We’ve just submitted our latest paper to the preprint arXiv (you can read more on the arXiv and its history here). We have done this for every paper we’ve submitted so far as a group; a list of our papers are here. Such preprint archiving is not very common in biology, but is in some other academic communities (notably physics, where the arXiv was established). It is great to see a larger number of quantitative population genetics papers appearing there, hopefully that trend will continue.
Having papers on the arXiv has been a uniformly positive experience:
1) It is great getting comments -from a broad range of people- that you can act on. For example, at least one department is holding a journal club on one of our arXived papers.
2) It is a permanently free copy of our papers. These are available as soon as we’ve written them, instead of after a year (or multi-year) wait that can accompany some iterations of the review process.
3) It is really nice to send someone a manuscript and not have to tell them to keep it to themselves, which always seemed slightly silly to me.
4) People can cite our papers and write blog posts about our papers, e.g. as people have done about our latest paper (Blog posts: here, here, here and here). I’ll hopefully write one shortly about it.
5) It is fun that previous versions of our papers are available (often corresponding to previous journal submissions). That allows people to look back on previous versions and see how our arguments have changed in response to criticism and review. I suspect no one will care to do so with our articles, but it would be great if we could look back at the different versions of now famous articles.
I’m sure there are a tonne of other reasons, but these are the ones that spring to mind.
I, and I’m sure other people, have worried about being scooped and beaten to publication due our arXived papers. But really this is silly as we’ve usually given talks, posters, etc on them at big conferences, so the idea that people somehow don’t know about our work before it appears in print is ridiculous. It is far better to get work out, once you consider it worthy of publication, so it can be read and cited by others.
We will continue to submit our papers there. I’m not sure what we’ll do with papers that don’t fit that criteria of the quantitative biology arXiv, as Nature proceedings shut up shop. But I’m sure we’ll work something out, and we’ll continue to explore other ways to have an open dialog about our work.
[UPDATE] should have noted that the inspiration for this post was seeing discussion by @mbeisen and @joe_pickrell.
[UPDATE 2]
A resource to find what journals permit preprint archiving.
Discussion of ESA’s negative policy on preprint archiving.
[Update 3]
Another biology blog on the joys of ArXiv http://ivory.idyll.org/blog/science-f-yeah.html
gcbias 
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This seems reasonable for people who present unpublished work at conferences, but what about those folks who wait until something is accepted/published before they present it in public? How can you convince them that preprint servers aren’t going to lead to scooping?
Thanks for commenting Rich.
To be honest I really can’t see the downside of submitting to the arXiv [journal and subject permitting] once you submit a paper. My point about being scooped was mainly to vocalize [or what ever the blog equivalent is] my secret worry and say how silly it is.
We all feel that rush to publish when we hear about a competitor working on the same topic, but my sense is that few people deliberately take the guts of another paper and publish it as their own. By putting our work out there in citable form early I feel that we are allowing others to start to build on our ideas and to credit us if they feel it is appropriate. In a paper we are about to submit we cite 4 different arXived preprints. I know I’ve benefited from seeing those preprints, and I’m glad to have a chance to cite them.
People can and do fail to cite even published papers, and frequently borrow ideas without even realizing it (I know I’m always shocked when I reread old papers how much of them I’ve accidentally reinvented or recycled). So I don’t feel like the arXiv is really any different from any journal.
My sense is that we [and certainly I] spend too much time worrying about these issues, when being more open would be of benefit to us all. That’s a set of somewhat random thoughts which don’t really answer your question, but hopefully shed more light on my thinking.
Graham
Graham, I guess by the time you’re submitting the paper, it’s unlikely you’re going to get scooped.
Great post! And thanks for the link. PeerJ is a new open access journal that will also offer preprints in the biological sciences, so it might be a good fit for things that don’t fit in arXiv (that’s where I’m planning on posting my next paper).
The only caveat I see is this: How do (especially print) journals react to the fact that they won’t get exclusive publishing rights? Does pre-publishing on arXiv impact your choice of journals?
You can lookup journals preprint policies here: http://www.sherpa.ac.uk/romeo/index.php. Some do take a hardline (see the link about ESA above). But many journals seem to have a vague policy, perhaps as they are slow to react to these things, which favours doing the right thing academically (i.e. making your article available). Also many high profile journals allow the preprint archives, and below that level there are more choices of journal (so more choice of preprint allowing journals).
Figshare may be another possibility. Although it is slightly different in look and feel than Nature Proceedings it seems like the replacement as it is also owned by Macmillan and appeared right around the time of the shutdown. Looks like its is picking up steam.
http://figshare.com
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