The Design Matrix: a Consilience of Clues
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The Design Matrix: A Consilience of Clues by Mike Gene & ARBOR VITAE PRESS ~ http://arborvitaepress.com Copyright© 2007 by Mike Gene. All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any informational storage and retrieval system, without permission in writing from the pub lisher, except for the inclusion ofbrief quotations in a review. Book Design: Robin P. Simonds "Face on Mars" photos courtesy NASA. Library of Congress Control Number: 2006937418 ISBN: 978-0-9786314-0-6 First Edition Printed in the United States 12 11 10 09 08 07 - 1 2 3 4 5 To Mary-for always believing in me. v TABLE oF CoNTENTS Introduction XI Part I -The Way 1 Chapter 1 Lessons from a Vanishing Face 3 The Face 5 What Can We Learn from the Vanishing Face? 7 The Face ofLife 11 A Fly in the Soup 13 The High-Resolution Face of Life 16 Chapter 2 The Explanatory Continuum 19 The Traditional Template 24 Inductive Gradualism 29 Stumping Darwin 34 Part II -The Clues 37 Chapter 3 Echoes ofTechnology 39 Misleading Metaphors? 43 A Convergence Between Biology and Engineering 54 Chapter 4 Error Correction Runs Deep 64 Proteins and Nucleic Acids 65 Encoding Life 68 Vll The Code 70 An Optimized Code 74 Proofreading 77 A Parity Code 80 Proofreading in the Light of Design 84 The Suspicion Deepens 86 Chapter 5 Welcome to the Machines 89 What's in a Machine? 95 Machines Point to Intelligent Design 98 Haven't We Heard This All Before? 101 The Nanotechnologists 103 Part III -The Challenges 111 Chapter 6 Ducks and Rabbits 113 Why Not Backtrack? 118 Evolvoid 119 Of Ducks and Rabbits 122 Do You See What I See? 124 Back to the Evidence 129 Chapter 7 Designing Evolution 137 Putting Darwin to Work 140 Front-Loading Evolution 146 Unpredictably Predictable 148 Selecting Your Surrogates 152 Multi-Tasking 159 Designed to Redesign 164 Flexibility 167 Chance Favors the Prepared Genome 173 Return of the Rabbit 179 viii Part IV-The Matrix 191 Chapter 8 Analogies and Discontinuities 193 Help from the Skeptics 195 The Power of Analogy 199 Deepening the Analogy 201 Weakening the Analogy 208 The Blind Watchmaker Returns 211 Irreducible Complexity 214 Possible Ways to Evolve Irreducible Complexity 219 Irreducible Complexity in the Matrix 226 The System-Dependent Core 231 Summing Up 235 Chapter 9 Rationality and Foresight 240 Rational Engineer versus the Tinkerer 243 Structural and Functional Decomposition 247 Attributes of Rational Design 252 The Plan 254 Looking Ahead 258 Chapter 10 The Design Matrix Unleashed 268 Taking the Matrix for a Test Drive 276 Getting Ready for the Qyest 286 Index 292 lX INTRODUCTION he decision to write this book was not an easy one, as argu ments about Intelligent Design and evolution generate a great deal of anxiety and hostility in our culture. The vast majority T of scientists do not view Intelligent Design as science and I happen to agree with them. Nevertheless, this scientific consensus has not stopped many people from trying to get Intelligent Design taught in the science classrooms of the public school systems. This creates an understand able resentment among those who highly value the place of science in our educational system. Because of the socio-political current that is attached to this debate, some may start with a false impression about the purpose of this book. Therefore, I should make it explicitly clear from the start that I did not write this book to help those seeking to change the way we teach science to our kids. I do not argue that design deserves to be known as science. At best, Intelligent Design may only be a nascent proto-science and thus does not belong in the public school curriculum. Nor does this book argue that evolution is false and deserves to be criticized in the public school curriculum. If the truth is to be told, I oppose such actions. So, you may ask, for what purpose would I write this type ofbook? It is my belief that there are people in the world like me-people who are tired of the heated debates, name-calling, innuendo, and political fights. Such people might find themselves in the middle ground and would rather focus on the hypotheses, the arguments, and the evidence. We might not be completely convinced that life was designed, yet we find the hypothesis to be tremendously intriguing. Rather than belaboring the concern as to whether the study of Intelligent Design should be labeled science, metaphysics, or religion, it is my belief that there are people who would rather just ponder the issues that are raised