jonathan eisen talk for #idweek: facilitating the spread of scientific knowledge via open science

Facilitating the Spread of Scientific Knowledge via Open Science

IDWeek 2013October 3, 2013

Jonathan A. EisenUniversity of California, Davis

@phylogenomics

Thursday, October 3, 13

Disclosures


My “Conversion”


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


J-

Can you get people to sign this and FAX it to me. 1-786-549-0137. Craig andClaire’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 ofpeople who have signed.

-M


Me and PLoS

• Joined founding Editorial Board of PLoS Biology

• Still not fully convinced about need for OA

• Worried more about push for full “Open Science”User agrees to

not publish genome level

analyses


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

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


Open Access Experiment

• 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

WMD - the Wolbachia of Male Destruction


Brotherly Love


Wolbachia in PLoS Biology


Wolbachia in PLoS Biology

• But still unclear to me whether this Open Access thing was a good idea or not


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?


http://en.wikipedia.org/wiki/Antenatal

http://en.wikipedia.org/wiki/Antenatal

http://en.wikipedia.org/wiki/Rho(D)_Immune_Globulin




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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


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 ....


Baby Lost

• Benjamin Augustin Eisen stillborn August 29, 2003


Disclosures


A Few Other Stories


Father’s Day


What is Open Science?


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


Open Science

• Papers and presentations• Data• Protocols• Samples• Software• Hardware• Classes and teaching materials• Communications


Open vs. Free


Citizen Science


Crowdfunding/Crowdsourcing


What Can You Do?


1. Make your public material open

• Making something public? Make it open

• Papers• Data• Software


• 2. Participate in open discussions post publication

• Post publication review• Blogs• Twitter• Meetings


3. Consider being more open pre-publication

• Data• Papers• Talks• Software• Ideas• Noteboook


4. Judge people by their contributions not surrogates

• Hiring• Promotion• Students


5. Embrace and use open material

• CC licensed figures for talks• Give credit• Remix and repurpose


6. Work for entities that are open


7. Do not support closed science


Many Exiting Barriers

• Impact factor• Money raising efforts• Conservative behaviors• Red herrings

• Lack of peer review• Cost of publishing• Journal copyright protects authors• Lobbyists


Genbank


Search BRCA1 human


Paid


BLAST Result


Blast Result



Blast Result

Plus - you are not allowed to share your alignments with anyone


A network of literature and data



Free = you can read all the papers



Open = Repurpose and share any part of your analysis w/ no restrictions. No lawyers. No fear.


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


Disclosures


jonathan eisen talk for #idweek: facilitating the spread of scientific knowledge via open science

Health & Medicine