Life's Ratchet: How Molecular Machines Extract Order from Chaos
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CHAPTER 4
Drexler, K. Eric. Engines of Creation 2.0. E-book. WOWIO, 2006. Available at www.wowio.com/users/product.asp?BookId=503.
Feynman, Richard. “There’s Plenty of Room at the Bottom.” Caltech Engineering and Science 23 (February 1960): 22–36. Available at www.zyvex.com/nanotech/feynman.html.
Nelson, Philip. Biological Physics: Energy, Information, Life. New York: W. H. Freeman, 2008.
Philips, Rob, and Stephen R. Quake. “The Biological Frontier of Physics.” Physics Today (May 2006): 38–43.
CHAPTER 5
Feynman, Richard. Feynman Lectures on Computation. Reading, Mass.: Perseus, 2000.
Gamow, George. Mr. Tompkins in Paperback. Canto ed. Cambridge: Cambridge University Press, 1993.
Mahon, Basil. The Man Who Changed Everything: The Life of James Clerk Maxwell. New York: Wiley, 2003.
CHAPTER 6
Astumian, R. Dean. “Making Molecules into Motors.” Scientific American (July 2001).
Astumian, R. Dean, and Peter Hänggi. “Brownian Motors.” Physics Today (November 2002): 33–39.
CHAPTER 7
Boyer, Paul. “Energy, Life, and ATP.” Nobel Lecture, December 8, 1997. Available at http://nobelprize.org/nobel_prizes/chemistry/laureates/1997/boyer-lecture.html.
Cooper, Geoffrey. The Cell: A Molecular Approach. Washington, D.C.: ASM Press, 1997.
Hoagland, Mahlon, and Bert Dodson. The Way Life Works. New York: Three Rivers Press, 1995.
Walker, John. “ATP Synthesis by Rotary Catalysis.” Nobel Lecture, December 8, 1997. Available at http://nobelprize.org/nobel_prizes/chemistry/laureates/1997/walker-lecture.html.
CHAPTER 8
Paley, William. Natural Theology. Available at “The Complete Works of Charles Darwin Online,” http://darwin-online.org.uk/content/frameset?itemID=A142&viewtype=text&pageseq=1.
CHAPTER 9
Alon, Uri. An Introduction to Systems Biology. Boca Raton, Fla.: Chapman & Hall/ CRC, 2007.
Margulis, Lynn, and Dorion Sagan. What Is Life? Berkeley: University of California Press, 1995.
Mayr, Ernst. This Is Biology: The Science of the Living World. Cambridge, Mass.: Harvard University Press, 1997.
Suggested Reading
This is an annotated list of books that I highly recommend for further reading. They may help clarify topics mentioned in the book, or continue a topic where the book left off.
ATOMISM
Greenblatt, Stephen. The Swerve: How the World Became Modern. New York: W. W. Norton, 2011. Delightful reading about impact of ancient Greek and Roman atomistic ideas on modern science.
COMPLEXITY
Kauffman, Stuart. At Home in the Universe: The Search for the Laws of Self-Organization and Complexity. New York: Oxford University Press, 1996. Thought-provoking ideas about self-organization, complexity, and the origin of life, from one of the best-known complexity theorists.
Waldrop, M. Mitchell. Complexity: The Emerging Science at the Edge of Order and Chaos. New York: Simon & Schuster, 1992. A highly readable, almost journalistic account of the early days of complexity research. Although the book is older, the topics discussed are just as relevant today as they were in the early 1990s.
DEVELOPMENT
Carroll, Sean. Endless Forms Most Beautiful: The New Science of Evo Devo. New York: Norton, 2005. This book and Carroll’s The Making of the Fittest, below, provide a superb introduction into evolutionary development (“evo devo”)— the theory of how bodies get their shapes and how these shapes evolve.
———. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. New York: W. W. Norton, 2006. See notes on Endless Forms Most Beautiful, above.
EVOLUTION
Dawkins, Richard. The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution. New York: Houghton Mifflin, 2004. My favorite Dawkins book (but all his books are recommended). A travel back in time, species by species, to the origin of life.
Pallen, Mark. The Rough Guide to Evolution. New York: Penguin Books, 2009. A quick, but surprisingly detailed introduction to evolution. A fun read.
Zimmer, Carl. Evolution: The Triumph of an Idea. New York: Harper Collins, 2001. A companion book to the highly recommended PBS TV series. Superb explanations, good writing, and many, many illustrations.
GENETICS
Ridley, Matt. Genome: The Autobiography of a Species in 23 Chapters. New York: Harper Perennial, 2000. A great introduction to the human genome. Each chapter covers a chromosome. The writing in this book is excellent.
MOLECULAR BIOLOGY
Harold, Franklin M. The Way of the Cell: Molecules, Organisms, and the Order of Life. New York: Oxford University Press, 2003. A very readable, popular introduction to cell biology.
