

English speakers need a verb that means "to provide OA to". It should be as succinct as "sell" for use in sentences such as, "We sell the print edition but ____ the digital edition."

Oh, the joys of verbing a noun. Here are my entries:

"Openpublished"; "to openpublish" (or "open-published", "to open-publish"). Apparently there is already a meaning of "open publishing", which is to make the process of publishing transparent (open peer review would be an aspect of this, as well as Indymedia and Wikinews), but I think the term is little used.
"Commoned"; "to common". Meaning "to place into the commons", as most OA publishing uses the Creative Commons licenses.
"Publicked"; "to publick". Meaning "to make public". It's an archaic word, used by Joyce in Finnegan's Wake, sometimes meaning "published", sometimes meaning "populated", and recently resurfacing to mean making a private message public.
"Freeshared"; "to freeshare" (echoing freeware and shareware). This term is already a synonym for freecycling, and for a defunct image upload site.
"Openshared"; "to openshare" (echoing open source and shareware). This term is already used for an icon that represents the open sharing of content - an icon that could be adopted by the open access movement.
"Copylefted"; "to copyleft". Using the existing term, which refers to Creative Commons and GNU GPL licenses among others.
Referring to libre and gratis: "Libred"; "to libre". "Gratised"; "to gratis".

Can you do better? Seize the glory by emailing Peter.

The Open Share icon is under a Creative Commons Attribution-Share Alike 3.0 Unported License from http://www.openshareicons.com/.

Article-level metrics

2010-02-03T20:17:00.006Z

Guys, are you sure you've thought this through? I mean, they're nice. They're fun. Data is fun. Seeing that somebody somewhere has read something you've written is satisfying and reassuring. It's good to know that you've sparked a conversation, and gotten people recommending you to their friends. But you think that it can't possibly go wrong? You think we should roll it out as the universal metric right now, and sort out the details later?

The impact factor is just data. It's nice for a publisher to know that people are reading the papers that they publish, and that all their hard work is having some effect. I can't believe that it would ever have been intended that such an absurd situation as the current practice of making and breaking careers according to a journal citation index should have arisen. Give out article-level metrics and they're soon going to stop being a bit of fun. People are going to use them and abuse them. It's what people do with data.

If you're going to reduce somebody's life's work to a number, it would certainly be less absurd to pick a number that is in some way relevant to that work, rather than relevant to the work that a whole bunch of other people did several years earlier. But only a little bit. What are article-level metrics representing? The quality of the work, or the controversy you've stirred up? The web-savviness of the field? The number of friends you have? There is already huge variation between the kinds of impact factors that medical journals get compared to, say, the sort that ecology journals get. What if, at the article level, breast cancer turns out to be inherently more comment-worthy than bowel cancer? If tenure and funding committees are willing to use something as absurd as an impact factor when making a decision, do you think that they're going to give a damn about the inherent variation in readership between fields? All those bowel cancer researchers better start reading up on their breast cancers now.

But what happens when article-level metrics really start to mean something? Give a large enough number of people an incentive to cheat and some of them are going to cheat. Remember when the World Journal of Gastroenterology boosted its impact factor with a little citation loading? How are you going to stop academics from doing what flickr users do to get themselves into the site's front-page "Explore" section for the day's best photos -- posting their stuff to "I'll leave an inane comment on yours if you leave an inane comment on mine" groups? What happens when academics spend ever increasing hours marketing their work to each other? How long is it going to be before journals and universities are competing for researchers by advertising how good their average article-level metrics are? Before journals and universities open departments dedicated to pressuring people into reading and commenting and blogging their articles?

What happens when pharmaceutical companies get in on the act? What about the ideas that get ignored for ten years, before it becomes apparent how important they are -- do the metrics count for the original paper, or for the review article that reignites the interest? What about the assholes, the trolls, the groupthink...?

Article-level metrics are a bit of fun. It's possible for them to remain a bit of fun. But it's going to take a lot of forethought and vigilance to make sure that is so.

Literature hack: context search

2010-02-01T20:45:00.005Z

Ryan Gregory has just started a new blog: Hackademe. It's a Lifehacker for academics, sharing his tips for scientists who are struggling to cope with all the shiny distractions around them. Here at Journalology towers, we have a whole bunch of these hacks lying around, and I hope we won't be treading on Ryan's toes if we share some of our literature searching and managing tips. (Though Ryan has already discussed reference manager software on his day old blog, so perhaps he has this one covered...)

A very simple one to get us started, then: install context search. Firefox comes with a built-in right-click tool for easy searching of Google for the text on the page that you have highlighted. Context search replaces that search Google tool with a search any-number-of-search-engines tool.

You can add all your own favourite search engines to the menu: just go to the search engine website and use the drop menu in the toolbar search box.

Now you can run through PubMed every unfamiliar gene, disease or researcher you stumble upon while reading, with three easy clicks and no typing. (Warning: novices may find themselves up at two in the morning having followed a long chain of context searches from cell signalling pathways to YouTube videos of snow ploughs on speeding trains.)

Dudes, I don't know how you coped in the olden days of typing your search terms into PubMed, and yet people seriously try to tell me that mankind once worked with "card catalogues" and "interlibrary loan". I'm not buying it, you guys.

A piece of peer review history

2010-01-31T01:30:00.003Z

I love browsing PubMed Central. How about this, from May 1985. The paper, Exaggerated responsiveness to thyrotrophin releasing hormone: a risk factor in women with coronary artery disease, by Fowler and Dean in the BMJ, is not in itself a work of unusual historical significance. But the associated sections in the document could be: is this where open peer-review began?

In a ~~comment posted~~ letter published the day after I was born, Thomas Walever said:

SIR,-I congratulate you on your publication of the paper by Drs J W Dean and P W B Fowler (25 May, p 1555) complete with the referees' comments and authors' replies. This correspondence indeed illustrates some of the problems with the peer review system. It was a help to know that others have had some of the same problems that we have had as authors. While comments made by referees are often helpful, it is indeed distressing when one does not agree with the criticism of the methods. This is especially true, it seems, for statistical matters; and this was well illustrated here. It has even happened that a major criticism was that something was not done which in fact had been done and was clearly stated to be so in the manuscript.

As a suggestion, perhaps matters might be improved if we had to sign our names to our reviews. There would be many problems with this, but the comments made to the authors would probably be more careful, considerate, and constructive. Some journals already suggest this as an option; perhaps the practice should be encouraged?

Twenty-five years on, and we do not have universal open peer-review. Further experiments have been conducted, though, led by the BMJ, which now uses signed reviews (but, so far as I can tell, does not publish the reviewer reports). In 1999, a blinded trial of open review by the BMJ editors found that open review didn't really make a difference to the quality of reports, and probably lengthened the time taken for review. Editor Richard Smith, campaigner for open-science and publishing reform, stubbornly decided to adopt it anyway, citing ethical reasons: you can not be tried by an anonymous judge. (In his editorial, Smith also declares his intentions to publish reports alongside the accepted papers, and introduce live community review, neither of which have come to fruition, so far as I can see.)

Other trials have had more positive findings regarding benefits of open review, such as more thorough reports, but the utilitarian merits of open review remain contested. This Nature Neruoscience editorial from 1999 complained (without evidence) that open review is likely to lead to "bland" and "timid" reviews, in which technical deficiencies are identified, but no comment is made regarding the interest level of a paper. If true, this would, of course, be a problem for high-end journals like Nature Neuroscience which select on the basis of interest level.

