Tuesday, January 6, 2015

Publish or Perish: an old system adapting to the digital era

    By Annie Chen and Michael Allegrezza
           When scientific publishing was developed in the 19th century, it was designed to overcome barriers that prevented scientists from disseminating their research findings efficiently. It was not feasible for scientists to arrange for typesetting, peer review, printing, and shipping of their results to every researcher in their field. As payment for these services offered by publishers, the researchers would transfer the exclusive copyrights for this material to the publisher, who would then charge subscribers access fees. To limit the printing costs associated with this system, journals only published articles with the most significant findings. Now, nearly 200 years later, we have computers, word processors, and the Internet. Information sharing has become easier than ever before, and it is nearly instantaneous. But the prevailing model of subscription-based publishing remains tethered to its pre-digital origins, and for the most part these publishers have used the Internet within this model, rather than as a tool to create a new and better system for sharing research.

Figure 1. Trend lines show an annual increase of 6.7%
for serials expenditures vs 2.9% for the Consumer Price
Index over the period 1986-2010, relative to 1986 prices.
In theory, digitization should have decreased costs of communicating science: (authors can perform many of the typesetting functions, articles can be uploaded online instead of printed and shipped, etc. In practice, however, digitization has actually increased the price of journals. Statistics from the Association of Research Libraries show that the amount spent on serials increased 6.7% per year between 1986 and 2011, while inflation as measured by the US Consumer Prices Index only rose 2.9% per year over the same period (Figure 1).1 Shawn Martin, a Penn Scholarly Communication Librarian, explained, “Penn pays at least twice for one article, but can pay up to 7 or more times for the same content,” in the process of hiring researchers to create the content, buying subscriptions from journals, and paying for reuse rights. To be fair, the transition phase from print to digital media has been costly for publishers because they have had to invest in infrastructure for digital availability while still producing print journals. Many publishers argue that while journal prices may have increased, the price per reader has actually decreased due to a surge in the ease of viewers accessing articles online.

Regardless of whether increasing journal prices was justified, a new model for academic publishing emerged in the 1990s in opposition: open access (OA). There are two ways of attaining open access: Gold OA, when the publisher makes the article freely accessible, and Green OA, which is self-archiving by the author. A few years ago, Laakso et al. conducted a quantitative analysis of the annual publication volumes of Direct OA journals from 1993 to 2009 and found that the development of open access could be described by three phases: Pioneering (1993-1999), Innovation (2000-2004), and Consolidation (2005-2009).2 During the pioneering years, there was high year-to-year growth of open access articles and journals, but the total numbers were still relatively small. OA publishing bloomed considerably from 2000 to 2009, growing from 19,500 articles and 740 journals to 191,850 articles and 4,769 journals, respectively. During the innovation years, new business models emerged. For example, BioMedCentral, later purchased by Springer in 2008, initiated the author charge. In 2004, some subscription-based journals began using a hybrid model, such as Springer’s Open Choice program, which gave authors the option of paying a fee to make their article openly available. During the consolidation phase, year-to-year growth for articles decreased from previous years but was still high, at about 20%.

The introduction of open access journals has sparked fierce and passionate debates among scientists. Proponents of open access believe scientific research should be available to everyone from anywhere in the world. Currently, subscription fees prevent many people from accessing the information they need. With open access, students and professors in low- and middle-income countries, health care professionals in resource-limited settings, and the general public would gain access to essential resources. For instance, Elizabeth Lowenthal, MD, at the Penn Center for AIDS Research, recently published a paper in PLoS One analyzing variables that influence adherence to retroviral drugs in HIV+ adolescents living in Botswana. Her decision to publish open access was because “the article will be of most direct use to clinicians working in Botswana and I wanted to make sure that it would be easy for them to access it.” Open access also provides re-use rights and may facilitate a more rapid exchange of ideas and increased interactions among scientists to generate new scientific information.

However, there may also be some downsides to increased access. Open access may increase the number of articles that people have to sift through to find important studies.3 Furthermore, people who do not know how to critically read scientific papers may be misled by articles with falsified data or flawed experiments. While these papers often get retracted later on, they may undermine the public’s confidence in scientists and medicine. Wakefield’s (retracted) article linking vaccines to autism, for example, may have contributed to the rise of the anti-vaccine movement in the US.4 Furthermore, many open access journals require authors to pay for their papers to be published to offset the cost of publication, and some people have taken advantage of this new payment system to make a profit through predatory journals (a list of predatory OA journals can be found here: http://scholarlyoa.com/publishers/). It is clear though, that the expansion of open access from 1993 until present time suggests that open access can be a sustainable alternative to the traditional model of subscription-based academic publishing.

