Journalology

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!