Life's Ratchet: How Molecular Machines Extract Order from Chaos
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Kinetic theory of matter, 133
Krebs cycle, 193, 194
Lac-operon, 235–236
Lagrange, Joseph Louis, 30
La Mettrie, Julien Offray de, 22–26, 60
clock analogy and, 25, 214
denial of soul, 24–25
irritability and, 24, 34
rejection of chance, 25–26
Landauer, Rolf, 131, 132
Laplace, Pierre-Simon, 30, 43, 54
Large Hadron Collider, 241
Laser trap, 173
Laser tweezers, 173–175
Lavoisier, Antoine, 29–30, 39, 193
Law of energy conservation, 37–38, 40, 41, 70, 74, 126–127
Law of errors, 54, 55
The Laws of the Game (Eigen), 66
Leeuwenhoek, Antonie Philips van, 22
Leibniz, Gottfried, 21, 37
Lenoir, Timothy, 32n
Liber De Ludo Aleae (Cardano), 49
Liebig, Justus von, 39, 193
Life
chance and necessity and, 214–215, 246
clock analogy, 25, 66, 214
complexity of, 245–246
defining, 1–2, 3–8, 229–230
as game of chance, 66
heat and, 17, 26–30
molecular machines and, 242, 243–244
noise and chaos and, 3
as process, 229–231
randomness and, 56–60
See also Living organisms
Life energy, 3–4
Life force, 3–4, 9–44, 243
animal heat, 26–30
animism, 11–12
atomism, 13–17
chaos as, 7–8
conservation of force and, 36–41
Darwin and, 41–44
energy and, 10–11
irritability and, 34–36
l’homme machine, 22–26
mechanical philosophy, 19–22, 30–34
medicine and, 18–19
origin of idea of, 11–13
vitalism, 12–13
See also Vital forces; Vitalism/vitalists
Life tables, 53–54
Ligase, 204
Liphardt, Jan, 135–136
Lipid molecules, cooperativity and, 104–106, 107
Liquids, molecular layers of, 118–120
Living organisms
clock analogy, 25, 66, 214
electricity and study of, 35–36
as open, dissipative systems, 86–87
watch analogy, 214–216
Loose coupling, 159, 160, 162–167
Loschmidt, Josef, 133
Loschmidt’s demon, 133
Lottery, 51–52
Lubrication, at nanoscale, 98
Lucretius, 14
Lysosomes, 169, 170
Machines, efficiency of, 126–127
Macroscopic world, order of, 68
Macrostates, 75–76
Magic, alchemy and, 18
Man a Machine (L’homme machine) (La Mettrie), 23, 24
Mass transport, in snow crystal growth, 102–103
Matei, George, 118
Matrix metalloproteinase (MMP), 209–211
cancer and, 234–235
Matrix metalloproteinase 1 (MMP-1), 210
Matrix metalloproteinase 2 (MMP-2), 234
Matrix metalloproteinase 14 (MMP-14), 233–234
Matter
graininess of, 98
kinetic theory of, 133
Maxwell, James Clerk, 55, 68, 69, 71, 125–126
Maxwell’s demon, 128–129, 131–132, 156
impossibility of realizing, 137
Smoluchowski’s simplified version, 138
Mayer, Julius Robert von, 37–38, 137
Mayow, John, 27–28
Mayr, Ernst, 94–95, 229, 230, 239
Meaning, information vs., 222–223
Mechanical energy, conversion from chemical energy to, 184–187
Mechanical philosophy, 19–26
conservation of energy and, 36–41
limitations of, 31–34
Mechanism, purpose vs., 41–44
Medicine
Galen and, 17–18
Harvey and, 19–20
Memory formation, 237
Mendel, Gregor, 43–44, 61
Méré, Chevalier de, 50
Messenger RNA (mRNA), 202, 208, 209
Micelles, 116
formation of, 104–105, 106, 107
Micrographia (Hooke), 4, 22
Microscope, invention of, 22
Microstates, 75–76, 77
Microtubule filaments, 108, 110
Microtubules, 90, 160, 169, 170
Mitchell, Peter, 194–195
Mitochondrion, 169, 170, 192–200
ADP/ATP and, 159
Mitosis, 182, 233
Mlodinow, Leonard, 54
MMP. See under Matrix metalloproteinase (MMP)
Moivre, Abraham de, 54
Molecular biology, 63–66
Molecular circuits, 121–122
Molecular feedback loop, 153–154
Molecular layers, of liquids, 118–120
