Life's Ratchet: How Molecular Machines Extract Order from Chaos (52 page)

Nucleotide bases,
201
,
202
,
205

Nucleus, cell,
169
,
170

Octamethyl-cyclo-tetrasiloxane (OMCTS),
118–120

Oils,
104
,
110
,
111

On Growth and Form
(Thompson),
7
,
57

The Onion
(newspaper),
144

“On the Nature of the Gene Mutation and the Gene Structure” (Delbrück et al.),
63

Open systems,
85–87

Operon,
235–236

Oral, Ahmet,
96

Order from order principle,
65–66

Origin of Species
(Darwin),
42
,
60

Osmosis,
211–212

Osmotic pressure,
105–106

Özer, Özgür,
96

Paley, William,
42
,
213–216

Pantoprazole,
232

Paracelsus,
18

Particle physics,
241–242

Pascal, Blaise,
50–53

Pascal’s triangle,
51–52
,
54

Patil, Shiva,
118–119

Paulze, Marie-Ann Pierrette,
29

Perpetuum mobile,
136–137

Perrin, Jean,
72

Persistent activation,
236–237

Pethica, John,
96–97

The Phenomenon of Man
(Chardin),
58

Philosophiae Naturalis Principia Mathematica
(Newton),
36

Phlogiston theory of fire,
29–30

Phosphoglucomutase,
150

Physical forces, explanation of life and,
60

Physical rules in nanoscience,
97–99

Physics

biology,
237–240

evolution and,
60–63

Rutherford on,
2

Physics Today
(journal),
144

Plato,
15
,
26

Pneuma,
15
,
17

Points, problem of,
50–53

Poker,
47–48

Positive feedback,
153

Power,
10

Power density of molecular machines,
144–145

Preformationism, mechanical philosophy and,
31–32

Prey
(Crichton),
92

Probability,
47–48

molecular motion and,
163
,
164
,
165

theory of,
48–50

Proceedings of the Natural History Society of Brünn
(journal),
43

Proceedings of the Royal Society
(journal),
137

Proctor, Bob,
10

Promoter,
206

Protein folding,
112–115
,
223

Protein shapes,
113–115

Protein synthesis,
200
,
207–209

Proteins,
107–108

enzymes and,
150

evolution of,
217–218

stability of,
117

See also
Molecular motors (motor proteins)

Proton-motive force,
196
,
197

Protons,
84

Pumps,
211–212

Purpose, mechanism
vs.,
41–44

Purposeful motion,
5
,
12
,
13
,
14
,
15
,
16

Pyruvate,
193

Pythagoras,
14
,
26

Quantitative analysis, life and,
19–20

Quantum-mechanical effects,
99–100

Quantum mechanics,
56
,
61

Quarks,
84
,
241

Quetelet, Adolphe,
54–55

Radiation

mutation and,
62
,
64

quantum mechanics and,
61

Ramanujan, Chandra,
96

Random motion,
5

Democritus and,
13
,
14

loose coupling and,
162–167

Randomness,
46–47
,
66
,
245

debate over,
56–60

molecular scale and,
7

physics and,
60–61

protein folding and,
115

See also
Chance

Random stacking,
79–80

Ratchet

evolution as,
225–226

Feynman’s,
138–141

Reductionism,
4–6
,
238–242

Regression toward the mean,
55–56

Regulation,
231–233
,
235–237

Regulatory networks,
235–237

Renaissance,
18

Rennin,
112

Repair enzymes,
64
,
117

Replication,
202–205

Repressor protein,
236

Reset step

ATP hydrolysis in myosin V and,
186–187

in kinesin-1,
181

for molecular machines,
155–158

Reversibility,
133–136

Reversible machine,
158

Ribosome,
207–209

evolution of,
219–220

Ritter, Johann Wilhelm,
36

RNA,
202
,
205–207

as enzyme,
219–220

translation and,
207–209

RNA polymerase,
206–207
,
208
,
209
,
236

Rohrer, Heinrich,
95

Russell, Bertrand,
244–245

Rutherford, Ernest,
2

Saint Augustine,
15

Saint Thomas Aquinas,
16

Sakamoto, Takeshi,
182–187

Scanning probe microscopes (SPMs),
94
,
95–96

Scanning tunneling microscope (STM),
95–96

Schleiden, Matthias Jakob,
33

Schlichta, Paul,
92
n

Scholasticism,
16

Schrödinger, Erwin,
6
,
63–66
,
116
,
214

Schrödinger’s cat,
128

Schwann, Theodor,
33

Science
(journal),
236

Scientific revolution,
21

Searson, Peter,
2

Second law of thermodynamics,
76–80

free energy and,
82

Maxwell on,
126

Maxwell’s demon and,
128–129
,
131–132

molecular machines and,
127–128

molecular storm and,
144

nanoscale systems and,
134–136

Smoluchowski’s trap door,
129–130

as statistical law,
130

violation of,
128–132

vital force and,
136–137

The Secret
(Byrne),
3
,
11

The Secret
(film),
10
n