StATS: Open Access Journals, part 2 (October 14, 2007).

I'm giving a talk at the Grand Rounds for CMH on Thursday, October 17.  I'm using PowerPoint for this talk, and here is a summary for my web pages.

Open-access (OA) journals and their impact on research and the practice of medicine.

This talk will cover the following topics:

  1. What is open-access (OA)?
  2. What are the historical antecedents to OA?
  3. What are the costs and benefits of OA?
  4. How you can help promote OA?

This presentation was inspired by a talk by Jim Pitman at the 2007 Joint Statistics Meetings and which is summarized on the web at

What is open-access (OA)?

Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions.

Some journals provide partial support to OA. They might:

OA is not public domain, because it does enforce several copyright restrictions. Restrictions vary by the journal. The most common restriction on copyright is the requirement that any user acknowledge the original source. Most OA journals allow the author to maintain the original copyright. This allows you to re-use your own work without having to get permission first.

OA is not (necessarily) low quality. OA is compatible with the peer-review process and is capable of producing research of high quality.

PLoS Biology is ranked as the most highly cited general biology journal by the Institute for Scientific Information (ISI), with an impact factor of 14.1.

There are several historical events which have laid the way for the OA publication.

1. The Internet (1974). The Internet and especially the World Wide Web have greatly reduced the costs of publishing and disseminating information. I don't have a good quote or source on this, but hopefully, my audience will take it on faith. I'm including a screen shot of the famous Al Gore quote about inventing the Internet.

During my service in the United States Congress, I took the initiative in creating the Internet.

2. GNU (1984) and FSF (1985). I will show a screenshot of the main page for GNU ( GNU stands for "GNU's Not Unix" (the acronym is a mathematical play on recursion). The GNU operating system, developed under the direction of Richard Stallman, represents the first major effort to produce a major software project where the software was freely distributed and where the source code for the software was openly published. The Free Software Foundation was set up to promote similar efforts for other software projects.

3. Cheap digital storage (1988). It's difficult to put a date on when digital storage became cheap, but one important development that allowed cheap digitial storage, was the discovery of giant magnetoresistance by Albert Fert and Peter Grunberg that won them the 2007 Nobel Prize in Physics. I am including a screenshot of the New York Times article mentioned below.

Dr. Fert, 69, and Dr. Grünberg, 68, each working independently in 1988, discovered an effect known as giant magnetoresistance, in which tiny changes in a magnetic field can produce huge changes in electrical resistance. The effect is at the heart of modern gadgets that record data, music or snippets of video as a dense magnetic patchwork of zeros and ones, which is then scanned by a small head and converted to electrical signals.

4. arXiv (1991). The development of preprint servers for papers in mathematics and physics. I will show a screenshot of the main page for arXiv (

arXiv (pronounced "archive", as if the "X" were the Greek letter Chi or Χ) is an archive for electronic preprints of scientific papers in the fields of mathematics, physics, computer science and quantitative biology which can be accessed via the Internet. In many fields of mathematics and physics, almost all scientific papers are placed on the arXiv. As of September 2007, contains over 440,000 e-prints, with roughly four thousand new e-prints added every month.

5. PubMed Central (2000). PubMed Central is a resource sponsored by NIH that allows journals to contribute their articles to an archive that is free and open to the public. When you are performing a PubMed search, you can set one of the search limits to restrict your search to articles that have the full free text available in PubMed Central.

PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature. Participation by publishers in PMC is voluntary, although participating journals must meet certain editorial and technical standards. PMC, itself, is not a publisher. Access to PMC is free and unrestricted.

6. The Public Library of Science (2001). The Public Library of Science (PLoS) is a publishing project that produces several journals (including PLoS Biology, PLoS Genetics, PLoS Computational Biology, PLoS Medicine, PLoS Neglected Tropical Diseases, PLoS ONE, and PLoS Pathogens). These journals require that the authors pay a fee for submission (currently $900) and make the content available for free under an open source license. I am inlcuding a screen shot from the PLoS main page (

PLoS is a nonprofit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource.