Molecular machines, 94, 122–124
activation energy and, 146–150
cancer and, 3
cellular functions of, 169–170
chaos and, 7, 138, 145–146, 158, 168, 212, 226, 230, 238, 242
coupling and, 159–168
efficiency of, 144
energy for, 158–159
enzymes and, 149–154
evolution of, 218–221, 226–227
Feynman’s ratchet, 138–141
free energy and, 157–159
molecular storm and, 7, 145–146
molecular tracks and, 154–155
motion of, 162–166
power density of, 144–145
regulation of, 231–233
reset step, 155–158
second law of thermodynamics and, 127–128
understanding life and, 242, 243–244
See also Maxwell’s demon
Molecular motors (motor proteins), 160–162, 170–192
ATPase and, 171–172
dynein, 170, 171
kinesin, 170, 171, 176–182
measurement of, 172–176
myosin, 170–171, 176, 182–192
Molecular scale, complexity of, 6–7
Molecular storm, 14, 72
creation of snowflake and, 83
evolution and, 225–226
free energy and, 83–85
harnessing energy of, 138–141
life force and, 243
molecular machines and, 7, 145–146
protein shape and, 114–115
reset step and, 157–158
role of random thermal noise of, 167–168
Molecular switching, 220, 237
cooperativity and, 121–122
Molecular tracks, 154–155
reset step and, 156
tight and loose coupling and, 159–166
Molecules
evolution of, 216–217
purposeful action and, 5
self-assembly of, 100–115
statistical mechanics and, 68–69
Monads, 21
Monastrol, 233, 234
Monod, Jacques, 144, 151
allostery and, 153
lac-operon pathway, 235–236
role of chance in history of life, 6, 57, 58–60, 224–225
Moore, Walther J., 63
Morgan, Thomas Hunt, 61
Motility assays, 90
Motion
atomic, 71–73
Brownian, 56, 71–72, 105–106, 129
hydrolysis of ATP and, 184–187
of kinesin-1, 176–181
loose coupling and, 162–167
molecular, 160–166
of myosin V, 176, 182–187
purposeful, 5, 12, 13, 14, 15, 16
random (see Random motion)
thermal (see Thermal noise (the
rmal motion))
tight coupling and, 160–162
Motor domain, 232
of kinesin-1 and myosin V, 176–177
in kinesins, 181
Muller, Hermann Joseph, 62
Müller, Johannes Peter, 38
Muscle, structure of, 188
Muscle cells, myosin II and, 187–189
Mutations, 62–63, 64
thermal motion and, 225–226
Myosin, 90, 170–171, 209
myosin I, 189, 192
myosin II, 167, 183, 184, 187–189
myosin V, 176, 182–187, 189, 192
myosin VI, 192
myosin VII, 192
myosin IX, 192
classes of, 170
family tree, 190–191
G proteins and, 220
superfamily, 189–192, 221
N terminus, kinesins and, 181
NAD+, 193
NADH, 193, 194
Nanobot, 93
Nanophysics, 90–91
Nanoscale, 91–94
assembly at, 100–115
energy equality at, 122–124
scanning probe microscopes, 94–96
violation of second law of thermodynamics and, 134–136
Nanoscience, 92–93
cooperativity, 104–106, 116–120
entropic forces, 106–110
hydrophobic forces, 110–112
molecular switching, 121–122
physical rules in, 97–99
quantum-mechanical effects, 99–100
thermal noise (thermal motion), 100, 122, 123–124
Nanostructures, creation of, 103
Nanotechnology, 5, 92
Natarajan, Arun, 2
Of Natural and Supernatural Things (Vesalius), 18
A Natural History of the Soul (La Mettrie), 23
Natural selection, 41–44
Natural Theology (Paley), 42, 214
Nature, La Mettrie and, 25–26
Naturphilosophie, 32
Necessity, chance vs., 6–8, 222, 224–225, 243, 246
Negative feedback, 153
Neutrons, 84
Newton, Isaac, 21–22, 36, 37
Newton’s cannonball, 128
Noise, life and, 3
Noji, Hiroyuki, 196–197
Noller, Harry, 219
Normal distribution, 54–55
Nuclear fusion, 84
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