By Humberto Debat *
(Researcher at IPAVE-CIAP-INTA, eLife and ASAPbio Ambassador)
-From novel peer-review solutions, collaborative manuscript writing, top science in open access journals, and the surge in deposition of preprints – Casey Greene, Randy Schekman and Richard Sever shared their perspectives on the current movement towards open science, and the great opportunities it offers for Latin American researchers.-
“…they have taken the strange resolution to be reasonable…Tomorrow they will be the whole planet. Perhaps what I say is not true, I hope it is prophetic.” Jorge Luis Borges
During the XVI Latin American Congress of Plant Physiology last November in the city of Córdoba, Argentina, a group of scientists from diverse backgrounds gathered to discuss preprints, open access and reproducibility in science. This was the final activity of the meeting, which was simultaneously broadcasted by eLife. The seminar was hosted at the National University of Cordoba, a public free-tuition institution that is over 400 years old. Overall, participants were excited at the impression that the status quo of academic publishing is shifting.
We started by providing a local perspective of science and technology in our region, particularly in Argentina, where we are experiencing a scientific collapse derived from a persistent economic crisis and aggressive government cuts in research budgets. We also introduced some venues that our country has provided to address open access of our scientific outputs such as the National System of Digital Repositories promoted by the former Ministry of Science (now downsized to a Secretariat), which contains over 173,000 open publications from Argentinian researchers. These repositories are integrated in a new portal harboring information from the R&D landscape in Argentina, developed in the context of current government practices encouraging open government. We also highlighted the meager use of preprint servers by our scientists, which might be associated to a limited level of awareness about preprints in general, or the fact that both funding agencies and hiring committees are still not considering these in evaluation.
After an introduction, our first speaker was Casey Greene, an Assistant Professor of Systems Pharmacology and Translational Therapeutics in the Perelman School of Medicine at the University of Pennsylvania, USA, where his team develops deep learning methods that integrate distinct large-scale datasets. Dr. Greene presented a range of projects he has been involved in, such as the biOverlay, which is a peer review overlay for the life sciences, oriented to provide an additional means for preprints to be formally assessed by open reviews. In addition, Dr. Greene introduced the collaborative authoring tool called Manubot developed with his post-doc Daniel Himmelstein, which is a system for writing scholarly manuscripts via GitHub that automates citations, references and versioning of manuscripts using git. Manubot, Dr. Greene said, was employed as a tool to write a multi-author review on Deep Learning, which received outstanding attention from both academics and general media. Questions from the audience included the topic of how Manubot could definitely date a manuscript’s existence through OpenTimestamps, in the context of priority claims, using the Bitcoin blockchain, which generated some feedback on Twitter. In addition, Dr. Greene commented on a study published recently analyzing Sci-Hub and its implications in global access to scientific literature. Further, Dr. Greene was asked to provide some background to an initiative he has supported entitled the Research Parasites Awards, celebrating rigorous secondary data analysis as a key role in the scientific ecosystem, encouraging reproducibility and open science practices. He pointed out that this prize has now been complemented by the Symbiont Award, recognizing exemplars in the good practices of data sharing.
The next speaker was Randy W. Schekman, a cell biologist at the University of California, Berkeley, USA, and a Nobel laureate for his groundbreaking work on cell membrane vesicle trafficking, former editor-in-chief of PNAS, who currently serves as EiC of eLife. Dr. Schekman has championed academic journal publishing reform and the promotion of open access publication. He also spoke passionately against the use of the Journal Impact Factor as a measure to assess scientific contributions and its exploitation by luxury-journals, which discourage replication studies. Dr. Schekman commented that he is one of the signatories of a letter to urge the Argentinian government to preserve its scientific system and prevent an imminent exodus of scientists. His presentation highlighted how eLife as an open access journal is concerned about the quality of the work it publishes, while oblivious about its impact factor. He commented on various actions he has promoted there, including early-career researchers as advisors, novel practices for the peer-review process, and diverse engagements oriented to target the challenges of reproducibility in science. He also discussed specific cases associated with the so called “reproducibility crisis”, such as failed efforts to confirm findings in high-profile scientific journals. When asked how he envisioned scientific publishing in ten years’ time, besides highlighting it was not much time, he suggested that the shift to immediate access and the use of preprints would probably keep its momentum. He pointed out that alternatives to the mostly monopolized closed platforms for peer-review processes should be discussed, which eventually could reduce costs and availability of novel avenues of academic dissemination. Dr. Schekman, after six inspiring and fruitful years leading eLife, will soon step down and will redirect his focus to a Parkinson’s organization.
