Advocating for change in the scientific enterprise
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Keynote at the UC Davis Training Program in Molecular & Cellular Biology Retreat on October 21, 2016 at Fallen Leaf Lake, Tahoe. Opinions are my own.
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Advocating for change in the scientific enterprise
- 1. Advocating for change in the scientific enterprise Jessica Polka Director, ASAPbio Visiting Scholar, Whitehead Institute Visiting Fellow, Harvard Medical School Twitter: @jessicapolka
- 2. The ivory tower is not a bubble • Interactions with other scientists can be intensely political • Dependent on public support/funds • Profoundly influenced by policies and infrastructure Daniel Parks/flickr
- 3. The way we do science is driven by social and political incentives What we measure • “Impact” (ie Journal Name/IF) • # of papers • Prestige of institution/mentors What we don’t measure • Reproducibility • Openness/sharing • Mentoring
- 4. Are these structural forces driving us to do the best science possible?
- 5. How did we get here?
- 6. 1945 The Wartime Deficit With mounting demands for scientists both for teaching and for research, we will enter the post-war period with a serious deficit in our trained scientific personnel.….for it takes at least 6 years from college entry to achieve a doctor's degree or its equivalent in science or engineering. WE MUST RENEW OUR SCIENTIFIC TALENT Centers of Basic Research Publicly and privately supported colleges and universities and the endowed research institutes must furnish both the new scientific knowledge and the trained research workers. Each year under this program 6,000 undergraduate scholarships would be made available to high school graduates, and 300 graduate fellowships would be offered to college graduates. The US research enterprise is built on a model of continuous expansion
- 9. 9 Academia is not diverse & inclusive enough Gibbs et al 2014
- 10. Age at independence has increased
- 11. Grant success rates are going down
- 12. Ron Vale, bioRxiv/PNAS 2015 More data now required to publish a paper
- 14. The environment is “hypercompetitive” What has changed? Less money, more people
- 15. Research funding grew, then shrank Center for American Progress “The doubling”
- 16. https://nexus.od.nih.gov/all/2016/05/31/how-many-researchers/ More applicants for research grants (but not more awardees)
- 17. And yet, more graduate students are enrolling than ever
- 18. Each PI is now graduating more students Ghaffarzadegan et al 2015 NSF data via FASEB
- 20. https://loop.nigms.nih.gov/2010/09/measuring-the-scientific-output-and-impact-of-nigms-grants/ But big labs are inefficient
- 21. Is biomedical research in trouble?
- 22. Solutions
- 23. So, what should you & I do?
- 24. Scientific citizenship • Awareness • Discussion • Organizing • Action • Datahound • Drugmonkey • Small Pond Science • Woman of Science • Local groups • Scientific societies • Communicate with congress – CLS, AFS • NIH RFIs • Twitter
- 25. Organizing - Postdocs taking a seat at the table Future of Research (FOR) • ~9 meetings across the US and Canada • Now a Massachusetts non-profit with a full- time Exec Director, Gary McDowell • Developing resources for postdocs (FLSA, etc) and students • Amplifying voices of postdocs through advocacy
- 26. Organizing - Scientific societies • The forum for scientific discussion • Leaders of culture change (see DORA) • Centers for science policy and communication • Interested in modernizing & the capturing the next generation
- 29. NIH Request for Information (RFI)
- 30. 195 responses!
- 31. Zach Chisholm, flickr Picking a problem
- 32. Publication is essential to scientific progress
- 34. Publishing has changed Ron Vale, bioRxiv/PNAS 2015
- 35. What to do about it? Problem: fast and open venues are not ‘impactful’ venues
- 36. A preprint is a manuscript posted online before journal-organized peer review
- 37. Preprints & journals are compatible Berg et al Science 2016
- 38. arXiv: 100,000 manuscripts per year Preprint servers have existed for 25 years In Biology
- 39. 0 100 200 300 400 500 600 700 800 900 1000 Jan-03 Jul-03 Jan-04 Jul-04 Jan-05 Jul-05 Jan-06 Jul-06 Jan-07 Jul-07 Jan-08 Jul-08 Jan-09 Jul-09 Jan-10 Jul-10 Jan-11 Jul-11 Jan-12 Jul-12 Jan-13 Jul-13 Jan-14 Jul-14 Jan-15 Jul-15 Jan-16 Jul-16 figshare (filtered by PrePubMed) Preprints.org (articles/reviews in bio/life/med) Nature Precedings (manuscripts, from search results) The Winnower F1000 Research PeerJ Preprints (bio/med/life) bioRxiv (from bioRxiv) arXiv (q-bio w/cross-lists, from arxiv.org stats) Version 1 | asapbio.org Preprints are taking off in biology
- 40. • Benefits of preprints • Concerns surrounding preprints • Taking action • Recent updates
- 41. Lack of access to literature Current problem Preprints are immediately available to everyone around the world
- 42. Preprints are publicly disclosed work that can be evaluated for a PhD thesis, postdoc positions, fellowships, or jobs. Training periods are long; students/postdocs wait to publish Current problem
- 43. Preprints are public documents that enable committees to see the most recent work of an applicant. Recent work is “invisible” to grant and promotion committees Current problem
