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AN EXAMINATION of CONTINGENCY in SYNTHETIC GENOMICS RESEARCH and IMPLICATIONS for NATIONAL SECURITY By

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AN EXAMINATION of CONTINGENCY in SYNTHETIC GENOMICS RESEARCH and IMPLICATIONS for NATIONAL SECURITY By AN EXAMINATION OF CONTINGENCY IN SYNTHETIC GENOMICS RESEARCH AND IMPLICATIONS FOR NATIONAL SECURITY by Shannon R. Fye-Marnien A Dissertation Submitted to the Graduate Faculty of George Mason University in Partial Fulfillment of The Requirements for the Degree of Doctor of Philosophy Biodefense Committee: Sonia Ben Ouagrham-Gormley, Chair Serguei Popov A. Trevor Thrall Kathleen M. Vogel Gregory Koblentz, Program Director Mark J. Rozell, Dean Date: Fall Semester 2015 George Mason University Fairfax, VA An Examination of Contingency in Synthetic Genomics Research and Implications for National Security A Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at George Mason University by Shannon R. Fye-Marnien Master of Science George Mason University, 2006 Bachelor of Science California State University, Sacramento, 2004 Director: Sonia Ben Ouagrham-Gormley, Chair, Professor Biodefense Program Fall Semester 2015 George Mason University Fairfax, VA Copyright 2015 Shannon R. Fye-Marnien All Rights Reserved ii DEDICATION This dissertation is dedicated to my beloved grandmother, Roberta Corbett Huffman, who is greatly missed. iii ACKNOWLEDGEMENTS This dissertation is the result of the encouragement and insight of many people. First and foremost, I would like to thank my committee members, Sonia Ben Ouagrham- Gormley, Kathleen Vogel, Serguei Popov, and Trevor Thrall, for providing input that has improved this project immensely. I am deeply honored to have worked with each of them. Thanks especially to my committee chair, Sonia Ben Ouagrham-Gormley, for her guidance and for helping me publish some of my research findings in a peer-reviewed journal (Sonia Ben Ouagrham-Gormley and Shannon R. Fye, “Restricted Science,” Frontiers in Public Health 2, no. 158 [2014]). This work would not have been possible without the researchers who allowed me to interview them. Many thanks to all of the people I interviewed, including Dr. John Glass, Dr. Ray Chuang, Dr. Tim Gardner, Dr. Brian Nosek, and several other researchers who wished to remain anonymous: All provided me with extremely valuable information. Thanks to the coworkers who have encouraged me, especially Anton Jareb, Dr. Denise Brown-Anderson, Dr. Steve Charbonneau, Carie Mullins, Elaine Gresham, Phil Smith, Raphael Perrino, Jason Hay, Carissa Christensen, Kathy Schvaneveldt, Dr. Shawn “Froggi” Jackson, and Dr. Jerome Holton. I am also grateful for all of the excellent professors I’ve had over the years whose passion for teaching left a lasting impression on me, especially Dr. Susanne W. Lindgren at California State University, Sacramento. Finally, I’m grateful to my parents, grandparents, husband, and friends for their love and encouragement. iv TABLE OF CONTENTS Page List of Tables ..................................................................................................................... ix List of Figures ..................................................................................................................... x List of Abbreviations ......................................................................................................... xi Abstract ............................................................................................................................. xii Chapter 1 Identifying the Potential Threats of Synthetic Genomics .................................. 1 Overview of Findings ...................................................................................................... 5 Methodology ................................................................................................................... 8 Dissertation Organization .............................................................................................. 11 Chapter 2 Synthetic Biology and Synthetic Genomics: Understanding the Technology, Current Concerns, and Threat-Prevention Policies ........................................................... 13 What are Synthetic Genomics and Synthetic Biology? ................................................ 14 Discourse on Biotechnological Advances and National Security ................................. 27 Technological Determinism ...................................................................................... 35 Inevitability of Nefarious Use ................................................................................... 38 Theoretical Possibilities ............................................................................................. 43 Threat-Mitigation Policies: Restricting Access to Dangerous Pathogens and Associated Genetic Material ............................................................................................................ 46 The Select Agent Rule ............................................................................................... 47 The Australia Group .................................................................................................. 49 Export Administration Regulations ........................................................................... 51 Biological and Toxin Weapons Convention .............................................................. 52 Chemical Weapons Convention ................................................................................ 53 Proposed New Framework to Address the Potential Threats of DNA Synthesis ......... 56 Screening Genetic Sequences .................................................................................... 58 Conducting Institutional Reviews of Synthetic Biology Experiments ...................... 64 Censoring Scientific Literature .................................................................................. 70 v Chapter 3 STS Literature: Evidence of Experimental Contngencies ................................ 73 Contingencies in Life Science Research ....................................................................... 74 Contingencies with PCR ............................................................................................ 74 Contingencies in Oligonucleotide Synthesis ............................................................. 77 Contingencies in Synthetic Genomics ....................................................................... 79 Contingencies in Synthesizing the Poliovirus: An STS Case Study ......................... 84 Contingencies in Synthesizing the phiX Bacteriophage: An STS Case Study .......... 88 The Role of Tacit Knowledge in Experimental Work .................................................. 92 Problems Transferring Tacit Knowledge .................................................................. 94 Methods for Acquiring and Transferring Tacit Knowledge ...................................... 97 Chapter 4 Difficulties Synthesizing Genes: Interviews with Gene Synthesis Firms ..... 106 Methodology ............................................................................................................... 107 Overview of the Gene Synthesis Process .................................................................... 108 Gene Design and Optimization ................................................................................ 109 Oligonucleotide Synthesis ....................................................................................... 110 Gene Assembly ........................................................................................................ 111 Cloning .................................................................................................................... 113 Verification .............................................................................................................. 114 Contingencies in Gene Synthesis ................................................................................ 116 Gene Design and Optimization ................................................................................ 117 Oligonucleotide Synthesis ....................................................................................... 118 Gene Assembly ........................................................................................................ 119 Cloning .................................................................................................................... 126 Verification .............................................................................................................. 127 Summary of Difficulties .......................................................................................... 131 Resolving Contingencies ............................................................................................. 132 Consulting SOPs ...................................................................................................... 132 Transferring Problem Sequences to More Experienced Researchers ...................... 135 Transferring Knowledge .......................................................................................... 139 What the Interviews Tell Us ........................................................................................ 144 Implications to National Security ................................................................................ 147 Chapter 5 Difficulties Assembling Genes and Genomes: A Case Study of JCVI’s Mycoplasma mycoides Synthesis and Assembly ............................................................ 149 vi Methodology ..............................................................................................................
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