Life's Ratchet: How Molecular Machines Extract Order from Chaos (48 page)

Continuum physics,
98

Control molecules,
152–154

Cooperativity,
104–106

of chemical bonds,
116–117

molecular switching and,
121–122

water molecules and,
117–120

Cow,
241–242

Creationists,
221–223
,
224
,
226

Crichton, Michael,
92

Crick, Francis,
6
,
201–202

Crystals,
64–65

CTP,
206

Cytosine,
201
,
202
,
205

Damping, of liquid layers,
118–120

Darwin, Charles,
71

chance
vs.
necessity and,
60

Paley and,
214

on question of Creation,
245–246

teleology and,
36

theory of evolution,
41–44

Dawkins, Richard,
222

The Day the Earth Stood Still
(film),
92

Delbrück, Max,
62
,
63
,
64

Democritus,
13
,
14
,
26
,
60

Depletion zone,
108
,
109

De rerum natura
(Lucretius),
14

Descartes, René,
214

energy conservation and,
37

on heat,
27

soul and,
4
,
20

The Description of the Human Body
(Descartes),
20

Despretz, César-Mansuète,
39

Development,
237

Dice,
49

Diffusion,
162
,
163
,
164
,
212

biased,
178

Diffusion limited,
103

Diffusion-limited aggregation,
103

Disorder, entropy and,
79

Dissipative systems,
86

Disulfide bridges,
116

DNA,
6
,
65

evolutionary changes in,
222

hydrogen bonds in,
116
,
201
,
205

information contained in,
222–223

as molecular track,
154–155

physical law and,
223

protein synthesis and,
115
,
200
,
207–209

as recipe,
100–101
,
223–224

replication of,
202–205

RNA and,
205–207

stability of,
116–117

structure of,
4
,
201–202

transcription,
202
,
205–207
,
208

translation,
207–209

DNA machines,
200–209

DNA operon,
236–237

DNA polymerase,
203
,
204

The Doctrine of Chances
(Moivre),
54

Drebbel, Cornelius,
22

Drexler, K. Eric,
94

Drift,
162
,
163

Drugs, regulation of molecular machines and,
232
,
233

Drunkard’s walk,
162

The Drunkard’s Walk
(Mlodinow),
54

Dualism,
20–21

Dulong, Pierre Louis,
39

Dynein,
169
,
170
,
171

Efficiency

of engines,
126–127

of human body,
136

Eigen, Manfred,
66
,
133

Einstein, Albert,
56
,
72
,
105–106
,
129

Electrical energy, conversion from chemical energy in cell,
193–194

Electricity, study of living organisms and,
35–36

Electromotor, F
₀
,
197–199

Electron-beam writers,
100

Electrons,
241

Electron transfer chain,
193–194

Electrostatic energy,
123
,
124

Elements, Greek conception of,
13
,
15
,
17
,
29

Embryology,
31–32
,
33

Endocytosis,
192

Energy,
69–70

activation,
146–150

chemical,
184–187
,
193–194

conversion of,
10–11
,
39–40
,
75–78

creation of snowflake and,
102–103

electrical,
193–194

electrostatic,
123
,
124

free,
80–83

gravitational,
70
,
74
,
77

gravitational potential,
134–135

heat,
70
,
73
,
74

mechanical,
184–187

at nanoscale,
122–124

open systems,
85–87

self-assembly and,
108–109

thermal,
70
,
73
,
74

See also
Free energy; Kinetic energy; Thermodynamics

Energy conservation,
10–11
,
37–41
,
70
,
73–74
,
126–127

Energy landscape

probability of motion and,
163
,
164

of protein,
113–114
,
115

Engines of Creation
(Drexler),
94

Entropic forces,
106–110

Entropy

big bang and,
84

creation of snowflake and,
102–103

defining,
76
,
79–80

free energy and,
81–82

Maxwell’s demon and,
131–132

self-assembly and,
108–110
,
111–112

See also
Second law of thermodynamics

Enzymes,
149–150

activation energy and,
149

allosteric,
151–154
,
155

cellular control and,
150–154

molecular machines as,
231–232

RNA as,
219–220

Epicurus,
14
,
15

Epigenesists,
31–32

Equality, Jarzynski’s,
134–136

Error law,
54
,
55

Escherichia coli,
lac-operon,
235–236

Eugenics,
55–56

European Molecular Biology Laboratory,
219

Evolution,
216–225

chance
vs.
necessity in,
222
,
225

Chardin and,
58

of molecular machines,
7
,
218–221
,
226–227

natural selection and,
41–44

physics and,
60–63

as ratchet,
225–226

Thompson and,
57–58

Ewald, Paul Peter,
63

Exclusion zone,
108
,
109

“Experimentally Demonstrable

Molecular Phenomena, Which Contradict Standard Thermodynamics” (Smoluchowski),
129

F
₀
unit, of ATP synthase,
197–200