Hoagland, Mahlon, and Bert Dodson. The Way Life Works. New York: Three Rivers Press, 1995. This book is also listed in sources, but I list it here again because I believe that everybody who has any interest in biology must have this book. It is a unique combination of humor and cartoons and a serious introduction to molecular biology. This is the best book to get you up to speed.
Lane, Nick. Power, Sex, Suicide: Mitochondria and the Meaning of Life. New York: Oxford University Press, 2005. A detailed, but very readable account of how energy is generated in cells, but it also branches out into many fundamental questions, such as why there are two sexes.
Rensberger, Boyce. Life Itself: Exploring the Realm of the Living Cell. New York: Oxford University Press, 1996. A well-written, popular introduction to cell and molecular biology.
MOLECULAR MACHINES
Jones, Richard. Soft Machines: Nanotechnology and Life. New York: Oxford University Press, 2007. Covers ground similar to Life’s Ratchet, but with less emphasis on the physics and more emphasis on nanotechnology. A good read.
Nelson, Philip. Biological Physics: Energy, Information, Life. New York: Freeman, 2008. Although I already listed this book in my sources, I list it here again because of its importance to Life’s Ratchet. This book inspired me to write the book in the first place. Biological Physics is the most interesting and well-written textbook I have ever read. However, it is quite technical, so buy it only if your calculus and physics are solid.
ORIGIN OF LIFE
Davies, Paul. The Fifth Miracle: The Search for the Origin and Meaning of Life. New York: Simon & Schuster, 2000. A very readable introduction to theories about life’s origin.
Hazen, Robert. Genesis: The Scientific Quest for Life’s Origin. Washington, D.C.: Joseph Henry Press, 2007. A very readable, personal account of an origin of life researchers. Up-to-date.
SELF-ORGANIZATION AND PATTERNS IN NATURE
Ball, Philip. The Self-Made Tapestry: Pattern Formation in Nature. New York: Oxford University Press, 2001. A detailed and beautifully illustrated account of the spontaneous formation of patterns in nature. A modern update of D’Arcy Thompson’s Growth and Form.
THERMODYNAMICS AND LIFE
Brown, Guy. The Energy of Life: The Science of What Makes Our Minds and Bodies Work. New York: Free Press, 1999. A popular account of how thermodynamics plays into human life, from the thermal motion in our cells to losing weight.
Kurzynski, Michal. The Thermodynamic Machinery of Life. The Frontiers Collection. Berlin and New York: Springer, 2006. A very technical, but profound discussion of thermodynamics and life.
Schneider, Eric. Into the Cool: Energy Flow, Thermodynamics, and Life. Chicago: University of Chicago Press, 2006. Discusses not only how life and the second law of thermodynamics are compatible, but how the second law is necessary to explain life.
Acknowledgments
A book that starts in ancient Greece and ends up with today’s cutting-edge research cannot possibly be created by one person alone. A number of people have, directly or indirectly, inspired, helped, worked on, or otherwise enabled me to write this book, and for this I thank them.
First, I thank my lovely and intelligent wife, artist and fellow science enthusiast Patricia Domanski, who
spent numerous hours reading, criticizing, editing, and correcting draft after draft, until the last vestiges of meandering sentences, dragging paragraphs, and useless words were removed. If there are any of them left, it is entirely my fault. My discussions with her inspired many ideas in the book, and I must especially thank her for having almost infinite patience with me.
I also thank my parents and teachers, who have instilled a great love for learning in me, a gift that has driven me to always want to learn and experience new things. One result of this gift is this book. I also thank Professor Herbert Granger from the Wayne State University Department of Philosophy, who set me straight on pre-Socratic philosophy; Professor Rafael Fridman (WSU Pathology) and Professor Heinrich Hoerber (now at University of Bristol), who got me started in biology-related research; and my physics colleague, Dr. Takeshi Sakamoto, who answered my many questions about molecular machines.
Last, but not least, I want to thank my agent, Russell Galen, who was so kind to take a chance on me, even though my first attempt at a book proposal was less than stellar, and my editors at Basic Books, T. J. Kelleher and Tisse Takagi, for all their valuable suggestions and support.
