bioRxiv, the Chan-Zuckerberg Initiative, #ASAPbio, and scooping

Gary McDowell May 13, 2017

The movement in the biological sciences to archive preprints, or complete scientific manuscripts that are uploaded by the authors to a public server, has grown dramatically and successfully since the first ASAPbio meeting I attended at the Howard Hughes Medical Institute in 2016. The growth of preprint archiving in biology over time has been dramatic, with many preprints being archived by a pre-existing server, bioRxiv.

The ASAPbio meeting grew an entire community, and an organization which is a self-professed "scientist-driven initiative" to look at preprints and their use. ASAPbio has advocated for a central service:

"The Wellcome Trust, National Institutes of Health, Medical Research Council (UK), Helmsley Trust, Howard Hughes Medical Institute (HHMI), European Research Council, Simons Foundation, Canadian Institutes for Health Research, Alfred P. Sloan Foundation, Department of Biotechnology (Government of India), Laura and John Arnold Foundation) have released a statement calling for further technology development and the creation of a central resource for preprints, which is being provisionally called the Central Service (CS). The CS will be a database that aggregates preprints from multiple sources, making them easier to read by humans and machines. These features will enable scientists to find new knowledge that can accelerate their research."

To produce this central service, ASAPbio issued a Request for Applications for proposals about what this service could/should look like, and also how governance by the community should work, in an open, transparent and accountable process.

Jessica Polka started working as Director of ASAPbio not very long after I left the ivory windmill so that I could tilt at it, and I have often marvelled at the observation that, even though I am very critical and indeed, sassy, about academia, I appear to have faced less pushback or concern generally than the specific effort targeting preprints. From the very beginning, there were various stakeholders with criticism of preprints from all sides of the publishing and academic world, and for some time I wondered whether preprints would take off due to the concerns many people had. It has often driven me to make the remark that "the preprints issue illustrates why we can't have nice things in biomedicine". Which is essentially the reason for this post.

I knew little to nothing of preprints when I went to the first ASAPbio meeting, but was an immediate convert, as it spoke immediately to my preferred way of doing science - openly, transparently, and inviting critique at all stages to defend and then modify my thesis. I also became a fan of the ASAPbio movement, as all my work revolves around increasing transparency in academia and holding all stakeholders accountable, and a system of community governance and open solicitation again fits my worldview.

Scooping in academia is the act of publishing work that someone else has been working on before they do, and is often described as a (inflated) deliberate phenomenon in academia. This has been a major source of concern around preprints, about whether a preprint establishes priority or not - if I archive a preprint, can someone else publish that work before me and "scoop" me? The issue seems to have been largely resolved, but it is ironic that this concern arose because, I now argue, ASAPbio is itself apparently about to be scooped.

The Chan-Zuckerberg Initative, a Limited Liability Company (LLC) set up by Priscilla Chan and Mark Zuckerberg with the scientific goal of "Helping cure, prevent or manage all diseases in our children’s lifetime" recently announced they are providing an undisclosed sum to Cold Spring Harbor Laboratory, a private non-profit research and educational institution with a publishing arm, which operates bioRxiv, as reported here in "BioRxiv preprint server gets funding from Chan Zuckerberg Initiative", to develop open source software, including manuscript conversion tools, and expand the server.

Shortly after this announcement, Leslie Vosshall, an advisory board member of bioRxiv and influential voice in the preprint movement, issued an open letter to Jessica Polka at ASAPbio calling for the abandonment of a central server as proposed by ASAPbio, and the adoption of bioRvix as the server of choice.

Is this a problem? Maybe not - I am a fan of all these initatives and the people involved; and it largely would achieve the goals of the ASAPbio movement. And certainly Vosshall took care to lay out her continued support for ASAPbio:

But let me lay out to you my unease about this situation, given the reasons I have followed the ASAPbio movement so willingly, and why I am now questioning whether I will continue to strongly advocate for preprints.

