Abstract
The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 693-805 |
| Number of pages | 113 |
| Journal | Journal of the History of Biology |
| Volume | 51 |
| Issue number | 4 |
| DOIs | |
| State | Published - Dec 1 2018 |
Keywords
- Bayh-Dole Act
- Bermuda Principles
- Big science
- Bioinformatics
- Biotechnology
- C. elegans
- Celera Genomics
- Co-production
- Community resource projects
- DNA Databank of Japan (DDBJ)
- DNA sequencing
- Data hoarding
- Data release
- Data sharing
- Databases
- Department of Energy (DOE)
- Ethical Legal and Social Implications (ELSI)
- European Bioinformatics Institute (EBI)
- GenBank
- Gene patenting
- Genetic mapping
- Genetics
- Genome commons
- Genomics
- Human Genome Project (HGP)
- Intellectual property
- Medical genetics
- Model organisms
- Molecular biology
- Moral economy of science
- National Center for Human Genome Research (NCHGR)
- National Human Genome Research Institute (NHGRI)
- National Institutes of Health (NIH)
- Nematode worm
- Open science
- Patents
- Physical mapping
- Post-genomics
- Public domain
- Reference sequence
- Science policy
- Wellcome Trust
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- History and Philosophy of Science
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In: Journal of the History of Biology, Vol. 51, No. 4, 01.12.2018, p. 693-805.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - The Bermuda Triangle
T2 - The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project
AU - Maxson Jones, Kathryn
AU - Ankeny, Rachel A.
AU - Cook-Deegan, Robert
N1 - Funding Information: US National Research Council (of the National Academy of Sciences) US National Science Foundation Office of Biological and Environmental Research (of the DOE) Office of Health and Environmental Research (of the DOE) Online Mendelian Inheritance in Man Oak Ridge National Laboratory Office of Scientific Research and Development Office of Technology Assessment (of the US Congress) Polymerase chain reaction Protein Data Bank (at the Brookhaven National Laboratory) Phil’s revised assembly program Phil’s revised editor Polycystic kidney disease Recombinant DNA Japanese Institute of Physical and Chemical Research Ribonucleic acid German genomic Resource Center (at the MPI in Berlin) Stanford Artificial Intelligence Laboratory Single Chromosome Workshop Single nucleotide polymorphism Japan Science and Technology Agency (also JST) Science and technology studies OR sequence-tagged site (meaning apparent with context) The Institute for Genomic Research University of California at San Francisco Unpublished in Journals and Available in Databases (Stephen Hilgartner’s term) The United Nations Educational, Scientific, and Cultural Organization United States Patent and Trademark Office Union of Soviet Socialist Republics Worm Community System Yeast artificial chromosome Funding Information: of the University of Sydney, Australia (‘‘The Ethos and Effects of Data-Sharing Rules: Examining the History of the ‘Bermuda Principles’ and Their Impact on US 21st Century Science,’’ Rachel A. Ankeny and Robert M. Cook-Deegan, 2011), and the Ewing Marion Kauffman Foundation. The contents of this publication are solely the responsibility of the authors, and do not reflect the views of their funders or employers. The charges associated with making this article open access were funded by an award from the Wellcome Library Open Access Fund. Funding Information: GBF GDB GESTEC HGI HGMP HGMW HGP HGS HHMI HTML HLA HUGO ICRF IHGSC IMB JGI JST KB LANL LLNL LMB MB MBL MIM MIT MPI MRC NCBI NCHGR NCI NHGRI NIH NINDS NLM European Community Ethical, Legal, and Social Implications (of genomics) European Molecular Biology Laboratory Energy Research and Development Administration Expressed sequence tag File transfer protocol Free and Open Source Software The five largest HGP sequencing centers after 1999 (the Sanger Centre, Washington University in St. Louis, the Broad Institute of Harvard and MIT, the DOE Joint Genome Institute, and the Baylor College of Medicine) German Research Centre for Biotechnology (in Braunschweig) Genome Database (at Johns Hopkins University) NIH Genome Science and Technology centers Human Genome Initiative (of the US DOE) Human Genome Mapping Programme (of the UK MRC) Human Genome Mapping Workshop Human Genome Project Human Genome Sciences Howard Hughes Medical Institute HyperText Markup Language Human Leukocyte Antigen Human Genome Organization Imperial Cancer Research Fund (in London) International Human Genome Sequencing Consortium Institute of Molecular Biotechnology (in Jena) Joint Genome Institute (of the DOE) Japan Science and Technology Agency (also STA) Kilobase (or Kb, kb) Los Alamos National Laboratory Lawrence Livermore National Laboratory Laboratory of Molecular Biology (University of Cambridge) Megabase (or Mb, mb) Marine Biological Laboratory (in Woods Hole, MA) Mendelian Inheritance in Man Massachusetts Institute of Technology Max Planck Institut für Molekulare Genetik (in Berlin) UK Medical Research Council US National Center for Biotechnology Information US National Center for Human