The Berkeley Science Review: Articles

Science Finds Its PLoS In The Sun
Is open-access publishing coming of age? (view PDF)
by Ben Gutman

Scientists are often perceived to be at the cutting edge of technology, but in one critical area they are stuck in the past. In the midst of the Information Age, when the Internet can rapidly deliver free information around the globe, scientists are still communicating with each other through closed, subscription-based journals. These expensive subscriptions make scientific research available only to those who can afford it, often preventing scientists from seeing the complete body of published works in their field. Or so say the founders of the Bay Area-based Public Library of Science (PLoS). This fall PLoS is taking an important step in its campaign to erase obstacles to the free and easy distribution of science: armed with initial funds of $9 million, it is launching a new online scientific journal intended to compete with top-tier scientific journals—and maybe even start a new trend in open-access publishing.

Lawrence Berkeley Lab scientist and Berkeley MCB professor Michael Eisen is oneof the cofounders of PLoS. He describes it as “a group of scientists who believe that science in general would be better off if the published results of scientific research were fully available.” He also believes the Internet has enormous potential for advancing scientific research. Most journals now offer their articles online as well as in print to paying subscribers, and are rapidly scanning in back issues (articles in Journal of the American Chemical Society are available online back to 1879). Berkeley recently canceled print subscriptions to journals offered by major scientific publisher Elsevier, choosing to rely on electronic versions instead. But Eisen envisions more than simply making research available to be read online by paying subscribers. According to the PLoS website, “open access” to scientific literature means “its free availability on the public Internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, to crawl them for indexing, to pass them as data to software, to make and dis- tribute derivative works, or to use them for any other lawful purpose.” Eisen sees a day when scientists will be able to “search the entire text of journal articles, [electronically] link to specific subsections, [and use the literature] in ways we haven’t even thought of yet.”

Eisen compares his vision of open-access research to public DNA-sequence databases that collate DNA codes discoveredby various researchers, explaining how the ability to systematically view whole genomes has revolutionized biology. If sequences were still published piecemeal in various journals, new fields such as genomics and Eisen’s own field of computational biology might not exist. Computational techniques employed daily, such as BLAST and homology searches, would never have been developed, he says. These tools, which allow biologists to search and compare genes and proteins across species and even kingdoms, elucidate everything from the function of the gene and genome to the pattern of evolution. In the scientific literature Eisen sees a similar trove of information to be mined by enterprising scientists in ways as yet unconceived, if only all the literature were available in a single, easily manipulated site. He and his PLoS colleagues have set out to make that possible.

This task has turned out to be easier said than done. Eisen first came upon the idea for a universal scientific literature database as a post doc some years ago with his then boss, now PloS cofounder, Dr. Patrick Brown of Stanford University. Eisen was working on microarrays, a biological tool used to study the activation of genes under various conditions. Huge amounts of prior data were require to understand the results generated by this technique. Says Eisen, “Pat Brown has a photographic memory, but it’s just not possible to know all the things you need to know. It just seemed logical to have all the information to interpret [the microarrays] in one place.” Biologists have been publishing research on the function of specific genes and proteins for years, but there was, and still is, no easy way to search through all of that information for general patterns.

Recognizing this need and the potential of the Internet, Eisen, Brown, and the third PLoS cofounder, Harold Varmus, Nobel Laureate and then director of the National Institutes of Health, set to work. The first attempt was the 1999 creation, by Varmus’s initiative at NIH, of PubMed Central—a free online repository for life-science publications. They hoped to convince publishers to voluntarily submit articles to PubMed Central some time after publication. The delay would allow publishers to continue to profit by charging customers for newly published material, but once the research was somewhat dated, it would become universally accessible. With a few exceptions, notably The Proceedings of the National Academy of Sciences (PNAS), this was not terribly successful.

The next approach was to formally create PLoS, and draft an open letter to scientific publishers. The letter, which Eisen terms “free market research,” outlined the broad desire among the scientific community for open access. It was widely termed a boycott, and was relatively unsuccessful. Signed by over 30,000 scientists from 180 countries, the letter asserted that the signers would not subscribe to, edit, or publish in journals that did not provide their content to a centralized repository such as PubMed Central within six months of publication. To their surprise, the journals disregarded these threats, and the boycott fell apart because the signing scientists couldn’t afford not to publish.

To hear Eisen tell it the journals were being obtuse, failing to grasp the obviousness of the new approach. He claims that the journals would not have lost subscribers and could have continued in much the present model. He points to the physics community, which for years has posted preprints on the website arXiv.org without destroying the physics journals. Dr. Nicholas Cozzarelli, a professor in the Berkeley Department of Molecular and Cell Biology and editor in chief of PNAS, generally agrees. PNAS follows a hybrid model, he explains, making content “freely available after six months, and immediately available to subscribers and in third-world countries.” However, he adds, “We are a breakeven journal. We don’t make a profit, nor incur losses, at least hopefully.” Other journals concerned with making a profit may not be willing to take a similar risk.

