Why I support BioRxiv and the emerging culture of preprint servers

If you are a biologist living in the world of the 90s, and there are many who do, you still have an urge to send your latest piece of work to one of those ‘glamour’ journals, as they are called now, and if you have done so, you are likely to be in the midst of suffering the slings and arrows of outrageous reviewing or, perhaps, of doing some more experiments in the hope to convince the reviewers –sorry, the editors- that you are a good citizen and that what you said the first time in the manuscript is, as you suggested, important and valid. You will be pinning down the recognition of your work, a fellowship, a grant or, perhaps even tenure, on THAT publication. As a consequence you will be worrying, a bit stressed and, certainly frustrated.

You might be beyond this first stage and, after more than six months and two or three rounds of reviews in one of those journals, a swift rejection on the comments of the ‘third reviewer’ (a shadow like ‘the third man’), worrying about being scooped will be considering what to do next: another of those journals?, something of the second tier?……no, not PLoSONE; not possibly BiologyOpen…that will be a last resort, those journals publish ‘anything’, don’t they? –well, actually, let me tell you they have an average acceptance rate of @60%, and manuscripts always have revision. But in any case, they are not ‘rated’…..they cannot possibly give you tenure, nor an interview, and of course, nobody reads them…..-wrong again because if you live in this world, you are really out of the real one. You obviously do not know that something is happening and that it is happening faster than many of us thought.

The most important thing that is moving is that we, the scientists as a collective, are beginning to realize that things need to change and that we can implement that change. We have realized that, in a manner that is easy to explain with hindsight, we have relinquished what is ours (intellectually and commercially) to a group of people (some of which were at one point our peers and colleagues) who have a very different aim, vision and ethos from ours. We want to publish our findings, share them with the community so that we can progress, get feedback from our peers so that we can improve our knowledge and our work. They want to sell journals and, more importantly, to keep a job behind a desk that also allows many of them to attend conferences to scout for publications, thus enjoying some of the good of what we do without the frustrations of the ‘other (our) side’. These people are called journal editors. Because traditionally we have had a well delineated interaction with them we have forgotten that things evolve and that right now journals and journal editors, together -let us not forget- with an increase in the quantity and the average quality of our output, have as their main job to select what is being published with criteria other than scientific quality. The result of this is a system that, in a more or less obscure manner, delays the publication of our work, imposes significant and absurd burdens on us and, basically, grinds us down. This feeds back on the Science which, as a result, is dumbed down and becomes tailored to the tastes and demands of journals and journal editors. In fact we are told all the time by those ‘glamour’ journals that a publication is an interaction between the editors, the reviewers and the scientists (read the somewhat amusing and worrying viewpoint of a Cell editor here (http://bit.ly/187zMkD). The journals see it as an equal contribution from each constituency! Many of us do not agree.

The result of this, as most of us know, is a system that is grinding to a halt, in which papers go through lengthy slow reviewing processes that tinker with their content or move from one journal to another with increasing frustration and desperation from the authors. That the papers improve in this process has less to do with the journals than with the fact that we continue to work on them because it is what we do. In parallel, young people, often the best, do not want to stay in Science and the fabric of our trade changes and selects for a new kind of person who works in a different manner. But there is an alternative world and what is happening is that this world is being chiselled out, fast and if we all work on it, the landscape will change, we shall regain control over what we do and this will be for the better.

You might have noticed that there are developments, with a basis on the Web. You SHOULD be aware of the discussions on Open Access publication and of San Francisco DORA. You might be aware of the existence of Blogs and Twitter, and if you are not you ought to because here we have a voice and one that is growing louder. It is here where you feel the sound of something coming up, of a different way of thinking about doing and reporting Science. It is too early to know whether it is better than what we have, or even what shape and form will it have but it is different and deserves a chance. And, what is interesting is that some of its parts have been tried and tested before. Enter BioRxiv (http://biorxiv.org/) a preprint server ran by Cold Spring Harbor (CSH) Press FOR the community of biologists. I support BioRxiv and the reasons for this are given below