Index
“About the Concept of Chance and . . . Laws of Probability in Physics” (Smoluchowski), 133
“About the conservation of force” (Helmholtz), 38
Acetyl, 193
Acetyl coenzyme A, 193
Actin, 90, 108, 110, 154, 171
Actin filaments, 169, 170
myosin and, 183, 186, 187–189
Activation energy, 146–150
Adenine, 201, 202, 205
ADP (adenosine diphosphate), 159
kinesin-1 and, 177–178, 179
loosely coupled motor and, 165
mitochondria and, 192
myosin V and, 184–186
tightly coupled motor and, 161–162
AFMs. See Atomic force microscopes (AFMs)
Ahmed Zewail Gold Medal Award, 195
Air, heat and, 28–29
Alchemy, 18
Aldini, Giovanni, 35, 36
Allosteric enzymes, 151–154, 155
“Allosteric Receptors” (Changeux), 152
Allostery, 153, 179, 231–232
Amino acids, 112, 113, 202
Amphiphilic molecules, 104–105, 107
Anaximander, 13
Anaximenes of Miletus, 13
Ando, Toshio, 183
De Anima (Aristotle), 12, 13–14
Animal heat, 26–30
Animism, 11–12, 14, 20–21
Aquinas, Thomas, 16
Aristotle
defining life, 3
purposeful motion and, 5, 14, 15, 16
scholasticism and, 16–17
vitalism and, 12–14, 60
Artificial nose, 95
Astumian, Dean, 144–145
Atomic force microscopes (AFMs), 2, 94–95, 96–97
Ando high-speed, 183
to measure stiffness and damping of liquid layers, 118–120
Atomic motion, 71–73
Atomic-scale energy dissipation, 97
Atomism/atomists, 13–17, 20, 21–22, 238–239
Atoms, 68
Democritus and, 14
existence of, 56
statistical mechanics and, 68–69
Voltaire and, 21
ATP (adenosine triphosphate), 158–159
conversion of food into, 192–194
hydrolysis of, 171–172, 177–181, 184–187, 192
kinesin-1 and binding and hydrolysis of, 177–181
loosely coupled motor and, 165, 166
motion and hydrolysis of, 184–187
myosin II and, 188, 189
myosin V and, 184
speed of molecular motor and concentration of, 174
tightly coupled (kinesin) motor and, 161–162
in transcription, 206
ATP synthase, 171, 195–199
ATPase, 171–172
Base pairing, 201–202
Bead assay, 175–176
Becher, Johann Joachim, 29
Bechhoefer, John, 132
Beeckman, Isaac, 20
Bennett, Charles, 131, 132
Bhalla, Upinder S., 236
Biased diffusion, 178
Big bang
free energy and, 84–85
life and, 7
Binnig, Gerd, 3, 94, 95
Binomial coefficient, 52
Biology
application of statistics to, 55–56
physics and, 237–240
thermodynamics and, 30
Biophysics, 90
Bistability, 237
Blackjack, 48
Block, Steven, 173, 174, 176, 177, 207
Blumenbach, Johann Friedrich, 32–33
Boerhaave, Herman, 28
Boltzmann, Ludwig
existence of atoms and, 56
kinetic theory of gases and, 68, 69, 71, 133
Quetelet and, 55
Boveri, Theodor, 61
Boyer, Paul, 195–196
Boyle, Robert, 27–28
Brillouin, Leon, 131
Brown, Robert, 33, 71–72
Brownian motion, 56, 71–72, 105–106, 129
Brownian motors, 144
Brownian ratchet, 166
Burnt-bridge mechanisms, 211
Bustamante, Carlos, 135–136
Byrne, Rhonda, 11
Byron (Lord), 34
C terminus, kinesins and, 181
c-subunits, of ATP synthase, 200
Caloric, 29, 70
Calvin and Hobbes (comic strip), 46
Cancer
matrix metalloproteinases and, 210, 234–235
molecular machines and, 3
Cancer drugs, 233, 234
Cardano, Gerolamo, 48–50
Cargo-binding domain, in kinesin-1, 177, 178, 232
Carnot, Sadi, 127
Casein, 111–112
Catholic Church
Descartes and, 20
Gassendi and, 20
soul and, 16
“Cause of Animal Heat” (Stevenson), 28
Cech, Tom, 219
Cell nucleus, 33, 71, 169, 170, 202, 208
Cells, 169–170
control of, 150–154
crowdedness of, 107–108
discovery of, 22
DNA, 200–209
entropic forces and, 108–110
matrix metalloproteinases, 209–211
mitochondria, 169, 170, 192–200
molecular motors (motor proteins), 170–192
movement of, 90–91
observation of, 4
pumps, 211–212
virtual, 236
Cell theory, 22, 33
Cellular membrane, 169, 170
Central dogma, 223
Central limit theorem, 54, 55
Chance, 45–66
history of gambling, 47–53
La Mettrie and, 25–26
life and, 214–215, 246
mutations and, 62
necessity vs., 6–8, 56–60, 66, 222, 224–225, 243, 246
randomness, 46–47, 56–60, 66
statistics, 53–56
variation and atomic physics, 60–63
What Is Life?, 6, 63–66, 225
Chance and Necessity (Monod), 6, 58–59
Changeux, Jean-Pierre, 151–152
Chaos atoms and molecules and, 68–69, 135
as life force, 3, 5, 7–8
molecular machines and, 7, 138, 145–146, 158, 168, 212, 226, 230, 238, 242