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Speed reading

The use of preprints has been well established in physical science research for decades. Is it time for the plant sciences to also embrace the format?

There has been a lot of interesting work reported in plant biology this year. “Pollinator foraging flexibility and coexistence of competing plants”1, “Chloroplast genome yields unusual seven-cluster structure C”2, “Perennial life-histories and demographic advantages may play contradictory roles in the evolution of plant mating systems”3, “Developmental and phenotypic plasticity of Arabidopsis thaliana accessions across an ambient temperature range”4, “The potato NLR immune receptor R3a does not contain non-canonical integrated domains”5; the list grows daily. You may see no obvious connection between these pieces of work, but a glance at the reference list below will show that they have all been presented on preprint servers instead of, or at least before, publication in conventional journals.

Preprints in science have a long history. Before the invention of the World Wide Web, it was common practice in fields such as astronomy and theoretical physics to circulate reports of recent discoveries by post or hand, both to announce that a particular scientist had made a particular observation and to put out drafts of ideas for constructive criticism by other scientists. During the 1980s, distribution of preprints moved from paper to e-mail, and quickly from individual e-mails to organized e-mailing lists. By 1991, one such list maintained by Joanne Cohn of Princeton's Institute of Advanced Study had become too big to manage manually (almost 200 people in over 20 countries), which prompted Los Alamos's Paul Ginsparg to automate the system (apparently writing the required scripts one evening while attending a workshop). And thus was the first preprint server created, initially called xxx.lanl.gov and now known as arXiv.org.

arXiv mainly holds studies in physical and ‘quantitative’ science, although some of the studies mentioned above can be found there13. A significant feature of arXiv is that articles can be revised and updated, something that is difficult to achieve in formal literature. Much that is originally posted on arXiv is never published elsewhere, as the criticism and commentary that accrues ‘post-publication’ can supply the validation provided by formal peer review in conventional journals.

arXiv is not the only preprint server that was developed in the 1990s, but while popular in physics and mathematics, preprint servers received little support in the life sciences. In 1999, then Director of the National Institutes of Health Harold Varmus proposed e-BioMed, much along the lines of arXiv.org — however, the preprint aspect of the project was dropped and it became PubMed Central, an open-access repository for already published studies. But times and attitudes change, and a number of preprint initiatives in biology have now been established, some as post-publication peer review journals such as F1000Research and PeerJ, while others are ‘pure’ preprint servers such as bioRχiv. Despite the similarity in names, this is not a part of arXiv.org (now run by Cornell University Library), but a separate entity administered by Cold Spring Harbor Laboratory. bioRχiv has an active plant biology section, in which refs 4,5 can be found.

The motivations for scientists to use preprint servers are clear. They provide a swift and relatively simple way to communicate new work. A paper can be uploaded within hours of completion. The format requirements tend to be straightforward and flexible, and there are no revisions needed before publication. The speed of presentation in a preprint server allows precedent over a discovery to be established, removing the fear of being ‘scooped’.

Preprints can be a way to solicit feedback on a study while it can easily be revised, improved or abandoned. This may be a reason to use a preprint in parallel with formal submission to a journal, in order to simultaneously take advantage of both conventional and post-publication peer review to create the best possible version of the study. Finally, a preprint can be a way to ensure that interdisciplinary work reaches disparate communities, such as when a plant biologist published a study involving sophisticated numerical analyses in a high-profile biology journal6, and then also posted it on arXiv.org so that mathematicians, who might have overlooked the work, would be sure to see it7.

However, there are concerns over the perceived status of preprints. In February this year, ASAPbio — an organization formed “to implement a sensible preprint system” — surveyed nearly 400 scientists (31% of whom had never posted a preprint) and found that 59% felt that a major disincentive to submitting a preprint was that some journals would not publish work that had already appeared as a preprint. Respondents’ opinions were evenly distributed along a range between ‘very likely’ and ‘very unlikely’ to submit their best work as a preprint, but this distribution changed dramatically if preprints established the priority of a discovery; if grant agencies and promotion committees saw them as evidence of productivity; and if all journals accepted preprints. In such a world, around 70% of the participants would have been ‘very likely’ to post preprints, and fewer than 10% would still not.

Preprints are a convenient way to present otherwise unpublished data, hypotheses and analysis, and we do not wish to prevent authors from making good use of them. Posting a study on a preprint server will not stop us from considering it for publication in Nature Plants. Of course, a preprint is not yet a substitute for a formally peer-reviewed publication. Rather, we feel they have a similar status to unpublished results or personal communication. It should also be noted that our reference lists are not restricted to formal publications, so preprints can be cited there. However, if the main conclusions of a study rely on data only presented in a preprint, we may ask authors to include those data in the study or provide additional direct support for those conclusions — even if that means repeating the experiments of another group.

We look forward to seeing how the use of preprints develops within the plant sciences, and listening to the diversity of opinion that they provoke.

References

  1. 1

    Revilla, T. A. & Křivan V. Preprint at http://arxiv.org/abs/1602.02569 (2016).

  2. 2

    Sadovsky, M. G., Bondar, E. I., Putintseva, Y. A. & Krutovsky, K. V. Preprint at http://arxiv.org/abs/1604.04398 (2016).

  3. 3

    Abu Awad, D., Tran, V.-C. & Billiard, S. Preprint at http://arxiv.org/abs/1604.06358 (2016).

  4. 4

    Ibanez, C. et al. Preprint at http://dx.doi.org/10.1101/017285 (2016).

  5. 5

    Giannakopoulou, A., Chaparro-Garcia, A. & Kamoun, S. Preprint at http://dx.doi.org/10.1101/056242 (2016).

  6. 6

    Williams, B. J., Johnston, I. G., Covshoff, S. & Hibberd, J. M. eLife 2, e00961 (2013).

    Article  Google Scholar 

  7. 7

    Williams, B. J., Johnston, I. G., Covshoff, S. & Hibberd, J. M. Preprint at http://arxiv.org/abs/1409.4978 (2014).

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Speed reading. Nature Plants 2, 16108 (2016). https://doi.org/10.1038/nplants.2016.108

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