From the NY Times: Biologists went rogue and publish directly on the Internet

By Lilian Nassi-Calò

Peer review is widely recognized as one of the most important steps of scholarly communication, because it ensures the validity, quality and credibility of research. It is also, however, the slowest step of the publishing process and may require a few months to a few years, if we consider that the article may not be accepted by the first journal it has been submitted to.

Scientific communication in the “Internet Age” considers these terms too long. Alternatives such as individualized publication of articles in journals and preprint repositories are gaining momentum and being consolidated in recent years. What’s more, one can associate preprints and post-publication peer review, according to participants ASAP Bio Conference, held in February 2016 at the Howard Hughes Medical Institute, US.

The SciELO program attended ASAP Bio and supports the current trend to accelerate the dissemination of research results, highlighting the continued publication of articles in journals it publishes and indexes. This type of publication was launched by the so-called Megajournals, such as the Public Library of Science (PLoS) collection and The BMJ (formerly British Medical Journal).

The prepublication online of articles in open access repositories aims mainly to accelerate the dissemination and sharing of research results and support the advancement of science. No less important is the intention of researchers to ensure the priority of their discovery. Moreover, pre-publication does not exclude the simultaneous or subsequent submission of the article to a journal, which would serve the purpose of meeting funding agencies requirements, career advancement and obtain recognition from peers.

A paper by Ronald Vale from The University of California at Berkeley and the Howard Hughes Medical Institute, US, deposited initially as a preprint1 and subsequently published in PNAS2 in 2015 thoroughly analyzes the aspects of pre-publication in biology. The author presents as main advantages of preprints the prompt availability of results; the increased scrutiny to which the article is exposed to the entire scientific community rather than two or three referees as in the classic peer review process; dissociation from the prestige of the journal title; and economy of resources. As the main disadvantages, Vale mentions the lack of peer review, which could lead to lower quality articles and information overload. However, the author points out that repositories have filter mechanisms to bar lesser scientific articles. Moreover, the reputation of the author and/or his institution is at stake and would prevent them from posting shoddy papers. About information overload, Vale believes that scientists are already overloaded with information, and it is sufficient to improve methods of literature search and retrieval to reduce it.

According to Vale, for the publication of preprints to become common and successful practice, in principle, it will require that two aspects are met. The first is that the scientific community – especially funding agencies – agrees to recognize preprints as relevant scientific production. The second is that journals accept to consider for publication material that have previously been deposited as preprints.

These aspects had already been assessed by the Open Science Initiative Working Group (OSI) in October 20143, sponsored by UNESCO. The resulting Report focuses on the reform of the current scientific publishing system through detailed analysis of topics such as Open Access, economic models of scientific publication, the evaluation of researchers’ performance and career advancement based on the journals’ prestige.

In a recent post on this blog, Jan Velterop4 takes up the topic of the scholarly publishing system reform through two controversial issues that are currently being discussed, the Sci-Hub website and hybrid journals. According to Velterop, the risk of both for scientific communication is not at their unethical aspect, but rather the fact that they prevent scientific publication to evolve according to the demands of modern scientific community.

The New York Times published on March 15 in its Science section5 an article on the ASAP Bio initiative, stating that Carol Greider of Johns Hopkins University, US, became the third biologist awarded with the Nobel Prize to publish her findings in an open access repository, bioRxiv, before submitting it to a scientific journal, considered the “official” publication. Through her Twitter account, Dr. Greider celebrates the publication in bioRxiv and inserts in the comment the hashtag #ASAPbio.

The preprint repository bioRxiv was created by the Cold Spring Harbor Laboratory along the same lines as arXiv, a traditional preprint repository in mathematics, physics, astrophysics and computer science, created in 1991 by Paul Ginsparg. Preprint files were considered as examples of “vertical openness” within open access scientific publishing by Adam Smith, rapporteur of the Workshop on Alternative Open Access Publishing Models6,7, or simply AlterOA, a conference that promoted a wide discussion on the future of Open Access in the European Union in October 2015.

BioRxiv is a relevant and timely initiative created three years ago, and with the support of scientists as Carol Greider, it is expected to grow and achieve the status of its predecessor arXiv. For now, however, it recorded last year 1,771 deposited articles, against millions published in traditional biomedical journals.

Since the support shown to bioRxiv during ASAP Bio, researchers are increasing the number of deposited articles. In the first quarter of 2016 (until March 18), the repository recorded 673 documents, nearly a third of the total articles deposited in 2015. And with the dissemination and support it has received, not only from renowned scientists, but also of young researchers, it is expected to increase further. Stephen Floor, a molecular biologist at the University of California, Berkeley, USA, tweeted “One need experience the liberating feeling of immediately communicating your results by preprint once to be hooked.” Steve Shea, a neuroscientist at Cold Spring Harbor Laboratory stated on his microblog “Our new paper. It languishes in review for 1.5 y, but u can read now and comment”, referring to the free access to their article recently filed in bioRxiv.

