Junior biomedical scientists and preprints

What’s a preprint?

A preprint is a manuscript in a finished form that has not yet been published in a traditional journal. It is essentially the document that you submit to a traditional journal for peer review, deposited on a server for anyone to access. The practice of publishing preprints is universal in the fields of physics and mathematics since the creation of the ArXiv preprint server in 1991, but the biological sciences have been slower to take up the preprint archiving model^1,2. A biological sciences preprint server, bioRxiv, is already in existence, and well used. At ASAPBio, Paul Ginsparg, founder of ArXiv, gave a keynote talk about the history of ArXiv which you can watch on the video stream. iBiology has also released a video with Youreka Science which explains what preprints are. Preprint publication, it has been proposed, could accelerate the dissemination of work and the pace of discovery³ (also in preprint format!).

What is being asked of the community?

There were many discussions on social media surrounding the ASAPBio meeting and aspects of scientific publishing; so many, in fact, that the original intention of the meeting was in danger of being drowned out in the noise. The focus of this meeting, like this paper, was to convince scientists to submit publications to preprint servers such as bioRxiv, before or at the same time as submission to a traditional journal of choice: adding a small step to the normal publication workflow. The goal of the meeting was to make sure that as many barriers as possible to that process could be removed, at journals, funding agencies and within the culture of biomedicine.

Why will I (as a junior scientist) preprint?

From the perspective of a junior scientist, there are several reasons that have convinced me to deposit my publications as preprints in the future (and, incidentally, have also convinced my current lab to do the same).

What are the reasons not to preprint?

Philosophical reasons given against preprinting generally revolve around: questions of whether they are recognized products or markers of productivity; the possibility of being scooped; and settling the issue of who has priority over a novel discovery.

To these, my simple answer was to talk to a physicist. I happened to see a tenured colleague from the physics department at Tufts on my return and explained what ASAPBio was about. When they asked why biologists don’t use preprints, and I gave the answers above, they replied that those were precisely the reasons they use preprints. In grants and tenure review, people recognize that the publication process is not under your control, but producing finished manuscripts and depositing them on a server, where they can be read, and then letting the publication process take its course is taken as an obvious part of the continuing process of science. In terms of being scooped, the manuscript has a DOI and is publicly available, and my physicist colleague told me they use preprints to explicitly avoid being scooped. In terms of priority of discovery, I have to agree with the view that publishing preprints by itself isn’t going to resolve or cause such disputes, unless the field decides to ignore contextual evidence for work in a scientific discovery. I must declare that establishing priority of discovery is not a personal goal, or certainly not one I am particularly concerned about in science, and so am perhaps not the best person to answer to that point, but there is a commentary piece at ASAPBio that directly addresses this topic.

In more practical terms, not all journals will accept preprints, but the vast majority do, with the exception of Cell Press, who publicly stated that preprints were possible to submit only through a vague, non-transparent process of contacting the editor to discuss the matter, with the caveat that the preprint should not have “been noticed” by the field. That they took this opportunity in front of an audience of junior scientists in particular was very surprising, especially as many of the other high impact factor journals, such as Science, Nature, PNAS, PLoS and others as described here in this list on Wikipedia will accept preprints. Indeed a group of publishers have drafted a statement actively encouraging the use of preprints and one of the commentary pieces for ASAPBio came from Genetics and G3 on the synergy that preprints and traditional publications could create. I will state here again for clarification that although there was an active discussion about post-publication peer review and extending that to the end of journals altogether, that was only one of the many areas of discussion and not the goal of the meeting, despite what might have been the impression.

There was also some discussion about health sciences, and publishing data that may give false hope to patients or be damaging if made publically available prior to peer review. On this point I will simply refer to Stephen Curry’s piece in the Guardian on the Zika virus, and the apparent embrace of open research in that context. We could well ask, why is this not the case for all research, not just for Zika, and recently, Ebola? The consensus at the meeting seemed to be that it was more, not less, important for medical research to be disseminated openly and rapidly. There have however been recent conflicts over the concept of “research parasitism” and data sharing in the medical literature⁸ and the battle for open data in the health sciences is a problem in itself. However I would argue that if you have submitted a piece for publication in a journal, then you are confident of those results and there shouldn’t be any serious harm (or any errors may be spotted more quickly, potentially) in a preprint of the article.

This comes down to a lot of what people seem to fear: which is that the literature will be overwhelmed with junk. David Stern wrote a commentary directly addressing this; essentially, it is very unlikely that people who publish junk will be rewarded for doing so. The peer review process is not perfect – no peer review process, to my eyes, is perfect – but added opportunities for review, dissemination, and replication can surely only benefit the scientific process. In addition, as Stern points out, your name is your brand and if you publish junk, your brand will be associated with junk. I would never (consciously) publish junk just to have a piece available and especially not in such an incredibly open and public format. The risks associated with doing so would be too great compared to depositing work I would stand behind publicly.

What next?

I have told you what I am doing and given my opinion and position after attending the meeting; but this is only to encourage more discussion. I and others, such as Samuel L. Díaz-Muñoz who wrote this commentary on a practical guide for young scientists, and James Fraser who wrote a commentary from the perspective of a junior faculty member, are interested in finding out what our community needs or wants, and hopes or fears about preprints. My impression is that firstly most people have not heard about preprints; my second is that there are some misconceptions about what they (and this meeting) were about. I hope this piece has given some clarification on these points but I am aware of my romantic disposition towards doing my science and am also in an environment and field where I don’t feel that some of the pressures people are most concerned about apply.

I am also not a fan of the current push towards “people not projects” as a model that should define biomedical research. Whilst there can be a place for such models, to help those who thrive in that kind of environment, we are pushing ever further into evaluating science on metrics and backgrounds of people, and looking less and less at the science itself. Preprints can provide evidence of the work and mind of the scientist in a more up-to-date fashion and, divorced from the impact factor of a particular journal, the work itself must be considered.

Ultimately I am excited about increasing the transparency and availability of science; increasing access to my work and enabling more discussion about its implications and improvement; and adding to the products that I can point to as evidence of my scientific endeavors in an attempt to reduce the time spent simply waiting around for publications to come out before applying for jobs and grants. Science is a continuous and reformative process and to me there is a great value in having science openly available for critique as well as having close scrutiny enforced through various models of peer review.