It's nearly ten years since the BMJ's switch to open review, and, so far as I know, the the model is still restricted to just a minority of medical journals and hardly any journals in other fields. The BMJ's initial hope to publish reviewer reports seems to have been forgotten. Open peer review seems to be just another area where publishers are still looking at new technology and discussing where they want to go, when everyone on the internet is asking "are you guys coming, or what?"

This is an edited re-post of something previously posted on cotch dot net.

Fraud epidemic in China?

2010-01-20T23:53:00.005Z

Last week's Nature included a news feature on scientific misconduct in China which contained the extraordinary (but not unbelievable) claim that a third of all researchers at "top institutions" in China admitted to plagiarism, falsification, or fabrication. The feature contains the extreme example of the systematic fabrication of crystal structures, but one would hope that the majority of the confessions of misconduct represent no more than the borrowing of a few paragraphs by those for whom English is not a first language (a crime, but not a hanging offence). But every publisher has its examples of photoshopped figures and impossible datasets, and it's hard to deny that certain countries pop up more often than others.

The fun part of the article, though, is the comments thread, which is full of readers' speculating about why China should have such a high-rate of misconduct. A drive for quick success and control of the sector by short-sighted bureaucrats with no actual understanding of science are suggested. A rapid expansion of science with a bottom-heavy hierarchy and insufficient supervision, or else the fierce competition and pressure in a publish-or-perish world. Perhaps it's just in the nature of communist societies? Even the impact factor is cited as a contributory cause, and the blame somehow shifted onto the publishers.

Nobody seems to consider the simple possibility that researchers from other countries might have access to better tools for disguising their fraud.

Reviewing Medical Hypotheses

2010-01-16T14:16:00.004Z

Zoë Corbyn writes in the Times Higher this week that Elsevier have "started an internal review" of legendary journal Medical Hypotheses following its publication last year of two hiv/aids denialism papers (covered in Bad Science here and Respectful Insolence here). One of the offending papers, lead-authored by notorious aids denialist Peter Duesberg, took an entire two days from submission to acceptance by the peer review shunning "journal", and had already been rejected from all of the real hiv/aids journals for making such embarrassing claims as that Uganda's population increase proves that hiv can not cause aids.

It would be a shame to loose the journal that gave us Ejaculation as a potential treatment of nasal congestion in mature males and the equally entertaining response, Ejaculation as a treatment for nasal congestion in men is inconvenient, unreliable and potentially hazardous, but at the same time, we have to consider whether we are really comfortable continuing to humour the confused outbursts of Bruce Charlton.

It's interesting to note that the best defence for the journal's existence that Corbyn could find was this: "while peer review worked for 'normal science', it also had the power to suppress radical ideas." The defence comes from intelligent design creationist Steve Fuller, whose ideas I don't think even Med Hypotheses sunk as low as publishing.

Hello!

2010-01-16T14:03:00.002Z

I am Joe. You might remember me from such websites as cotch dot net, friendfeed, and twitter. I work for a STM publishing company, formerly editing molecular biology journals, but now helping them develop their web publishing technology. I will be posting my ill-considered thoughts about science publishing alongside Matt's on Journalology, so that I don't have to bore the readers of my real blog with them. Do follow my vanity site for updates on all my other blogging.

Defining Open Access: Gratis vs Libre

2008-08-27T22:30:00.006Z

Peter Suber and Steven Harnad have introduced two new terms into the Open Access lexicon: gratis and libre.

I'll let Peter explain:

"When the Bethesda and Berlin statements came out (June and October 2003) they followed the Budapest statement in calling for the removal of both price and permission barriers. As a result, all three components of the Budapest-Bethesda-Berlin (BBB) definition of OA now call for both sorts of free online access.

But unfortunately we still don't have widely accepted terms for the two sorts of free online access: (1) the kind which removes price barriers alone and (2) the kind which removes price barriers and at least some permission barriers. This gap in our vocabulary has caused confusion and conflicts, not least because it created pressure to use the term "open access" for each. For now, my choice is to use "gratis" and "libre". They are accurate, neutral, and descriptive. In the neighboring domain of free and open source software, they exactly express the distinction I have in mind".

Gratis is cost free
It means free to read.

Libre is cost free & permission free
It means free to use.

Heather Morrison is a fan of these new terms, and I think they are going to catch on (although some are confused). I do still think that 'real' open access is more than just giving it away for free - permission barriers matter, and others like Jim Till agree. That the initial suggestions for gratis and libre were 'weak OA' and 'strong OA' speaks volumes.

A short post about Bentham Open

2008-08-27T10:59:00.000Z

I've had my eye on Bentham Open since before various bloggers, Peter Suber and Richard Poynder raised concerns about their email marketing and the recruitment of their editorial boards.

When they launched they copied some of their instructions for authors verbatim from the BMC-series journals, but the below really took the biscuit. Spot the difference. They stopped using that logo pretty sharpish; I think someone put a shot across their bows...

My view of Scientific Journals International

2008-08-20T22:24:00.008Z

Richard Poynder, Gunther Eysenbach and others have been investigating the practices of some of the new Open Access publishers, such as Bentham Open, Libertas Academica and Scientific Journals International (SJI). The fear is that an unscrupulous publisher might look on Open Access as a way to make a fast buck (in a "Gold Rush"), hoping to take advantage of the goodwill that many researchers have towards Open Access journals. There's a fine line between being a respectable Open Access publisher and a vanity publisher, and that line is held by rigorous peer review and good editorial processes. Quite rightly, a spotlight is being shone on the way that publishers are marketing themselves, recruiting editorial board members and conducting peer review. BioMed Central has faced similar scrutiny, and has weathered it.

Richard Poynder is a well-respected freelance journalist with an interest in the Open Access movement. He is known for his incisive interviews, and he has recently been asking whether anyone knows about SJI. His questions were prompted by researchers wondering about SJI:

"What kind of quality can I expect from a journal titled “Journal of Electronic Book”? Not to be too harsh, but it might be grouped with another journal such as “Journal of Gooder Grammar”."

"Nowhere on the website could I find any indication of who is actually behind these journals"

"SJI sometimes speaks of itself as a publisher of journals (plural) and sometimes of one multi-disciplinary journal (singular)."

"The fact that some of the lead authors of articles are using lycos and aol as email addresses really raises alarms"

In response, Zinath Rehana, co-founder of SJI, sent a lengthy post to the SPARC Open Access Forum, threatening to sue Richard Poynder and others for libel. This response is not very measured.

"Dr. Niaz [the founder of SJI] is also well aware of the realities of prejudice and racism, and knows how to deal with them with legal actions"

"Why is there such hostility toward an Asian American immigrant of 25 years?".

To bring the issue of race into this as Zinath Rehana has done is uncalled for. Dr Niaz's institution, St. Cloud State University, may have problems with racism but that does not mean that it is lurking around every corner. I see no reason to believe that Richard Poynder is motivated by racism. The further implication that Richard Poynder is in some way anti-Open Access is simply incorrect. I believe that Zinath Rehana was mistaken if she was hoping to garner support in the Open Access movement with her post to SOAF. Dorothea Salo isn't impressed, for starters. I think that it is best to answer legitimate concerns with openness rather than threats of legal action.

Zinath Rehana calls on other Open Access publishers for help against unfair criticism, but then goes on to criticise BioMed Central and PLoS for being unsustainable and profligate. The picture she paints of BioMed Central is not one I recognise - we're getting more submissions than ever, and rumour has it that we're 'in the black'. SJI claims that article processing charges are not scalable, when that's exactly what they are. Zinath Rehana also neglects to mention the waiver schemes operated by PLoS and BioMed Central for authors who have difficulty paying. I don't think that criticising PLoS and BioMed Central is the best way to make friends in the Open Access movement.

While biomedical publishing is edging towards being open, SJI may be going the other way.