Genome Research US National Cancer Institute US National Human Genome Research Institute US National Institutes of Health US National Institute of Neurological Disorders and Stroke US National Library of Medicine Funding Information: Various German, French, and Japanese institutions were also represented. The German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) boasted considerable attendance, including Frank Laplace as the administrator for the German human genome program (DHGP) (1996 Bermuda Programme and Participants List). DHGP biologists in attendance included Hans Lehrach, formerly of the ICRF in London, and André Rosenthal, from the Max Planck Institut für Molekulare Genetik (MPI) in Berlin and the Institute of Molecular Biotechnology (IMB) in Jena, respectively (Unterhuber 1995; Rosenthal interview 2011). Jean Weissenbach was a French genetic mapper at Généthon and also the head of the new French national sequencing center, Genoscope, funded by the basic research agency the Centre National de la Recherche Scientifique (CNRS). Masahira Hattori of the University of Tokyo and Naotake Ogasawara of the Nara Institute of Science and Technology were also at this 1996 meeting, funded by the STA (Hattori to KMJ 2012). Yoshiyuki Sakaki of Funding Information: Efforts in Japan, in turn, led the world in other areas of physical mapping, technology development, and sequencing. In 1981, Akiyoshi Wada had secured funding from the Science and Technology Council of Japan through the Science and Technology Agency (STA, or JST [About JST 2009]) for a project called ‘‘Extraction, Analysis, and Synthesis of DNA,’’ which became ‘‘Generic Basic Technologies to Support Cancer Research’’ in 1984 (Cook-Deegan 1994, p. 215). The initiative, closely tied to traditions of robotics and automation in Japan, soon gained industry support, including from Fuji Photo and Hitachi, alongside a headquarters at the elite RIKEN Institute for Physical and Chemical Research in Tsukuba Science City around 1985 (Ibid.).43 The Japanese-US competition in genomics was particularly intense, given the trade tensions between the two nations that had lasted throughout the 1980s. Yet as the leader of the Japanese sequencing projects, Akiyoshi Wada had stimulated international efforts to organize a coordinated human genome project, visiting the US in 1986 to promote such Funding Information: Predictably, the US cohort in Bermuda in 1996 was the largest, followed by the British (Fig. 2; also, 1996 Bermuda Programme and Participants List). The Americans in attendance included James Watson, who had been the inaugural director of the NIH HGP (1996 Wellcome Trust Bermuda Meeting Report); Francis Collins, now the director of the US NCHGR; Aristides Patrinos, the director of the Office of Biological and Environmental Research (OBER) at the DOE; Mark Guyer, the assistant director of the NCHGR and the program officer responsible for grants administration; Jane Peterson, an NIH program officer overseeing sequencing grants; and J. Craig Venter and Mark Adams, both of TIGR in Maryland. Michael Morgan organized and hosted the meeting on the behalf of the Wellcome Trust, and three colleagues from the Trust accompanied him. Sohaila Rastan joined from the MRC, although this British medical research agency—one of several research councils responsible for academic research and development in the UK (e.g., Balmer 1996b, p. 255, n. 4)—would ‘‘not be spending significant amounts of money on production sequencing’’ in the human genome (Guyer to Collins 1996; also, 1996 Wellcome Trust Bermuda Meeting Report). Four scientists, including John Sulston and Jane Rogers, both of whom attended all three Bermuda meetings, attended from the Sanger Centre, meaning that the NIH, the DOE, and the Wellcome Trust all were able to send both extramural grantees and intramural employees as their representatives to the meeting (1996 Bermuda Programme and Participants List; Rogers interview 2012). Funding Information: Most attendees, including our interviewees, saw the 1996 International Strategy Meeting in Bermuda as crucial, enabling the alignment of working priorities and technological strategies (Collins interview 2012; Hillier interview 2012; Morgan and Wallace interview 2012; Rogers interview 2012; Weissenbach interview 2012). The meeting was repeated in 1997 and 1998, in the same location and at the same time of year. Alongside the Wellcome Trust, the funding for later meetings came from the NIH, the DOE, the Japanese Society for the Promotion of Science, and the UK MRC (1997 Bermuda Meeting Report; 1998 Bermuda Meeting Report). The core of the attendance remained relatively stable, though some minor shuffling did occur. Elbert Branscomb of the DOE’s Joint Genome Institute (JGI), founded in 1997, attended the second and third Bermuda meetings, as did the BMBF genomics administrator Ursula Hurtenbach (1997 Bermuda Revised Delegates List; 1998 Bermuda Programme and Provisional Delegates List). The Netherlands’ Gert-Jan van Ommen and Australia’s John Mattick joined the group in 1997 (1997 Bermuda Revised Delegates List); and the