Dynamics of Complex Systems Index

Inde x Bold numerals identify a key or defining reference. Numbers followed by the letter “f” indicate figures. 7±2 rule, 9, 348, 356, 362, 424, 623, 87 associative memory, 302-4, 331. See neural -helix, 423-4, 454, 467 network—attractor abstraction, 396, 404 assumptions, 89, 91-95, 102, 244, 258, 548, 652, 689 accept, 195, 489. See Monte Carlo logic, 236 activated dynamics, 173 asymmetry, 464, 563, 576, 615, 617, 716 activated processes, 57, 95 asymptotic, 482, 502 activation and inhibition, 629, 638, 641, 658, 690, 695 asynchronous, 300, 307, 632 active sites, 423, 470 attention, 416 activity, 5, 297, 300, 417, 622 attractor, 23, 116, 622, 625. See also neural network acyclic matrix, 192, 204, 227 attributes, 339, 394-5, 611 adaptive, 4, 298, 376, 426, 573, 574-5, 818-9 audition, 329. See also sensory processing address (location), 11, 303, 416 avalanches, 565-6 adiabatic process, 63 , 69, 83, 724 average, 39, 43, 90-1, 148, 179, 186, 188, 272 adrenaline (epinephrine, norepinephrine), 296, 396-7, Avogadro’s number, 13, 723 824 awareness, 416 affinity, 478, 620 axon, 297, 399, 418 aggregation, 92, 478, 502-27, 565, 676 aggression, 566, 615-9 -sheet, 424, 454, 467 alien life, 701 back-flow assumption, 102 align, 166 back-propagation algorithm 323, 325 alleles, 543, 605-11, 613 bacteria, 536-7 alphabet, 214 ballistic, 111, 192, 198, 204, 476 altruism, 566, 604, 615-9 barriers. See energy— barrier amino acids, 421-2 basin of attraction, 212, 302 -322, 377, 407, 470 glycine, 429f behaviorism, 404-5, 757 proline, 459 bias, 48, 52, 111, 182, 542, 558, 560, 611 propensity, 431 bifurcation, 32, 33f, 283 amorphous solid, 211 binary digit (bit), 214 analog/analogy, 256, 784, 786, 788-91, 816, 820 binary variable, 19, 97, 114, 146, 220, 299, 543 analytic continuation, 282 binomial coefficients, 44 AND (&), 237, 403 bipartite lattice, 162, 446 animals, 93, 386-7, 529 bloodstream, 296, 396, 418 anneal, 90, 106-108, 211. See also ensemble, simulated Boltzmann constant, 68 ant, 618 Boltzmann distribution, 84 anticorrelated, 255 Boltzmann factor, 97, 182 antiferromagnet. See magnet Boltzmann probability, 70-1, 77, 90, 94, 97, 146, antifreeze proteins, 183 190, 192 apes, 414, 602 Boltzmann normalization, 73 approximations, 186, 272, 425 Boolean algebra, 239, 716 area, 62, 75-6, 253 boredom, 391, 398 artificial intelligence, 296, 340, 758, 775-81 bottleneck. See entropy ASCII, 216, 218 boundary, 446-8, 465-6, 471, 487 aspects. See attributes boundary conditions, 114, 132, 257, 447-56 associations, 392, 394, 410 brain, 296, 328-9, 365, 393 839 840 Index Brownian dynamics, 198 completeness (logic), 240, 403 bubble chamber, 183-4 complex by design, 621 complex material, 92, 348, 366-70, 701, 791 canonical ensemble, 71, 97 complex organism, 92, 348, 366-70, 529, 623, 701, 751, Cantor set, 259 791 capacity. See memory—capacity complex systems, 2, 91-95, 745 casino, 54-6 field of, 1-2, 700, 789 catalyst, 536-7 complexity, 2, 6, 12-4, 162, 214, 269, 292-3, 406, 530-1, categorization, 303, 343 602, 695, 700-1, 703, 791 causality, 255 algorithmic, 235, 253, 693, 705-15, 724, 730 cell, 113, 297, 421, 536-7, 619, 622, 667. See also behavioral, 92, 716, 741, 752-7 cellular automaton, neuron, glial cell collective, 6, 746-51, 806-9 membrane, 536, 678, 688 computational, 269, 409 adhesion, 678 estimation, 704, 759-79, 814-5 differentiate, 621-6. See specialization frozen information, 719-22 division, 621 human intuition, 761-6 intercellular fluid, 629 human value, 778 pigment (melanophore), 627, 676 increase, 529, 532, 559-62, 597, 602, 619, 808-9, programmed cell death, 678 824-5 cellular automaton (CA), 9, 112-145, 187, 250, 477, limits, 781, 825 488-527, 627-48, 665-7, 690. See lattice gas, of a human being, 759-779 majority rule of numbers, 714 machine (CAM), 122 of physical systems, 716 Margolus (partitioned) rule, 133-139, 494 of sets, 715 mod2 rule, 114-120 plants and animals, 770-1, 816 multiple spaces, 132 profile, 14, 717, 722, 725-51, 755, 759, 805-15 pattern formation, 627-48, 665-7, 690 recognition, 715, 757-9 763 polymer, 488-98 transition, 805-25 center of mass, 485 components. See part , subdivision central control, 796-804, 823 composite patterns, 333-335, 340, 342, 345, 347-8, 372, central limit theorem, 47-52, 56, 110, 174, 197, 222, 309 389, 403, 407, 538, 611-4 cerebellum, 365, 414 compression, 232, 256-8, 692-3, 706, 764, 767, 773, 775 cerebrum, 337, 365 compulsion, 306, 397-8 chain . See polymer computation, theory of, 6, 112, 235-258, 694, 703, 706 chain of influence, 368, 612. See also order computer, 6, 253, 776. See development—program, channels, 331, 338, 339, 475-7, 555, 564, 598 pseudo-random numbers chaos, 32 -4, 120, 258, 283-8, 570, 579, 666, 725, 737, architectures, 112, 497 759 cellular automaton machines, 122, 488 characters, 216 memory, 11, 303 chemical, 60, 296-7, 392, 396, 418, 470, 478, 627, 648, nonuniversal, 409 787 parallel, 113, 187, 331, 488-9, 491, 497, 508, 597 catalysis, 652, 655 simulations, 7, 9, 19, 33, 40, 113, 476, 186-214 , 288, chemical switch, 687 305, 312-319, 347, 419, 424, 488-508, 513-6, stoichiometry, 653 519-27, 632, 779-80 reaction, 137, 629, 652-8 universal, 122, 236, 403, 409, 530, 777 classification, 304, 394-5, 701 concentration . See density chromosome, 537, 605, 611 condensation, 122 Church-Turing hypothesis, 236 conditional probability, 223 cluster, 180, 446 conformations, 425, 428 cognition, 404. See also mind conjugate gradient, 210 coherence, 13, 746-51, 806-8. See collective, cooperative consciousness, 329, 394, 411-6, 419. See also attention coherent noise, 355 consumption, 530, 562, 695-6 coherent transition, 432 contingent . See conditional coin toss, 38, 40, 41, 217, 256 continuity equation, 57, 649 collective, 153, 169, 456, 529, 533, 566, 604, 620, 819, continuum, 57, 78, 109, 251, 543, 551 821-2. See also coherent, cooperative, social control, 622, 804 collision, 84, 96-7, 103 convexity, 224, 739 communication, 214, 233, 489, 530, 707, 812 Conway’s Game of Life, 123, 127-130, 251, 641 communism, 799, 822 cooperative, 106, 179, 270, 431, 441, 454, 468, 530, 548, compass directions, 493, 496, 520 696, 818. See also collective compatibility, 343, 412 coordination, 809, 812-4 competition, 530, 532, 535, 548, 550, 582, 615-6 coordination number, 155  Index 841 corporation, 783-7, 789-90, 792, 799-803, 806 dinosaurs, 535, 566, 571 corpus collosum, 338 disjunctive normal form, 241 correlation, 13, 91, 155, 166-170, 222, 254-6, 268-9, disordered phase, 154 306, 308, 333, 335, 338, 340, 409, 434, 481, dissipative, 476, 550, 737 485, 500-1, 604-11, 746-51, 809. dissociation . See subdivision See also independent distinguishable. See indistinguishable function, 500 DNA, 421, 424, 477, 530, 532, 536, 542, 605, 611, length, 91, 94, 168, 227, 480, 638, 743 622. See also genome time, 91, 94, 177, 743 non-coding, 767 cost function . See minimization persistence length, 480 counting, 77, 94, 150 dolphins, 387 covalent bond, 421 double well potential, 96 covering, 261-3 DOWN, 146 creation, 532 dreams, 385, 387-8, 389, 407. See also sleep— creativity, 253, 296, 396, 406-9, 419, 780 REM Crick, 387 critical cluster . See critical nucleus ecosystem, 529, 697 critical nucleus, 182, 446-54, 465 effective field . See mean field critical temperature. See phase transition effectiveness, 582 critical value, 311 efficiency, 586, 590 crossover, 268, 468, 512, 538, 611 eigenvalues, 204 cubic lattice, 152, 162, 463 Einstein-Podalsky-Rosen paradox, 113 Curie temperature, 153. See phase transition elastic string, 484 current, 102, 109, 193, 204, 648 electrochemical pulse, 