The Cosmic Machine The Cosmic Machine The Science That Runs Our Universe and the Story Behind It Scott Bembenek San Diego Copyright © 2016 Scott Bembenek All rights reserved. This book was professionally published by the author Scott Bembenek through Zoari Press. This book or parts thereof may not be reproduced in any form, stored in any retrieval system, or transmitted in any form by any means – electronic, mechanical, photocopy, recording, or otherwise – without prior written permission of the author. If you would like to seek written permission, or have other questions about the book, contact the author at: scottbembenek.com The Cosmic Machine: The Science That Runs Our Universe and the Story Behind It Published by Zoari Press San Diego, CA, USA ISBN: 978-0-9979341-0-6 Library of Congress Control Number: 2016913451 First Edition Printed in the United States of America For Ariana and Zoey, May you find the answers to all of life’s difficult questions. About the Author scottbembenek.com Scott Damian Bembenek grew up in the small town of Delavan, Wisconsin (population of approximately 5,000 at that time). Scott’s passion for science began around the age of five. Throughout his childhood, “science” took on a variety of forms, involving such things as batteries, circuits, magnets, anything electronic, insects, frogs, toads, salamanders, turtles, fish, etc. He conducted new “experiments” on a weekly (sometimes daily) basis, much to the astonishment of his (exceptionally patient) mother. Scott attended Carroll College (now Carroll University) in Waukesha, Wisconsin. There he further pursued his interest in chemistry, especially organic chemistry. However, by the end of his third year it was clear that his real interest was physical chemistry, a more theoretical, less laboratory-intensive version of chemistry. Indeed, Scott’s skills weren’t in the laboratory, which should have been clear to him much sooner since the laboratory potion of classes always brought down his grade – unlike for his fellow students. During this time his interest in physics grew. In his last year in college, Scott was fortunate to be able to take graduate-level classes and conduct research in physics under the direction of his advisor, as part of a self-designed curriculum toward a BS in chemistry and physics, which he received in 1993. Scott did his graduate work at the University of Kansas in Lawrence, where he investigated the dynamics of complex liquid systems using computer simulations and theoretical techniques. His work on supercooled liquids and glasses remains well cited even today. Scott received his PhD with honors in 1997 in theoretical chemical physics. Thereafter, he was awarded a National Research Council Fellowship and joined the Army Research Laboratory in Aberdeen, MD. There he used computational and theoretical techniques to study the dynamics of explosives. Scott pioneered a new approach to parameterizing interaction potentials necessary for accurate computer simulations. His work was well recognized, and upon the completion of his fellowship, he was immediately offered a full-time position. However, Scott had other plans. Intent on pursuing a career in academia, Scott took a research associate position (and a 50% salary cut) at Colorado State University. While computer simulations once again played a role in his work, the majority of his time at the office involved “old-school, paper and pencil” theoretical physics on fluid systems. In fact, his paper A Kinetic Theory for Dilute Dipolar Systems required more than 300 pages of derivations! When his term at Colorado State was finishing up after two years, he began looking for permanent employment. He attended a recruiting session at the university held by Johnson & Johnson that gave an overview of the drug discovery research at its San Diego site and potential employment opportunities. Although scheduled for an interview the following day, he had intended to pass on the opportunity. Some wise advice from a friend convinced him otherwise. Currently, he is a Principal Scientist in the Computer-Aided Drug Discovery group at Johnson & Johnson Pharmaceutical Research & Development in San Diego, CA, where he has worked since 2002. During his time there, he has made substantial contributions to numerous drug discovery projects and has worked in a variety of disease areas. Contents I The First Law: Energy 1 Nothing for Free 3 The Conservation of Work 2 Swinging, Falling, and Rolling 6 The Initial Foundations of Energy 3 Untangling the Mess 18 Energy, Momentum, Force, and Matter 4 The Missing Link 25 Heat: The Final Piece in the Energy Puzzle II Nature’s Compensation: Entropy 5 Thoughts of Heat Engines 