"We employ an innovative quadruple-blind review system, where the referees, authors and editors remain anonymous throughout the peer-review process. Names of the chief editor or associate editors are not published on SJI Web site. Authors or reviewers cannot contact the editors to influence the review process deliberately or unintentionally"

Quadruple blind? Does this mean that there is no editorial accountability? I believe that it is essential that people know who runs a journal, but authors and readers seem to have to take the editorial processes at SJI on trust.

The payment model of SJI is unusual. They charge article processing charges, but ask for more money the more authors there are. Articles do not cost more to process if they have more authors. This payment model might lead to authors being unfairly left off papers to save a group money. If authors do pay the fee it may be a canny move by SJI because the number of authors on scientific articles increases year by year.

There is an impressively long list of journals, but many are "Coming soon..." when you follow the links. How many active journals are there? There is an Editorial Board, but this spans across all the journals. The journals have no scopes to my knowledge, no information on indexing, and I can find no information on the license under which the articles are published.

Importantly, there is no official information available on how peer review is conducted: who selects reviewers, who makes editorial decisions, how many reviewers are used, what are the editorial policies and standards? The only information we have about the peer review at SJI is from an anonymous comment on the Open Access blog. I hope that this is not an accurate or representative depiction. If it is, I would advise those running SJI to read and adopt the policies of the World Association of Medical Editors.

We need answers, not legal action.

This post is my opinion, and not that of BioMed Central

[Post edited 22/8/08 - I had not realised that Zinath Rehana is female]

Scientific Journals International on the attack

2008-08-20T22:02:00.004Z

The message below was sent to the SPARC Open Access Forum by Scientific Journals International, who Richard Poynder has been investigating.

---

Someone has posted false rumors and misinformation about SJI on your forum. We contacted Dr. Suber and he advised us to send our response to you. We would truly appreciate it if you kindly post the attached response on your forum. Please do not hesitate to contact us should you have any questions.

Best regards.

Zinath A. Rehana (Zinia)
Co-founder of SJI
info@scientificjournals.org
http://www.scientificjournals.org

Lies, fear and smear campaigns against SJI and other OA journals

It has come to our attention that a couple of individuals and organizations are propagating libelous, deceptive, misleading and false information and rumors about SJI (as well as other open-access journals) via emails and blogs. We are taking legal actions against such fraudulent and libelous activities.

The email campaign is being carried out by an individual by the name of Megan Voss. We need your help in identifying any other individuals or
organizations who may be involved in such fraudulent and libelous activities. If you receive any fraudulent and suspicious emails or reports,
please forward them to us so that we can collect additional evidence for our legal actions.

We are also collecting evidence of libelous propaganda carried out by Richard Poynder. He has posted false and distorted information about SJI and other open-access publishers on several blogs. He is not affiliated with any reputable news media. We could not find any information about his academic background or professional media experience other than a few "freelance stories" he has written.

This individual has been harassing our staff and Board members with ridiculous and pointless questions, intimidation, and "bullying" tactics.
He scared away one of our new Board members from Yale University by posing false rumors and misleading questions to him. Consequently, he has withdrawn from our Advisory Board.

When Mr. Poynder contacted us for the first time, our founder had asked him about his affiliation. He said he was not affiliated with any news media. His approach came out to be arrogant, ignorant, disrespectful, and hostile.

Our founder Dr. Niaz is a very busy man. He is a Senior Fulbright Scholar who now serves as the Director of Graduate Studies in the Department of Mass Communications at Saint Cloud State University. He is currently working on several book projects simultaneously. His university Web site is located at http://web.stcloudstate.edu/nahmed/. He does not have time to deal with such an arrogant individual. Moreover, when Mr. Poynder called him from U.K. the connection was not very clear and Dr. Niaz was about to go to an important meeting. So, he asked him to send his questions via email and later referred him to SJI Web site and his university Web site as many of the questions have already been answered there.

Dr. Niaz is accustomed to dealing with polite, respectful and legitimate journalists. In connection to his other online initiative (Idea Trade
Network www.newideatrade.com), Dr. Niaz had been interviewed by CNN, CBS, MarketWatch, Washington Post, Star Tribune and other leading news media from around the world (www.newideatrade.com/mediacoverage.htm). SJI is still in its initial phase and we have not had the time to carry out any publicity campaigns. We are only beginning to get coverage in the news media about SJI.

Dr. Niaz is also well aware of the realities of prejudice and racism, and knows how to deal with them with legal actions. As a US citizen, he knows
his rights and has the courage to fight for his rights. Nonetheless, when Mr. Poynder approached him with an arrogant and disrespectful manner, he just did not have the time to put up with such unprofessional conduct and asked the staff to respond to his questions.

Mr. Poynder then asked a number of idiotic questions that made it clear to us that he was neither knowledgeable nor had a deeper understanding of the innovative ideas and approaches that are being developed in the open-access publishing world. In fact, he did not seem to be interested in anything other than a few false rumors that have been circulated on the Internet. At one point, he demanded that we give him the names of three authors whose papers had been rejected. Our staff found this to be very childish and ludicrous. They told him that hundreds of papers are being accepted or rejected on a regular basis. If he wants to write a story based on false rumors that open-access journals do not conduct peer-reviews then he can ask the sources of these rumors (or anyone else) to verify this by submitting their own papers to see if they go through a peer-review process. One can also become a reviewer for an open-access journal to see if he or she is asked to review any manuscripts. Our staff also told him that he can contact hundreds of authors whose papers have been published to see if they were peer-reviewed. Each article that is published on SJI includes the author's email address. We have records of all email exchanges between SJI and Mr. Poynder and will produce the same in the Court of Law if needed. In his blog postings, Mr. Poynder has misrepresented the facts and suppressed the truth. He conveniently omitted the fact that our staff had told him to contact hundreds of SJI authors who have had peer-reviewed articles published. He also distorted the facts about his email exchange with some of the Advisory Board members. It is clearly stated on our Web site, that the Advisory Board members are responsible for providing advice and guidance for the ongoing development of SJI, and that it is the Review Board members (more than 3,000 and growing) who are asked to serve as peer reviewers. Surprisingly Mr. Poynder disregarded this fact and began to harass our Advisory Board members with misleading emails, and then posted false and distorted information on several blogs.

We are also appalled by the level of his disrespect, arrogance, and hostility toward our founder Dr. Niaz. In several blogs he stated that Dr. Niaz "described himself as the director of Graduate Studies in the Department of Mass Communications at Saint Cloud State University." Any respectable professional whether he or she is a journalist, a scholar or anyone else can easily verify this fact by contacting the university or by
checking the university Web site. In fact, even though he was referred to the university Web site, he never mentioned any of the facts about Dr. Niaz that can be verified in five minutes. He never mentioned that Dr. Niaz is a Senior Fulbright Scholar, and a tenured full professor at a major state university in Minnesota where he has served for the past 17 years. Instead, he states that Dr. Niaz "described himself as the director of Graduate Studies.."

Mr. Poynder calls himself a "freelance journalist." Sadly, it is not journalism he is practicing. It is trash, it is distortion, it is fear-mongering, it is smear campaign. It is a disgrace to the profession of journalism.

One can only wonder about the motivations for such distrust, hatred and disrespect toward someone (he has never seen or met). Why is there such hostility toward an Asian American immigrant of 25 years who has made only positive contributions to this country like millions of other immigrants whose creativity and innovations have made this nation great?