297, 418 cycle, 25-34, 116, 127, 283, 306, 405, 738-40 electroencephalography (EEG), 386, 388-9 elementary particles, 183, 292 Darwin, 532 emergence, 2, 5, 10-2, 292-4, 625, 822 data compression . See compression emotions, 396 death, 123, 387, 535, 575, 821 encoding, 232, 249, 257, 298 decay (exponential), 20, 104, 168, 267, 501 endochrine-system, 396 decimation, 270, 276 energy, 393 decoding, 232 barrier, 95, 103, 182, 193, 195, 426, 430, decomposition of memories, 388, 407 447-8, 457-8, 467, 474-7, 510, 555-6, 575 decoration, 461-2 consumption/flow, 537 deduction, 236 in evolution (fitness), 532, 550-2 de Gennes, 478 fluctuations, 73, 89 degrees of freedom, 34, 112, 145 landscape, 398, 550 delta function, 40 neural network, 301, 324 democracy, 789, 822 polymer, 479-83 dendrites, 297 protein, 429-30 density, 57, 66, 481, 486, 648, 652, 674 surface, 92 detailed balance, 193, 494, 498 thermodynamics, 58, 66 deterministic, 35, 113, 186-188, 255, 625, 738. well, 95 See also chain of influence English, 13, 218, 231 determinism, 411, 569-72 ensemble, 9, 19, 38, 84, 91, 186, 188, 219, 226, design and engineering, 623, 625, 691-695 , 781 234, 255, 439, 489, 550, 566, 713 Devaney, 36 annealed, 90 development (biology), 6, 530, 533, 537, 548, 569, canonical, 71 621-5 , 691, 766, 769 microcanonical, 71 blueprint, 622, 692 quenched, 90, 94, 224, 308, 435 program, 622-3, 625 entropy, 13, 58, 62-3 , 64, 68, 100, 220-1, 477, 533, dictatorship, 797-8, 804, 823 537, 558, 560, 596, 717-23 diencephalon, 397 bottleneck, 193, 475-7 differential equation, 9, 19, 139, 187, 257, 289, 577, Ising model, 148-151, 220-1 648-51 polymer, 479 diffusion, 97, 108-112, 197-8, 476-7, 483, 506, 648, 695 environment, 5, 8, 410-1, 529-32, 541, 552, constant, 110, 507, 520, 525, 565, 629, 663, 666 572-4, 604, 617, 619, 622, 693, 716, 752-7, driven (biased), 111-2, 445, 470-1, 517, 532 808-9, 819, 824 equation, 110, 648-9 enzymes, 423-4, 470, 474 digit, 214 equilibrium, 13, 59-66, 94, 95, 190, 505, 539, 595 dimension . See fractal far from, 476, 612-3, 627, 630, 653-4 dimensionality, 169, 430, 482, 567, 692-3 equipartition theorem, 80 842 Index ergodic theorem, 90, 94, 188, 190, 637, 716, 721, extensive, 60, 62, 66, 69, 268, 456 781 external field, 153. See magnetic field nonergodic, 107, 153, 173, 179, 235, 611, 716, 718, 743 factorial, 45, 78-9. See Sterling’s approximation source, 226-31 factory, 806, 808 error, 47, 201-203, 292, 335, 406-9, 501, 507, 515, 625, failure. See neural network—failure 693, 731, 733 false (F), 236 error function (erf( x)), 330 fast processes, 90 eukaryotes, 536-7 feedback, 298, 397, 616 evolution, 410, 528-620, 625-6. See fitness, resources, feedforward . See neural network selection Fermi function, 99 artificial, 620 ferromagnet . See magnet artificial selection, 535, 559, 571 fetus, 624, 691 bravery, 618 Fibonacci numbers, 707, 710 coevolution, 590 field . See external field, local field, magnetic field collective, 604, 614-9 fight or flight response, 396 convergent, 535 filter, 369, 374, 376, 404, 410, 812 driving force, 541 fitness, 531-3, 542, 546-9 , 563, 574, 586, 589, 696 equilibrium, 539, 554, 568, 595 and population ratios, 552, 566-9, 589-90, 697 extinction, 535, 541, 568, 573, 597, 601, 603, 697 class, 591 eye color, 544 collective, 603-4, 612, 619 forest fire, 573, 603 domain of viability, 546-8 fossil, 535, 537, 566 energy valley (well), 555, 564, 574 heritable traits, 530, 532, 604, 637 global, 533, 566-9, 590, 598, 601, 619 horse, 535, 543 landscape, 550-1, 553-9, 615 incremental changes, 532, 538-42, 554-9, 615, 617, maximum, 593 619 neutral, 546, 599 interactions, 530, 548, 562-6, 569, 614, 620 neutralist/selectionist, 546, 549, 555, 562 gene-centered view, 604-5, 613-4 viability, 546-9, 593, 611, 613 global, 533, 566-9, 590, 598, 619 fixation, 306, 397-8 