Life's Ratchet: How Molecular Machines Extract Order from Chaos (46 page)

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.

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.

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.

“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