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The Model Worm: a Controlled Reduction

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The Model Worm: a Controlled Reduction The Model Worm: A Controlled Reduction by Michal Arciszewski A Thesis Presented to The University of Guelph In partial fulfillment of requirements for the degree of Doctor of Philosophy in Philosophy Guelph, Ontario, Canada ©Michal Arciszewski, 2013 ABSTRACT THE MODEL WORM: A CONTROLLED REDUCTION. Michal Arciszewski Advisor: University of Guelph, 2013 Professor Andrew Wayne This thesis will argue that reduction is best viewed as a hypothesis about scientific unification: that the relation of reduction between theories at distinct levels is best understood as a relation of unification wherein empirically discovered differences can be explained at a single theoretical level. This unification occurs when a single base- level theory retains and explains a diverse range of upper-level phenomena from multiple upper-level theories, while at the same time dispensing with the upper-level theories themselves. This hypothesis, when applied to the relationships between biology and chemistry, is called molecular reduction. This is a novel understanding of intertheoretic relations, and it is shown to differ from both Nagelean reductions and explanatory pluralism. Molecular reductions occur when a biological theory and a molecular theory represent identical things. Representation will be seen to occur through idealised models that only represent specific limited properties of the target system: an idealised model only represents the explicit parameters (the structure) of the target system. In order to demonstrate an intertheoretic identity between two theories it will be necessary to avoid the misrepresentation one theory‘s target phenomena by another theory. Representation will be modeled in terms of a bijective functional relationship between the two. In this way, an intertheoretic identity requires that the functional relationship be both surjective and injective, and so the theories to be isomorphic with respect to how they model the target phenomena. When this obtains, there is significant methodological interaction between the theories. This interaction is at the heart of a molecular reduction. Molecular reductions have been designed to show that this kind of intertheoretic identity can be observed when two models, a biological one and a molecular one, both represent the causal structure of an experimental phenomenon. The case study examined here consists of models of the induction of dauer arrest. Here, the target phenomenon is the causal structure of developmental bifurcations, and this target phenomenon is also represented by a molecular model. Both the biological and molecular models are representing the same set of phenomena: a causal structure in experimental conditions. Despite the fact that this identity holds in biologically limited conditions and does not result in a general biological explanation, this case study gives some evidence in favour of a more general unification, and hence molecular reduction, of biology. The unification is through molecular chemistry, which consists of general molecular properties of many disparate biological systems that can also be modeled as governed by molecular laws. This identity unifies biology by having the single molecular model represent more biologically disparate target phenomena. This kind of intertheoretic identity supports the hypothesis of scientific unification, that the causal structure of diverse experimental phenomena from biology can be represented by a molecular models. Key terms: hypothesis of scientific unification, molecular reduction, representation, misrepresentation, idealised models, bijective functions, isomorphism, methodological interaction. iv ACKNOWLEDGEMENTS I first need to thank Andrew Wayne for his unending support and patience, this project would not have succeeded without his guidance. I must also thank my family for the encouragement. And most importantly I thank my children Stanislaw and Wojtek for giving me the purpose to complete this work. To them this thesis is dedicated. v TABLE OF CONTENTS Abstract .......................................................................................................................... ii Acknowledgements ....................................................................................................... iv Table of Contents ........................................................................................................... v List of figures ................................................................................................................. x Abbreviations ................................................................................................................ xi CHAPTER I ................................................................................................................... 1 1.1Molecular Reductions ................................................................................... 1 1.2 The Induction of Dauer Arrest in Caenorhabditis elegans: A Molecular Reduction ................................................................................................................... 4 1.2.1 Arresting as Dauer: The Biological Phenomenon and the Molecular Model ..................................................................................................................... 5 1.2.2 Triangulating Molecular Reductions: Not Nagelean, Not Ruthless Reduction and Not Integration ............................................................................... 8 1.3 What Is The Hypothesis Of Unity? ........................................................... 11 1.4 Inter-Level Causal Explanations ............................................................... 13 1.5Logic Of The Unity Of Science Vs. The Hypothesis Of Scientific Unity . 16 1.6 Disunity Or Autonomy As Descriptions Of Intertheoretic Relations ....... 22 1.6.1 The Problem Of Competing Hypotheses ............................................ 25 vi 1.7 Molecular Reductions Are Distinct From Multi-Level Integration .......... 28 1.8 The Direction ............................................................................................. 30 1.9 A Summary ................................................................................................ 34 CHAPTER II THE STRUCTURE OF METHODOLOGICAL INTERACTION .... 40 2.1 Methodological Interaction In Molecular Reductions ............................... 40 2.2 Scientific Representation ........................................................................... 42 2.2.1 Theories .............................................................................................. 44 2.2.2 Models ................................................................................................ 46 2.2.3 Empirical Models Of Intertheoretic Relations ................................... 56 2.3 The Logic Of Methodological Interaction And Autonomy ....................... 62 2.3.1 The Methodological Criterion For Interaction .................................. 62 2.3.2 Methodological Autonomy ................................................................. 68 2.4 Conclusions ............................................................................................... 76 CHAPTER III THE PROPOSED KINDS OF METHODOLOGICAL INTERACTION ........................................................................................................... 79 3.1 Attempts To Establish Methodological Interaction ................................... 79 3.2 Reductive Identities ................................................................................... 81 3.2.1 Traditional Reduction With Bridge Laws .......................................... 81 3.2.2 Inter-level Reductive Explanations .................................................... 92 vii 3.2.3 Mathematical Limits And Structural Isomorphisms .......................... 96 3.2.4 Reductive Identities: Molecular Reductions .................................... 101 3.3 Explanatory Integration ........................................................................... 103 3.3.1 Novel Theories ................................................................................. 104 3.2.2 Integration Though Local Constraints .............................................. 107 3.4. Integrations Are Distinct From Reductions: Local Constraints Do Not Establish Intertheoretic Identities .......................................................................... 115 CHAPTER IV NAVIGATING THE METHODOLOGICAL GAPS WITH LESS ERROR ...................................................................................................................... 119 4.1 Representing A Common Failure: Misrepresentation ............................ 119 4.2 Characterising Methodological Interaction Through Representations .... 123 4.2.1 Failure To Represent Is Lack Of Isomorphism ................................ 126 4.2.2 Methodological Interaction Through Representations ..................... 127 4.2.3 Misrepresentation In Inter-Level Relations ...................................... 131 4.3 A Model Of Methodological Error ........................................................ 134 4.3.1 Failure Of Mapping .......................................................................... 136 4.3.2 Failure Of Injection .......................................................................... 136 4.3.3 Failure Of Surjection ........................................................................ 141 4.4 A Failure Of Surjection Is Not A Failure Of Reduction ......................... 145 viii 4.5 Conclusions
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