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The Emergence of a New Human Superorganism After Organ The Emergence of a New Human Superorganism After Organ Transplantation by G. V. Ramesh Prasad A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Philosophy Waterloo, Ontario, Canada 2017 © G. V. Ramesh Prasad 2017 Examining Committee Membership The following served on the Examining Committee for this thesis. The decision of the Examining Committee is by majority vote. External Examiner Dr. Maya Goldenberg Associate Professor Department of Philosophy University of Guelph Supervisor Dr. Paul Thagard Distinguished Professor Emeritus Department of Philosophy University of Waterloo Internal Member Dr. John Turri Professor, Canada Research Chair in Philosophy and Cognitive Science Department of Philosophy University of Waterloo Internal-External Member Dr. J. David Spafford Associate Professor Department of Biology University of Waterloo Other Member(s) Dr. Christopher Lowry Assistant Professor Department of Philosophy University of Waterloo ii Author’s Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. iii Abstract The biological human being is an emergent human superorganism consisting of the human organism physiologically integrated with other organisms. The persistence of a superorganism in space and time requires communication among its organisms. This communication occurs through immune processes at the biological boundaries of these organisms. Immune processes also repair disrupted boundaries, with this repair resulting in either health or disease processes depending on how the boundaries are restored. Health, disease, and biological personal identity all emerge from the mode of arrangement of, and communication of biological information among the superorganism’s parts. The study of solid organ transplantation enables the ontology of the biological human being as a superorganism by bringing together the structural and functional boundaries of different organisms in a way that communication can be better understood. By understanding that organ transplant recipients are not just non-transplanted patients with an extra part, but are newly emergent human superorganisms, we can better understand both post-transplant health and disease and target our therapies more effectively. Successful reintegration of the superorganism after disruption may be relevant to many health processes, and therefore to the goals of medicine in general. iv Acknowledgements I thank the University of Waterloo for providing me with the rare opportunity to expand my intellectual horizons by pursuing formal higher education in Philosophy, a discipline quite different from Medicine. This structured project that has come to define my forties would not have been possible anywhere else in the world. I thank my supervisor, Dr. Paul Thagard, for so willingly accepting me as his graduate student. His ready availability and great enthusiasm for the project made my experience very special. I am very grateful for all his insightful comments and constant encouragement. Dr. Thagard is a true gentleman, and I am a better person because of him. I thank Dr. John Turri, certainly one of the nicest people in the world, for his great guidance and mentorship during all my years of philosophical training. Dr. Christopher Lowry so willingly served on my committee and provided helpful suggestions. Dr. Shannon Dea and Dr. Gerry Callaghan introduced me to the wonders of barrier-free undergraduate philosophy. Dr. Carla Fehr made a great difference to my pursuit of doctoral studies when she said, “we will make this happen”. Memorable courses taught by Drs. David DeVidi, Mathieu Doucet, Doreen Fraser, Patricia Marino, and Joseph Novak all helped in my professional development as a philosopher. I thank my colleagues at St. Michael's Hospital, Toronto, for allowing me the scheduling flexibility to pursue this dream. I sometimes had to reschedule patient clinics to travel to Waterloo, and that would never have been possible unless others were willing to share some of the clinical work. Dr. Jeffrey Zaltzman and Dr. Martin Schreiber were always willing to discuss the Philosophy of Medicine with me, despite their own busy schedules. This thesis was mostly written in my office. I thank my three children for providing the singular reason to come home at night, and my staff and patients for giving me the powerful incentive to go to work every morning. v Dedication This thesis is dedicated to my parents, who are my first teachers, best friends, most ardent cheerleaders, ideal role models, and greatest source of inspiration. vi Table of Contents List of Abbreviations ix Preface 1 1 Biological Human Beings and Solid Organ Transplantation 4 1.1 Dissertation hypothesis 4 1.2 The biological human being 5 1.3 Addressing the limitations of solid organ transplantation 12 1.4 Splitting the human being into organism and superorganism 16 1.5 Is a human being with a transplant a different kind of human being? 