Preprint Publication: The Force Awakens or the Revenge of the Undead?

April 5, 2016

Physicists do it, economists do it, but biologists? Not so much. I am talking about publishing on preprint servers which is standard practice for researchers in many disciplines except among biologists who have largely resisted posting their results prior to publication in a scientific journal. That is, until now.

About 10 years ago, I came across arXiv (pronounced Archive), the physics preprint server now hosted by the Cornell University Library. Here physicists who study a different set of very small things from the ones studied by microbiologists post their papers in advance of peer review. At the time, I was working at NIH on the important science policy issue of public access to NIH-funded research publications, and indeed I was struck by the rapid pace that such quick publication allowed and the (relative) collegiality that seemed to reign among physicists. Since then, the arXiv repository has expanded to cover other fields including quantitative biology. Yet many biologists are only just discovering the arXiv repository along with the idea that there is value in preprints. It would be interesting—and possibly transformative—if biologists would adopt the preprint model, posting results for open peer review instead of waiting for publication in a peer-reviewed journal. And that may happen soon, especially given the interest of funding agencies to consider preprints for funding decisions and research evaluation.

How did we get here? There are two main reasons that biologists are increasingly interested in preprints.

First, thanks to the leadership of Richard Sever and John Inglis, Cold Spring Harbor Laboratory Press has developed a dedicated biological sciences repository for preprints, similar to arXiv, under the name of bioRXiv.

Second, a February 2016 meeting of an ad hoc group called ASAPbio at the Howard Hughes Medical Institute headquarters in Chevy Chase, Md., under the leadership of Ron Vale and others gave preprints a big push.

I attended that ASAPbio meeting and led an exciting working group on the perspective of funding agencies toward preprints. The enthusiasm among the 70 or so scientists present was palpable.

Often confounded with preprints, there is another new publishing model, called post-publication review. It is important to distinguish between preprint and post-publication review, because they reflect two different models and pursue two different goals. A preprint is simply the posting of a manuscript on a server like bioRXiv, either before or at the same time that the paper is submitted for peer-reviewed journal publication. People can see the posted article, comment or even conduct a full review of the paper, if they wish. However, a preprint posting does not constitute publication so authors can submit the manuscript to a traditional peer-reviewed journal as original material. Most journals including all ASM journals now accept manuscripts that have already appeared on preprint servers for review. Preprint does not substitute for traditional peer-reviewed journal publication.

The post-publication review model is a different kettle of fish. The Faculty of 1000 has a new post-publication review platform called F1000 Research. The PLoS group is also developing one. In this model, a posted manuscript is reviewed publicly (F1000 commissions public reviewers) where everyone can chime in on the manuscript’s strengths and weaknesses. Once two public reviewers have provided strongly positive reviews, the posted manuscript automatically becomes a publication. It cannot be submitted to another journal since it is now published in F1000 Research, and as such is indexed in PubMed.

This model of post-publication review is intriguing, although it seems somewhat chaotic. I also believe that post-publication review could create a system where it would be difficult to distinguish signal from noise. I am currently not a supporter of this model, because I am convinced that the editors and dedicated reviewers at good peer-reviewed journals, such as the ASM journals, add significant value. At the ASAPbio meeting, I heard significant consensus on the value of preprints while on the post-publication review model, there was significant disagreement.

Also at ASAPbio I heard a lot of discussions about the role of preprints in establishing priority of discovery, with the role of peer-reviewed publications in journals having the function to determine relevance and impact—through peer-review first, and through citations afterwards. The role of preprints in separating these two functions, currently combined in the journal publication, is indeed interesting and articulated very well in a paper by Vale and Hyman.

While establishing priority is very important, it is generally relevant for only a very small fraction of discoveries. There is something else that is very relevant which surprisingly was not discussed at all during the ASAPbio meeting.

I did not hear enough about professional societies in the preprint era. Yet, professional societies are the forums for their disciplines. None of the invited speakers spoke to this perspective and, while I tried to raise it during the discussion, there just wasn’t enough time, and the meeting was not structured to incorporate this essential perspective. Yet for professional societies like ASM, it is critical. Preprint publication could offer exciting opportunities for professional societies, for other nonprofit publishers and, most of all, for scientific vitality. But it could also affect nonprofit publishers in unexpected ways.

Consider this from the ASM vantage point. Our mission is to advance the microbial sciences. If we believe that preprints are so important to advancing science, how can we ignore this innovation in publishing?

Personally I can see important opportunities for ASM in preprints. Scientific communication is undergoing its greatest transformation since the printed scientific journal appeared 350 years ago. Today, scientists communicate through multiple digital communities. The old-time scholarly association formed around a common interest and a common (and slow) journal was the original scientific social network. Today, the landscape looks very different. With Uber, I can order a car right to where I am standing now, with Amazon I can get a delivery to my home tomorrow morning. In our time, scientific interests and cross-disciplinary collaborations don’t stay within neat borders and cannot wait for months or years, since we live in the culture (and the technological means) of here and now. Professional societies like ASM need to provide real value for our members and ultimately for our science, considering our member’s expectations, needs and preferences, in the realm of what is technologically possible and helpful to advance microbial sciences. Because of this, supporting preprint publication should be part of ASM’s value for its members.

I realize that not everyone in the global scientific enterprise is convinced that preprints are a good thing, but I see a wealth of timely information emerging through preprints, catalyzing new experiments, collaborations and insights. I believe that preprints represent a new resource for professional societies to tap, to encourage and to promote.

There has never been a scientific age as exciting nor as quickly evolving as our own, and here at ASM, we are determined to play a significant role in the acceleration of microbial sciences. As ASM’s new Chief Executive Officer, I have some thoughts and I could not be more excited about the future of ASM as the global forum for microbial sciences—both digitally and non!

Author: Stefano Bertuzzi

Stefano Bertuzzi
Stefano Bertuzzi is the CEO of the American Society for Microbiology.