Category Archives: Commentary

We encourage readers to submit “white papers” describing their position on one or more topics relating to preprints to be displayed on the website. Please contact Ron Vale at Ron.Vale -at- ucsf.edu.

Some thoughts on ASAPbio

Angela DePace, Assistant Professor, Department of Systems Biology, Harvard Medical School

I believe strongly in open access (mainly because everyone deserves access to the scientific literature, but also because of the immorality of making large profits from free academic labor and the unsustainability of library subscription prices).  I also believe in open peer review; I strive to write critiques that I would be happy to read to the author in person.  It took me longer than it should have to start signing my reviews, but I recently did, and so far so good. I also think that post publication peer review would be a huge step forward for decreasing publication time and increasing the accuracy of the literature, as it would be a more visible record of vetting by the community rather than a select few.

At this stage in my career I’ve come up with a compromise to accommodate these values while still trying to work within the system enough to effectively recruit people and compete for funding, which I think are the things potentially most affected by where I choose to publish.

Continue reading

Preprints & Scholarly Publishers: A Synergy

GENETICS and G3: Genes|Genomes|Genetics, peer-reviewed, peer-edited journals published by the Genetics Society of America (GSA), are proud to support the posting of preprints. Here, we outline our experience in a draft statement.

Since 2012, in response to requests from members of our community, the GSA Journals have supported the posting of preprints. In 2015, we were among the first to partner with bioRxiv. Authors can submit a manuscript for peer review at GENETICS or G3 while simultaneously submitting the manuscript to bioRxiv as a preprint. As part of a pilot project, it is now possible to submit preprints from bioRxiv directly to our journals for review. Thus, we and other journals are already conducting the type of experiment proposed by ASAPbio. So far, few authors (<8%) opt to post preprints on bioRxiv before their paper is submitted to our journals for review.

Continue reading

Open pre-print peer review: a call for greater transparency in the evaluation of manuscripts

Lachlan Coin, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
Darya Vanichkina, Centenary Institute, University of Sydney, Sydney, Australia
Alicia Oshlack, Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia

Transparency and openness are extremely beneficial for science.  The immediate and open publication of findings via preprint servers results in rapid dissemination of scientific discovery amongst researchers.   However, under the status quo, preprints are peer-reviewed by journals in a manner which is completely non-transparent to the reader;  and are commonly published in a subscription journal.  As a result, only the draft submission is openly available.  The reviews and the authors’ response are locked away forever.  Readers are asked to trust the journals implicit guarantee that each manuscript has gone through the same robust peer-review process.   However, the reliability of the peer-review process at high profile journals is somewhat of  a myth, as is demonstrated by a trend towards a higher retraction index with higher impact factor [1]. This practice of hiding reviews is damaging to scientific progress and to the general trust in the academic publishing system overall, since readers cannot see which aspects of the study were questioned and whether some aspects – which the reader may consider critical  – were ever questioned at all.

Continue reading

Fix the incentive structure and the preprints will follow

David L. Stern
Janelia Research Campus
HHMI

I have been following the discussion about preprints closely over the past few months and I am won over by the arguments that science papers should be made available freely to everyone as soon as authors feel that the work is complete. Posting papers to preprint servers is one good solution; I imagine there are others. (I prefer to call such documents open papers to remove the stigma associated with calling the work “pre” anything.) However, the discussion about the future of open papers has been imbalanced, with too much emphasis on the consequences of open papers for peer review and too little discussion of the fact that scientists are driven to publish in journals because of the existing incentive structure. The CV, and, specifically, journal names (and impact factors, journal reputation, etc.) are used extensively to judge scientists in competitions for jobs, promotions, and grant money. This is the main impediment to widespread adoption of open papers. I have heard many arguments about how it is too hard to change the structure of these competitions and that we should, instead, focus on producing great science in open papers, and let the culture-shift follow. In contrast, I think it is easier to change the incentive structure first; widespread adoption of open-papers will follow, like water flowing downhill.

Continue reading

Open Scholar: Using Existing Infrastructure to Transform Peer Review

Gary McDowell, Future of Research and Tufts University, and Pandelis Perakakis, Mind, Brain and Behaviour Research Centre, University of Granada, Spain

Please address any correspondence to garymcdow@gmail.com and peraka@ugr.es

In reforming the culture of peer review and moving towards a system that embraces the use and recognition of pre-print servers, we are cognizant of the need to avoid re-inventing the wheel, by identifying and using existing infrastructure and initiatives that can assist in furthering this goal.