Besides the aspect of publication speed – and consequent immediate attribution of authorship – another factor motivates scientists to deposit their articles initially in preprint repositories, which is the concept of science as a public good. Research is largely funded by public resources which come from taxes paid by everyone. There is nothing fairer than reciprocate by providing the results as soon as possible in open access on the Internet. Harold Varmus, another Nobel awarded researcher, former director of the NIH, historical supporter of Open Access and one of ASAP Bio organizers, said at a conference that was widely twitted “Varmus: conversations should also think about science as public good. Preprints can be good for careers…” and “we also must fulfill our contract to the public who supports our ability to do research.”

However, researchers, especially those at the beginning of their careers, are reluctant to deposit their articles in preprint repositories for fear that by doing so they are potentially decreasing the chance – already small – to have their papers accepted for publication in leading journals such as Nature, Cell or Science. The first two journals adopt as policy treating preprints with the same priority as not pre-published manuscripts. Others, however, do not consider preprints at all and some, such as Cell, advise authors who wish to deposit preprints to previously consult the journal. Since publications in high profile journals can define a researcher’s career, many of them prefer not to risk this possibility by publishing preprints.

In fact, many researchers are divided between the advantages of having their results quickly published online and the advantages of traditional publishing, including peer review, that leads to the improvement of the manuscript and brings recognition associated with the journal prestige. Another Nobel awarded scientist, Randy Schekman of University of California, Berkeley, US, and editor of eLife received the following comment tweeted by a colleague “Schekman reinforces importance of peer review to vet + improve papers and the importance of our role as reviewers #ASAPbio“.

Emergencies in public health such as H1N1 flu epidemics of in 2009, Ebola in 2014 and current Zika virus outbreak led journals to make freely available articles previously beyond paywall to facilitate and promote the work of researchers around the world in finding diagnoses tests, treatments and vaccines. The rapid proliferation of Zika virus outbreaks, initially in the Americas, and now spreading to every continent, lead many journals to declare that they will not penalize researchers who published preprints before submitting their articles. The reaction of scientists was to question why draw a line at Zika virus and not extend the benefit to all?

The determination to make scientific articles freely accessible to everyone has led a researcher in Kazakhstan to pirating subscription scholarly papers and make them available online at Sci-Hub. Researchers speculated that if preprints were the rule, there would be no need to pirate articles. Richard Sever, responsible for bioRxiv server at Cold Spring Harbor Laboratory shared on his Twitter account: “24-48 hr to post on bioRxiv. Anyone in the world with a computer can read it. Just sayin’”

Proponents of classic publishing system argue against preprints claiming that are detrimental to quality science. Emilie Marcus, editor at Cell, reported at ASAP Bio conference that in conversation with over 100 scientists editors of the renowned journal found that what drives researchers to deposit preprints is primarily to ensure the authorship of the discovery and the longing to do it could compromise the quality of the work.

Preprint supporters counter argue that researchers have a reputation to uphold to and would not publish, even as preprints, poor quality papers. Anyway, articles deposited in bioRxiv, for example, are clearly marked to indicate that “contain information that has not yet accepted or endorsed by the medical and scientific community.” Any researcher is aware, too, that there are numerous peer reviewed articles demonstrably flawed, and for many, post-publication peer review would be a more accurate and fair way to exert quality control.

In fact, scientists do not intend to break with the traditional system of scientific publishing through preprints, they just want both to co-exist. Others go further, as the Dean of Harvard Medical School, US, Jeffrey S. Flier, stating that disturbing scholarly publication can be good for science. He wrote on his Twitter “Will preprints disrupt bioscience publishing? Perhaps they should. Disruption is needed, for many reasons.”

Some researchers, however, do not see with good eyes a competition between journals and preprints. If university libraries drop out journal subscriptions on behalf of preprints, journals, in retaliation, may revoke their permission to use them, forcing scientists to make a difficult choice.

The preprints movement may depend on another movement started by biologists themselves, the Declaration on Research Assessment (DORA), signed in 2012, which recommends not using the impact factor to evaluate researchers for hiring and career promotion8. ASAP Bio advocates claim that a cultural change is needed in order to evaluate publications, based on the essence of the content and not where they were published. According to Michael Eisen, an ASAP Bio advocate, this discussion is more than opportune, “it’s pretty amazing that it took 20 years for ‘scientists should post their work on the Internet’ to not be viewed as radical #ASAPbio“. Everything indicates that this is the direction to go.