growth rate models, 577-81 fixed point, 21-38, 209, 275-83, 306 migrations and domains, 535, 572-4, 789 flock, 529, 746-51 model limitations, 552, 556-7, 563, 566-9, 575-6, Fletcher, 719 595-6, 598-601, 604 Flory, 481 Monte Carlo random walk model, 550-76, 595-7, fluctuations, 89, 169, 586, 616 619 fluid, 57, 483-8, 619 molecular, 531, 538, 618-20 food web, 536, 565 mule, 547, 613 force, 62, 75, 484, 489 niches (specialization), 602, 697, 816 Fourier representation, 47, 49, 51, 272-3 persistence, 535, 697 fractal, 9, 258-63, 744, 759 physical constraints, 547-8 stochastic, 262, 744 punctuated equilibria, 565-6 free energy, 72, 85, 100, 191, 479-83, 533, 558 randomness & history, 548, 568, 569-72 ideal gas, 79 rate of, 603-4, 612 Ising model, 148, 156 renewable-resource model, 582-6, 591-6, 599, 697 free will, 411 reproduction and selection models, 576-604, 596, freezing transition, 106, 430 599, 601, 603, 620 Freud, 329 social, 617-9, 808 frontal lobes, 414 space and time, 572-4, 603 frustration, 162, 467-8, 819 space of possibilities, 543-6 function, 4, 421, 426, 623 survival, 550, 608, 816 fundamental constants, table of, 723 survival of the fittest, 599 fundamental law, 292 systematic change, 540-1, 554, 564, 592 trait distribution, 543-6 Gaia, 787 trait divergence, 541, 546, 555, 564, 567, 574, 597, galaxies, 187, 292 605, 611, 619, 697 gambling, 41, 54-6 tree of life, 597, 697 gamete, 537 excitatory synapse, 298, 301 gas, 58, 60, 62, 85, 137 experiment, 90-1, 389-93, 404, 414, 419, 471, 503, 519, ideal 64, 74-85, 718, 722, 727-35 530, 626, 676, 688, 700, 720, 759 Gaussian distribution, 46, 50-1, 54, 110, 112, 174, 309, exploration of space, 425, 475, 503, 550, 553 479-80, 484, 539, 543, 558, 648, 732 exponential. See decay, growth Gaussian integral, 51, 79, 81, 189  Inde x 843 gene, 538, 604-5, 613, 622, 688 hydrodynamics, 4, 34, 139, 142, 483-9, 507, 515-6 generalization, 35, 186, 196, 227, 396, 495 hydrogen bonds, 423-4, 467 neural network, 303-4, 324, 335, 403-4 hydrophilic and hydrophobic, 523-4, 536 genetic, 298, 410-1, 611, 637, 674. See also genome hypothalamus, 397 genome, 530, 532, 542-9, 557-9, 574, 695 length, 545, 559, 766-771 ice, 86-7, 90, 183, 719 Geszti, 388 ideal gas. See gas giraffe, 626, 641-8 imagination, 406-9 glass, 4, 89, 95, 105, 193, 211, 430, 719, 743 immune system, 617, 620, 702, 820 Glauber dynamics, 173 -185, 195, 302, 316, 378, 631 imprint, 298, 394. See also Hebbian imprinting glial cell, 417-8 impurities, 106, 182-3 glider, 127 in vitro, 424, 519 global economy, 700, 796-815, 820-5 in vivo, 9, 424, 519 Gödel’s theorem, 252, 715 independent, 41, 44, 91, 166, 168, 216, 226, 228, 254-6, grammar . See language, linguistics 333, 338, 409, 427, 434, 435, 451, 465, 500, 538, graphical method, 21, 155, 243 545, 571-2, 605, 610, 611, 614, 747, 759. See also ground state, 164-166 correlation growth (exponential), 20, 425-7, 449, 453, 457-8, 468, indistinguishable, 78, 80-2 577, 595. See also nucleation and growth individual, 529, 534, 604, 617, 637, 700, 784-7, 803-5, 808, 820-2 halt (Turing machine), 245 individuality, 408, 409-10 halting problem, 251-2, 713, 715 industrial revolution, 796 Hamiltonian (energy function), 270 inference, 236, 254, 689 Hamlet, 11, 303 influence, 269, 297. See also interdependence Hamming distance, 307, 311, 394 infinite, 252 Hardy-Weinberg theorem, 606 information, 6, 12, 214-235, 253-4, 530, 532, 536-7, harmonic well, 101 617, 622, 693-4, 700, 703, 713, 809, 819 Hartmann, 389 processing. See higher information-processing heart attack, 34, 821 transfer . See communication heat transfer, 58, 62, 64 inhibitory synapse, 298, 301 Hebb, 298 inhomogeneous, 263, 435, 454, 458-471 Hebbian imprinting, 173, 298, 301 , 306, 319, 349, 373, initial conditions, 20, 94, 116, 132, 140, 258, 469-70, 396 471, 518-9, 570-1, 