Anyone with an average level of intelligence and knowledge about the history of this country knows the fact that this is a land of immigrants. In terms of innovations, just look around and see what is happening in the world of new media and Web commerce. Google, Amazon.com, YouTube.com, Hotmail.com and hundreds of other new technologies, products and services have been developed by recent immigrants who came to this country for some of the same reasons the early immigrants came-for better opportunities where they could utilize their creativity and inventiveness. It is this great diversity of people and their innovations that have made this country great. Unfortunately, out of millions of good hearted and open minded people, there are a few who do not know their own history, nor do they allow their prejudiced minds to open up to the true realities that could alter their misperceptions. In the end, they harm a lot of well-intentioned law-abiding hard-working citizens whose creativity and innovations could benefit not only the institution or corporation they work for but also all citizens including the prejudiced and the fear-mongers.

Aside from prejudice and hatred, we are also aware of the professional jealousy and hostility that exist in every domain of human endeavors. The scholarly publishing world is no different.

Opposition to open access

Opposition to open access has largely been from traditional subscription-based journal publishers, whose business model depends upon
providing access to research only to those who will pay for journal subscriptions. Many conventional publishers actively oppose open access,
because it will cut into their profitability.

Some organizations representing subscription-based traditional publishers in the United States are currently lobbying the government against open-access publishing. These organizations include, The Association of American Publishers and its lobbying organization PRISM. In fact, soon after the launch of the European petition for open access, the well-known traditional journal Nature reported that subscription-based publishers were preparing to spend hundreds of thousands of dollars to counter open-access support.

According to news reports, some traditional publishers and a few of their misguided allies in the academia as well as a few spin-doctors in the media are engaged in misinformation campaigns against open access journals. Disinformation and distortions are also being propagated by a few bloggers who have no journalistic background and have no knowledge about the ethics or social responsibility of the media in contemporary society. These individuals have never worked for a reputable media outlet, nor do they have any academic training in journalism. Nonetheless, they are engaged in deceptive campaigns of fear and smear. Some traditional publishers are also actively trying to thwart the open access movement and are lobbying to delay or dilute government policies regarding open access.

The Association of Research Libraries has responded recently by stating, "This effort is clearly aimed at preserving established publishing
conventions and the revenues of established publishers" (source http://www.ala.org/ala/acrl/acrlpubs/crlnews/backissues2008/may08/librarybud
getsscholcomm.cfm). These lobbyists and their spin-doctors try to capitalize on the fact that some people will accept spin or misinformation without checking to see if there is any factual information to back it up. For example, some of these organizations and their spin doctors are
spreading misinformation that open access journals do not conduct peer-reviews of articles. One of the leading advocates of open access
publishing Peter Suber states ".they are using.the 'sky is falling on peer review' as a fear tactic....this is like Microsoft campaigning to make
Google go away...(source http://www.earlham.edu/%7Epeters/fos/2007_09_30_fosblogarchive.html).

Many top university presses such as MIT Press, Columbia University Press, and Oxford University Press are now dissociating themselves with these
lobbying organizations of the traditional publishers. Cambridge University Press and Rockefeller University Press have recently publicly criticized
PRISM and its activities (source http://www.earlham.edu/%7Epeters/fos/2007/10/mit-press-dissociates-itself-from-prism.html).

Legal action

SJI is now collecting evidence for its legal action against individuals and organizations who are propagating libelous, deceptive, misleading and false information and rumors about SJI (as well as other open-access journals). We are also issuing a "fraud alert" to more than 3,000 scholars who are involved with SJI to monitor and report to SJI of any libelous and misinformation campaigns against SJI and other open-access publishers. We urge other open-access publishers to do the same. Since some of the traditional journal publishers, their spin doctors, bloggers, and a few misguided allies in the academia, are carrying out organized campaigns of lies, distortions, fear and smear, the open-access publishers must organize themselves to expose these activities and take legal actions using libel laws to stop such campaigns of lies and distortions.

As with Mr. Poynder's misinformation campaigns, we would like to give him one opportunity to issue an apology and a retraction on the blogs where he posted his libelous statements. If he complies, we would not pursue legal actions against him and we will be glad to talk to him about SJI. Had Mr. Poynder approached us with an open mind and in a collegial manner, we could have shared a lot of information about our experience in developing SJI into a sustainable open-access publisher that is profitable and at the same time affordable for authors and their funding agencies. Such information could be valuable to other open-access publishers that are struggling to sustain their operation.

Unsolved issues in the open-access publishing model

Many open-access publishers have been unable to come up with economically sustainable business models. They have not been able to use a business model that is efficient and profitable for the publisher and at the same time affordable for the authors and their funding sources. Most of the open-access journals are sustained by grants and endowments as well as subsidies from universities, foundations, government agencies, and
professional societies or associations. A handful of large open-access publishers have sustained their operation without reaching profitability by
continuing to raise the article processing fee which is their primary source of revenues. For example, Biomed Central now charges $1,700-$1,900 per article while PLoS charges $2,100-$2,750 per article (source http://pln.palinet.org/wiki/index.php/Open_access_controversies).

Critics have argued that the escalating processing fees of these open-access journals are becoming a barrier that may destroy what it originally wanted to foster. In very few disciplines (other than medical and life sciences) do scholars have sufficient funds from grants and other sources to pay such high article processing fees. In many fields, funding at the university, foundation, or government agency level is scattered, uncommon or rare. Even in medical and life sciences, many researchers and scholars in less funded institutions as well as independent researchers are unable to pay such high article processing fees. In fields such as Social Sciences and Humanities, many authors are engaged in significant research without grants, and therefore, may not have the funds to pay for the prohibitive article processing fees.

One of the reasons why the major open-access journals have experienced difficulty in reaching profitability is that they maintain a very high cost
structure of operation which carries extremely high overhead and administrative costs. These include a plethora of big-expense offices and a
stable of high salaried professional editors, executives, programmers, and database administrators.

For a major traditional journal, the average cost of producing an article is approximately $2750. For open-access publishing, the cost is in the range of $500-$2500 per article (source http://library.queensu.ca/webir/planning/e-journal_publishing_support.htm). These expenses are split among editorial costs, electronic composition and production, journal information system, manuscript management system, electronic archiving, overhead expenses, and administrative costs. The publication fee or article processing fee must cover the costs of publishing the accepted article plus the cost of reviewing the number of articles the journal rejects for each accepted article. Since costs per accepted paper rise with the rejection rate of papers, the fee usually rises as the rejection rate goes up and acceptance rate goes down.

Such high cost structure demands sizeable revenue streams to offset it. However, the major open-access journals have not explored all possible
streams of revenues. Instead, they have relied heavily on article processing fees and institutional memberships that pay the processing fees
for university faculty and researchers. However, as they continued to raise their fees, it has become unaffordable for many authors and institutions.

There is also a serious problem with the fee structure of major open-access journals. Their article processing fee or institutional membership fee is not scalable. They charge a flat article processing fee for publishing each article no matter how many authors collaborate in writing the article. If an article is written by one author, he or she pays the same high processing fee as an article that has five authors (Biomed Central charges $1,700-$1,900 per article while PLoS charges $2,100-$2,750 per article). This fee structure is not fair or affordable for an individual author whose research may not have been supported by a grant and therefore, he or she has to pay the processing fee out of pocket.

The major open-access journals also charge a flat fee for their institutional membership. Such membership fees have also been rising at a
rapid pace. For example, in 2005, BioMed Central charged libraries up to $4,658 per year. The cost then jumped to $31,625 in 2006. These charges have continued to soar in 2007 and 2008. Many institutions have begun to cancel their memberships. The scientific and medical library at Yale University recently announced that it would cease its BioMed Central institutional membership (source http://www2.library.yale.edu/movabletype/scilib/archive/2007/08/library_drops_b_1.html). The Yale library noted that it paid $31,625 to cover the cost of publication in BioMed Central's journals by their authors in 2006.

