Science Wants to Be Open:If Only We Could Get Out of Its Way

BOSC2012July 12, 2012

Jonathan A. EisenUniversity of California, Davis

@phylogenomics

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Disclosures

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My “Conversion”

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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

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The Letter

We support the establishment of an online public library that would provide the full contents of the published record of research and scholarly discourse in medicine and the life sciences in a freely accessible, fully searchable, interlinked form. Establishment of this public library would vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences.We recognize that the publishers of our scientific journals have a legitimate right to a fair financial return for their role in scientific communication. We believe, however, that the permanent, archival record of scientific research and ideas should neither be owned nor controlled by publishers, but should belong to the public and should be freely available through an international online public library.To encourage the publishers of our journals to support this endeavor, we pledge that, beginning in September 2001, we will publish in, edit or review for, and personally subscribe to only those scholarly and scientific journals that have agreed to grant unrestricted free distribution rights to any and all original research reports that they have published, through PubMed Central and similar online public resources, within 6 months of their initial publication date.

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The Letter

We support the establishment of an online public library that would provide the full contents of the published record of research and scholarly discourse in medicine and the life sciences in a freely accessible, fully searchable, interlinked form. Establishment of this public library would vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences.We recognize that the publishers of our scientific journals have a legitimate right to a fair financial return for their role in scientific communication. We believe, however, that the permanent, archival record of scientific research and ideas should neither be owned nor controlled by publishers, but should belong to the public and should be freely available through an international online public library.To encourage the publishers of our journals to support this endeavor, we pledge that, beginning in September 2001, we will publish in, edit or review for, and personally subscribe to only those scholarly and scientific journals that have agreed to grant unrestricted free distribution rights to any and all original research reports that they have published, through PubMed Central and similar online public resources, within 6 months of their initial publication date.

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J-

Can you get people to sign this and FAX it to me. 1-786-549-0137. Craig andClaires 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

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PLoS After the Letter (2003)

• > 25,000 people signed the letter• Small increase in open access support

• But not enough• So PLoS announced the launch of their own journals•PLoS Biology•PLoS Medicine

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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

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Ft. Lauderdale Agreement

• Feb 2003 meeting in Ft. Lauderdale on “Genome Sequencing Data Release Policies”

• Follow up to the “Bermuda Accord”• Debate about how open to be with data• NHGRI had supported a similar policy to TIGRs

(see http://www.genome.gov/10506537)• Sean Eddy gave a talk that convinced me that

these restrictions we in direct conflict with the whole point of giving money to places to generate the data

• So I did what any scientist should do - some experiments

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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

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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

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Brotherly Love

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Wolbachia in PLoS Biology

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Experiments in Progress …

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

• Then real life intervened

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Lack of Access

• Scientist without access

• Would access have helped?

• Is limiting access useful or needed?

• Goal of much of scientific and medical research is to spread knowledge

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Father’s Day

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OA Publishing

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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

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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

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Open vs. Free

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Search BRCA1 human

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Search BRCA1 human

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Search BRCA1 human

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

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Paid

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BLAST

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BLAST

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BLAST Result

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Blast Result

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

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Blast Result

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

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A network of literature

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A network of literature and data

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A network of literature and data

Free = you can read all the papers

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A network of literature and data

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

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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

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Many Exiting Barriers

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

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

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Other Areas of Open Science

• Open data• Open source software• Open discussion• Open resources• Open review

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Why Can You Do?

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1. Make your public material open

• Making something public? Make it open

• Papers• Data• Software

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• 2. Participate in open discussions post publication

• Post publication review• Blogs• Twitter• Meetings

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3. Consider being more open pre-publication

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

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4. Judge people by their contributions not surrogates

• Hiring• Promotion• Students

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5. Embrace and use open material

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

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6. Work for entities that are open

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7. Do not support closed science

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Disclosures

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