Realizing that presenting the idea of open access and even making a threat didn’t reshape the world of scientific publishing, Eisen and company undertook a new approach. They decided to demonstrate the feasibility of open access and of a fundamentally new business model for scientific publishing. They would create their own journals operating in an open-access, author- funded system, aiming to compete with top-tier journals such as Science, Nature, and Cell and demonstrate that this model is economically viable. They hope to ultimately convince all of scientific publishing to follow their lead. This may be a more effective approach. “If this is a great idea, lots of people will consider it,” says Don Kennedy, editor of Science. “Every time something clever succeeds you look at it.”

Cozzarelli agrees: “I think this is a great idea. It’s obvious that this is the way to go. The question is … how to make the transition.… It is difficult for existing journalsto try this model … [but] if they succeed many journals will allow, and many will not.” The first PLoS journal, premiering this October, will be called PLoS Biology, and is backed by a $9 million grant from the newly created Gordon and Betty Moore Foundation (Gordon Moore of Intel and Moore’s Law fame is a Berkeley graduate). PLoS has also secured the editorial services of Vivian Siegel, the well-known former editor of Cell.

What is different about the PLoS journals is that authors will be charged to publish an article. Eisen says this will reverse the current outdated business model of scientific publishing, whereby the costs are borne by the consumer of scientific information. If publishing is done on the Internet, costs are fixed, and extra copies cost no more to produce. The research can therefore be dis- tributed for free, reaching the broadest possible audience, and the fixed cost is borne by the producer.

But this author fee also poses potential problems. While journals in some fields already charge authors to publish (as well as charging for subscriptions), the proposed $1,500 fee is two to five times higher than standard. In biology it is new; few biology journals currently charge authors to publish. Cozzarelli, who sits on the editorial board of PLoS Biology, says the fee could make things difficult for authors if they don’t receive additional funding. “If, as PLoS hopes, the money currently given to libraries by institutions and granting agencies, is instead given to authors, then the model will likely succeed,” he says. “If not, then something is lost.”

Will funding agencies agree to make publication fees a standard part of scientific grants? In fields in which the author-funded system already exists, grants tend to include publication costs. A set of journals published in Britain by BioMed Central (BMC) is already based on an author-funded, open-access model, but the difference, apart from BMC being for profit and PLoS not, seems to be in their reach. PLoS, according to Eisen, intends to lead from the top. A lofty goal, admits Cozzarelli: “I think it would be a great success if PLoS were as reputable as The Journal of Biological Chemistry.” (JBC is a high-quality journal, but not the most prestigious.) BMC is taking a more grassroots approach, establishing a broad stable of mostly niche publications, from BMC Ecology and Journal of Biology to Filaria Journal and BMC Palliative Care. Perhaps both approaches will be necessary to convince other journals of the feasibility of open access. Eisen is confident that PLoS Biology will succeed in attracting top-notch research. He expects to have “about a dozen outstanding papers” in October’s premier issue.

Kennedy of Science agrees that PLoS Biology “might very well become a serious competitor. We welcome them into the business.” However, he is not rushing to adopt the open-access model, much to Eisen’s dismay. Eisen feels that Science’s publisher, the American Association for the Advancement of Science (AAAS), should lead the charge toward open-access publishing. He points out that AAAS is a notfor- profit publisher with a well-established, successful journal, and the stated mission “To advance science and innovation through the world for the benefit of all people … [and] foster communication among scientists, engineers and the public.” For his part, Kennedy says, “It’s a mystery to me why [Eisen] is so particularly critical of Science.” He explains that Science is very different from its commercial competitors, already giving away much free content, and denies that Science is a profitable magazine, since members of AAAS receive subscriptions as part of their dues. “Subscriptions and ad revenue may exceed costs, or may not,” he notes, since it “depends on how you cost account every subscriber.”

That open-access publishing is still very much an experiment is made clear by several qualms raised even by supporters. Robert Tjian, editorial-board member of Cell and professor in the MCB department, highlights an interesting concern: if publishers are being paid per article there is an incentive to publish more articles. As he says, “The biggest challenge is to make sure that there are enough filters so that not everything gets in. The other way to deal with that is to charge more per paper, but that gets back to limiting access.” On the whole, however, he is supportive of the experiment, and while he doesn’t know whether Cell will eventually follow suit, he, along with Cozzarelli, puts the final judgment in the hands of young scientists. “The real clientele,” says Tjian, “is the students and post docs. If [PLoS] can convince them that it’s better to publish in the new electronic journals than in Science and Nature then they’ll have succeeded. But right now I’m not sure what would make a student do that.”

Will PLoS Biology succeed? With its considerable bankroll and all-star cast, it is off to a strong start. But PLoS will truly be a success only when all scientific research is freely available to all scientists, without the barriers of subscription fees and fragmented, unconnected information. While that goal is still far off, open access may one day change the way that science is done.

Ben Gutman is a graduate student in the Department of Plant and Microbial Biology.

Want to know more?
www.plos.org
www.sciencemag.org
www.nature.com
www.biomedcentral.com

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