Japanese sequencing leader Yoshiyuki Sakaki as well as Fumihiko Kikuchi, from the University of Tokyo and JST, respectively, traveled from Japan in 1998 (1998 Bermuda Programme and Provisional Delegates List). Finally, in this third year of the Bermuda strategy meetings, the weather cleared, enabling the delegates to take scooter rides (1998 Meeting Photographs). Funding Information: Table 1 Summary of Principles Agreed Upon at the First International Strategy Meeting on Human Genome Sequencing (Bermuda, 25–28 February 1996) as reported by HUGO The following principles were endorsed by all participants. These included officers from, and scientists supported by, the Wellcome Trust, the U.K. Medical Research Council, the NIH NCHGR (National Center for Human Genome Research), the DOE (U.S. Department of Energy), the German Human Genome Programme, the European Commission, HUGO (Human Genome Organisation), and the Human Genome Project of Japan. It was noted that some centres may find it difficult to implement these principles because of legal constraints and it was, therefore, important that funding agencies were urged to foster these policies Primary genomic sequence should be in the public domain It was agreed that all human genomic sequence information, generated by centres funded for large-scale human sequencing, should be freely available and in the public domain in order to encourage research and development and to maximise its benefit to society Primary genomic sequence should be rapidly released Sequence assemblies should be released as soon as possible; in some centres, assemblies of greater than 1 Kb would be released automatically on a daily basis Finished annotated sequence should be submitted immediately to the public databases It was agreed that these principles should apply for all human genomic sequence generated by large-scale sequencing centres, funded for the public good, in order to prevent such centres establishing a privileged position in the exploitation and control of human sequence information Coordination In order to promote coordination of activities, it was agreed that large-scale sequencing centres should inform HUGO of their intention to sequence particular regions of the genome. HUGO would present this information on their World Wide Web page and direct users to the Web pages of individual centres for more detailed information regarding the current status of sequencing in specific regions. This mechanism should enable centres to declare their intentions in a general framework while also allowing more detailed interrogation at the local level Funding Information: Stephen Hilgartner has argued that a new ‘‘governing frame’’ materialized as fledgling genome scientists struggled with the exigencies of communication and the territorial politics of smaller-scale, mostly bench-based molecular biology around 1990, precipitating the adoption of new data-sharing policies (Hilgartner 1998, 2004a, 2013, 2017, esp. Chaps. 3–4).9 The necessity of rapid sharing to monitor the HGP’s progress and quality became apparent under these uncharted circumstances, giving rise to what Hilgartner calls the ‘‘‘when’ question’’ regarding the mandated release of HGP-funded data (Hilgartner 2017, Chap. 6, esp. p. 167). Heavy-handed control via policy by the NIH, the US Department of Energy (DOE), and later the UK Wellcome Trust was written into the HGP from the beginning (Hilgartner 2004a, p. 124, 2013, pp. 404–406, 2017), for instance, especially through prescriptive (though often revised) 5-year policy plans (Collins and Galas 1993; Collins 1995, 1998). Deliberate efforts by the HGP’s leadership resulted in policies for the rapid sharing of genetic, physical, and genomic maps, the precursors to sequencing in the HGP, by 1992 (NIH, DOE Guidelines Encourage Sharing of Data, Resources 1993; Hilgartner 1998).10 Whether they were ready for journal publication or not, according to these 1992 policies, all of the HGP’s maps and early sequences funded by the NIH or the DOE were to be deposited into the public biomolecular databases within 6 months of their generation (NIH, DOE Guidelines Encourage Sharing of Data, Resources 1993). Yet in this instance, as Hallam Stevens has demonstrated, while the imperatives of new kinds of biological projects indeed engendered the need for rapid data sharing, scientists and administrators in the HGP were nevertheless relying on technological infrastructures, biomolecular databases, already in place, thereby raising the question of how these technologies were already influencing sharing practices in the life sciences (Stevens 2017). Funding Information: The US HGP continued to gestate through 1986 and 1987. In 1986, the DOE announced its Human Genome Initiative (HGI), allocating $5.3 million to the national laboratory network for resource and technology development (Human Genome Program Report, ii). Also in 1986, the National Research Council (NRC) of the US National Academy of Sciences investigated the feasibility of mapping and sequencing large genomes, with Sydney Brenner representing the viewpoints of the UK mappers and sequencers