632, 637, 676 hemispheres, 337, 365 inner product, 306-7 heterogeneous, 60 input-output, 300-1, 322 heteropolymer, 435, 519-25 intensive, 10, 60, 66 heterozygous, 606 interactions, 5, 12, 58, 66, 84, 145, 269, 430, 435, 471, hexadecimal, 215 530, 548, 551, 557, 562-6, 615, 630, 695, 812 hexagonal honeycomb lattice, 162 local, 467, 471 hierarchy, 347, 364-70, 367, 373, 410. See also spin glass long-range, 170-173, 367, 456, 466, 468, 471, 565-6, control, 797-815 569, 629-30, 695 higher information processing, 296, 328, 371, 393 infinite-range, 171, 367 hippocampus, 393, 416 interdependence, 12, 92, 426-7, 471, 536, 565-6, 590, history, 131, 700, 793-5, 806, 810-15, 824 601, 605, 617, 620, 751, 784-7, 791-6, 824 homogeneous, 35, 58, 60, 113, 435, 627, 637 evolution of, 614-9 homologue, 538, 605-6 internal dialog, 404-6, 407, 418 homopolymer, 435, 477, 520 inverse, 118, 133, 306 homozygous, 606-7 invertible, 232, 254, 712 Hopfield, 173, 387. See neural network-attractor irreducible matrix, 192, 203, 227 hopping, 95, 110, 432, 507 irrelevant, 258, 278-9, 288, 293, 452, 564, 637 Horne, 385 irreversible, 62, 503-5, 510, 724-5 horse, 535 Ising model, 64, 145-186, 188, 194, 258, 270-83, 301-2, human being, 89, 369, 562, 602, 615-9, 701, 740, 756, 430-1, 468, 544, 548, 627, 629-30, 719. 758, 760, 775-81, 815, 818 See also dimensionality communication, 233-235 iterative map, 9, 19, 35, 39, 187, 209, 274, 576, 612, 666, consciousness, 414 819 error, 406-9 superstable point, 286 thought, 253-4, 404, 407 iterative refinement, 36-8, 207-14, 289 information processing, 296, 328, 371, 393 rights, 784-5 human civilization, 7, 699-701, 782-825 joint probability, 41, 43, 166 Huxley, 804 844 Index Kelvin temperature scale, 64 Markov chain, 39, 191-2, 198, 203, 576, 226-31, 234, kinetic energy, 78, 192, 429, 476 551-2, 713, 738 kinetic pathways, 426, 470, 472-7, 510, 518-9, 525 mass, 58, 75, 486, 566 kinetic theory of gases, 74 Master equation, 56, 104, 109, 432 kinetics, 102, 153, 173-186, 473, 503 material, 58-9, 91, 211 knots, 518 growth 142-144 Koch curve, 263-4 Mathematica, 201 Kolmogorov complexity. See complexity— matrix, 194, 203, 289, 291 algorithmic Mattis model, 172-3, 468-9 mean field, 154-160, 170, 269, 445, 481-2, 485, L-system, 686 508-10, 548, 563-4, 604-11, 614, 620, 695 label, 303, 341, 416, 492 mechanical work. See work landscape. See energy meiosis, 537-8, 605, 611 language, 296, 329, 340-5, 702, 761 memory, 11, 173, 255, 298, 302-4, 328, 389, 393, lattice. See cellular automaton, multigrid 404, 407. See decomposition, neural lattice gas, 139, 141-3, 691 network left-right universe, 333-338, 372, 409 capacity, 305, 308, 331, 345-364, 372 levels of description, 292-4, 329, 620, 744 consolidation, 385-7 Library of Congress, 232, 622, 816 content-addressable, 302-4, 338 life, 7, 89, 123, 293, 366, 529-42, 621, 624, 702, 740, false, 404, 407 789-91 forget, 404 phenomenology, 530, 534-6, 549, 571-2 reimprinting, 374-385 senescence, 535, 604, 687 repetition, 397-8 traits, 534-5 retrieval, 302-4, 394 variety/diversity, 5, 534, 549, 555, 573, 816 short-term, 348, 405, 774 life expectancy, 820-21 spurious, 316, 319-22, 373, 408 lifetime of the earth, 533 metastable, 183, 446, 454, 465 lifetime of the universe, 254, 552 microcanonical ensemble, 71 linguistics, 340. See also language microorganisms, 571-2. See prokaryotes Lindenmayer, 686 microscopic, 10, 58, 66, 187, 278, 293, 570-2, 726, 775 linear stability analysis, 68, 671-3, 690 microstate, 13, 66 limb, 626, 678, 687 Migdal-Kadanoff transformation, 279-82 lobotomy, 389 military, 4, 803, 812, 896 local field, 302, 308, 431, 435, 467. See also magnetic mind, 298, 329, 371, 393-419 field minimization, 207-214, 324-32 local process, 510, 554 Mitchison, 387 local properties, 60, 61f, 92 mod2 rule. See cellular automaton