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BIOLOGICAL SYSTEMATICS and EVOLUTIONARY THEORY By BIOLOGICAL SYSTEMATICS AND EVOLUTIONARY THEORY by Aleta Quinn BA, University of Maryland, 2005 BS, University of Maryland, 2005 Submitted to the Graduate Faculty of The Kenneth P. Dietrich School of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2015 UNIVERSITY OF PITTSBURGH KENNETH P. DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation was presented by Aleta Quinn It was defended on July 1, 2015 and approved by James Lennox, PhD, History & Philosophy of Science Sandra Mitchell, PhD, History & Philosophy of Science Kenneth Schaffner, PhD, History & Philosophy of Science Jeffrey Schwartz, PhD, Anthropology Dissertation Director: James Lennox, PhD, History & Philosophy of Science ii Copyright © by Aleta Quinn 2015 iii BIOLOGICAL SYSTEMATICS AND EVOLUTIONARY THEORY Aleta Quinn, PhD University of Pittsburgh, 2015 In this dissertation I examine the role of evolutionary theory in systematics (the science that discovers biodiversity). Following Darwin’s revolution, systematists have aimed to reconstruct the past. My dissertation analyzes common but mistaken assumptions about sciences that reconstruct the past by tracing the assumptions to J.S. Mill. Drawing on Mill’s contemporary, William Whewell, I critique Mill’s assumptions and develop an alternative and more complete account of systematic inference as inference to the best explanation. First, I analyze the inadequate view: that scientists use causal theories to hypothesize what past chains of events must have been, and then form hypotheses that identify segments of a network of events and causal transactions between events. This model assumes that scientists can identify events in the world by reference to neatly delineated properties, and that discovering causal laws is simply a matter of testing what regularities hold between events so delineated. Twentieth century philosophers of science tacitly adopted this assumption in otherwise distinct models of explanation. As Whewell pointed out in his critique of Mill, the problem with this assumption is that the delineation of events via properties is itself the hard part of science. Drawing on Whewell’s philosophy of science, and my work as a member of a team of systematists revising the genus Bassaricyon, I show how historical scientists avoid the problems of the inadequate view. Whewell’s account of historical science and of consilience provide a better foothold for understanding systematics. Whewell’s consilience describes the fit between a single hypothesis and lines of reasoning that draw on distinct conceptual structures. My analysis clarifies the significance of two revolutions in systematics. Whereas pre-Darwinian systematists used consilience as an evidentiary criterion without explicit justification, after Darwin’s revolution iv consilience can be understood as a form of inference to the best explanation. I show that the adoption of Hennig’s phylogenetic framework formalized methodological principles at the core of Whewell’s philosophy of historical science. I conclude by showing how two challenges that are frequently pressed against inference to the best explanation are met in the context of phylogenetic inference. v TABLE OF CONTENTS PREFACE .......................................................................................................................................................................... ix 1.0 INTRODUCTION ..................................................................................................................................................... 1 2.0 MILL’S PHILOSOPHY OF SCIENCE .................................................................................................................. 6 2.1 MILL’S INDUCTION AND CAUSAL REASONING ................................................................................. 6 2.1.1 Induction: Particulars and General Propositions ........................................................................................ 6 2.1.2 Justifying Induction: Causal Necessity........................................................................................................ 12 2.1.3 Justifying Induction: Relevant Resemblances ............................................................................................ 21 2.1.4 Mill’s Causal Ontology .................................................................................................................................. 23 2.2 NATURAL KINDS .............................................................................................................................................. 24 2.2.1 Mill on Natural Kinds ................................................................................................................................... 24 2.2.2 Scientific Investigation: Biological Natural Kinds .................................................................................... 31 2.2.3 Justifying Mill’s Natural Kinds ..................................................................................................................... 35 3.0 WHEWELL’S PHILOSOPHY OF SCIENCE ................................................................................................... 40 3.1 WHEWELL’S INDUCTION AND CRITIQUE OF MILL ........................................................................ 41 3.1.1 The Role of Concepts in Science ................................................................................................................ 41 3.1.2 Concepts and Causes in Kepler’s Discovery ............................................................................................. 46 3.1.3 Concepts and Causes in Classificatory Science ......................................................................................... 51 3.2 WHEWELL ON NATURAL AFFINITY ....................................................................................................... 53 3.2.1 Goals and Problems of Classification ........................................................................................................ 53 3.2.2 Successful Classificatory Science ................................................................................................................. 61 3.2.3 Justifying Natural Affinity ............................................................................................................................ 65 vi 3.3 WHEWELL’S NATURAL THEOLOGY ....................................................................................................... 68 4.0 NETWORK ASSUMPTIONS AND THE RELEVANCE PROBLEM ....................................................... 73 4.1 THE NETWORK ASSUMPTIONS AND MODELS OF EXPLANATION ........................................ 74 4.1.1 The Network Assumptions and the Covering Law Model ..................................................................... 74 4.1.2 The Network Assumptions and Historical Explanation ......................................................................... 76 4.2 THE NETWORK ASSUMPTIONS AND THE RELEVANCE PROBLEM ........................................ 82 4.2.1 The ‘Hard Part’ Objection ............................................................................................................................ 82 4.2.2 The Conceptual Structure of Science ......................................................................................................... 86 4.2.3 Event Chains and Historical Hypotheses .................................................................................................. 90 5.0 HISTORICAL HYPOTHESES .............................................................................................................................. 95 5.1 HISTORICAL HYPOTHESES AND CAUSAL DEPENDENCE ........................................................... 96 5.1.1 Historical Causal Reasoning ......................................................................................................................... 96 5.1.2 Historical Hypotheses and Whewell’s Practice of Historical Architecture ......................................... 101 5.2 SYSTEMATICS AS HISTORICAL SCIENCE ............................................................................................ 108 5.2.1 Lamarck and Gegenbaur ............................................................................................................................. 108 5.2.2 Hennig’s Methodology and Tree Diagrams ............................................................................................. 112 6.0 PHYLOGENETIC INFERENCE TO THE BEST EXPLANATION ...................................................... 123 6.1 THE UNDERCONSIDERATION OBJECTION AND THE PROBLEM OF EVIDENCE ......... 125 6.2 CONSILIENCE AND THE TAUTOLOGY OBJECTION .................................................................... 141 7.0 CONCLUSION ....................................................................................................................................................... 158 BIBLIOGRAPHY .......................................................................................................................................................... 160 vii LIST OF FIGURES 5.1. A square space with equal semicircular arches. Whewell's (1830) plate I, figure 1. ...................................... 103 5.2. Church with two side aisles and only semicircular vaults. Whewell’s (1830) plate IV, figure 6. ................ 104 5.3. Vaulting a rectangular space using pointed and semicircular arches.
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