and Maynard Olson bringing further first-hand experience to the study.33 In 1987, a DOE committee recommended a 15-year project to map and sequence the human genome (Human Genome Program Report, ii). Shortly thereafter, the DOE and the NIH began allocating explicit funding for mapping and sequencing, securing their first official HGP budgets from Congress (Cook-Deegan 1994, pp. 99–106, 142–147, 355–356). Finally, on August 7, 1987, the OTA hosted the workshop that dovetailed from the notorious 1986 CSHL Funding Information: ABI Applied Biosystems ACeDB A C. elegans Data Base AFM Association Franc¸aise contre les Myopathies (French Muscular Dystrophy Association) BAC Bacterial artificial chromosome BBN Bolt, Beranek, and Newman BITNET Because It’s There NETwork, or Because It’s Time NETwork BMBF Bundesministerium für Bildung und Forschung (German Federal Ministry of Education and Research) Complementary DNA Centre d’Etude du Polymorphisme Humain (Center for the Study of Human Polymorphisms, now Foundation Jean-Dausset-CEPH) Centre National de la Recherche Scientifique (French basic research agency) Consensus editor Contiguous DNA sequence Cold Spring Harbor Laboratory DNA Databank of Japan Declaration of Exceptional Circumstances Deutsche Forschungsgemeinschaft (German basic research agency) German Human Genome Project Deutsches Zentrum für Luft-und Raumfahrt (the German Aerospace Centre) Funding Information: Cook-Deegan Archive: ‘‘The Robert Cook-Deegan Human Genome Archive,’’ containing the full scope of archival materials for Cook-Deegan’s The Gene Wars: Science, Politics, and the Human Genome (1994), created with partial support from the Duke University Center for Public Genomics (2004-2016), a Center of Excellence in ELSI Research co-funded by the NHGRI and the DOE (P50-HG-003391). https://bioethics.georgetown.edu/library-materials/digital-collections/robert-cook-deegan-human-genome-archive/. Funding Information: the University of Tokyo directed the Japanese human sequencing efforts focused on chromosomes 4, 14, 16, 21, and 22, with other aspects of the Japanese HGP under the direction of Ken-ichi Matsubara of Osaka University (1996 Wellcome Trust Bermuda Meeting Report). Neither Sakaki nor Matsubara attended the 1996 Bermuda meeting, though they would have been made aware of the proceedings, and remained closely involved with the HGP’s data-sharing politics in the years to come. While the STA’s funding for the HGP focused on human sequencing, additional support for the Japanese HGP came from the Monbusho (the Ministry of Education, Science, and Culture) and the Ministry of Health and Welfare (Ibid.). Funding Information: The HGP began officially in 1990. The initial planning document prepared by the NIH and the DOE, Understanding Our Genetic Inheritance, implicitly acknowledged the NIH as the lead agency, with an NIH-to-DOE funding ratio of 2:1 (pp. 30–37). The National Science Foundation (NSF), National Institute for Standards and Technology, and several Department of Defense research and development agencies were also expected to play less conspicuous roles (Palca 1989). The main goal of the new project was to develop a human reference genome, to be accomplished by a ‘‘multi-phase program’’ in which the initial phase would encompass refining the genetic map, beginning the construction of a physical map, and investing in more accurate, efficient, and affordable DNA sequencing (Understanding Our Genetic Inheritance, pp. 5–6). Partly to encourage data sharing and quality control, a digitally compatible language of ‘‘sequence-tagged Publisher Copyright: © 2018, The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
AB - The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
KW - Bayh-Dole Act
KW - Bermuda Principles
KW - Big science
KW - Bioinformatics
KW - Biotechnology
KW - C. elegans
KW - Celera Genomics
KW - Co-production
KW - Community resource projects
KW - DNA Databank of Japan (DDBJ)
KW - DNA sequencing
KW - Data hoarding
KW - Data release
KW - Data sharing
KW - Databases
KW - Department of Energy (DOE)
KW - Ethical Legal and Social Implications (ELSI)
KW - European Bioinformatics Institute (EBI)
KW - GenBank
KW - Gene patenting
KW - Genetic mapping
KW - Genetics
KW - Genome commons
KW - Genomics
KW - Human Genome Project (HGP)
KW - Intellectual property
KW - Medical genetics
KW - Model organisms
KW - Molecular biology
KW - Moral economy of science
KW - National Center for Human Genome Research (NCHGR)
KW - National Human Genome Research Institute (NHGRI)
KW - National Institutes of Health (NIH)
KW - Nematode worm
KW - Open science
KW - Patents
KW - Physical mapping
KW - Post-genomics
KW - Public domain
KW - Reference sequence
KW - Science policy
KW - Wellcome Trust
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UR - http://www.scopus.com/inward/citedby.url?scp=85055991028&partnerID=8YFLogxK
U2 - 10.1007/s10739-018-9538-7
DO - 10.1007/s10739-018-9538-7
M3 - Article
C2 - 30390178
AN - SCOPUS:85055991028
SN - 0022-5010
VL - 51
SP - 693
EP - 805
JO - Journal of the History of Biology
JF - Journal of the History of Biology
IS - 4
ER -