by design and evolution. The most important reason for writing this book is that I, like most au thors, believe I have something to say. If we push aside all the politics, rheto- Xl ric, and concerns about what we should and should not do with the concept of Intelligent Design, I remain intrigued by the concept and evidences and continue to ponder the topic. I do not come to you as one with a precon ceived belief that life was, indeed, designed. I come to you with nagging suspicions that there may really be something solid behind the hypothesis that life was designed. These suspicions are like 'splinters in my mind' that will not go away if left unattended. What you will find in this book is the beginning of a journey. Writing in the journal Science in 1977, Nobel Laureate Francois Jacob once offered some truly profound words that have been the inspiration of this book: To produce a valuable observation, one has first to have an idea of what to observe, a preconception of what is possible. Scientific advances often come from uncovering a hitherto unseen aspect of things as a result, not so much of using new instruments, but rather of looking at objects from a different angle. This look is necessarily guided by a certain idea of what this so-called reality might be. It always involves a certain conception about the unknown, that is, about what lies beyond that which one has logical or experimental reasons to believe. This book is indeed about looking at objects from a different angle and hav ing a certain conception about reality that is beyond current logical or ex perimental reasons to believe. It is the first step in an investigation. You are invited to join along. The Design Matrix is broken into four parts. Part I is entitled "The Way," as we start our journey by pondering new ways to think about Intelligent Design. In Chapter 1, arguments about the existence of the Face on Mars are considered, as these arguments provide important lessons that will help guide our perspective. In Chapter 2, I explore the conventional ways of thinking about design and biology and suggest a somewhat different way of approaching these issues. The approach I raise is not radical or novel; it has just been neglected. In Part II, "The Clues," I outline features of biology that can fuel our new approach as they point toward design. It will be crucial to remember Xll that I offer such features only as clues and not proofs. I have personally found these clues to be haunting and worthy of closer examination. It will then be my goal to help the reader move beyond the level of merely having hunches backed up by clues. But before we can get to this, we will confront the challenges that we face in Part III. In Chapter 6, we meet Darwin's Theory of Evolution, learn ing to respect it, as well as expand our way of thinking about this theory. Chapter 7 highlights the possibilities on ways that design and evolution can actually co-exist, opening new doors for thinking about design. Finally, in Part IV, I progressively outline a method for tentatively infer ring the existence of design and helping us move beyond the suspicions-the Design Matrix. It is an open-ended method that can be used by both sides of this dispute to assess a design inference and it is my hope that you will find it easy to understand and use. After explaining the Design Matrix, I take it for a test drive to see how it scores things that are known to be designed by humans, along with various biological features. In Volume 2 that is eventu ally to follow, I will use it, and more, to explore the living world. I have come to find myself in the highly unusual position of writing a book about design and evolution while using a pseudonym. Why would I make such a choice? My interest in this topic is a function of the Internet and my chosen handle for the Internet has long been Mike Gene. Idly surf ing the internet forums one day, I stumbled across many heated arguments on Intelligent Design approximately a year after Michael Behe's book, Dar win's Black Box, was published. I found this "buzz" interesting and intrigu ing, while also noting that the author was a reputable biochemist at a main stream university, rather than a typical author of creationist literature. As I read through the exchanges, and explored the Internet to better familiarize myself with Behe and his new argument, I must admit that I admired him for having such temerity. Having long had an affinity for the underdog, I decided to join the fray, since Behe's supporters on the forum seemed outgunned and outnumbered.