phdp / article_preprint Goto Github PK

While I would really like to submit to PLOS Biology (its both open access and popular), I'm not sure our paper fits in any of their "Article Types": http://www.plosbiology.org/static/guidelines.action

...the closest is "Community Pages" but it's for societies...

This was just posted to figshare:
http://figshare.com/articles/Data_for_arXiv_submissions_by_subject_and_year/96966

The data makes it pretty clear that biology is way behind. The numbers grow, but from 0% to 1%. The only other section we're behind is finance.

This could be some useful figures and/or a graph for the paper.

Hi @PhDP,
Can you please update my GitHub username from karthikram to karthik in the README? thanks!

I don't think that the cross-pollination argument is going to sell particularly well for a couple of reasons. First, we're basically saying that bio folks did the work, published it, and then because the physicists don't read the relevant literature that the biologists also need to be posting to arXiv to communicate with them. Second, it's not particularly clear how preprints are different in allowing for communication across disciplinary boundaries. Yes, the math and physics folks hang out on arXiv, but what if I post my preprint elsewhere or what if I just published in a physic journal like Physical Review E.

It's not that I don't agree with the main point, it's just that I don't feel it's going to accomplish our main goal of getting biologists more engaged with preprints. So, I'd suggest using the Conclusion to revisit our major themes and discuss some success stories from biology like Titus Brown's recent post.

Again, I'm happy to do the work here, I just wasn't sure that everyone would agree with my vision so I thought we should talk about it first.

http://www.frontiersin.org/computational_neuroscience/10.3389/fncom.2012.00079/abstract

I have several more small revisions but I'll wait till Ethan is finished with his round.

The arXiv section feels quite long compared to the other preprint sections. In some ways this is justified given it's long history ad importance, but it also feels excessively detailed for our purposes. In particular the second paragraph is largely about the details of the submission process, which I think could easily be cut. The third paragraph could be shortened extensively and merged with the final paragraph.

I'm happy to do the editing, I just thought that I'd open this for discussion before doing the work.

Sorry, I only came across this because Ethan and I were discussing version control etc, and he pointed to this repo. Took a look at the article, and the department is listed as "bology", and I'm pretty sure it should be "biology".

BTW, very cool that you guys did this using Github.

This doesn't need to be an in depth exploration, but just quoting some times from the annual editorials in big journals like Ecology, Evolution, etc. should help give some real context. We can then magnify this by pointing out that many papers are submitted to and rejected by several journals (often based primarily on impact) meaning that realized delay in getting the idea out could be 1-2 years (this is probably about right for me personally for first submission to final, on paper, publication). In other words, we're not talking about the literature being weeks or even months behind the cutting edge thought, but probably a year or more.

This paper, like much else written on the subject, focuses on ArXiv and the physics community as the historical example (no worries, putting a astrophysics paper on ArXiv was my introduction to scientific publishing too). But apparently preprints have a long (longer?) history in economics which might deserve a hat-tip too: Paul Krugman eloquently whines about this on his blog

Computer science culture has taken a different tact towards preprints by publishing conference proceedings. don't know much of the detail here but sounds like a similar story, where pressure for faster publishing helped this more preprint-like format become considered more on par with full publication.

KR is supported by NSF DEB-1021553.

POS has had their first successful publication. Here is today's blog post about it:
http://www.peerageofscience.org/public/blog.php?blog=27

Paper section: https://github.com/PhDP/arXiv_paper/blob/master/ms.tex#L105

So far we've been treating this an ecology/evolution issue, but I'm wondering if it doesn't really apply to biology more generally. Certainly none of the folks in my department who do cell & molecular work post preprints and I suspect that this is just as much of a problem in those disciplines. Broadening to Biology more generally will both reach more people and make a better argument for a general journal.

Thoughts?

I love this section. The process behind this manuscript is really cool. However, I don't feel like this section benefits the paper. Part of what we're fighting here is the perception that only weird open science types use preprint servers and this just confirms that suspicion. We also want this piece to be short and to the point so that it accomplishes it's main goal and this is just one more paragraph of text for folks to read.

Should we highlight the process? Absolutely. But I think we're better off doing it in some blog posts to accompany the posting of the ms to arXiv and the publication of the paper.

In clarifying misconceptions, this paper should address the difference between submitting your accepted manuscript to a preprint server, vs. posting your manuscript to the preprint server prior to submission to a journal.

• The Sherpa/Romeo database identifies which publishers will permit a person to post to ArXiv or other servers after acceptance, as determined by the copyright terms of the Journal. (Presumably in order to provide open access to content more than faster dissemination. Still, Sherpa/Romeo database should be mentioned and explained. Folks will wonder why it says Ecology Letters permits preprints on ArXiv).
• This paper seems to focus on journal policies that would invoke the "Ingelfinger Rule", rejecting submissions that appear on ArXiv on the grounds that they have already been published. (Might consider using this term and historical context in the medical community).

Obviously the second case implies the first, but not vice versa.