OPEN SOURCE BIOINFORMATICS:THE INTERSECTION BETWEEN FORMAL INTELLECTUAL PROPERTY LAWS AND USER GENERATED LAWS IN THE SCIENTIFIC RESEARCH COMMONS Thesis submitted to the Faculty of Law at the University of Tasmania for the degree of Doctor of Philosophy by James Scheibner, BComp-LLB (Hons), Grad Cert Research Centre for Law and Genetics,University of Tasmania November 2018 99,950 Words Declaration of Originality This thesis contains no material which has been accepted for a degree or diploma by the University of Tasmania or any other institution, except by way of background information and duly acknowledged in this thesis, and to the best of my knowledge and belief no material previously published or written by another person except where due acknowledgement is made in the text of this thesis, nor does the thesis contain any material which infringes copyright Authority of Access This thesis may be made available for loan and limited copyright and communication in accordance with the Copyright Act 1968. Statement of Ethical Conduct The research associated with this thesis abides the international and Australian cods on human and animal experimentation, the guidelines by the Australian Government’s Office of the Gene Technology Regulator and the rulings of the Safety, Ethics and Institutional Biosafety Committees of the University. DATE OF SUBMISSION 26 November 2018 SIGNED DATE - JAMES KEVIN SCHEIBNER i Open Source Bioinformatics: The Intersection between Formal Intellectual Property Laws and User Generated Laws in the Scientific Research Commons This thesis examines the interplay between national copyright and patent laws, and informal user generated norms in the governance of open source bioinformatics projects. Bioinformatics describes an interdisciplinary merger between computer science, statistics and molecular biology for quantitative biology analysis. As for many computationally driven scientific fields, there is a strong initiative both by researchers inside and outside the field to encourage collaborative research through open source software and data licensing. However, a trend towards seeking exclusive copyright and patent protection for bioinformatics algorithms could foster exclusivity and discourage collaboration in bioinformatics. Whether this effect exists within bioinformatics research, and if so is best resolved through national copyright and patent reform or private ordering strategies (which are already present through open source licensing) is a matter of open debate. This thesis explores these issues using a mixed methods, grounded theory framework that compares open licensing of bioinformatics software across the US, the EU, Australia and New Zealand. This framework operates on three levels: firstly, with a doctrinal analysis of copyright and patent laws (as well as related sui generis rights for data compilations); secondly, with a quantitative analysis of patent applications in bioinformatics and forward citation rates for patent publication pairs to determine whether the grant of these patents has a negative effect on citation rates; and thirdly, through semi-structured interviewing of bioinformaticians who release open source software and also seek patent protection. Each of these layers of analysis reveals that national patent laws do not appear to have a significant effect on the formation and governance of open source bioinformatics communities, but law reform targeted at encouraging private ordering strategies through copyright licensing might have a positive effect. This thesis concludes by offering recommendations on assessing how private ordering strategies in open source bioinformatics can be improved to encourage collaborative research. ii Acknowledgements It feels as if a lifetime ago I decided to return to University and undertake a doctorate of laws. The process has been arduous and testing at times, but I need to offer some thanks to those who made it possible. First and foremost, I am indebted to my supervisors, Professor Dianne Nicol and Dr Jane Nielsen. From when I started my journey as a doctoral student to our last impromptu supervision meeting, they have always unconditionally supported me. In my darkest hours following an operation gone horribly wrong, they inspired me to keep going and finish what I had started. I credit my evolution as an academic researcher to their steady, patient guidance. I must also thank two research supervisors who were heavily involved at different stages of the PhD, namely Dr Janet Hope and Associate Professor Michael Charleston of the School of Physical Sciences. Janet was instrumental during the nascent stages of the thesis in helping me collect my ideas and prepare a cogent narrative. Likewise, Michael was instrumental in helping me develop an understanding of the field of bioinformatics. I also must thank the academic and library staff at the Faculty of Law, who put up for me for far too long, first as an undergraduate student and later as a postgraduate student. In particular, my