Preprint at work and at work for preprints

A couple of weeks ago I wrote about our experience getting rejected during the review process, at the R1-R2 stage, for novelty reasons. Another group had submitted and published a competing manuscript after our initial submission. This all happened while we had posted the preprint of our manuscript on biorxiv several months prior.  Our story ended well. After some noise the editors reconsidered and invited us to resubmit. You can read the whole story here.

A couple of months have passed since the graceful turn around of PLoS. We were able to address the remaining reviewer’s concerns. So now our manuscript is improved and finally fully approved be the peer review process. You can read the accepted version of the manuscript here, all previous versions here and a short media snipped here. ///In case you are interested in improving crops be intergenus transfer of immune receptors I recommend these papers in wheat, rice and Arabidopsis.///

….this whole story was only possible with PLoS, who actually cares about the community it serves. Imagine a AAAS or Nature group journal, I bet they would have simply swept us aside.

Enough of the background story….Was it worth all the hassle? Do preprints work in my field (of plant biology)? Would I post a preprint of my work again?

Yes it was worth all the hassle. I truly think we were treated unfairly as it simply isn’t good manners to reject a manuscript due to novelty reasons alone during the review process. The journal already engaged you and asked for more. Now it simply drops you like a hot potato?!? No one wants a dirty potato off the floor! Our preprint simply made our case stronger and public.

Yes it was worth all the hassle. Our preprint got over 1500 visits and 500 pdf downloads before publication with PLoS. Doesn’t sound much to you…well it is well more than none while hidden away in a pile of papers of a busy reviewer.

I think it is (very) early days for preprints in plant biology. Several (senior) PIs told me that it doesn’t work, it isn’t good for your career, it hurts early career researchers, the field is too competitive….well that’s their opinion not mine. Others have written good posts of why to support preprints (here, here, here, here)  so I won’t repeat all that jazz here (yet see below). The plant biology community in particular though can only profit from more openness including preprints, post publication peer review (PPPR), public peer review (PPR) and similar new ways of improving the peer review/publication process. I tend to wonder if many of the high profile retractions (here and here) and falsification accusations (here and here) could have been avoided in a more transparent culture. Impossible to tell in hindsight yet well worth striving for in near future. More transparency and openness is really the only way forward…

Yes of course! Every time I have the chance I will post my manuscript on a pre-print server at time of submission. I deem it ready to go public so no reason to hold back! /// I even hope to  get feedback on a preprint someday./// This decisions of course also depends on my co-authors and our journal choice. ///See (not fully up-to-date) policies here. And no in my experience AAAS does not support preprints./// Also the American Society of Plant Biology (ASPB) wasn’t really supportive of preprints up to very recently. Thankfully this has changed due to lobbying efforts of several of its members (including myself) as you can read here and here. ASPB hasn’t publicly announced this change however I hope they follow in the footsteps of other big societies such as American Phytopathological Society (APS), Amercian Society of Microbiology (ASM), and Genetics Society of America (GSA) to only name a few. It is great to see scientific societies listening to their memberships.

Yes preprints work as long as we work for them. It will be great to see preprints fully take of in (plant) biology including pre-publication reviews such as here.  I can only agree with others that the whole publication experience needs to be improved. Researchers should not feel like ‘beggars can’t be choosers’ when it comes to publication and sharing their knowledge. Hidden away peer review might help improve your manuscript in many, but for sure not all cases. It doesn’t appear to be the best way to decide on accept/reject of your manuscript (see also here) and thereby deciding on your future in academia.

ASPB members and Plant Physiology/The Plant Cell authors for pre-prints

///Disclaimer: This is a copy of our request to the American Society of Plant Biology to support pre-prints.///

ASPB members and Plant Physiology/The Plant Cell authors for pre-prints

Based on a recent discussion on twitter we discovered that the American Society for Plant Biology (ASPB) currently discourages preprint deposition on publically available archives such as http://biorxiv.org/, http://arxiv.org/ or https://peerj.com/preprints/. We as engaged members representing a wide variety of plant biologist would like to encourage ASPB to change its stance and allow deposition of a pre-print when submitting to Plant Cell and Plant Physiology. Pre-print compatible policies are quickly becoming the norm at other journals ASPB members publish in, including: Nature Publishing Group, PLOS, PeerJ, Cold Spring Harbor Press, Science, PNAS, eLife, Frontiers journals, EMBO, Development, and Evolution (http://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy). We do not want to be in the position to have to chose between a pre-print and submission to these outstanding community journals.

Potential benefits to the plant science community include:

  • fast dissemination of important new discoveries in the field
  • fast dissemination of work in progress
  • public visibility of successive revised versions of a manuscript
  • feedback during the review process potentially leading to improved manuscripts. (See for example haldanessieve.org)
  • straightforward way to establish precedence

Thanks for considering our request:

If inclined, edit, sign, and distribute widely here.