The immediate question by many to Vosshall's proposal was whether bioRxiv would transition to open governance, and thus far I have not been satisfied that this will happen. Certainly there have been many tweets to the contrary, including many light-hearted ones by Richard Sever, co-founder of bioRxiv (UPDATE: this tweet is referencing the development of the bioRN preprint server from Elsevier):

As someone who is the Director of an independent non-profit, I find the lack of a clear statement addressing people's concerns deeply unsettling. In the weeks since the announcement no clear and substantial statement has been issued on what the terms of this agreement are, how much it is, what this will entail - and particularly, there seems to be no clear commitment to open governance by the community. I could also assert that Future of Research is free, not for profit and not for sale, but frankly I have no actual control over any of those things - and Future of Research is an *independent* non-profit. My board, theoretically, could at any time decide to change these aspects. I can provide no assurance of that, and this lack of concrete reassurance is what leads me to express my concerns here. So I am unsure how Richard is able to dismiss this so readily as not being an issue. It is an issue. Please, please, address it.

I am surprised somewhat by the general acceptance of this situtation by many of my colleagues, and I suppose it reflects that people are happy to see something happen if they generally agree with it, rather than adhering to the principles of community and scientific need. The community has been going through an open process of assessing its needs and that process has literally stalled - ASAPbio just announced a four-month hiatus in its process until it is clear what is happening, and we are left somewhat in the balance because it looks like the community will allow their decision-making process to be deferred to a particular group, which is something I am disappointed by given that it happens all too often with our scientific process.

The analogy may be too simplistic, because they are completely different models, but imagine a situation similarly arising giving Elsevier a load of funding for its preprint server to do the same thing as bioRxiv. There would be complete uproar in our community. I know, I know, Elsevier is a for-profit publisher and bioRxiv is not for profit (at least, for now - again, I can only verify its future status from a few tweets, although I am sure they do not mean to be so deliberately dismissive of this concern as they surely find it to be completely unfounded). But the general principle to my admittedly inexperienced eyes is the same, and this is where my concern arises. We appear to be moving from an open, community-based decision-making process to handing this deliberation over to what is, certainly for now, a relatively closed group. We are not removing or weakening the gatekeepers to how we publish; we could merely be changing the guard. Because, to take this to its most sinister and cynical conclusion, what we might now expect is that to put your preprints in anywhere that isn't bioRxiv will to have published "in some crap server". We could very easily replicate the impact factor-chasing nonsense with preprint-chasing nonsense, if extreme care is not taken right now. That really must be avoided.

You're probably right, I'm likely over-reacting. To be honest with you, I have no real way of knowing, and in the way things play out in our system, that gives me great concern. I also have no idea if hosting everything at bioRxiv is the best thing scientifically; I was able to participate in and observe the experiment and rigorous scientific discussion at ASAPbio, but now it that decision-making may become more restricted, and closed. This doesn't seem to be figuring as largely in the discussion as I might have hoped, though I have had many conversations recently with people who don't find bioRxiv meets their needs (for non-philosophical reasons) who seem equally frustrated.

What I hope to get from this is a concrete and clear commitment to open governance and community input from bioRxiv in the manner ASAPbio has been doing, if the community decides this is the way to go. I would also like to see genuine recognition from the community that while bioRxiv may suit your needs, it does not suit everyone's, and the community is trying to have a scientific evaluation of preprinting as a community, to figure out current and future needs. 

Let me lay out all of my conflicts: this post is written in entirely a personal capacity, with no prior knowledge or involvement of anyone named or from these groups of organizations, but I am part of the working team at OpenScholar (which works with a preprint server and self-journaling site, The Self-Journals of Science); the Executive Director of Future of Research, which advocates for transparency and accountability in academia; a member of the Steering Committee of Rescuing Biomedical Research (which the original #ASAPbio founders are affiliated with, I have joined however only last month); and a friend and overall fanboy of Jessica Polka, the Director of ASAPbio. I currently find posting preprints to be fun. This post is based on my own impressions and concerns in this situation and I am somewhat melodramatic.