My experience publishing scientific research has ranged from receiving valuable critical and constructive feedback to receiving vague, utterly unsubstantiated criticisms. One example, however, stands apart. I want to share it, to spread the word for the good practice.
Last autumn, I measured changes in the composition of the ribosomes that defy our decades-old understand of this structure. Exceptional claims require exceptional evidence; I did my best to test the evidence, and by the time I was ready to submit a manuscript to a peer-reviewed journal, I was too impatient to wait for a few months before I start receiving feedback, before I know what my peers thought about the work. This impatience gave me the final push to try the new preprint server for biology research, bioRxiv. There are very many good idealistic reasons why we should all use it and a few pragmatic fears that inhibit its use. I tried it. I uploaded my manuscript.
My experience exceeded my expectations, by far! I received very constructive and thoughtful feedback from some of the most knowledgeable experts in the field, both by emails and comments on the server. Is not this what publication is supposed to do, to disseminate widely the results to our colleagues and solicit their feedback? BioRxiv worked marvelously in this regard, providing all essential aspects of publishing research results!
How about the stamp of approval of a “prestigious” journal/magazine? We see increasing number of cases undermining the credibility of this stamp. Still, I am far from denying the value of critical peer feedback; it is a very valuable initial screening, and I already got this feedback from bioRxiv. The ultimate stamp of validation is when the work is successfully reproduced by independent researchers and tested again and again over the coming decades. Of course I cannot be 100% certain that my work (or any other recent work) will survive this test of time and no peer-reviewed journal can tell me that, only time can. The essential functions of peer-reviewed journals — providing a wide dissemination and initial feedback from peers — is also provided by bioRxiv only much faster and at no expense. Use it! Let’s make publishing about sharing results and critical feedback, not about journal/magazine politics.
Slavov N., Semrau S., Airoldi E.M., Budnik B., van Oudenaarden A. (2014)
Variable stoichiometry among core ribosomal proteins, bioRxiv, PDF, doi:http://dx.doi.org/10.1101/005553
Slavov Lab Blog 
Nikolai,
This is wonderful! I definitely think this is the way to go. I’ve been thinking of doing the same thing lately with some papers we’ve been struggling to publish (I’m so sick of this, grumble grumble!), but I’ve been a bit scared off because of unclear rules about whether this constitutes “publication” at some journals. Thoughts? I saw on Wikipedia that they have a list of journals and their policies, but it still seems somewhat unclear.
Arjun
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Hi Arjun,
We also had a very positive experience with our pre-print and I would encourage you to give it a go. Although we were not as lucky as Nikolai with regard to feedback from peers (we got only a handful of emails, although they were very helpful), the pre-print gave very good exposure (~1000 views in the first month) and we could see a clear increase in the requests for the tools we present in the paper. Some promotion on the web certainly helped, which should be easy for you with your blog and twitter followers.
As for journal policy the Wikipedia list is a good start, but it is probably a good idea to check directly on the journal website as well. In any case posting requires that you know which journal you want to target, including a second choice. Our work ended up in PNAS and since they have published an editorial clearly stating that pre-prints are ok we did not even mention it during the submission and it never came up later on. I think that is fine when policy is clear, but in other cases you will have to contact the editor before posting.
Another question is what the underlying feeling at the journal is independent from their official policy. My guess is that while progressive publishers such as Elife or PLOS embrace pre-prints, the dinosaurs probably see it as a potential threat to their business model (let’s hope they are right). Nevertheless it is encouraging to see that pre-prints also appear in high profile journals of the second category, including such with murky pre-print policies. Ideally the pre-print metrics will help you with the journal as it could serve as a indication that your work is of interest to the field or a wider audience. Another aspect to consider is that the pre-print might help you with the reviewers. I think most of your colleagues will appreciate that you openly share your results and those that end up reviewing your paper might therefore approach it with a positive attitude.
Lastly I would not underestimate the feel-good factor of doing something you believe in.
Hope that helps.
Fillip
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Arjun,
I have an update from my bioRxiv preprint: It was read by a professor (whom I did not know) who liked it and wrote to me to encourage me to apply for a faculty position in his institution, one of the premier research institutions in USA.
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Hi Arjun,
I had this concern as well. For many good journals (such as PNAS, PLoS, eLife and others) a preprint does not affect adversely publishing in these journals while some other journals are more in the grey zone. My guess is that the latter journals do not want the papers to be published as preprints but they also do not want to be on the wrong side of history and oppose a practice that can clearly benefit science and that is embraced by many progressive scientists. I know of quite a few colleges who posted their papers on the bioRxiv before submission to journals and are very happy with their decision to post on the bioRxiv and the consequences.
For me personally, the big question is whether preprints are visible and widely read. If they are read only by your evil competitors and nobody else, that would be a problem. However, bioRxiv preprints seem to get very good visibility and many preprints get as many views as published papers in mid-tier journals; that is de facto publication in the sense that the results have been shared with the community and are citable even though peer-reviewed journals consider the papers preprints and are willing to take them for review and formal peer-reviewed publication. My experience was particularly positive: thanks to my bioRxiv preprint, I started collaborations and got feedback from some of the most senior professors in the field while my paper is still in the formal peer-review pipe line. Publishing a preprint is also great for collaborating and sharing your results. In fact, it might be one of the most potent antidotes to the hyper secretive cultures that has come to dominate some communities.
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We also had a stellar experience of quickly receiving helpful, detailed reviews for a preprint — ours was in PeerJ Preprints.
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I will upload my latest manuscript to BioRxiv soon. I have no intention of publishing it further than this. It will be “made public” and thus by definition “be published”. I have no wish to change the meanings in the English language. During preparation of the manuscript I have approached many in diverse fields to provide feedback and I have been very happy that they have happily done so. So the manuscript is peer reviewed, just not the way formal journals would like one to do so. I will invite anyone to comment on it as regards methodology, interpretation, and logic goes. But in a manner not anonymously unlike in journal peer review. The manuscript will never have an IF as a result.
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