Life's Ratchet: How Molecular Machines Extract Order from Chaos
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nanoscale and, 91, 123–124, 135, 158
thermal motion and, 145–146, 168, 205, 226
Chaperonin molecules, 114, 223
Chardin, Pierre Teilhard de, 57, 58, 60
Cheese making, 111–112
Chemical bonds
cooperativity of, 116
energy, 123, 124
See also Hydrogen bonds
Chemical energy
conversion into electrical energy, 193–194
conversion into mechanical energy, 184–187
Chemical reactions
activation energy and, 146–150
temperature and, 109
Chemi-osmotic process, 194
Christianity, material world and, 15–17
Chromokinesin, 182
Chromosomes, 61–62
Clock, as analogy for living organism, 25, 66, 214
Coefficient of correlation, 56
Coenzyme A, 193
Coiled coil, of kinesin-1, 177
Collagen
assembly of, 108–110
MMPs and, 209–210
Competitive inhibition, 151
Computer analogy of life, 25n, 230
Conservation of energy, 10–11, 37–41, 70, 73–74, 126–127
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, F0, 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
F0 unit, of ATP synthase, 197–200
F1 unit, of ATP synthase, 196–198, 199
De fabrica (Vesalius), 19
FADH2, 193, 194
FCS. See Fluorescence correlation spectroscopy (FCS)
Feedback loops
DNA and, 223–224, 235–236
molecular, 153–154, 231, 233
self-activating, 237
Fermat, Pierre de, 50–51, 52
Fernel, Jean François, 27
Feynman, Richard, nanoscience and, 91–92, 93, 97, 98, 100
Feynman’s ratchet, 138–141
Fibers, 154
Filaments, 154
Financial crisis of 2008, cooperativity and, 121
Fire, 29–30
First law of thermodynamics, 73
Flagella, self-assembly of, 110
Flavobacterium, 217–218, 220
Flemming, Walther, 61
Fludd, Robert, 20
Fluorescence correlation spectros
copy
(FCS), 175, 210
Fluorescence-based single-molecular techniques, 175–176
Fluorescent markers, for motor proteins, 175–176
Focused-ion beams, 100
Fokker-Planck equation, 163
Food, conversion into ATP energy, 192–194
Force, 10
entropic, 106–110
generated by hydrolysis of ATP, 172
hydrophobic, 111–112, 116
molecular motion and, 163
proton-motive, 196, 197
See also Life force; Vital forces
Frame-shift mutation, 217
Frankenstein (Shelley), 34–35
Franklin, Benjamin, 28
Free energy, 80–83
molecular machines and, 157–159
molecular storm and, 83–85
motion of kinesin-1 and, 179–180
reset step and, 157–158
self-assembly of molecules and, 101
FRET, 175
Friction, 28, 37, 70, 74, 77, 87, 134–136
Fridman, Rafael, 210, 233–234
Frog leg experiments, 35, 38–40
G proteins, 220
Galen, 17, 19, 27
Galileo, 21, 22, 128
Galton, Francis, 55–56
Galvani, Luigi, 35, 38
Gambling, 47–53
Games, interplay of necessity and chance in, 66
Gamow, George, 130
Gassendi, Pierre, 20–21
Gauss, Carl Friedrich, 54
Gavin, Sean, 241
Gedankenexperiment, 127–128
Gene, 202
Schrödinger and, 64–65
Genetic code, 202
Genetics, 43–44, 61–62
Gerber, Christoph, 94–95
Gibbs, Josiah Willard, 68
Glucose, 193, 194
Gluons, 241
God
Chardin and, 58
La Mettrie and, 25–26
materialist philosophy and, 20–21
randomness and, 46–47
reason and, 15
soul and, 16
theory of evolution and, 42–43, 44
Goldberg, Gregory, 209–210
Goldberg’s law of physics, 209
Golgi apparatus, 169, 170
Gradients, machines and, 127
Graininess of matter, 98
Graunt, John, 53
Gravitational energy, 70, 74, 77
Gravitational potential energy, 134–135
Gravity, 84–85
Greek philosophy, life force and, 12–17
Grimble, Ralph, 96
GTP, 206
Guanine, 201, 202, 205
Hänggi, Peter, 144–145
Harvey, William, 19–20, 26
Heart
function of, 19–20
heat and, 26–27
Heat
generation of animal, 26–30
life and, 17
as motion, 37
Heat energy, 70, 73, 74
Heinlein, Robert, 94
Helicase, 203, 204–205, 209
Helium, 84, 85
Helmholtz, Hermann von, 36–37, 63
biophysics and, 90
conservation of energy and, 37, 38–41, 60, 70, 126–127, 137
energy from food, 193
evolution and, 44
Helmont, Jan Baptist van, 27
Heredity, 61–62, 64
Hexagonal close-packing, 103
Hippocrates, 17
Hoerber, Heinrich, 3
Hohenheim, Phillippus Aureolus Theophrastus Bombastus von, 18
Holism, 5, 238–242
L’homme machine, 22–26
Hooke, Robert, 4, 22, 28, 33, 67
Human body
efficiency of, 136
as machine, 19–22
physical nature of, 24–26
transformation of energy by, 10–11
Human Genome Project, 224
Huxley, Andrew, 187
Huxley, Thomas Henry, 42, 217
Hydrogen, 84, 85
Hydrogen bonds
in DNA, 116, 201, 205
in water, 110–111
Hydrolysis of ATP, 171–172, 177–181, 184–187, 192
Hydrophilic head, of lipid molecules, 104–105, 107
Hydrophobic force, 111–112, 116
Hydrophobic tail, of lipid molecules, 104–105, 107
Ideal gas law, 65
Information, meaning vs., 222–223
Inheritance, 43–44, 61–62
Inhibition of enzymes, 151–154
Inhibitory binding, 231–232
Instability, creation of snowflake and, 102
Intelligent design, 223, 245
Interfaces, in nanoscale, 98–99
Irreducibility argument, 221–222
Irreversibility, 133–134, 158
Irritability, 24, 34–36
experiments disproving vital forces as necessary for, 38–40
Isoleucine, 151–152
Iyengar, Ravi, 236
Jacob, François, 153, 235
Janssen, Hans, 22
Janssen, Zacharias, 22
Jarzynski, Christopher, 134–136
Jeffries, Steve, 96
John the Evangelist, 15
Joule, James, 37
Jun, Yonggun, 132
Kant, Immanuel, 32–33
KIF1B, 182
Kielmeyer, Carl Friedrich, 33
Kinesin motors, 160–162, 167
Kinesins, 169, 170, 171, 209
kinesin-1, 176–181, 232
kinesin-2, 182, 232
kinesin-3, 182, 232
kinesin-5, 182, 233
kinesin-7, 232
classes of, 170
family of, 181–182
G proteins and, 220
measuring speed of, 173–174
regulation of, 232–233
superfamily, 221
Kinetic energy, 70, 72–75, 74, 85
Jarzynski’s equality and, 134–136
Kinetic theory of gases, 60, 71