It turns out that Physics and Maths, which evolved to some maturity before the 80s and 90s, had developed efficient ways to report their findings. Less dependent on the opinion of ‘modern journal editor” –though of course this is an impossible. Being aware that peer review is important and that peer review is best when it is done in the open, they established a preprint server, arxiv (http://arxiv.org/ and http://en.wikipedia.org/wiki/ArXiv), where you can deposit a manuscript before sending it off for publication in a peer reviewed journal. By posting your work in arxiv, you make it available to the community, open it up for comments and, as you receive a doi, it becomes a citable and searchable object. The preprint can be updated and the comments it receives can be seen and read by everybody. One day you decide your work is ready to be sent to a peer reviewed journal and you do so. Nature and Science (amongst many others) accept papers that have been posted in arxiv. Over the years biologists with an inclination for the quantitative –evolutionary biologists, bioinformaticians, system biologists- have started to publish in arxiv and, indeed, there is a section/category called ‘quantitative biology’. But although asymptotically all Biology is/should be quantitative, there is more to Biology than quantitative biology. There is cell and developmental biology, molecular biology, genetics, biochemistry. In fact, it is clear that these are areas where researchers have not yet caught up with change and need educating in the new ways so that they can be recruited to the future. There are several preprint servers open to Biology (FigShare, PeerJ and F1000Research being some) and you should look at the interesting article on “The case for Open preprints in Biology’ by Desjardins-Proulx et al (http://bit.ly/13jj4b4) and consider the pros and cons of this culture. It is with all this in mind that BioRxiv is born. On the notion that arxiv is not going to expand to other categories of Biology, CSH Press decided to launch BioRxiv, with arxiv as a model, and the aim of expanding the preprint culture to molecular and cell biologists. Now, yes….wait a moment, don’t throw all the questions at the same time. I shall address what I feel are the most important ones and the hope that you will join this enterprise, and let you make up your mind about the project.

1. The first and most obvious question is that if there is arxiv, why have BioRxiv? Why don’t we submit our papers to arxiv? It is clear, though I agree that it has not been explicitly stated, that arxiv is not going to expand its categories beyond ‘quantitative biology’ and therefore it is a good thing to have a home for the rest of Biology. It is in this regard that it is important to notice that Paul Ginsparg, founder of arxiv, is in the advisory board of BioRxiv. While it is true that names on such boards do not mean much (not difficult to find interesting conflicts in members of many such boards of many journals), the fact that he is arxiv says, in one way or another, that he endorses BioRxiv.

Also, it is important to realize that while CSH Press is indeed a publisher, it does its job within the context of an institution that has served Biology enormously well over the years and I, like others, see this as another contribution to the field and one that is prescient. This leads me to the second point. Indeed I am sure that BioRxiv does not grow out of thin air and that CSH Press is and will be subsidizing the project.

I do not see BioRxiv as fragmentary but as an attempt to reach to a significant constituency of biologists that we need on board to effect progress.

2. There have been some voices making the reasonable point that a commercial publisher, which is not Open Access, should not be doing something like this, that after a free run under a well known commercial name, once the community is hooked, they will charge and, in the long run, CSH will make money out of this. In some way this is the model of PeerJ or F1000Research –though the costs are very modest-. To this I say, let us wait and see. I want to believe that CSH Press will work on the arxiv model rather than a commercial one, and I do for two reasons. The first one because I do not think that this is in their books. The second one because even if this is in their minds, things are moving fast and by the time they would try to do this, the game will have caught up with them; they will not be able to. But I genuinely believe that they will not do it and it they do, like many of us, I will be disappointed.

3. What about others? Why BioRxiv and not PeerJ, or F1000Research? Well, you have a choice and this is not bad and, as I have said, in these two there are, already, clear and explicit commercial reasons for their development.

There are other questions but, I do not want to go on more than is necessary here so, allow me to get back to the question at the beginning: why I support the spirit of arxiv/BioRxiv ?

