Jonathan Eisen talk for #IDWeek: Facilitating the Spread of Scientific Knowledge via Open Science

1. Facilitating the Spread of Scientific
Knowledge via Open Science
IDWeek 2013
October 3, 2013
Jonathan A. Eisen
University of California, Davis
@phylogenomics
Thursday, October 3, 13

2. Disclosures
Thursday, October 3, 13

3. My “Conversion”
Thursday, October 3, 13

4. Public Library of Science (PLoS)
• Started in 2000 by
•Harold Varmus
•Pat Brown
•Michael Eisen
• First action was to circulate an
open letter on publishing
Thursday, October 3, 13

5. JCan you get people to sign this and FAX it to me.
1-786-549-0137. Craig and
Claire’s sigs would be greatly appreciated.
I assume I can put your name on it, no?
I set up a site http://www.publiclibraryofscience.org
to keep lists of
people who have signed.
-M
Thursday, October 3, 13

6. Me and PLoS
User agrees to
not publish
genome level
analyses
Thursday, October 3, 13
• Joined founding
Editorial Board of
PLoS Biology
• Still not fully
convinced about
need for OA
• Worried more about
push for full “Open
Science”

7. Open Data Experiment
• Unrestricted data
access policy on
Tetrahymena thermophila
• First time done at
TIGR
• Many people
published papers
before we did
• But many more helped
with our paper
1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2 Department
of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass Spectrometry,
York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences, Marquette
University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center for
Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of
America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago,
Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont,
California, United States of America, 8 Department of Biology, University of Texas at San Antonio,
San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University of
Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of Molecular
and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America,
11 Department of Computer Science and Engineering, University of Washington, Seattle,
Washington, United States of America, 12 Department of Cellular Biology, University of Georgia,
Athens, Georgia, United States of America, 13 Department of Biological Sciences, University of
Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology, University of Rochester,
Rochester, New York, United States of America, 15 Canadian Institute for Advanced Research,
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, 16
Department of Genetics, Stanford University, Stanford, California, United States of America, 17
Department of Molecular, Cellular, and Developmental Biology, University of California Santa
Barbara, Santa Barbara, California, United States of America
Thursday, October 3, 13
Thanks for the message about the
genome, that is a nice surprise. Lots of
Bacillus DNA in there unfortunately but
we are going to go wild looking in it.
Patrick

8. Open Access Experiment
WMD - the
Wolbachia of
Male
Destruction
Thursday, October 3, 13
• Had published one paper in an
Open Access journal (Genome
Biology)
• We were working on a paper on
the first Wolbachia genome
• Wolbachia are maternally
transmitted parasites that target
males in many species
• In filarial nematodes appear to
be mutualistic symbionts
• Our paper was being recruited
by Nature and Science

9. Brotherly Love
Thursday, October 3, 13

10. Wolbachia in PLoS Biology
Thursday, October 3, 13

11. Wolbachia in PLoS Biology
• But still unclear to me whether this
Open Access thing was a good idea or
not
Thursday, October 3, 13

12. Thursday, October 3, 13

13. RhoGam
• Supplier
• RhoGAM should be administered within 72 hours of
known or suspected exposure to Rh-positive red
blood cells.
• Wikipedia
• It is given by intramuscular injection as part of
modern routine antenatal care at about 28 weeks of
pregnancy, and within 72 hours after childbirth.[5] It
is also given after antenatal pathological events that
are likely to cause a feto-maternal hemorrhage.[6]
• Question
• What happens if you do it even later?
Thursday, October 3, 13

14. Thursday, October 3, 13

15. Thursday, October 3, 13

16. You can purchase online access to this
article (and all its versions) for a 24hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Thursday, October 3, 13

17. Access Blocked - What Next?
• Bought lots of articles
• Tried to contact experts
• Got friends to get some articles from libraries
• Got more and more pissed off
Thursday, October 3, 13

18. Medical Guesswork
• Wife got Rhogam 11 days after blood exposure
• Other treatments became in part guesswork as
well
• Note, doctors at this time were spectacular
• They even asked for assistance in finding out
answers to some treatment questions
• In theory, the scientific / medical literature could
help ....
Thursday, October 3, 13

19. Baby Lost
• Benjamin Augustin Eisen stillborn August
29, 2003
Thursday, October 3, 13

20. Disclosures
Thursday, October 3, 13

21. A Few Other Stories
Thursday, October 3, 13

22. Father’s Day
Thursday, October 3, 13

23. Thursday, October 3, 13

24. Thursday, October 3, 13

25. Thursday, October 3, 13

26. Thursday, October 3, 13

27. What is Open Science?
Thursday, October 3, 13

28. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
Thursday, October 3, 13

29. Open Access
• Free, immediate access online
Unrestricted distribution and re-use
Author retains rights to attribution
Papers are immediately deposited in a
public online archive, such as PubMed Central
Bethesda Principles, April 2003
Thursday, October 3, 13

30. Open Science
• Papers and presentations
• Data
• Protocols
• Samples
• Software
• Hardware
• Classes and teaching materials
• Communications
Thursday, October 3, 13

31. Open vs. Free
Thursday, October 3, 13

32. Citizen Science
Thursday, October 3, 13

33. Crowdfunding/Crowdsourcing
Thursday, October 3, 13

34. What Can You Do?
Thursday, October 3, 13

35. 1. Make your public material open
• Making something public? Make it open
• Papers
• Data
• Software
Thursday, October 3, 13

36. • 2. Participate in open discussions
post publication
• Post publication review
• Blogs
• Twitter
• Meetings
Thursday, October 3, 13

37. 3. Consider being more open
pre-publication
• Data
• Papers
• Talks
• Software
• Ideas
• Noteboook
Thursday, October 3, 13

38. 4. Judge people by their
contributions not surrogates
• Hiring
• Promotion
• Students
Thursday, October 3, 13

39. 5. Embrace and use open material
• CC licensed figures for talks
• Give credit
• Remix and repurpose
Thursday, October 3, 13

40. 6. Work for entities that are open
Thursday, October 3, 13

41. 7. Do not support closed science
Thursday, October 3, 13

42. Many Exiting Barriers
• Impact factor
• Money raising efforts
• Conservative behaviors
• Red herrings
• Lack of peer review
• Cost of publishing
• Journal copyright protects authors
• Lobbyists
Thursday, October 3, 13

43. Genbank
Thursday, October 3, 13

44. Search BRCA1 human
Thursday, October 3, 13

45. Search BRCA1 human
Thursday, October 3, 13

46. Search BRCA1 human
You can purchase online access to this
article (and all its versions) for a 24hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Thursday, October 3, 13

47. Paid
Thursday, October 3, 13

48. BLAST Result
Thursday, October 3, 13

49. Blast Result
You can purchase online access to this
article (and all its versions) for a 24hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
Thursday, October 3, 13

50. Blast Result
Plus - you are not allowed to share your
alignments with anyone
Thursday, October 3, 13

51. A network of literature and data
Thursday, October 3, 13

52. A network of literature and data
Free = you can read all the papers
Thursday, October 3, 13

53. A network of literature and data
Open = Repurpose and share any
part of your analysis w/ no
restrictions. No lawyers. No fear.
Thursday, October 3, 13

54. Educational Benefits of OA
• No debate about “fair use”
• No need for password’s or logins for
course web sites
• No lawyers have to be involved
• Material from OA publications can be
repackaged for any purpose
Thursday, October 3, 13

55. Disclosures
Thursday, October 3, 13