local relaxation time, 454 model, 228, 278-9, 296, 365, 393, 419, 427, 507, 529-30, logic, 253, 296, 399 538, 576, 600, 632, 688, 690, 692, 705-16, 757, propositional, 236-239 788, 818 theory of. See computation molecular dynamics, 186-187, 488-9 logistic map . See quadratic iterative map momentum, 13, 66, 190-2, 198 long-range. See interactions—long-range monkey, 414 Lotka-Volterra predator prey model, 586 monomer, 477 Lyaponov exponents, 737 Monte Carlo 173, 188-203, 226, 302, 476, 550, 631. See computer—simulations errors, 201-203 macroscopic, 10, 58, 66, 187, 278, 293, 570-2, 726, 775 evolution, 531 macrostate, 13, 66 local moves, 197, 491 magnet, 58-9, 94, 145, 152, 270, 367, 630, 719 Metropolis, 194, 495, 550-1 antiferromagnet, 152, 160-6, 171, 431, 435, 440, minimization, 210, 550 446, 629 nonlocal moves, 198, 213, 502-3, 575, 614 ferromagnet, 152-160, 170, 431, 435, 440, 446, polymer, 488-527 468-9, 611, 629 time, 508 magnetic bubble memories, 630 walkers, 550, 614 magnetic field, 58, 146, 153, 179 motor control, 296, 329, 337, 414 magnetic resonance imaging (MRI), 392, 404, 624 multigrid, 258, 282, 288-92, 293 magnetization, 58-9, 148-9, 179, 221 mutation, 537-8, 538, 590 majority rule, 114-5, 320 man-made, 293 Margolus rule, 133-139, 494 NAND ,242 market, 813-4 nanotechnology, 781  Index 845 nation-state, 700, 783, 787, 789-91, 806 or (|), 237 natural language. See language orbit, 25 natural process, 62, 64 order, 476, 518, 527, 740 nature versus nurture, 410-1, 776 ordered phase, 154 Navier-Stokes equation, 139, 142, 485-6 organ, 626, 678 Nazis, 786 organization by design, 6, 527, 530, 625, 691 neighborhood, 113, 463-5, 492-3, 496-8 origin of complex organisms, 528-620, 824-5 neighbors, 151, 179, 367, 463-5 origin of life, 528-620 network, 626, 797, 805, 812-3 orthogonal patterns, 373-4 neural network, 7, 295-419, 622, 631. See activity, oscillator, 20, 306, 484, 586, 632, 666 hierarchy, pattern oscillation frequency, 101, 103, 140 activity bias, 417 outer product, 305 attractor, 11, 173, 298, 300-5, 306-332, 338, 393, overload catastrophe, 305, 332, 372-8, 390. 401, 405, 412, 414, 462, 468-71, 772 See memory—capacity auto-associative. See neural network—attractor biological, 297-8, 320, 337, 772 palimpsest memory, 319, 372, 375-8 capacity. See memory—capacity parallel processing, 331, 338, 426-7, 432-71, 473, 476, dilution, 345, 364 488, 534, 602. See also computer failure, 306, 319, 335-6, 390, 397-8, 405, 407, 416. parameter space, 275, 632, 665 See also overload parenthesis, 238 feedforward, 298, 300, 322-328, 328-9, 338, 393-4, parse, 341 401, 405, 412, 414, 462, 471 part, 5, 11, 60, 92, 94, 259, 604-20, 792, 820-2. hidden layers, 324 See also subdivision Hebbian imprinting. See Hebbian imprinting partition function, 73, 101, 148, 191, 272 Hopfield . See neural network—attractor parts of speech, 341 objective, 372, 404 pattern, 11, 298, 301-4, 324, 393-4, 611, 614, 622, subdivided, 328-365, 371-4, 462 625-85, 818 training, 301, 322, 371 evolved random, 380-5, 627-48 plasticity, 298 pattern formation, 530, 621-85, 690, 819. neuromuscular control, 805 See reaction-diffusion neuron (nerve cell), 11, 296-7, 623, 772, 805 activation and inhibition, 627-85 metaneuron, 418 activator-inhibitor model, 659, 668 refractory period, 307, 405 activator-substrate model, 659, 689 neuron probe, 392-3 animal skins, 614, 622, 625-85 neurophysiology, 329, 345, 365 CA models, 627-48 Newton, 258 evolution, 695-8 Newtonian mechanics, 58, 75, 90, 191, 489, 532, 787 fast and slow diffusers, 690 Newton’s laws, 62, 75, 187, 476, 486, 787 pattern recognition, 296, 304, 324, 394-5, 403, 612 Newton’s method, 36 Pázmándi, 388 noise, 218, 316, 581. See fluctuations, temperature periodic. See cycle noise (standard deviation). See signal-to-noise analysis Perron-Frobenius theorem, 