7. Budapest Open Access Initiative (2001). This meeting, held in Budapest and sponsored by the Open Society Institute.

The Open Society Institute (OSI), a private operating and grantmaking foundation, aims to shape public policy to promote democratic governance, human rights, and economic, legal, and social reform. On a local level, OSI implements a range of initiatives to support the rule of law, education, public health, and independent media. At the same time, OSI works to build alliances across borders and continents on issues such as combating corruption and rights abuses.

George Soros is founder and chairman of the Open Society Institute and the Soros foundations network. He is also the chairman of Soros Fund Management LLC.

The first paragraph of this initiative reads:

An old tradition and a new technology have converged to make possible an unprecedented public good. The old tradition is the willingness of scientists and scholars to publish the fruits of their research in scholarly journals without payment, for the sake of inquiry and knowledge. The new technology is the internet. The public good they make possible is the world-wide electronic distribution of the peer-reviewed journal literature and completely free and unrestricted access to it by all scientists, scholars, teachers, students, and other curious minds. Removing access barriers to this literature will accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge.

8. Ancestor (2007).

9. Journal of Topology (2008).

Who pays the bills? There are many economic models for publication, but the most common models are:

There are also hybrid models that combine these two approaches. Other revenues, such as advertising, apply equally well to both models.

Academic journals are "paradise" for commercial publishers.

First the public pays for most scientific research through, for example, the National Science Foundation. Then universities pay the salaries of scientists who do virtually all the writing, reviewing and editing. Universities sometimes even provide free office space to journals. Finally, authors typically sign over their copyright to publishers, who can sometimes bring in many millions of dollars a year in subscriptions for a single high-priced journal — subscriptions paid by university libraries supported by tax dollars and tuition.

Who benefits from OA? Although there is controversy over the general benefits versus costs of OA, some parties clearly benefit:

OA increases research visibility. There are many studies that have shown this, but one of the best looked at a series of articles published between June and December 2004 in the Proceedings of the National Academy of Sciences. The researchers tracked the publications over time to see how often they were cited by other publications.

A total of 1,492 original research articles were analyzed: 212 (14.2% of all articles) were OA articles paid by the author, and 1,280 (85.8%) were non-OA articles. In April 2005 (mean 206 d after publication), 627 (49.0%) of the non-OA articles versus 78 (36.8%) of the OA articles were not cited (relative risk = 1.3 [95% Confidence Interval: 1.1–1.6]; p = 0.001). 6 mo later (mean 288 d after publication), non-OA articles were still more likely to be uncited (non-OA: 172 [13.6%], OA: 11 [5.2%]; relative risk = 2.6 [1.4–4.7]; p < 0.001). The average number of citations of OA articles was higher compared to non-OA articles (April 2005: 1.5 [SD = 2.5] versus 1.2 [SD = 2.0]; Z = 3.123; p = 0.002; October 2005: 6.4 [SD = 10.4] versus 4.5 [SD = 4.9]; Z = 4.058; p < 0.001).

Various groups have offered support for OA. Here are some important ones.

The Medical Library Association (MLA) supports both the concept of open access to information generated from federally funded scientific and medical research and current copyright law, and maintains that having access to timely, relevant, and accurate information is vital to the health of our nation and its education and research programs.

Beginning May 2, 2005, NIH-funded investigators are requested to submit to the NIH National Library of Medicine's (NLM) PubMed Central (PMC) an electronic version of the author's final manuscript upon acceptance for publication, resulting from research supported, in whole or in part, with direct costs from NIH. The author's final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process.

[The Wellcome Trust] requires electronic copies of any research papers that have been accepted for publication in a peer-reviewed journal, and are supported in whole or in part by Wellcome Trust funding, to be deposited into PubMed Central (PMC) or UK PMC once established, to be made freely available as soon as possible and in any event within six months of the journal publisher's official date of final publication.  (Note: according to WIkipedia, The Wellcome Trust is a United Kingdom-based charity established in 1936 to administer the fortune of the American-born pharmaceutical magnate Sir Henry Wellcome. Its income was derived from what was originally called Burroughs Wellcome & Co, later renamed in the UK as the Wellcome Foundation Ltd (Wellcome plc). The trust is the world's second richest medical charity after the Bill and Melinda Gates Foundation, with net assets at 30 September 2006 of over £13.4 billion ($26.8 billion). The trust states its mission as being "to foster and promote research with the aim of improving human and animal health." In addition to funding biomedical research, it supports the public understanding of science.)

