Archive | July, 2013

Thoughts on arXiv and journals

9 Jul

One of the best things about working at Stanford is having lunch outside with my colleagues almost every day. Last Friday it was fairly cold (70 degrees orso, 20°C) but we are a tough bunch and we were sitting outside.

One of the newer people in the lab asked to the others: “do you publish your manuscripts on the arXiv?” What followed was a brief discussion of the pros and cons of publishing on the arXiv before a paper is published in a journal. Here is my summary.

Screen shot 2013-07-09 at 2.49.11 PM

Pros and cons of publishing on the arXiv


1. Science goes faster when we share our results faster.

2. Published papers will be better if more people can give feedback early on.

3. There is some evidence (though not from a randomized trial) that papers get cited more when they are first published on the arXiv.

4. Getting your paper “out there” before it is accepted by a journal takes away some of the stress of getting the paper accepted by a journal. Others can already see what you’ve done, and an arXiv-ed paper looks much better on your CV than “in preparation.”

5. In quantitative biology, the arXiv is cool and you will look like a modern 21st century scientist if you publish on the arXiv. But don’t try to impress a physicist with your new-found arXiv-fondness, because they already used the arXiv before most current graduate students were born. If you go for hip, consider publishing your preprint on Figshare, because they allow you to keep track of traffic, and PeerJ Preprints is another new option.

6. If you’re in evolutionary biology, you can benefit from exposure on Haldane’s Sieve if you publish on arXiv (or another preprint server).


1. The paper may still change a lot and you cannot remove the arXiv-ed version (though you can add a newer version, and I think it is unlikely that anyone looks at an old version).

2. Some journals don’t like to publish arXiv-ed papers, see this list:

3. If many people read the arXiv-ed version, they may not bother reading the improved journal-version.

Honestly, I am not too convinced of these cons.

So should do away with publishing in peer-reviewed journals?

I don’t think so. Despite everything that is wrong with journals, I think they are very useful.
Ask yourself: when was the last time you really took the time to read through a paper by someone you didn’t know?
Right, I think that may have been when you were reviewing a paper! And chances are that you were reviewing that paper because an editor asked you. There is not yet a system – outside of journals – that makes sure that a paper gets read & scrutinized by at least a few people. When I tried to publish a somewhat controversial paper on HIV last year, I was annoyed with the peer review system, because I felt it was unfair to a newby in the field. But without the review system, chances are that my paper would have been ignored entirely. If it wasn’t for journals, how would a person who is not yet known in the field get the attention of the community?

Editors are important hubs in our scientific community

Of course, there are reviewers who do not take their task seriously, and there are scientists who do take time to read papers by unknown scientists even if they are not reviewing, but I bet that both are rather small minorities. I like to review papers, I am happy that my papers get reviewed, and I think that the editors who organize it all are important hubs in our scientific community. We shouldn’t do away with that!