The major open-access publishers expected academic institutions to support author fees with massive reallocations from library acquisitions budgets. However, relying too heavily on article processing fees puts open-access journals at a disadvantage compared to traditional journals, which are supported centrally through library budgets. Many universities have pointed out that libraries cannot simply transfer their acquisitions budget from subscriptions to open access overnight, since access to the subscription-only journals is important for their researchers.

What can other open-access journals learn from the experience of SJI? SJI combines the open-access model with innovative approaches to address the problems in the current scholarly publishing system at the worldwide level. SJI is still in its development phase. We are learning and trying new ideas and approaches on an ongoing basis. That is the key to achieving success in any online venture. As we provide high quality services at lesser cost, SJI continues to thrive and our base of support grows stronger every day, while other open-access journals struggle to merely sustain their operations with the help of grants and institutional subsidies.

SJI operates using a lean publishing model. While other major open-access publishers spend millions in big-expense offices and high salaried
professional editors, executives, and programmers, SJI gets by, operating from a tiny 150 sq ft office with several part-time staff. Instead of
hiring high salaried professional editors, executives, and programmers, SJI has built a devoted community of more than 3,000 scholars, researchers, programmers, management and marketing faculty and professionals who serve SJI as volunteer advisors, reviewers, editors, and technical experts. The fee structure of SJI is scalable and fair to the authors. For newer journals, SJI charges $99 per article with $99 for each additional author. For the older journals, the fee is $199 per article with $99 for each additional author. The experience of SJI clearly indicates that researchers and their host institutions and funding agencies are willing to pay reasonable and affordable article processing fees for the sake of faster and fairer access and greater exposure of their work.

SJI is also able to reduce costs of publishing by requiring the authors to perform the final formatting of their articles for publication. The authors
are also asked to seek professional editing services if SJI reviewers and editors have recommended such revisions.

SJI is in the process of employing open-source software to automate many tasks including early assessment of papers to identify possible duplicate submissions or repurposing material from other papers. This automation will further reduce our administrative costs.

SJI has developed several alternative models of sustainability and profitability and is using innovative ways to generate revenues that are missing from other journals. We have found numerous creative ways and a wide range of revenue streams that allow us to share and distribute the costs of open-access publishing across all interested stakeholders-not just article processing fees from authors. Such alternative streams of revenues help us keep our article processing fees low enough to attract thousands of authors and researchers who do not have sponsors or grants, and consequently, cannot afford to pay the high processing fees of other major publishers.

SJI has also realized that every kind of digital content can be made available through open access publishing--from texts and data to audio,
video and multi-media contents. SJI is probably the only open-access publisher that publishes peer-reviewed creative work (poetry, paintings,
music, films, novels, video and multimedia) on its Journal of Creative Work. Moreover, our standard scientific journals are complemented by several unique and innovative journals such as Journal of Dissertations, Journal of Patents & Trademarks, Journal of Reviews, Journal of Electronic Books, Journal of Biography & Autobiography, Journal of Current Events & Issues, Journal of Interdisciplinary and Multidisciplinary Research, Journal of Research Data, Journal of Bibliographies, Journal of Monographs, and Journal of Research Abstracts.

Any scholar or any organization planning to launch an open-access journal can feel free to contact us for helpful advice and suggestions. Existing open-access journals that are struggling to survive can also contact us for more information on how to become sustainable and profitable, and affordable at the same time. We never stop learning. But, one has to start somewhere.

Journalology round-ups return!

2008-08-03T22:49:00.002Z

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.
http://www.searchguide.se/oa/eng/

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".

Citations

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".
http://www.sciencemag.org/cgi/reprint/sci;321/5887/329a.pdf
http://www.sciencemag.org/cgi/reprint/321/5887/395.pdf

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.
GB: 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...

Bioinformation Journal: making sure "open access" means open access

2008-08-03T22:17:00.005Z

When looking at the journal Bioinformation, I spotted the tagline

"It is free to publish, open access and online immediately upon acceptance"

This is wrong, as like the BioMed Central journals this journal usually charges an article processing charge. This got me digging a bit further.

They state on the published articles that

"This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited"

OK, although a non-commercial license isn't great, as Peter Murray-Rust has explained. Yet when I tried to right click on the page, a notice popped up:

"Sorry! Copying of these contents for potential editing and reproduction is not permitted. However, you have access to read, know and print contents for non-commercial processes".

This is not consistent with open access; it is a restriction of reuse. It also prevents 'fair use'.

The journal states that

"The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes"

It is usual among open access journals that the authors retain copyright, and a Creative Commons Attribution license is applied. As the Budapest Statement on Open Access put it "The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited".

I emailed the editors and received a brief reply from Prof Kangueane. Now, a couple of weeks later, the tagline reads

"It is open access and online immediately upon acceptance"

Excellent. The right-click restriction also appears to be gone. I will leave it up to their authors and editors to lobby them to change from a CC-BY-NC to a CC-BY license, but it seems that Biomedical Informatics Publishing Group and Bioinformation are now doing things right.

Funding for publication ethics research

2007-12-16T16:18:00.000Z

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.

Journalology roundup #13 - plagiarism special

2007-11-17T22:35:00.000Z

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

2007-11-17T22:34:00.000Z

The wonderful Piled Higher and Deeper comic.

This Is The Truth

2007-11-01T12:53:00.000Z

- 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.

Journalology roundup #12

2007-10-29T21:15:00.000Z

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

2007-10-29T15:55:00.000Z

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!

2007-10-29T15:44:00.000Z

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

2007-10-29T14:20:00.000Z

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.

Published at last!

2007-09-21T17:51:00.000Z

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...

Journalology roundup #11

2007-09-20T21:59:00.000Z

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

2007-09-20T20:57:00.000Z

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!
S PARC
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!

----

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:

Hey, Facebook, breastfeeding is not obscene!(Official petition to Facebook)

Recently, Facebook has started 'pulling a myspace' by not allowing people to post profile pictures of babies nursing. The pictures have been reported as 'obscene' and have been removed- their posters warned not to repost or fear being kicked off of Facebook.

We're wondering: what about a baby breastfeeding is obscene? Especially in comparison to MANY other pictures posted all over Facebook that really are obscene.

Facebook, we expect more from you, and we expect you to realize that nursing moms everywhere have a right to show pictures of their babies eating, just like bottle-fed babies have a right to be seen. In an effort to appease the closed-minded, you are only serving to be detrimental to babies, women, and society.

**Facebook, allow breastfeeding pictures, and stop classifying them as obscene!**

Multiple Stab Wounds May Be Harmful To Monkeys

2007-09-08T14:56:00.000Z

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.

Journalology blog statistics

2007-09-02T18:06:00.000Z

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!

2007-09-02T17:26:00.000Z

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

Journalology roundup #10

2007-09-02T16:46:00.000Z

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

2007-09-02T15:46:00.000Z

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.

Modelling the needed population of tooth fairies

2007-08-18T14:40:00.000Z

The posting on the Bad Science blog of articles from an issue of Homeopathy about the memory of water has let to quite a lot of critical appraisal of the science behind these articles.

My favourite quote from these discussions is from a comment on the Good Math blog regarding the modelling of dilution and succussion ('shaking' in homeopathy):

"Nobody models the needed population of tooth fairies".

A new way to find reviewers - the ouija board

2007-08-12T22:07:00.000Z

Authors of manuscripts submitted to our journals can suggest potential peer reviewers.
A recent submitting author took advantage of this to suggest...

His former supervisor

Wait, it gets better....