- 44. The immediate visibility of preprints enables invitations to meetings, new collaborations, etc. Your most recent work is also invisible to your colleagues Current problem Also more feedback on your manuscript than 2-3 anonymous peer reviewers
- 45. Lack of transparency and length of review creates difficulties for establishing priority of discovery Current problem Preprints have a time stamp and DOI number; public evidence of what work was done when
- 46. Information is being held within laboratories for longer periods of time With preprints, new knowledge is immediately accessible, allowing research overall to advance. Current problem
- 47. Concern: We can’t be trusted to share our work before peer review • Reputation is important Flickr/NASA Goddard
- 48. Concern: Journals won’t accept my preprint Nature and Nature journals, Science, PNAS, Cell, eLife, J. Cell Biology, EMBO, ASM journals Oxford Press journals, J. Biol. Chemistry MBoC Genetics J. Neuroscience ……. Search Wikipedia: list of academic journals by preprint policy Contains links to original policies
- 49. Concern: How can we ensure ethical disclosure of data? Preprint servers should (and already do!): • Screen for human subjects research • Ensure that authors agree to posting • Expect that methods are present and complete
- 50. Concern: How should preprints be covered in the media? Cell phones & cancer Vaccines & autism
- 51. Concern: I’m going to get scooped http://asapbio.org/preprint-info/preprint-faq Paul Ginsparg, founder of arXiv on scooping: “It can’t happen, since arXiv postings are accepted as date-stamped priority claims. Eventually I came to understand that biologists do not use “scoop” in the standard journalistic sense… Instead “scooping” in the context of biology research appears to mean using information or ideas without proper attribution.” http://asapbio.org/drafts/draft1 Draft statement on disclosing & crediting scientific work “As responsible citizens of the scientific community, we...will fairly cite original work presented as a preprint in our own scientific papers, just as we would cite a journal publication. We will acknowledge such work, as appropriate, in our presentations at scientific meetings.” ie: preprints are public but not obviously well-respected
- 52. Posting preprints is a good experience 392 responses. Results at asapbio.org/survey
- 53. Accelerating Science and Publication in biology Feb. 16/17, 2016 at HHMI Headquarters Strong consensus that broader use of preprints could become a valuable addition to the journal system (Organizers: Daniel Colόn-Ramos, Jessica Polka, Harold Varmus, Ron Vale)
- 54. Moving preprints forward Scientists University Promotion Committees Journals Funding Agencies .org
- 55. Encouraging the productive use of preprints • Visibility • Network effects • Easy to find • Standards • Screening • Citation • Preservation, access, licensing • Policies • Funders • Journals • Institutions #ASAPbio ASAPbio Ambassadors
- 56. Encouraging the productive use of preprints • Visibility • Network effects • Easy to find • Standards • Screening • Citation • Preservation, access, licensing • Policies • Funders • Journals • Institutions
- 57. A new kind of marketplace for papers October 4, 2016
- 58. UCSC & The Rockefeller University job ads Sept 26 2016
- 59. In the interests of accelerating scientific discovery, the Biohub will establish a publication policy for open and rapid dissemination of research results: all Investigators will be required to post manuscripts on Arxiv on the date of submission to peer- reviewed journals. https://med.stanford.edu/rmg/funding/chan_zuckerberg.html
- 60. If a scientist wants to cite an interim research product in an NIH application or report, the citation should meet certain standards. These standards might include: •Ensuring the document is preserved, findable, and freely accessible to people and machines •Links to other versions and associate data and resources •Attribution and disclosure of authorship, funding, competing interests, licensing, and other issues used in high-quality scholarly publication •A clear statement that the product is preliminary, and the level of peer-review it has received (if any) Note, NIH does not intend to require awardees to create interim research products.
- 61. Encouraging the productive use of preprints • Visibility • Network effects • Easy to find • Standards • Screening • Citation • Preservation, access, licensing • Policies • Funders • Journals • Institutions Proposing community-governed infrastructure (like PubMed Central) for preprints
- 63. Robots are going to steal our jobs (and this is wonderful) Nanopub.org Subject, object, predicate Blog post on scholarly kitchen
- 64. Only ~6% of articles can be practically reused Total articles (PubMed): 24.5 million articles Free to read (PMC): 4 million articles Open to download/reuse (OA PMC subset): 1.4 million articles
- 65. Thank you ASAPbio Co-organizers Ron Vale (UCSF) James Fraser (UCSF) Daniel Colόn-Ramos (Yale) Harold Varmus (Cornell) ASAPbio Funding Simons Sloan Arnold Moore Jessica.polka@gmail.com, @jessicapolka Mentors etc Pam Silver Iain Cheeseman ASCB FOR Funding Open Philanthropy Project FOR colleagues Kristin Krukenberg Sarah Mazilli Gary McDowell David Riglar & many others