Is being scooped the flip-side of a pre-print !?! It wasn’t for us with PLoS

Update 01/14, 11 PM, (Late night update while single dad…): The previous title of this blog-post read “Is being scooped the flip-side of a pre-print !?! It was for us.”. However the last night email from PLoS, while I was talking with my co-first author in Israel where it is already morning, made me change the title. To my surprise and with loads of awe and respect PLoS reconsidered their call of rejecting our manuscript based on the novelty issue caused by the publication of a competing manuscript (see details below). Now instead of considering novelty the editors gave us the opportunity to address the remaining reviewers comments within 60 days. AWESOME and OUTSTANDING. We will forge ahead and do so in the weeks to come and resubmit in due time. It is great to see PLoS taking this important issue seriously. Looking forward to read their updated editorial policies on their website soon so in future there won’t be any confusion about pre-prints and being scooped during the review process. Today PLoS improved the publishing landscape once again. That’s what I *love* about PLoS. Way to Go!

Go Pre-Print Go!

Update: A better title might have been -> Posting a preprint before a paper is in press puts you at risk for being scooped.

Update #2, January 07, 2014 ~ 5PM PST: PLoS got in touch and will have a ‘second’ look at the case. That is absolutely something I appreciate about PLoS actually listening to its community. I hope the major outcome of all this is that PLoS openly declares its editorial standards on preprints and (independently) on being ‘scooped’ during the review process. This is especially important for papers that got submitted after the initial PLoS submission date, because no one really knows where papers get passed around.

Let me get this straight right away. I love open science, open access, the idea of pre-prints and doing good reproducible science. Ever since I heard about the concept of pre-prints I started to put my articles on pre-print server, as much as possible, for everyone to enjoy while the manuscript is under review see here, here and here. This means people can actually read the science well before publication, which is often more than 6 months earlier. Also I really like the idea of and PLoS itself having worked with them on open access topics several time. I am also know to be more critical with fiends I like ;).

Here is the story so far in brief.

June 11, 2014 Submission of manuscript to a PLoS journal and deposition on biorxiv.

July 16, 2014 Rejection of manuscript after full review at this particular PLoS journal.

July 25, 2014 Re-submission of manuscript to another PLoS journal. Back to back with another paper of collaborators showing something similar in another plants species. This gets accepted December 4, 2014, also after major revisions.

September 10, 2014 Preliminary acceptance with major revisions within 60 days.

November 16, 2014 Re-submission of majorly revised version. Submission letter indicated that alternative study was published in another journal. (Initial submission August 12, 2014 and acceptance October 28, 2014. Author declare on pubmed that they missed our pre-print study and will add citation in the final print version (here).

December 19, 2014 Rejection of our manuscript based on novelty and one specific experimental request, which we could have addressed within 2-3 weeks if possible (more details below if wanted).

December 20, 2014 Rebuttal of decision. Citing that we had pre-print out and that authors of other competing study omitted our pre-print at time of submission of their paper.

January 07, 2015 Rejection of our rebuttal due to the following editorial practice. I will cite this here straight, because we looked for editorial guidance in regards of pre-prints and competing publications during the review process on the PLoS webpage. Without success!

‘From an editorial perspective, a work would not be considered novel if a similar paper is published before the work is fully accepted for publication. Although we fully understand this is a difficult situation for you and your co-authors, we could not neglect the fact that Lu and associates reported a similar story in a highly regarded, peer-reviewed scientific journal, which reduced both the significance and novelty of your work. We realized that the situation might be a bit tricky with the deposition of your manuscript onto an online pre-print server before the submission of the paper by Lu et al. While PLOS journals are “pre-print friendly”, we do not have a specific policy regarding scooping. Nonetheless, we can assure you that none of the authors in the published paper served as a reviewer for this manuscript and there is no conflict-of-interest issues during the handling of your manuscript by PLOS xxxxxx.’

I am fine with having my paper rejected because reviewers are not satisfied and it is not deemed novel enough at the initial stage of reviewing. That is simply part of the game. Problem here is the missing transparency. PLoS is ‘pre-print friendly’ (here and here) however does not honor submission date*. Of course putting a manuscript on a pre-print server at the point of initial submission exposes you to the risk of being scooped by other folks scrambling to publish their data in time while you in review and revising. Especially in a culture that for now does not ‘honor’ and cite pre-prints.In this case being ‘friendly’ doesn’t really support pre-prints. You can be scooped during the review process anyway.

Will deposit my manuscripts on pre-print servers at time of submission? YES, as much as possible!! I think these are exciting times for biology.

Will I submit to PLoS ‘higher tire’ journals at the same time? NO!! Not without a straight editorial policy on pre-prints and being scooped during the review process.

Update 01/14, 11 PM: Yes with the new and hopefully clear cut editorial policy on pre-prints and being scooped in the review process I will always again submit my paper to PLoS and a pre-print server at the same time. Way to Go!

Update after short twitter discussion. It is not clear if author’s of the competing paper knew about our pre-print. This is only speculative. Main point is #1 they MIGHT have rushed for publication having heard of pre-print or manuscript another way.  #2 journals like PLoS need to get their editorial policies straight about pre-prints and getting scooped during the review process. Honoring submission date will become more important with more pre-prints out.

*Even though only ONE specific additional second round experiment was request. This confirmatory experiment could have been addressed easily. I am willing to post the whole review process and communication without names up here if folks of PLoS don’t mind so you can judge for themselves.