[The Max Planck Institute's] mission of disseminating knowledge is only half complete if the information is not made widely and readily available to society. New possibilities of knowledge dissemination not only through the classical form but also and increasingly through the open access paradigm via the Internet have to be supported. We define open access as a comprehensive source of human knowledge and cultural heritage that has been approved by the scientific community. (Note: according to Wikipedia, The Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V. (abbreviated MPG, meaning Max Planck Society for the Advancement of Science) is an independent German non-profit research organization funded by the federal and state governments. The Max Planck Society has a world-leading reputation as a science & technology research organization. In 2006, the Times Higher Education Supplement rankings[1] of non-university research institutions (based on international peer review by academics) placed the Max Planck Society as no.1 in the world for science research, and no.3 in technology research (behind AT&T and the Argonne National Laboratory in the United States).

What you can do to support OA. Jim Pitman has a list of recommendations that I have excerpted for my talk.




Summary. OA journals offer digital content at no cost and with limited copyright restrictions. OA journals offer benefits to medical professionals in developing countries, improve the visibility of your research. Since so much of the research endeavor is supported by taxpayer money, there is an obligation to offer this research openly and without limitation. There are many things that you can do to promote OA.

Here are some resources I probably will not use in my talk.

What does the term "free" in "free software" really mean?

The term "free software" is sometimes misunderstood--it has nothing to do with price. It is about freedom. Here, therefore, is the definition of free software. A program is free software, for you, a particular user, if:

Since "free" refers to freedom, not to price, there is no contradiction between selling copies and free software. In fact, the freedom to sell copies is crucial: collections of free software sold on CD-ROMs are important for the community, and selling them is an important way to raise funds for free software development. Therefore, a program that people are not free to include on these collections is not free software.

Note that this quote is from a book, that sells for $24.95, but which includes the entire contents online for free.

The Ingelfinger Rule and its relationship to pre-publication.

The following quote is a bit dated, but shows is consistent with the medical journals hostility towards pre-publication. Michael Gottlieb had noted in 1981 an unusual series of five patients with Pneumocystis carinii and wanted to get word out rapidly about this.

"I've got something here that's bigger than Legionnaire's," he said. "What's the shortest time between submission and publication?"

The editor explained it would take three months to send the story around to a panel of expert reviewers who would make sure that it was scientifically sound. There would be another delay between the time the review was finished and the publication date, he said. He didn't need to tell Gottlieb about eh ironclad rule that the journal, like virtually all major scientific publications, maintained about the secrecy of material about to be published. If there was any leak whatsoever to the popular press about the research, the journal would pull the story from its pages.

"We'd like to see it," the editor concluded. "Sounds interesting, but there's no way we can guarantee that it will be published."

But this is an emergency, Gottlieb thought as he hung up the phone in frustration. You don't just run business as usual in an emergency.

And the Band Played On, Randy Shilts, page 63.

In fairness to gated journals, they do offer better alternatives today in a medical emergency. Nevertheless, many medical journals today do not allow pre-publication in an archive repository. This is part of a controversial policy called the Ingelfinger rule.

Ingelfinger rule: The policy of considering a manuscript for publication only if its substance has not been submitted or reported elsewhere. This policy was promulgated in 1969 by Franz J. Ingelfinger, then the editor of The New England Journal of Medicine. The aim of the Ingelfinger rule was to protect the Journal from publishing material that had already been published and thus had lost its originality.

Another nice resource about the Ingelfinger Rule is

Pro/con debate about "author pays" model. There is a nice pair of articles in the BMJ which take opposite viewpoints about OA and the "author pays" model of research.

A sharply critical view of Open Access was published by Nature.

BioMed Centeral has a list of 11 myths about OA.

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