192, 203-7 , 226 nonanalytic, 267, 487 perturbation, 367, 587, 625, 665, 668 nonequilibrium, 62, 89, 108, 596, 703 phase, 60 noninvertible, 254 phase transition, 10, 85-89, 168, 611. See nucleation nonlinear, 25, 299, 546, 551, 652, 655, 695-6 and growth nonuniform, 732 diagram, 87, 160, 469 nonuniversal, 235, 409, 531, 714, 777 disorder-to-order, 429, 469 NOR, 242 first-order, 86, 179, 440, 446, 469 not (^ ), 237 glass, 105, 193, 721 nucleation and growth, 179, 445-54, 465-6, 470 kinetic, 112, 123, 142 nucleation time, 449 lower & upper critical dimensions, 170 number of components, 5, 94, 296, 424-7, 435, 771, 820 magnetic, 153-5 number of states, 12-3, 67-74, 150, 538, 559 second-order, 87, 156, 269, 278, 745 number of particles, 60, 66, 92, 137 temperature 86, 153, 5 phase separation, 211, 509 O (order) 439. See scaling phenome, 530, 542-9, 557-9, 574-5, 605, 695 objects, 339, 394 phenomenological approach, 404-5, 531-3, 688-9 observer, 14, 254, 268, 716, 752-9 philosophy (egoism), 614-9 obsession, 306, 397-8 physiology, 366, 369, 387 Occam’s razor, 257, 688, 731 physiology and behavior, 542, 575, 611. See phenome optimization, 533, 545. See also minimization Picasso, 408 846 Inde x piston, 58, 62, 83 folding, 7, 423-7, 518, 526-7, 532, 534 Planck’s constant, 13, 78 folding problem, 424, 518 plants, 92, 529, 770-1, 816 frustration, 467-8 point particles, 58, 75 fundamental folding problem, 425-7 polyethylene, 477 globular, 423, 518 polymer, 198, 268, 421, 471, 476 -527, 536 kinetic effects. See kinetic pathways ball-and-string model, 489-91 local interaction model, 467-8 bond fluctuation algorithm, 491 molten globule, 518-9 collapse, 426, 477, 503-527 nucleation and growth model, 454 collapse time, 517, 525 persistence length, 480 connectivity, 491, 493, 496-7, 506, 520 predictive models, 431 contour, 508, 510, 512 primary structure, 421, 468 curvature, 510, 515 quaternary structure, 423-4 end-to-end distance, 478, 489, 512 secondary structure, 423-4, 454, 465 end-dominated collapse, 508, 517-9 short and long range interactions, 467 ends, 508, 510, 520 space & time partition model, 465 excluded volume, 480-527 structure, 421-4 flexibility, 480, 495-7 tertiary structure, 423-4, 454, 465 knots, 518 three-dimensional (3-d) structure, 423-5, 468 melt, 497, 519 turns, 424 one-space algorithm, 492-6, 520-5 proteolytic reactions, 474 persistence length, 480 pseudo-random numbers, 198-200, 253, 258, 713 precipitate, 478 psychology, 329, 393-419, 757 radius of gyration, 498 psychotherapy, 398 relaxation and diffusion, 483-8, 489 reptation, 502-3, 519 quadratic iterative map, 26-38, 127, 283-8, 578 ring, 519 quantum, 13, 35, 62, 66, 78, 99, 187, 270, 429 scaling, 477-88, 499-502, 509-17 quench, 90, 106-108, 211, 430. See also ensemble simulations, 488-508, 513-6, 519-27 quantum, 718, 727, 781 smoothing, 512 quasi-equilibrium, 653 two-space algorithm, 488, 496-502, 505-8, 513-6 quasi-static, 653-4 polymerase, 537 question, 332, 427, 703, 823 polysaccharides, 421, 477, 536 polystyrene, 477 Ramachandran plot, 429f population dynamics, 530, 577, 604-20, 612 random, 34, 195, 216, 232, 233, 256, 485, 494, 532, 548, position, 13, 66, 187, 190-2, 479 570-2, 606, 632, 637, 818. See pseudo-random positron emission tomography (PET), 392, 404 numbers postsynaptic potential, 302 numbers, 198, 253, 508 potential energy, 95, 192, 429 patterns, 306-8, 312, 374-5 power law, 168, 267, 427, 499-502, 511-2, 515, 543, 566 variable, 38 predator-prey, 562, 565, 576, 586-90, 599, 603, 615, random walk, 40-56, 108-112, 194, 223, 268, 306, 617, 626 308-12, 359, 476, 478-9, 485, 506, 532, 560, 648. prediction, 32, 255, 389, 424, 431, 515, 688, 789, 818, See self-avoiding random walk 823. See chaos reaction-diffusion, 627, 652, 658, 676, 690, 695 pressure, 10, 58, 60, 62, 74-77, 80-85, 486 read-write