The final speaker of the event was Dr. Richard Sever, Assistant Director and Executive Editor for CSH Perspectives and CSH Protocols. Cold Spring Harbor (CSH) Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. CSH has advanced the spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology. As a highlight in an editorial published over 14 years ago by Dr. Sever in the Journal of Cell Science, he promoted open access as an online publishing model, joined the HINARI initiative, which gives third-world countries instant free access to the scientific literature and supported a shift away from copyright transfer practices. Dr. Sever is the co-founder of bioRxiv, the most important preprint server in the life sciences. He focused his presentation on this platform, which is growing exponentially and it serves as a hub that connects pre-publication discussion of new results with formally published journal articles. He introduced new initiatives aimed to rethink and improve the peer review process. When asked about how bioRxiv would handle the incremental number of submissions if the trend keeps growing, he responded that the system is prepared and scalable, and as long as the platform maintains its focus in basic screening and leaves peer-review to other avenues, bioRxiv can manage the flow. Dr. Sever was also asked about new forms of rapid scientific dissemination, such as micropublishing, or more wide-ranging platforms as the Peerj Preprints server, which accepts submissions of incomplete versions of articles and he argued that bioRxiv is oriented to the posting of “complete but unpublished manuscripts”. Dr. Sever commented on how bioRxiv is accelerating scientific communication/discovery by quoting a presentation where Stephen Quake reasoned that – if the typical delay of publication is removed, after ten years there would be a fivefold acceleration of scientific discovery. Besides the many benefits associated to the adoption of preprints, Dr. Sever highlighted a general change of publishing culture, which can be observed in a trend of the scientific community of timely dissemination of knowledge, which would accelerate the pace of research advance.
Following the event, the discussion continued on various platforms. Among them, I would like to mention Sarvenaz Sarabipour, a postdoctoral fellow at the Institute for Computational Medicine, Johns Hopkins University, USA, a distinguished biochemist and an ambassador for eLife, who followed the seminar online. Dr. Sarabipour commented: “It was great to hear from the speakers on a number of critical issues affecting researchers today, one of which is open science practices that greatly benefit researchers via exchange of knowledge and skills among nations of all economies. My take on this informative webinar was that:
- How we read and contribute to the scientific literature matters and requires more attention from all researchers in life sciences. Open access resources can spark creativity and collaboration within and among nations.
- Reproducibility is a chronic, complex and enormously time-consuming issue, and addressing it requires action from researchers and funders. Open access publishing options such as preprints can help address the reproducibility challenges that are ongoing in the industry and academic research alike.
- To encourage researchers to publish their manuscripts on open access platforms such as preprint servers prior to journal submission, scoop protection should be offered by all journals.
- More collaboration is required to arrive at a consensus on where and to what detail research methods need to be described to facilitate screening preprints better.”
As a closing, perhaps it is worth emphasizing here one of the most important features of preprints for scientists based in peripheral countries as myself: they provide both free of charge access as well as publishing without cost. Article processing charges and subscription-based access to scientific literature are asymmetrical barriers, which affect more directly the researchers from low income regions. Preprints provide an inclusive avenue for researchers to comply with open access practices – encouraging open science, which is the fundamental basis of science reproducibility. I hope this event and the great speakers, who kindly shared their perspectives, may have served as a means to promote these good practices in our region.
*The author would like to thank Kornelia Korzec for the original idea, helpful comments, and also Steven Burgess for editing of this post.