University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Experiments, Simulations, and Lessons from Experimental Evolution Emily Parke University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biology Commons, and the Philosophy Commons Recommended Citation Parke, Emily, "Experiments, Simulations, and Lessons from Experimental Evolution" (2015). Publicly Accessible Penn Dissertations. 1114. https://repository.upenn.edu/edissertations/1114 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1114 For more information, please contact [email protected]. Experiments, Simulations, and Lessons from Experimental Evolution Abstract Philosophers and scientists have sought to draw methodological distinctions among different kinds of experiments, and between experimentation and other scientific methodologies. This dissertation focuses on two such cases: hypothesis-testing versus exploratory experiments, and experiment versus simulation. I draw on examples from experimental evolution--evolving organisms in a controlled laboratory setting to study evolution via natural selection in real time--to challenge the way we think about these distinctions. In the case of hypothesis-testing versus exploratory experiments, philosophers have distinguished these categories in terms of the role of theory in experiment. I discuss examples from experimental evolution which occupy the poorly characterized middle ground between the two categories. I argue that we should take more seriously the point that multiple theoretical backgrounds can come into play at multiple points in an experiment, and propose some new contributions toward clarifying the conceptual space of experimental inquiry. In the case of experiment versus simulation, people have attempted to clearly delineate cases of science into these two categories, and base judgments about their epistemic value on these categorizations. I discuss and reject two arguments for the epistemic superiority of experiments over simulations: (1) Experiments put scientists in a better position to make valid inferences about the natural world; (2) Experiments are a superior source of surprises or novel insights. Both of these claims are false as generalizations across science. Focusing on the experiment/simulation distinction as a basis for in-principle judgments about epistemic value focuses us on the wrong issues. This leaves us with a question: What should we focus on instead? I offer preliminary considerations for a framework for evaluating inferences from objects of study to targets of inquiry in the world, which departs from the problematic custom of basing such evaluations on questions like "Was it an experiment or a simulation?" This framework is based on the ideas of capturing relevant similarities while appropriately accounting for what researchers already know and what they are trying to learn by asking the scientific question at hand. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Philosophy First Advisor Michael Weisberg Keywords experimental evolution, experiments, exploratory experiments, hypothesis testing, simulations, surprise Subject Categories Biology | Philosophy This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/1114 EXPERIMENTS, SIMULATIONS, AND LESSONS FROM EXPERIMENTAL EVOLUTION Emily C. Parke A DISSERTATION in Philosophy Presented to the Faculties of the University of Pennsylvania in Partial Fulfllment of the Requirements for the Degree of Doctor of Philosophy 2015 Supervisor of Dissertation ________________________ Michael Weisberg, Associate Professor of Philosophy Graduate Group Chairperson ________________________ Michael Weisberg, Associate Professor of Philosophy Dissertation Committee Karen Detlefsen, Associate Professor of Philosophy and Education Daniel Singer, Assistant Professor of Philosophy Paul Sniegowski, Professor of Biology EXPERIMENTS, SIMULATIONS, AND LESSONS FROM EXPERIMENTAL EVOLUTION COPYRIGHT 2015 Emily Carter Parke ACKNOWLEDGMENT I am immensely grateful to my committee members, all of whom have inspired, challenged, and encouraged me not only in writing this dissertation but throughout my years as a graduate student. Michael Weisberg has been a great source of insight and support, always encouraging me to develop my own projects while guiding me to take them in fruitful directions and ofering knowledgeable feedback every step of the way. I have benefted from all of his advice over the years, on everything from how to give talks to which font to use, and feel very lucky to have him as a supervisor. I am thankful to Karen Detlefsen for her support and generosity with her time, wealth of knowledge on the history and philosophy of