Life's Ratchet: How Molecular Machines Extract Order from Chaos (53 page)

Self-assembly,
100–115

energy
vs.
entropy and,
108–110

of micelles,
104–105
,
106
,
107

of snowflakes,
101–103

Sellers, Jim,
183–184

Shape

of molecular machines,
146

myosin II and cellular,
187

of protein,
113–115

Shelley, Mary Wollstonecraft,
34–35

Shelley, Percy Bysshe,
34

SHRIMP,
175

Signaling pathways,
235–237

Sisyphus,
156–158

Smoluchowski, Marian von,
129–130

on chance and laws of probability,
133

simplified version of Maxwell’s demon,
138

Snowflakes, formation of,
82–83
,
101–103

Sodium-potassium pump,
212

Soul,
12–14
,
16

Descartes and,
20

La Mettrie’s denial of,
24–25

Spacey, Kevin,
48

SPMs.
See
Scanning probe microscopes (SPMs) Spudich, Jim,
175–176

Stahl, Georg Ernst,
29

Stars,
85

Statistical mechanics,
3
,
60–61
,
68–69

molecular motion and,
163

Schrödinger and,
65
,
69

Statistics,
53–56

Steam engines, as analogy for life,
25
n

Stevenson, John,
28

Stiffness, of molecule-thick water layers,
118–120

STM.
See
Scanning tunneling microscope (STM)

Stoics,
15
,
60

The Strategy of Life
(Lenoir),
32
n

Subba-Rao, Venkatesh,
101

Supernovae,
85

Surface-to-volume ratio, in nanoscale,
98–99

Sutton, Walther,
61

Swerve,
14

Systems biology,
235–237

Szilard, Leo,
131

Targeted drug delivery,
93–94

Teleomechanism,
32–34

Temperature

free energy and,
80–81

molecular motor speed and,
167–168

motion of kinesin and,
179

self-assembly and,
109

Thales,
13

The Theory of Heat
(Maxwell),
126

Theory of probability,
48–50

“There’s Plenty of Room at the Bottom” (Feynman),
91–92
,
93

Thermal energy,
70
,
73
,
74

Thermal noise (thermal motion),
72
,
100

cellular activity and,
65

chaos and,
145–146
,
168
,
205
,
226

molecular machines and,
122
,
123–124
,
174

mutations and,
225–226

Thermodynamic equilibrium,
85

Thermodynamics,
60

biology and,
30

first law of,
73

second law of (
see
Second law of thermodynamics)

This Is Biology
(Mayr),
229

Thompson, Benjamin (Count Rumford),
29
,
70

Thompson, D’Arcy Wentworth, role of chance in history of life,
7
,
57–58
,
60
,
224–225

Threonine,
151–152

L-Threonine deaminase,
151–152
,
153

Thymine,
201
,
202

Tight coupling,
159–162
,
166
,
167

Timaeus
(Plato),
26

Timoféeff, Nikolai,
62
,
63
,
64

TIMP-2,
233–234

TIRF,
175

Topoisomerase,
203
,
204

Tourney, Christopher,
92
n

Transactions of the Scientific Society of Göttingen
(journal),
62

Transcription,
202
,
205–207
,
208

Transfer RNA (tRNA),
207–209

Transistor,
122

Transition state, in chemical reactions,
146–147
,
148

Translation,
202
,
207–209

tRNA synthetases,
208–209

Tropomyosin,
189

Tunneling,
95–96
21
(film),
48

Universe,
243–246

Uracil,
205–206

UTP,
206

The Vengeful Faculty
(La Mettrie),
23

Vesalius, Andreas,
19

Vesalius, Basilius,
18

Vesicles,
106
,
107
,
182

Vibrational energy, ATP/ADP conversion and,
159

Vinci, Leonardo da,
49

Virchow, Rudolf,
33

Virtual cells,
236

Viruses, self-assembly of,
110

Viscosity,
98

Vital forces,
32–33

experiments disproving necessity of,
38–40

explanation of life and,
60

impossibility of
perpetuum mobile
and,
137

See also
Vitalism/vitalists

“Vitalisms and Animalisms” (Monod),
58–59

Vitalism/vitalists,
7
,
12–13
,
14
,
15
,
238–239

chance
vs.
necessity and,
60

conservation of energy and repudiation of,
36–41

discrediting of,
60

epigenesis and,
31–32

Galen and,
17

irritability and,
34–36

teleomechanism and,
32–34

Voltage, across the membrane,
194

Voltaire,
21
,
58

Waiting state,
177–178

Walker, John E.,
195

Walking transport motors

kinesin-1,
176–181
,
232

myosin V,
176
,
182–187
,
189
,
192

Wallace, Alfred Russell,
41

Watch, as analogy for living organism,
214–216

Water molecules

cooperativity and,
117–120

hydrogen bonds and,
110–111

Watson, James,
6
,
201–202

Wave mechanics,
63

Weinberg, Steven,
241

Weizman Institute of Science,
219

“What I Believe” (Russell),
244–245

What Is Life?
(Schrödinger),
6
,
63–64
,
225

Xenophanes,
13

X-synthase,
171

Yanagida, Toshio,
167
,
179

Young’s modulus,
98

Zeno of Citium,
15

Zimmer, Karl,
62
,
63
,
64