33 The Thermodynamic Origins of Entropy 6 Dissipation 43 The Relationship Between Heat and Work 7 The Preferred Direction 52 Entropy as Nature’s Signpost 8 The Other Side of Entropy 58 Entropy’s Connection to Matter and Atoms III The Pieces: Atoms 9 Speculations of Atoms 71 Thoughts of Existence Pave the Way for Atoms 10 Two New Philosophies 80 Rational Versus Spiritual View of Nature 11 Realizing Atoms 90 The Physical Foundations of the Atom 12 Final Doubts to Rest 101 The Atom as Physical Reality vi IV Uncertainty: Quantum Mechanics 13 Discrete 113 Energy’s Devious Secret 14 Light Quanta 126 Particles and Waves: The Beginning 15 The Quantum Atom 138 Revisiting the Atom 16 Quantum Mechanics 150 Nature’s Lottery Epilogue 179 From Here to There Bibliography 181 vii Preface As I sat with the “final version” of the manuscript, looking it over for “one last time” (a lie I had told myself so many times before, and each time fully believing it), I sighed; this time I had it. A brief conversation with a friend had started me down this long, often wayward, journey of writing my first popular science book, or, as I like to call it, a “science story.” My friend had recounted to me something they had read by a popular science writer. I was intrigued – not so much by the story itself (honestly, I have forgotten both the writer and the story), but rather by my friend’s excitement with what they had read. Let’s face it: science doesn’t often incite this response in the majority of people. So, as a scientist myself, it was uniquely rewarding for me to witness that enlightened moment my friend had experienced; I wanted to create those types of insightful science moments for others. Moreover, there’s a long, rich history of pivotal scientific achievements that have been clouded or simply ignored by the current popular science literature, and I wanted to bring these to light as well. It was these reflections that motivated me to write a popular science book. Thus began a journey that started in August of 2009. I was originally convinced that I could finish this project in two years. However, in the ensuing two years many things happened: I suffered paralysis in my left hand in a martial arts training accident but continued to write, before surgery and during the almost two-year recovery process, albeit a bit at a slower pace; got married and had four ceremonies (two in San Diego, one in Wisconsin, and one in China); took on more responsibility at work (I still have my day job); lost my mom; and became a dad. While all these things undoubtedly contributed to the extended time frame, they’re not the main reasons. I had a particular vision for the book, and I refused to publish it until it was realized. This, in addition to my bit of OCD and touch of perfectionism, resulted in a much-extended timeline. Nonetheless, I think (and I hope you do too) it was worth it. As I see it, a major stumbling block for the popularity of science is its presentation. It’s often presented in a very dry, dull manner. Many of you have taken those classes, seen those videos, heard those talks … and so have I. Clearly, for me (and other scientists) those things weren’t major setbacks – we became scientists, after all. Sure, we found some of those things boring, too (yes, scientists are human beings), while other parts of it we found quite exciting. For me the bottom line is this: science is a passion. My passion for science began when I was very young, around five years old. Back then “science” was about taking apart electronics and performing experiments – all humane! – on insects and garden-variety suburban amphibians. In fact, I will never forget when in second grade I went to our (very small) school library to check out a book on how electricity worked. In a quite discouraging tone the librarian said, “Wouldn’t you much rather check out a book with a nice story?” To which I replied, “Nope.” For most of my childhood I suffered from pretty bad allergies and asthma, which meant I missed a lot of school. The routine that was set up early in my academic life was this: I stayed home from school, Mom picked up my homework from my teachers, and I worked on it at home – sort of a power version of home schooling, if you will. And I always worked ahead when it came to my science and math classes. I guess you can say that science kept me engaged in school viii during those rather difficult years, providing me with a perspective that persisted into adulthood and has remained with me ever since. You see, I’ve been a scientist for a long time now, officially since 1997 when I got my PhD in theoretical chemical physics. Like I said, I became a scientist because I have a passion for it.