His dead former supervisor

Wait, wait, it gets even better.....

His dead former supervisor, indicated with (deceased)

Guys, who last had the ouija board?

13 ways to get your manuscript rejected

2007-07-17T00:27:00.000Z

I've seen a couple of good guides to getting your work published in a peer reviewed journal. But how to ensure that you get it rejected?

1. Don't write in clear English. Hell, forget clear English, don't even write in English. Editors who insist on good English are probably just pining for the days of the Empire. The more incomprehensible the better. Ignore simple grammatical rules like the use of articles, and don't run a spell check. Spell check is for losers. Certainly don't get it copyedited - good lord, that'd just be throwing good money after bad.

2. Never cite prior work. Be like this correspondent to a physics journal*, who gaily admits that "The only time I access previous articles is when the referee forces me to". Oh joy.

3. Try and try again. So your work has been rejected several times over? Play the lottery of peer review, and eventually you'll slip it past the reviewers! Reviewers love it when they see an article for the fourth time, with none of their advice acted on. No, really, they do**. ***

4. Argue. Argue. Argue. The reviewers hate you; you hate the reviewers. Don't be diplomatic: let loose the vitriol. The editor won't mind, they'll obviously take your side. After all, who the hell do the reviewers think they are? Oh, you mean the editor picked them because they think that they're experts in the field? Then the editor's an idiot too!

5. Do you know who I am?! Editors are always delighted when an author points out their eminent qualifications in a rebuttal, while ignoring all scientific substance for the reasons for rejection**.

6. Use Word Art to brighten up your article**. It shows your playful side.

7. Go completely off the wall. Five dimensional alien brains?** Bring it on.

A typical day in the editorial office.
Image credit Shira Golding on Flickr, Creative Commons Attribution Non-Commercial 2.0

8. Ethics committee? What ethics committee? Oh, yeah, right, we've got an, er, ethics committee. What do you mean, it can't just be me, my dog, and my next door neighbour?!** You mean we actually had to ask the patients before we experimented on them!?!**

9. You're a hero. Patients adore you as their saviour and the scientific community are all paid lap-dogs of big pharma. You know what results you want, so what's a little data misrepresentation between friends?**

10. ID. The reviewers and editors won't mind if you slip just a little bit of Creationist terminology into the scientific peer-reviewed literature...**

11. Photoshop rules!!! Pesky band in the way? Just photoshop it! Transformation failed? Just photoshop it!**

12. Copy. Has someone else said it better than you ever could? Copy! Copy! Has someone else done the experiments better than you ever could? Definitely copy!

13. Don't support your conclusions. Who needs to spend hours preparing supporting data? Loser! It just takes a few quick keystrokes to write "Data not shown".

Be sure to also check out Horacio Plotkin's sage advice.

* Thanks to the Blog of the "Editor's Bookshelf" for helping me to find that letter again.
** Any resemblance of this blog post to real events or persons is, um, entirely coincidental.
*** Stop messing about and submit it to Biology Direct!

Not being clear about authorship is lying

2007-07-12T21:49:00.001Z

That blunt statement is the start of the title of an editorial in the March/April issue of the National Medical Journal of India, "Not being clear about authorship is lying and damages the scientific record" by Charlotte England, Matt Hodgkinson and Pritpal Tamber. Yes, that's right, I'm published. Very exciting.

The online version isn't available yet; I'll see if I can get permission to reproduce the text here. I forgot to speak to Pritt about an 'Authors' addendum' when he submitted it, so the journal retains copyright and their permissions policy is that "The published manuscript may not be reproduced elsewhere, wholly or in part, without the prior written permission of the Journal".

I can, however, post an early version that I drafted with Charlotte, which formed the skeleton for the finished editorial. It bears little resemblance to the final version, so I'm in no danger of breaching copyright.

------

Misattribution of authorship is corrupting the scientific and medical literature. Those who do not deserve to be included within the byline of research articles can be found listed despite this, the recipients of ‘gift’ authorship. The efforts of others go unrecognised by readers of articles since they have vanished to become ‘ghost’ authors. Why this abuse of the scientific record happens may be the same as why much corruption occurs – the opportunity for reward without effort, and the influence of money. Transparency can counter the temptation to misattribute authorship, but this requires the cooperation of journal editors, authors, and the authors’ institutions.

Authorship criteria

Authorship is intended to give credit to those who conducted the published work, as well as to highlight those who should take responsibility for the content of the published article. In order to make clear who deserves to be an author, criteria for authorship have been drafted, the most widely known being those of the International Committee of Medical Journal Editors (ICMJE). These classify an author as someone who has substantially contributed to a published study and suggest that authorship credit should be given when an individual meets each of three criteria: 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising critically for intellectual content; 3) final approval of the version to be published [1]. Many journals have since adopted these guidelines in their instructions for authors.

Policies on declaration of authorship often vary between journals. For example, the BMJ asks that authors explain their contribution in their own words [8], while JAMA has a checklist [9]. Research by the Croatian Medical Journal has shown that the structure of author contribution forms can significantly alter the number of contributions reported for each author, and therefore declared contributions should not always be taken at face value [Marusic et al., 2006].

Rising numbers of authors

Since the ICJME guidelines were first published in 1979, there has been a steady rise in the number of listed authors. The most significant aspect of this increase has been the inclusion of senior researchers such as department chairs or professors as either first or last authors [2]. This trend towards increasing numbers of authors is not exclusive to international journals such as the BMJ, as the Indian Journal of Pathology and Microbiology has also seen a 10-15% increase over two decades in the number of articles that have five or more authors [3]. However, this trend is not universal, since the number of authors of articles published in Indian Pediatrics has remained stable over the years [4]. It is not clear whether the increase in the number of authors can be attributed to an increase in the number of scientists being active in research or whether the inclusion of senior scientists as an author is due to the laboratory hierarchy, in other words whether a senior author has been ’gifted’ authorship solely due to their position.

Gift authorship

Honorary or gift authorship is known to frequently occur in biomedical publishing – one study in a French university suggested that up to 60% of senior researchers have received gift authorship by failing to meet all three of the ICJME criteria [5]. The prevalence of gift authorship has been seen to range from 0.5% of research papers in JAMA [6] to 39% of Cochrane systematic reviews [7]. Failure to meet ICJME criteria for authorship can be attributed to several possibilities. Due to the way in which the reviews are compiled, Cochrane authors may not be involved in the original draft or the ongoing revisions, thereby failing to meet all three criteria [7]. It is seen worldwide that the head of a department may insist on being listed as an author on any article issuing from their department, regardless of their own input [5], but in particular it has been acknowledged that authors listed on Indian research papers have a tendency to follow a traditional hierarchal order, where the most senior individual is listed first, followed in descending order by everyone else involved in the study [3]. The tendency to bow to authority has been criticised by Inder Verma, who has argued that “Science is best carried out in an irreverent environment, where the status quo is challenged, often at the risk of offending superiors. But the Indian scientific enterprise frowns on questioning authority and rewards obedience. Senior scientists are too often selected by seniority and rank, rather than their ability and achievements” [18].