In addition to facilitating access to scientific articles, the Internet has also created opportunities to improve the peer review process. Peer review was designed to evaluate the technical merit of a paper and to select papers that make significant contributions to a field. Scientists supporting the traditional model of publishing argue that the peer review process in some open access journals may not be as rigorous, and this may lead to the emergence of a “Wild West” in academic publishing. Last year, reporter John Bohannon from Science magazine sent a flawed paper to 304 open access journals, and of the 255 journals that responded, 157 accepted the paper, suggesting little or no peer review process in these journals.5 However, even high-impact journals publish papers with flawed experiments.6 Michael Eisen, co-founder of PLoS, wrote, “While they pocket our billions, with elegant sleight of hand, they get us to ignore the fact that crappy papers routinely get into high-profile journals simply because they deal with sexy topics…. Every time they publish because it is sexy, and not because it is right, science is distorted. It distorts research. It distorts funding. And it often distorts public policy.”7 Nature, for example, published two articles last year about acid-bath stem cell induction, which were later retracted due to data manipulation. However, according to Randy Sheckman, editor-in-chief of eLife, “these papers will generate thousands of citations for Nature, so they will profit from those papers even if they are retracted.”8

With digital communication, peer review for a manuscript could shift from a rigid gate controlled by 3 or 4 people, who might not even be active scientists, into a more dynamic, transparent, and ongoing process with feedback from thousands of scientists. Various social media platforms with these capabilities already exist, including ResearchGate9 and PubMedCommons.10 Some open access journals are using different strategies to address these issues in peer review. eLIFE, for example, employs a fast, streamlined peer review process to decrease the amount of time from submission to publication while maintaining high-quality science. On the other hand, PLoS One, one of the journals published by the Public Library of Science, judges articles based on technical merit alone, not on the novelty.

We polled a few scientists at Penn who had recently published for their thoughts on open access and peer review. Most people did not experience a difference in the peer review process at an open access journal compared to non-open access. The exception was at eLIFE, where reviewers’ comments were prompt, and the communication between reviewers and editors is “a step in the right direction,” according to Amita Sehgal, PhD. To improve the peer review process, some suggested a blind process to help eliminate potential bias towards well-known labs or against lesser-known labs.

The digital revolution is changing the culture of academic publishing, albeit slowly. In 2009, the NIH updated their Public Access Policy to require that any published research conducted with NIH grants be available on PubMed Central 12 months after publication.11 Just last month, the publisher Macmillan announced that all research papers in Nature and its sister journals will be made free to access online in a read-only format that can be annotated but not copied, printed or downloaded. However, only journal subscribers and some media outlets will be able to share links to the free full-text, read-only versions.12 Critics such as Michael Eisen13 and John Wilbanks14 have labeled this change merely a public relations ploy to appeal to demands without actually increasing access. It will be interesting to see if other publishers follow this trend.

Scientific communication has yet to reap the full benefits in efficiency made possible by the Internet. The current system is still less than ideal at furthering ideas and research with minimal waste of resources. But this generation of young researchers is more optimistic and may revolutionize scientific publishing as we know it. “I think [open access is] the future for all scientific publications,” says Bo Li, a postdoc at Penn. “I hope all research articles will be freely accessible to everyone in the world.”

A companion opinion article by Penn PhD student Brian S. Cole can be found here.

This article appeared in the Penn Science Policy January 2015 newsletter

Annie Chen
Michael Allegrezza

1Ware M, Mabe M. (2012) The stm report. http://www.stm-assoc.org/2012_12_11_STM_Report_2012.pdf
2Laakso M, Welling P, Bukvova, H, et al. (2011) The development of open access journal publishing from 1993 to 2009. PLoS ONE.
3Hannay, T. (2014) Stop the deluge of scientific research. The Guardian: Higher Education Network Blog. http://www.theguardian.com/higher-education-network/blog/2014/aug/05/why-we-should-publish-less-scientific-research.
4Wakefield AJ, Murch SH, Anthony A, Linnell, et al. (1998) Ileal lymphoid nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children [retracted]. Lancet. 351:637-41.
5Bohannon, J. (2013) Who’s afraid of peer review? Science. 342(6154): 60-65. DOI: 10.1126/science.342.6154.60
6Wolfe-Simon F, Switzer Blum J, Kulp TR, et al. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332(6034) 1163-6. doi: 10.1126/science.1197258.
7Eisen M. (2013) I confess, I wrote the Arsenic DNA paper to expose flaws in peer-review at subscription based journals. it is NOT junk. http://www.michaeleisen.org/blog/?p=1439.
8(2014) Episode 12. The eLIFE podcast. http://elifesciences.org/podcast/episode12
9ResearchGate. http://www.researchgate.net/
10PubMed Commons. http://www.ncbi.nlm.nih.gov/pubmedcommons/
11NIH Public Access Policy Details. http://publicaccess.nih.gov/policy.htm
12Baynes G, Hulme L, MacDonald S. (2014) Articles on nature.com to be made widely available to read and share to support collaborative research. Nature. http://www.nature.com/press_releases/share-nature-content.html
13Eisen M. (2014) Is Nature’s “free to view” a magnanimous gesture or a cynical ploy?. it is NOT junk. http://www.michaeleisen.org/blog/?p=1668
14Van Noorden R. (2014) Nature promotes read-only sharing by subscribers. Nature. http://www.nature.com/news/nature-promotes-read-only-sharing-by-subscribers-1.16460

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