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Advocating for change in the scientific enterprise
Jessica PolkaDirector, ASAPbio
Visiting Scholar, Whitehead InstituteVisiting Fellow, Harvard Medical School
Twitter: @jessicapolka
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
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
Are these structural forces driving us to do the best science possible?
How did we get here?
1945
The Wartime DeficitWith 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 ResearchPublicly 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
Times have changed
9
Academia is not diverse & inclusive enough
Gibbs et al 2014
Age at independence has increased
Grant success rates are going down
Ron Vale, bioRxiv/PNAS 2015
More data now required to publish a paper
Retractions are increasing
https://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/
The environment is “hypercompetitive”
What has changed?
Less money, more people
Research funding grew, then shrank
Center for American Progress
“The doubling”
https://nexus.od.nih.gov/all/2016/05/31/how-many-researchers/
More applicants for research grants (but not more awardees)
And yet, more graduate students are enrolling than ever
Each PI is now graduating more students
Ghaffarzadegan et al 2015NSF data via FASEB
http://www.theatlantic.com/business/archive/2013/02/the-phd-bust-americas-awful-market-for-young-scientists-in-7-charts/273339/
https://loop.nigms.nih.gov/2010/09/measuring-the-scientific-output-and-impact-of-nigms-grants/
But big labs are inefficient
Is biomedical research in trouble?
Solutions
So, what should you & I do?
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
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
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
Communicating with congress
Communicating with congress
NIH Request for Information (RFI)
195 responses!
Zach Chisholm, flickr
Picking a problem
Publication is essential to scientific progress
Adapted from http://asapbio.org/survey
Publishing has changed
Ron Vale, bioRxiv/PNAS 2015
What to do about it?
Problem: fast and open venues are not ‘impactful’ venues
A preprint is a manuscript posted online before journal-organized peer review
Preprints & journals are compatible
Berg et al Science 2016
arXiv: 100,000 manuscripts per year
Preprint servers have existed for 25 years
In Biology
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arXiv (q-bio w/cross-lists, from arxiv.org stats)bioRxiv (from bioRxiv)PeerJ Preprints (bio/med/life)F1000 ResearchThe WinnowerNature Precedings (manuscripts, from search results)Preprints.org (articles/reviews in bio/life/med)figshare (filtered by PrePubMed)
Version 1 | asapbio.org
Preprints are taking off in biology
• Benefits of preprints• Concerns surrounding preprints• Taking action• Recent updates
Lack of access to literature
Current problem
Preprints are immediately available to everyone around
the world
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
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
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 manuscriptthan 2-3 anonymous peer reviewers
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
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
Concern: We can’t be trusted to share our work before peer review
• Reputation is importantFlickr/NASA Goddard
Concern: Journals won’t accept my preprintNature and Nature journals, Science,PNAS,Cell,eLife,J. Cell Biology, EMBO,ASM journalsOxford Press journals,J. Biol. ChemistryMBoCGeneticsJ. Neuroscience…….
Search Wikipedia: list of academic journals by preprint policyContains links to original policies
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
Concern: How should preprints be covered in the media?
Cell phones & cancer Vaccines & autism
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
Posting preprints is a good experience
392 responses. Results at asapbio.org/survey
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)
Moving preprints forward
Scientists
University Promotion Committees
Journals
Funding Agencies
.org
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
Encouraging the productive use of preprints
• Visibility• Network effects • Easy to find
• Standards• Screening• Citation• Preservation, access, licensing
• Policies• Funders• Journals• Institutions
A new kind of marketplace for papersOctober 4, 2016
UCSC & The Rockefeller University job adsSept 26 2016
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
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.
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
Layers
Overlay journals
Annotation layers
Robots are going to steal our jobs (and this is wonderful)
Nanopub.org
Subject, object, predicate
Blog post on scholarly kitchen
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
Thank youASAPbio Co-organizersRon Vale (UCSF)James Fraser (UCSF)Daniel Colόn-Ramos (Yale)Harold Varmus (Cornell)
ASAPbio FundingSimonsSloanArnoldMoore
[email protected], @jessicapolka
Mentors etcPam SilverIain CheesemanASCB
FOR FundingOpen Philanthropy Project
FOR colleaguesKristin KrukenbergSarah MazilliGary McDowellDavid Riglar& many others