Ghost authorship

Further issues arise with the concept of ghost authorship, where individuals do not receive acknowledgement of their contributions to a manuscript. This failure to disclose contributions is generally regarded as an unethical practice because of the potential conflicts of interest that may be present, such as resulting from the use of a professional medical writer by pharmaceutical or communication companies. The prevalence of ghost writing is not as great as that of gift authorship, with around 10% of manuscripts being written by ‘ghosts’ [7, 12]. However, there is a danger that pharmaceutical company-employed writers can ensure that the medical intervention in question is shown in the best possible light, and editors and readers will be unaware of the potential bias. There have even been reported cases where a medical communications company working on behalf of a pharmaceutical company will send potential “authors” a draft article, complete with a title page containing their name [13]. Provided the involvement of a professional writer in a manuscript is made as transparent as possible by acknowledging their contribution, their involvement can serve to improve the quality of articles [14]. The best way to deal with the potential issues surrounding the use of ghost writers is to ensure that not only is their involvement made plain, either within the byline if they meet the criteria for authorship, or in an acknowledgments section, but their competing interests, such as their employment by the sponsoring company, should also be stated. The present rapid growth in clinical trials in India run by foreign pharmaceutical companies makes this issue of increasing importance to Indian researchers [19].

Why authorship criteria matter

The reasons why authorship criteria should be adhered to and declared can be as mundane as making life easier for editors who are trying to find appropriate peer reviewers! Frequent gift authorship can make someone with little knowledge of a subject appear to be an expert, and lead to them being inappropriately invited to review. As has been discussed, ghost authors or unacknowledged contributors may have links to pharmaceutical companies, introducing a competing interest that will remain hidden. However, the issue of the ethics of authorship and contributorship is not only of interest to journal editors. Medical professionals have an obligation to behave ethically, and under the Medical Council of India Code of Ethics Regulations [15] they should “expose, without fear or favour, incompetent or corrupt, dishonest or unethical conduct”. The code specifically states in regard to signing professional certificates, reports and other documents that “Any registered practitioner who is shown to have signed or given under his name and authority any such certificate, notification, report or document of a similar character which is untrue, misleading or improper, is liable to have his name deleted from the Register”. Handing out a gift authorship or knowingly suppressing the involvement of a ghost could well fall within these regulations.

A further hazard of accepting undeserved authorship is highlighted by a case of fraud involving the University of California, San Diego. As Harold Sox and Drummond Rennie recount, “Slutsky had published 137 papers with 93 different coauthors when someone noticed anomalies in a few of his publications. The university's response was exemplary. [They] contacted Slutsky's coauthors and held them responsible for defending the integrity of every published paper”. They rightly conclude that “the guilty scientist's coauthors bear primary responsibility for publicly validating or retracting their joint publications” [10].

It is important that credit is given when credit is due because authors need to be accountable for the work they publish. This is especially important in cases where one of the authors is found to have produced fraudulent data, thereby affecting research that cites this data. Once there is suspicion that one research article contains fraudulent data, all other manuscripts from that group of authors need to be called into doubt [10, 11]. These matters are incredibly serious and co-authors should be involved in raising doubts about data as well as employers and journals. As an author, they should accept responsibility for that manuscript, even if their actions were not at fault.

Junior researchers who find themselves locked in a dispute over authorship can turn to the guidelines of the Committee on Publications ethics [17]. These guidelines advise that researchers start discussing authorship when they plan the research project. This is sage advice. The failure to agree authorship of a research project has previously seen researchers resort to legal action [16].

Conclusions

The corruption of the hard-won right to be recognised as an author of a scientific article can be countered by requiring authorship contribution declarations on all manuscripts, and requiring acknowledgment of anyone else who contributed. Despite the existence of journal policies on authorship, it is difficult for editors to enforce these policies. Editors do not have full knowledge of who contributed; only the authors and contributors can themselves say for sure. To avoid disputes, researchers should follow journal guidelines, and as COPE recommends collaborators should discuss authorship at the inception of a research project. As journals rely on authors’ institutions to arbitrate disputes between authors, institutions should have their own code of conduct for authorship, and be prepared to follow up on cases of authorship misconduct, be it gift or ghost authorship.

References

International Committee of Medical Journal Editors. Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Writing and Editing for Biomedical Publication. Updated February 2006 [http://www.icmje.org/#author]
Drenth JP: Multiple authorship: the contribution of senior authors. JAMA 1998 Jul 15;280(3):219-21.
Kakkar N: Authorship trends in the Indian Journal of Pathology and Microbiology: going the global way? J Clin Pathol 2004 Jun;57(6):670.
Sohi I, Kakkar N: Author numbers in Indian Pediatrics--going against the tide! Indian Pediatr 2004 Dec;41(12):1286-7.
Pignatelli B, Maisonneuve H, Chapuis F: Authorship ignorance: views of researchers in French clinical settings. J Med Ethics 2005, 31(10):578-81
Bates T, Anic A, Marusic M, Marusic A: Authorship criteria and disclosure of contributions: comparison of 3 general medical journals with different author contribution forms.JAMA 2004, 292(1):86-8
Mowatt G, Shirran L, Grimshaw JM, Rennie D, Flanagin A, Yank V, MacLennan G, Gotzsche PC, Bero LA: Prevalence of honorary and ghost authorship in Cochrane reviews. JAMA 2002, 287(21):2769-71.
http://www.bmj.com/advice/article_submission.shtml#author
http://jama.ama-assn.org/cgi/data/295/1/103/DC1/1
Sox HC, Rennie D: Research misconduct, retraction, and cleansing the medical literature: lessons from the Poehlman case. Ann Intern Med 2006 Apr 18;144(8):609-13.
Flanagin A, Carey LA, Fontanarosa PB, Phillips SG, Pace BP, Lundberg GD, Rennie D: Prevalence of articles with honorary authors and ghost authors in peer-reviewed medical journals. JAMA 1998 Jul 15;280(3):222-4.
Fugh-Berman A: The corporate coauthor. J Gen Intern Med 2005 Jun;20(6):546-8.
Jacobs A, Carpenter J, Donnelly J, Klapproth JF, Gertel A, Hall G, Jones AH, Laing S, Lang T, Langdon-Neuner E, Wager L, Whittington R; European Medical Writers Association's Ghostwriting Task Force: The involvement of professional medical writers in medical publications: results of a Delphi study. Curr Med Res Opin 2005, 21(2):311-6
Jacobs A, Wager E: European Medical Writers Association (EMWA) guidelines on the role of medical writers in developing peer-reviewed publications. Curr Med Res Opin 2005, 21(2), 317–321 http://www.emwa.org/Mum/EMWAguidelines.pdf
Medical Council of India Code of Ethics Regulations, 2002 (Published in Part III, Section 4 of the Gazette of India, dated 6^th April,2002) http://www.mciindia.org/know/rules/ethics.htm
Abbott A: Dispute over first authorship lands researchers in dock. Nature 2002, 419(6902):4.
Tim Albert, Elizabeth Wager: How to handle authorship disputes: a guide for new researchers. COPE Report 2003. http://www.publicationethics.org.uk/reports/2003/2003pdf12.pdf
Verma I: Then and now. Nature 2005 Jul 28;436(7050):478-9. http://www.nature.com/nature/journal/v436/n7050/full/436478a.html
Srinivasan S, Loff B: Medical research in India. Lancet 2006 Jun 17;367(9527):1962-4.

Open Choice takes a beating

2007-07-10T23:25:00.000Z

I've been impressed with the way that publishers have begun the shift to open access with schemes such as Springer's Open Choice, offering authors the choice to have their article made open access in an otherwise subscription journal, depending on the payment of a fee ($3000 for Springer).

Stevan Harnad has criticised Open Choice, arguing against double payment (readers and authors in effect paying for the same article), and what Stevan sees as the way that paying for open access publication is a distraction from self-archiving.

Now, Open Choice is being criticised from another front: researchers such as Peter Murray-Rust who are keen on open access publication, but who find that Open Choice does not quite meet the usual standards they expect of open access.