Notes

1. VALE, R.D. Accelerating Scientific Publication in Biology. bioRxiv. 2015. DOI: 10.1101/022368. No prelo.

2. VALE, R.D. Accelerating Scientific Publication in Biology. PNAS. 2015, vol. 112, nº 44, pp. 13439-13446. DOI: 10.1073/pnas.1511912112. Available from: http://www.pnas.org/content/112/44/13439

3. THE OPEN SCIENCE INITIATIVE WORKING GROUP. Mapping the Future of Scholarly Publishing. Janeiro 2015. Available from: http://nationalscience.org/wp-content/uploads/2015/02/OSI-report-Feb-2015.pdf

4. VELTEROP, J. On the dangers of SciHub and hybrid journals. SciELO in Perspective. [viewed 27 March 2016]. Available from: http://blog.scielo.org/en/2016/03/22/on-the-dangers-of-scihub-and-hybrid-journals/

5. ARMON, A. Handful of Biologists Went Rogue and Published Directly to Internet. The New York Times. 2016. Available from: http://nyti.ms/22iEqpz

6. Report of the Workshop on Alternative Open Access Publishing Models. European Commission. 2015. Available from: http://ec.europa.eu/digital-agenda/en/news/report-workshop-alternative-open-access-publishing-models

7. NASSI-CALÒ, L. Results of the workshop AlterOA: recommendations for the future of open access. SciELO in Perspective. [viewed 18 March 2016]. Available from: http://blog.scielo.org/en/2016/01/28/results-of-the-workshop-alteroa-recommendations-for-the-future-of-open-access/

8. NASSI-CALÒ, L. Declaration recommends eliminate the use of Impact factor for research evaluation. SciELO in Perspective. [viewed 19 March 2016]. Available from: http://blog.scielo.org/en/2013/07/16/declaration-recommends-eliminate-the-use-of-impact-factor-for-research-evaluation/

References

ARMON, A. Handful of Biologists Went Rogue and Published Directly to Internet. The New York Times. 2016. Available from: http://nyti.ms/22iEqpz

EISEN, M. and VOSSHALL, L.V. Coupling Pre-Prints and Post-Publication Peer Review for Fast, Cheap, Fair, and Effective Science Publishing [Originally published in Michael Eisen’s blog “it is not junk”]. SciELO em Perspectiva. [viewed 18 March 2016]. Available from: http://www.michaeleisen.org/blog/?p=1820

Mapping the Future of Scholarly Publishing. The open science initiative working group. 2015. Available from: http://nationalscience.org/wp-content/uploads/2015/02/OSI-report-Feb-2015.pdf

NASSI-CALÒ, L. Declaration recommends eliminate the use of Impact factor for research evaluation. SciELO in Perspective. [viewed 19 March 2016]. Available from: http://blog.scielo.org/en/2013/07/16/declaration-recommends-eliminate-the-use-of-impact-factor-for-research-evaluation/

NASSI-CALÒ, L. Results of the workshop AlterOA: recommendations for the future of open access. SciELO in Perspective. [viewed 18 March 2016]. Available from: http://blog.scielo.org/en/2016/01/28/results-of-the-workshop-alteroa-recommendations-for-the-future-of-open-access/

PACKER, A., et al. Speeding up research communication: the actions of SciELO. SciELO in Perspective. [viewed 18 March 2016]. Available from: http://blog.scielo.org/en/2016/03/10/speeding-up-research-communication-the-actions-of-scielo/

Report of the Workshop on Alternative Open Access Publishing Models. European Commission. 2015. Available from: http://ec.europa.eu/digital-agenda/en/news/report-workshop-alternative-open-access-publishing-models

VALE, R.D. Accelerating Scientific Publication in Biology. bioRxiv. 2015. DOI: 10.1101/022368. No prelo.

VALE, R.D. Accelerating Scientific Publication in Biology. PNAS. 2015, vol. 112, nº 44, pp. 13439-13446. DOI: 10.1073/pnas.1511912112. Available from: http://www.pnas.org/content/112/44/13439

VELTEROP, J. On the dangers of SciHub and hybrid journals. SciELO in Perspective. [viewed 27 March 2016]. Available from: http://blog.scielo.org/en/2016/03/22/on-the-dangers-of-scihub-and-hybrid-journals/

External Links

arXiv – http://arxiv.org/

ASAP Bio – http://asapbio.org/

bioRxiv – http://biorxiv.org/

Sci Hub – https://sci-hub.io/

 

lilianAbout Lilian Nassi-Calò

Lilian Nassi-Calò studied chemistry at Instituto de Química – USP, holds a doctorate in Biochemistry by the same institution and a post-doctorate as an Alexander von Humboldt fellow in Wuerzburg, Germany. After her studies, she was a professor and researcher at IQ-USP. She also worked as an industrial chemist and presently she is Coordinator of Scientific Communication at BIREME/PAHO/WHO and a collaborator of SciELO.

 

Translated from the original in portuguese by Lilian Nassi-Calò.

 

How to cite this post [ISO 690/2010]:

NASSI-CALÒ, L. From the NY Times: Biologists went rogue and publish directly on the Internet [online]. SciELO in Perspective, 2016 [viewed ]. Available from: http://blog.scielo.org/en/2016/04/07/from-the-ny-times-biologists-went-rogue-and-publish-directly-on-the-internet/

 

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