There is one thing very clear to many of us: after the battle of Open Access, the next target of the community should be to improve Peer Review as a way to redress the balance of control over our work and regain some decision making power over our work. The Peer Review issue is large, complex, out of control and with many edges that make quick fixes difficult. It is made more complex by the fact that it is an emergent property of the system, to which we all make a contribution. BioRxiv represents a way to show confidence in our work (as physicists do with arxiv), to shift the emphasis back to the content of research rather than on the presentation and the branding associated with journal names. To put emphasis on the WHAT rather than on the WHERE. Placing your draft (when you deem it ready for this) here will give it a doi and make, effectively, a publication. It will mean that while not the final product, you are ready to state the facts and to receive comments that, in an open manner, could improve the manuscript. Posting your work in BioRxiv will say that you are confident about it.

If journals are smart, they should be able to use this resource and in the long run, they will. In an ideal world, they could use the comments as part of the review process and even fish for papers there. If we are all in it, this is what should happen with time. Like so much, this is in our hands as a community. I have discussed the advantages of preprint servers before, particularly in the context of DORA (http://amapress.gen.cam.ac.uk/?p=1239) and I suggest you read them. There is much to be gained by young researchers here.

One of the reasons for supporting BioRxiv is the one that some people do not like and the one they have used to pan it. It is that by being championed by CSH it makes a call to molecular, cell and developmental biologists who are the more traditional, brand bound and less progressive members of the community. These people know about CSH and they might be more prone to dip their feet into something that is provided to them by someone they know and use. And we need these people because their students and postdocs are the future. They need to know and we need them on board.

This is not a time for utopias but for finding ways to regain control over what we do, how we evaluate and how we present it. There is little doubt that the preprint culture will win. The issue is, as ever, what form we want it to take. The model of arxiv is proven, tested and successful and I see BioRxiv as a way to teach biologists the value of that culture. We have already deposited a manuscript there, and will do the same with more in the future. I encourage you to do the same. If the purpose of a publication is to show what you have done to the community and put it to tests and comments, there is little doubt that arxiv and BioRxiv will help you fulfil that goal. If the purpose is to get the seal of approval of a publisher then, it is a different game….but then, let us not fool ourselves and believe that we are doing science, we are doing a cross between journalism, literature and salesmanship. To worry about the WHERE rather than about the WHAT is to show a lack of confidence which should not be part of the culture of Science.

4 thoughts on “Why I support BioRxiv and the emerging culture of preprint servers

  1. This is a great post and I share many similar sentiments but I wonder why authors should send their work to a traditional journal after posting their work on a repository. You admit that preprints are actual publications and you outline all the benefits that they have over traditional journals so if the “preprint” system is advantageous in all aspects that matter scientifically why should we prop up the old failing system?

    • @Josh Nicholson (can’t seem to reply directly).

      The (part) answer is to be found in the experience of arXiv where pre-prints are works-in-progress – self-admittedly “draft” and open to and inviting criticism. Following revision, the “publication” of the final manuscript provides the definitive article. In other words, the preprint is simply a part of a process. Of course, nothing is final as emerging models of post-publication review are testament, however, like in software, there is still a need to declare a “golden master” even when science continues. This is the cornerstone of publication and although modern communication technology has rendered the idea of “going to press” obsolete, we need markers of confidence or maturity in order to provide some points of fixation (as well as providing “scientific currency” in the true sense. While a pre-print accrues a DOI, it’s content may change – something that, aside from corrigenda, doesn’t typically occur to published work which enters the literature, warts and all (all papers should be written to reflect their inherent imperfection).

      Of course, this may simply be a segue to a different mode of “publication” where documents as immutable objects disappear. But that Brave New World isn’t here yet.

  2. I completely agree with the sentiments you discuss above. Particularly ‘delays the publication of our work, imposes significant and absurd burdens on us and, basically, grinds us down’ coupled with ‘In parallel, young people, often the best, do not want to stay in Science and the fabric of our trade changes and selects for a new kind of person who works in a different manner’. As a young ambitous scientist I am currently considering leaving academic research as the system is getting the better of me.

    If you are interested in some of my thoughts, you can read about them here. This blog post may resonate with your points.

    http://diylifesci.wordpress.com/2013/07/14/quick-wins-rather-than-asking-truely-pertinant-questions/

  3. Pingback: A Bio-Archive for the Future of Publication | John Innes SVC

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