Peter Murray-Rust has resigned from the editorial board of a Springer journal in protest at the way that Open Choice is working. In particular, he is concerned at the lack of visibility or explanation of Open Choice, other than just a small logo
as well as the way that Springer retains copyright to the articles (Open Choice articles seem to be © Springer, although information on the Springer site states that "if authors choose open access in the Springer Open Choice program, they will not be required to transfer their copyright to Springer"). One of his real concerns is about the transparency of permissions to reuse the work, a criticism that has also recently been raised about self-archiving with the battle cry, 'Free is not open!' (it is unusual to see Stevan and Jan Velterop, Springer's open access champion on the same side of an argument). Jan has responded to Peter, to which Peter has replied, clarifying his worries.

One thing that Peter noted really did surprise me. Although readers can access Open Choice articles without charge, on the page there is a link that invites readers to 'Add to shopping cart'. There is also a 'Request Permissions' link, which if you follow tells you that "To request reuse of content from this Springer Science+Business Media journal, please e-mail Springer Rights & Permissions directly at permissions.heidelberg@springer.com for assistance". No mention of Open Choice.

Click the link to 'Add to shopping cart', and you are told that you can purchase it (for $32 in this case). I thought that it was unlikely that a reader would really be able to proceed with the purchase of an article that is actually open access, but I got all the way to being asked for my credit card details with no warning that I was about to pay for something that was free! This problem of people paying for articles that they could access for free elsewhere is an issue with self-archiving, but it really shouldn't be possible when the publisher has already been paid by the author!

As if criticisms of double payment weren't bad enough, this appears to be triple payment (subscribers to the journal, authors, and readers of the individual article who purchase it without realising it is open access). I wonder how many readers have made this mistake, if any? I take no delight in highlighting this criticism of Springer, as the blind spots in their implementation of open access are surprising considering Jan Velterop's genuine dedication to the cause of open access (his blog is called The Parachute, because 'it only works when it is open'). I'm sure that Jan will be working to fix these glitches in Open Choice.

Journalology roundup #9

2007-07-10T22:54:00.000Z

Mentors of tomorrow. "Everyone knows bad peer review when they come across it — but too few are nurturing good referees".

Physicians and researchers have different needs. "Alex Williamson is publishing director at the BMJ Group, the publishing arm of the British Medical Association (BMA). We ask her about the role of journals in clinical medicine". A pity to see the BMJ Group being ambivalent about open access, especially as the BMJ is a good example of a high-profile medical journal publishing open access research.

Is physics the new biomedicine? "A new set of physics and maths journals are planned for BioMed Central. Siân Harris finds out why this open-access publisher is branching out from biomedical sciences". All about the launch of Chemistry Central and PhysMath Central.

Researcher accused of breaching research ethics faces GMC. "A former senior lecturer at the UK Institute of Psychiatry repeatedly breached research ethics guidelines and lied to study sponsors while building an international reputation as a leading researcher, according to charges laid by the General Medical Council. The GMC's fitness to practise committee heard that Tonmoy Sharma, who left the Institute of Psychiatry as a clinical senior lecturer in 2001, falsely claimed to have sought and received approval from ethics committees for several studies. He is also accused of recruiting patients by telephone without informing their carers; offering financial inducements to research subjects; breaching agreed research protocols; lying in a job application; posing as a professor; and in one case threatening a patient with withdrawal of treatment if she left a study".

PLoS journal retracts phylogenetics paper. "Computational Biology journal pulls paper about estimating the accuracy of phylogenetic trees, in what colleagues deem an exemplary process".

New site pits 'published' vs. 'posted'. "Nature Precedings raises questions over the value of sharing findings before submitting to peer review".

Search skills needed for new Web world. "Consumers now regularly go to the Web to look for medical information or to gain from the experience of people with similar ailments. They also take that information to their doctors, who have to contend with this new found influence on their patient relationships (whether they actually appreciate it or not!). And now even doctors are using Web searches more, sometimes for fairly sophisticated diagnostic reasons. However, all of this makes several basic assumptions: that people basically know what they want, even if they don't know the details, and that they basically know how to go about getting it from the Web. Au contraire, at least according to a couple of recent articles in the online journal BMC Medicine. One points to a study of Swiss people -- generally considered a very literate and knowledgeable lot -- that concluded there is a "consistent and dramatic" lack of knowledge in the general public about medical matters. The other is about a project that examined the search skills of people trying to get medical information from the Web, and found them lacking".

Copyright and research: an academic publisher’s perspective. "As a publisher working on the legal and rights’ side of the business at present, but who used to be a Commissioning Editor responsible for research books in the Humanities, the author finds himself sympathetic to the needs of academic authors and keen to find ways of ensuring that their copyright interests are adequately protected"... "A full-scale tilt into unrestricted Open Access would be too big a shift. Someone has to pay, and it can be argued that the current mildly regulated framework which ‘publisher-controlled’ copyright represents does the job quite well: of keeping the economics in equilibrium". Peter Suber has commented.

Retrovirology editorial compares impact factors and H-factors.

Reviewing Reviewers. "This weekend I have been poring over statistics provided by a journal for which I do some editorial work. In addition to data related to how the journal is doing (impact factor, ranking among journals in related fields etc.), there are also lists of reviewers: who did reviews, how many each has done, and how long the reviews took. It's amazing to contemplate these lists, first of all because they are a testament to the huge amount of work reviewers do in the name of 'professional service'. I have done my share of complaining about reviews of my own manuscripts, so it's good to be reminded from time to time that, despite some unethical and rude reviewers, the system of peer review is an impressive thing in terms of its scope and time involved".

Do scientists really believe in open science? "I am writing this post as a collection of the current status and opinions of “Open Science”. The main reason being I have a new audience; I am working for the CARMEN e-Neuroscience project. This has exposed me, first hand, to a domain of the life-sciences to which data sharing and publicly exposing methodologies has not been readily adopted, largely it is claimed due to the size of the data in question and sensitive privacy issues".

Clinical trial results often overstate benefits of treatment. "Failings in the way that clinical trials are designed and presented may lead doctors to overstate the benefit of treatments, experts warned last week. The conference on clinical trials, organised by the James Lind Alliance and the Lancet and held at the Royal Society of Medicine in London, also heard that key groups of participants were often excluded from clinical studies and as a result were denied the benefits of evidence based medicine. Stephen Holgate, professor of immunopharmacology at Southampton University, said that children and elderly people were "especially neglected" in this area".

For free or for fee? Dilemma of small scientific journals. "Biomedical publishing is becoming increasingly dominated by multinational companies, advertising research articles at the international market, presenting them electronically through web-based services, and distributing them to readers-consumers. It seems that they will soon become the sole publishers for the majority of biomedical journals. In the past decade, however, we witnessed a quiet revolution in the whole structure of scientific communication, influenced by new technologies and initiatives such as Open Access, PubMedCentral, PLoS, and BioMedCentral. The Croatian Medical Journal (CMJ) has recently been approached by two major publishing companies and offered to become one of the journals in their group. The editorial decision was to join neither of the publishers".

Journal of Biology celebrates its fifth anniversary. Hidden away in a table in this editorial is the calculation of the 'unofficial impact factor' for J Biol for 2005 - 20.1. Not bad, if I say so myself...

Free is not open. The CMAJ congratulated its former editors for the launch of Open Medicine - and got the response that, thanks all the same, but you're not open access.

Free medical textbooks. The 'Flying Publisher' describes their project to publish free medical textbooks.

Biomedical Journals and Global Poverty: Is HINARI a Step Backwards? "Our experience in Peru with the Health InterNetwork Access to Research Initiative (HINARI), an initiative managed by the World Health Organization that helps promote access to scientific information by providing free (or low cost) online access to major science journals, is not as accessible as hoped for and, in fact, is getting worse".