Open Scholar (http://www.openscholar.org.uk/, @os_soc) is an open, collectively governed organisation of volunteer researchers that was founded to develop concrete alternatives to the problem of journal-dependent scientific evaluation and communication. We identify the problem of journals and publishers not on whether they offer free or paid access to their content, but on the fact that they all treat knowledge as a material resource that accrues value from exclusivity. However, contrary to material goods, the more knowledge is freely shared, the more value it obtains. It is therefore to the benefit of society and science itself that knowledge, in the form of scientific articles, is made available instantly and in all available means. Such a way to disseminate articles also enforces a private and local way to evaluate them, which brings a lot of perverse incentives in scientists’ collective endeavor. Fortunately, the infrastructure already exists to permit the instant sharing  of all research material. Continue reading

bioRxiv: a progress report

John R. Inglis and Richard Sever, Cold Spring Harbor Laboratory
Please address any correspondence to inglis@cshl.edu and sever@cshl.edu

bioRxiv (biorxiv.org) is a not-for-profit, online archiving and distribution service for preprints[1] of research papers in the life sciences. It was launched in November 2013 by Cold Spring Harbor Laboratory, a research and educational institution, and receives financial support from the Laboratory and The Lourie Foundation.  Scientists have shared their work and ideas through the Laboratory’s meetings, courses, and publications for more than eighty years.  bioRxiv extends that mission for the digital age by enabling scientists to make findings immediately available to the research community worldwide and receive feedback on draft manuscripts before submitting them to journals. There is no charge to post or read papers on bioRxiv. Continue reading

ASAPbio and Preprints – A Perspective from a Junior Faculty Member

James Fraser, UCSF

Can we move towards more open and rapid sharing of scientific results without putting younger scientists careers at risk?  Ideally we want evaluation (of candidates for faculty positions, of promotion of Assistant Professors, of graduate students for fellowships, or of grants for funding) to be thorough and based entirely on a careful study of the science. Young scientists are optimistic about more open and transparent evaluation systems. But we are also worried about the pragmatics of careers as the system is in flux.  Will  preprints be helpful to trainees and junior faculty who are in the most fragile situation with regard to publishing and career advancement?  Could preprints even be harmful to young scientists, perhaps making them vulnerable to getting scooped and thus be dangerous?  My experiences as a non-tenured junior faculty have uncovered many positives of preprints.  My relatively new laboratory (my faculty appointment began in 2013) has started using them and experienced many benefits, and we are not turning back.   Our celebrations when a paper is posted on BioRxiv are joyous and dwarf the, often exhausted, feelings we experience when the work is eventually published in traditional venues. Continue reading

Draft Statement Regarding Pre-Posting of Articles

Developed for Discussion at ASAPbio by The Royal Society, PLOS, eLife, and EMBO Press

We are committed to increasing the accessibility of research and ensuring that it is communicated as rapidly as possible. To accelerate this process, we encourage researchers to deposit early versions of articles they intend to submit to a peer-reviewed journal in appropriate subject repositories such as arXiv and bioRxiv. The manuscript submitted to a journal, an earlier draft, or any part thereof may be deposited at any time and made freely available.

Continue reading

What Defines “Priority of Discovery” in the Life Sciences?

Ronald D. Vale1 and Anthony A. Hyman2
1Dept. of Cellular and Molecular Pharmacology, University of California San Francisco and The Howard Hughes Medical Institute, San Francisco, USA
2Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Address correspondence to: vale@ucsf.edu and hyman@mpi-cbg.de

Summary

A scientist’s job is to make a discovery and then broadly disseminate this new knowledge, so as to benefit the scientific mission and society overall.  In exchange for releasing this knowledge, the scientist wishes to be acknowledged for their original contribution.  This pact, which is embodied in the term “priority of discovery”, is crucial to the process, culture and reward system of science. Yet for something so fundamental to the scientific enterprise, the rules behind “priority of discovery” are rarely discussed, written about, or even taught.  Here, we break down  “priority of discovery” into two steps: 1) disclosure, in which the discovery is released from an individual or small group of scientists to the world-wide community, and 2) validation, in which other scientists assess both the accuracy and importance of the work.  Scientific disclosure is a discrete event, although we argue it has different rules and meaning from a public disclosure as defined by patent law.  Acquiring validation is a more complex process that starts with peer review and is followed by an extended period in which the experiments are repeated and the concepts are considered.  Currently, in the life sciences, both of these steps are embodied in publication through a peer-reviewed journal.  However, we propose that biologists could be better served by separating the steps, with the first step of disclosure occurring through a preprint server, followed by a second step of validation occurring through a journal publication or potentially other community-recognized mechanisms that achieve the same goals.  This division of these steps is embedded in the practices of the physics and mathematics communities. We also believe that “priority” is not simply a race for the first time-stamp, but rather that quality plays a critical role in how scientists ultimately judge discoveries. Continue reading

Pre-prints: building a practical guide and Q&As for junior scientists

Samuel L. Díaz-Muñoz
Center for Genomics and Systems Biology and Department of Biology, New York University

Pre-prints of research articles have been proposed as a way to advance scientific progress, establish priority of discovery, and ameliorate some of the current shortcomings of the peer review process. All these traits are intended to accelerate the pace of innovation. Innovation, mostly, but not invariably, is fueled by new researchers with different ideas. However, as academic science has become more competitive, junior researchers have become especially attuned to the power of incentives for career progress, which may not be aligned with increasing the pace of scientific discovery. Continue reading