special thanks must go to Professor Don Chalmers, Professor Margaret Otlowski, Dr Lynden Griggs, Dr Elise Histed, Dr Jeremy Prichard, Associate Professor Heather Forrest and Dr Jeff McGee. I owe an enormous debt too to Professor Gino Dal Pont, who very generously read a draft of my thesis to ensure that the findings were coherent. I also must thank the incredibly tight knit and supportive postgraduate cohort at the Faculty of Law, who often patiently and kindly listened to the nervous mutterings of their anxious colleague. In particular, Dr Moshood Abdussalam, Jan Charbonneau, Dr John Liddicoat, Dr Kerryn Brent, Dr Philippa McCormack, Joseph Wenta and Dr Jason Allen Grant deserve special credit for their patience and sage advice. Last but most definitely not least, I must thank the tireless and dedicated library staff at the Law Library, particularly Chris Hurburgh, Carolyn Jarvis and Deb Bowering. Not only were they all very tolerant in handling my frequent inter-library loan requests, but they were also a constant source of good counsel and sympathy. I must also thank the University of Tasmania Graduate Research Office, who granted me part of the McDougall Postgraduate Scholarship and the Sir Henry Baker Memorial Fellowship. These scholarships allowed me to attend the 2018 Conference of the Commons at the University of Utrecht, and the IP Academics Conference at the University of Sydney. These were invaluable experiences that allowed me to meet key researchers in my field and eventually complete my thesis. In addition, I must thank Linda Kahl, Tania Bubela and Osmat Jefferson, all of whom gave me excellent advice on the direction of my thesis. Although I cannot name them, I must also thank my interviewees who contributed to this project via their interview responses. iii Finally, I must thank my friends and family who supported me during this thesis, particularly my brother Angus, Tim, Nick, Alex, India, Megan and Jez. Last, but certainly not least, I must thank my mother Tethys, who knows how hard completing a PhD is from personal experience, and worked tirelessly to help with drafting and editing my thesis. The King said "The third question is, how many seconds of time are there in eternity." Then said the shepherd boy, "in Lower Pomerania is the Diamond Mountain, which is two miles and a half high, two miles and a half wide, and two miles and a half in depth; every hundred years a little bird comes and sharpens its beak on it, and when the whole mountain is worn away by this, then the first second of eternity will be over." - Household Tales, by the Brothers Grimm. iv Contents INTRODUCTION 1 Scientific Background 2 Sociological Background 4 Legal and Economic Background 6 Research Questions 8 Methods and Methodology 9 Scope of Research and Original Contribution to Knowledge 12 Thesis Outline 13 1 A HISTORICAL AND TECHNICAL OVERVIEW OF COMPUTATIONAL BIOLOGY 16 1.1 INTRODUCTION . 17 1.2 THE PRE-HISTORY OF BIOINFORMATICS - FROM ‘OLD BIOLOGY’ TO ‘NEW BIOLOGY’ . 18 1.2.1 Defining Computational Biology and Bioinformatics . 18 1.2.2 Sequences and Sequencing - 1945 to 1972 . 20 1.2.3 The Rise of Quantitative Approaches to Molecular Biology and Genomics 22 1.3 THE EVOLUTION OF COMPUTER SCIENCE AND SOFTWARE ENGINEERING . 22 1.3.1 The Evolution of Programming Languages - 1954 to 1960 . 22 1.3.2 Operating Systems and Cyberinfrastructure - 1969 onwards . 25 1.4 THE MERGER OF MOLECULAR BIOLOGY AND COMPUTER SCIENCE - THE ORIGINS OF COMPUTATIONAL BIOLOGY . 27 1.4.1 Automating Genome Sequencing and Recombinant DNA . 27 1.4.2 The ‘Atlas of Protein Sequence and Structure’ - The First Sequence Compilations and Bioinformatics Algorithms . 29 1.4.3 Networked Databases and Bioinformatics - from the Atlas to GenBank . 31 v 1.4.4 From Sequence Databases to Large Scale Computational Biology - The Role of Computational Biology in the Human Genome Project and the International HapMap Project . 32 1.4.5 After the HGP and HapMap - Next Generation Sequencing and The Expansion of Bioinformatics Algorithms and Databases . 38 1.4.6 Beyond Bioinformatics Databases and Software - Systems and Synthetic Biology . 40 1.5 PRELIMINARY CONCLUSIONS ON THE NATURE OF BIOINFORMATICS AND IMPLICATIONS FOR THE PRESENT STUDY . 43 1.5.1 Reproducibility and Computational Biology . 43 1.5.2 Sustainability and Bioinformatics . 44 1.6 CONCLUSION . 46 2 COPYRIGHT IN CODE: A COMPARATIVE JURISDICTIONAL ANALYSIS OF DIVERGENT COPYRIGHT LAWS ON SOFTWARE 48 2.1 INTRODUCTION . 49 2.2 THE BOUNDARIES OF COPYRIGHT LAW . 50 2.2.1 A Brief History and Definitional Grounding in Copyright Law . 50 2.2.2 How Software Became Copyrightable . 51 2.2.3 Diffusion of Copyright Protection for Software . 54 2.3 THE SCOPE OF COPYRIGHT PROTECTION FOR SOFTWARE . 55 2.3.1 Copyright for Software in the US . 55 2.3.2 Scope of Copyright Protection for Software in the European Union . 57 2.3.3 The EU Sui Generis Database Right and Future EU Copyright Reform . 59 2.3.4 Copyright Protection for Software in Australia and New Zealand .