18 1.6 Structure of dissertation 22 2 The Diversity of Life 26 2.1 Biological hierarchies and relationships 26 2.2 The meaning of species 29 2.3 The meaning of organism 37 2.4 The meaning of individual 46 2.5 Why the organism-individual distinction is still problematic 52 2.6 Reconciling organism, species, and individual 60 2.7 Individual versus superorganism 64 2.8 A summary of species, organism, individual, and superorganism 65 3 The Human Organism and the Human Superorganism 67 3.1 Types of superorganisms 69 3.2 Size and composition of the human microbiota 72 3.3 Functions of the human microbiota 79 3.4 Relation of the microbiota to the human body: The intervening 84 boundary 3.5 Is the human being a superorganism or a community? 97 vii 3.6 The human superorganism and therapy: Probiotics and fecal microbiota 99 transplantation 3.7 Xenotransplantation 103 3.8 Breakdown of the superorganism 107 3.9 A summary of the human organism and human superorganism 109 4 The Immune System in Organisms and Superorganisms 112 4.1 Searching for a mechanism of the human organism and superorganism 113 4.2 The immune system as a collection of mechanisms 123 4.3 The immune response to other organisms 132 4.4 The immune response in solid organ transplantation 139 4.5 Rejection of the organ transplant 146 4.6 Interactions between the transplanted organ and non-human organisms 153 4.7 Accessing the messages of the immune system 157 4.8 Transplant tolerance and immune privilege 166 4.9 A summary of the immune system in organisms and superorganisms 172 5 Transplantation and Biological Emergence 176 5.1 Emergent processes in solid organ transplantation 177 5.2 The transplant recipient with emergent processes 182 5.3 The organ transplant as a part of a new whole 192 5.4 Boundaries and biological identity after organ transplantation 199 5.5 A summary of emergence in organ transplantation 202 6 Disease, Health, and the Human Superorganism 205 6.1 Disease and health as emergent processes 208 6.2 Using solid organ transplantation to understand health and disease 213 6.3 Establishing and maintaining the healthy human superorganism 225 7 Summary and Conclusion 237 Bibliography 246 viii List of Abbreviations CRISPR/Cas9 clustered regularly interspaced short palindromic repeats/ clustered regularly interspaced short palindromic repeats-associated system DNA Deoxyribonucleic Acid FMT fecal microbiota transplantation MHC major histocompatibility complex PAMP pathogen-associated molecular patterns SOT solid organ transplantation ix Preface Medicine is largely concerned with the diagnosis, causes, and treatment of disease. Correspondingly, much of our medical knowledge relates to the basic biological processes that are involved in supporting the healthy functioning of the human body (Thagard 2011). End-stage failure of a solid organ such as the kidney, liver, heart, or lung is among the most serious diseases that can afflict the human body. Organ failure results in severe morbidity and even death. The most effective therapy for irreversible end-stage organ failure in humans is the functional replacement of the failed organ. In the case of kidney failure, long-term functional replacement of the failed kidneys is possible with the help of a machine, in a process called dialysis. However, there are no similarly effective long-term, machine-based therapies to sustain life when many of the other solid organs fail. Besides machines, another means of replacing the function of a failed solid organ is with a better functioning organ transferred from another human being, in a process called solid organ transplantation, or SOT. SOT is one of the most significant medical advances of the past century. In SOT, a healthier organ effectively replaces the seriously diseased or failed organ. This healthier transplanted organ connects to the rest of the body, sometimes in a different location while leaving the failed organs intact in their usual location, such as in the case of a kidney transplant. In other instances, the new healthier organ is implanted in the same location as the diseased organ removed from that location, as in the case of a liver, heart, or lung transplant. In all these cases, the transplanted organ is now in an environment that is new for that organ. The human being is also in a new situation after the organ transplant, since it now contains a new organ from a different human being. One important clinical motivation for SOT is to provide relief from serious human disease. Another clinical motivation is to prolong human life after one or more essential organs fail (Wolfe 1999). SOT has the remarkable ability to provide a significant improvement in the quality of life of patients with end-stage organ failure (Evans 1985). 1 Important measures of quality of life such as appetite, strength, endurance, cognition, and the ability to eat a normal diet as well as travel are vastly improved.
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