the life sciences, and meticulous feedback on my writing. I am grateful to Paul Sniegowski for his thoughtful mentorship, inspiring conversations about science and philosophy and teaching, and for welcoming me into his lab and patiently teaching me so much about biology over the years. I was fortunate to have Dan Singer join my committee in my last two years at Penn, and have appreciated his careful comments on my work which have helped improve my attention to detail, his knowledge and perspective on formal matters, and general encouragement as I fnished the PhD. While not on my ofcial committee, I am also particularly indebted to three other mentors: Mark Bedau, for his ongoing advising, encouragement, and comments on everything I’ve written in the last 11+ years; Zoltan Domotor, who has been a valuable resource on all matters in philosophy of science; and Mary Morgan, whose work has been an important source of inspiration, for many great discussions and feedback on my work. I am grateful to all of my past and present colleagues in philosophy at Penn, in particular the members of Science Club, and to my fellow members of the Sniegowski Lab for being so welcoming and teaching me everything I know about experimental science: Matthew Gazzara, Angela Halstead, Meredith Hyun, Dave Katzianer, Kate Kerpen, Brooks Martino, Eugene Raynes, Kathleen Sproufske, Ben Sprung, and especially Chris Gentile, Mitra Eghbal, and Tanya Singh. I have also beneftted from feedback (both written and in conversations) on portions of the material in this dissertation from a number of others: Wes Anderson, David Barack, Matt Bateman, Brett Calcott, Mark Colyvan, Lindley Darden, Alkistis Elliott-Graves, Karen Kovaca, Peter Godfrey-Smith, Ben Kerr, J. J. LaTourelle, Alan Love, Margaret Morrison, Valerie Racine, Eric Saidel, Carlos Santana, Kyle Stanford, Kim Sterelny, and Michael Travisano. Finally thanks to my husband Brett, who is a constant source of support, inspiration, and good conversations about biology and philosophy and everything else. iii ABSTRACT EXPERIMENTS, SIMULATIONS, AND LESSONS FROM EXPERIMENTAL EVOLUTION Emily C. Parke Michael Weisberg Philosophers and scientists have sought to draw methodological distinctions among diferent kinds of experiments, and between experimentation and other scientifc methodologies. Tis dissertation focuses on two such cases: hypothesis-testing versus exploratory experiments, and experiment versus simulation. I draw on examples from experimental evolution—evolving organisms in a controlled laboratory setting to study evolution via natural selection in real time—to challenge the way we think about these distinctions. In the case of hypothesis-testing versus exploratory experiments, philosophers have distinguished these categories in terms of the role of theory in experiment. I discuss examples from experimental evolution which occupy the poorly characterized middle ground between the two categories. I argue that we should take more seriously the point that multiple theoretical backgrounds can come into play at multiple points in an experiment, and propose some new contributions toward clarifying the conceptual space of experimental inquiry. In the case of experiment versus simulation, people have attempted to clearly delineate cases of science into these two categories, and base judgments about their epistemic value on these categorizations. I discuss and reject two arguments for the epistemic superiority of experiments over simulations: (1) Experiments put scientists in a better position to make valid inferences about the natural world; (2) Experiments are a superior source of surprises or novel insights. Both of these claims are false as generalizations across science. Focusing on the experiment/simulation iv distinction as a basis for in-principle judgments about epistemic value focuses us on the wrong issues. Tis leaves us with a question: What should we focus on instead? I ofer preliminary considerations for a framework for evaluating inferences from objects of study to targets of inquiry in the world, which departs from the problematic custom of basing such evaluations on questions like “Was it an experiment or a simulation?” Tis framework is based on the ideas of capturing relevant similarities while appropriately accounting for what researchers already know and what they are trying to learn by asking the scientifc question at hand. v TABLE OF CONTENTS 1. Experiments 1 1.1.What is an Experiment? 1 1.2.Diferent Kinds of Experiments 8 1.3.Overview of the Dissertation 10 2. Experimental Evolution 13 2.1.Lenski’s Long-Term Evolution Experiment 16 2.1.1. High Mutation Rates 21 2.1.2. Punctuated