head, 244 prior knowledge, 235 real numbers, 20, 33, 251, 299 probability current 102, 109 real world, 89, 254 probability distribution, 38, 44, 53, 216, 234, 479-80, recipient, 234, 412, 711 551. See conditional probability recognition, 398-403, 616, 715, 757-9, 763 prokaryotes, 536-7, 571, 602 reductionism, 11, 533 proof by contradiction, 205-6, 252, 498 reject, 194-5, 489, 616. See Monte Carlo propagation, 470 relationships, 8, 394, 404 propositions (logic), 236 relaxation, 57, 95, 102-5, 214, 290, 427-71, 473-477, protein, 366, 420-527, 536. See -helix, -sheet, 483, 551 conformation, relaxation time, polymer relaxation time, 104, 177, 420-427 , 500, 517, 525. amino-acid sequence. See protein—primary See also correlation time structure relearning, 374 backbone, 423 relevant, 258, 278-9, 288, 297, 481, 564, 606 dihedral angles, 427 reliable, 403, 507, 625 driving force for folding, 453, 471 religion, 532, 776-8 excited states, 439-40 renormalization, 89, 168, 258, 269-88, 293, 454, 462, extrusion, 519 481, 504  Index 847 replication, 537. See self-replication, reproduction signal-to-noise analysis, 305, 308-12, 347, 352-64, 374 representation, 692-3, 716, 759 silicon, 142, 211, 299 reproduction, 123, 530-1, 533, 535-6, 548, 562, 575-6, simplicity, 257, 292-3, 488, 505, 818 590, 695-6, 789 Simpson’s rule, 201 asexual, 612 simulated annealing, 211 sexual, 531, 535, 543, 604-14, 620, 694, 696 size, 60, 536 resolution. See scale sleep, 371-93, 407, 419. See also dreams resources, 535, 539, 550, 600, 612, 695, 697, 813-4 creativity and, 407 multiple, 600-4, 611, 619, 620, 697 cycle, 386 retrieval. See memory deprivation, 386-7, 390-2 reversible, 62, 83, 117 doctors, 386, 391 revolution, 797-9 hypnogram, 386 ribosome, 519 insomnia, 386 RNA, 421, 536 phenomenology and theory, 385-8 robot, 253, 781 rapid eye movement (REM), 386-8 robust, 92, 403, 506-7, 519, 525 slow wave (SWS), 386, 389 root mean square (RMS), 43, 48, 52 substances, 389, 392 Rouse relaxation, 483-488, 502, 511 slow processes, 90 social behavior, 604, 614-20, 626, 695, 700, 779. sandpile model, 566 See human civilization, evolution—social scaffolding, 692, 812 ostracism, 616-7 scale, 5, 32, 168, 258, 283, 638, 700, 806, 809 social consequences, 616 length, 89, 91, 168, 629, 668, 673, 725, 774. social policy, 783-7 See also correlation length socialization, 617 time (separation of ), 89, 94, 97, 106-8, 193, 653 solvent, 478, 504, 510 time, 5-6, 421, 425-6, 471, 473, 533, 571, 593-5, 725. soul, 775 See also correlation time, relaxation time source, 219, 819 scaling, 258, 267-9 , 282, 293, 427, 435, 471, 477-488, Soviet Union, 799-800, 809, 821-2 509-17, 525, 667 space-time, 19, 113, 131, 188, 254-5, 269, 572 dynamic, 483 space partitioning, 133, 488, 491, 497 exponent, 267-8, 482, 506, 511-8 specialization, 2, 602, 617, 816-9. See differentiation function, 267, 512 species, 529, 603, 604, 614 schizophrenia, 392 specific heat, 74, 89 science, 1-3, 257, 776-8, 783 specific knowledge, 711 select, 174, 194, 375, 489, 508, 518, 520, 819 spin, 146, 270, 301, 431, 629 selection, 409-10, 531-2, 537-8, 539 , 552, 559, 561-2, spin glass, 172, 311, 320, 466 572, 576, 585, 596, 605, 615-6 engineered . See neural network—attractor and entropy, 596 spontaneous generation, 532 by organism, 573 spontaneous magnetization, 153 scope of, 599, 620 spring, 484. See oscillator self-action, 26, 300, 307 stable fixed point . See fixed point, attractor self-averaging, 168 standard deviation, 52, 498 self-avoiding random walk, 481, 512 Star Trek, 538, 788, 818 self-awareness, 296, 389, 411-6 starvation, 618 self-consistency, 154, 293, 397, 405, 549, 564, 692, 809, state of a system, 19. See also pattern, conformation 819 statistical approach, 365 self-image, 413 statistical mechanics, 6, 10, 58, 66-89, 270 self-organization, 6, 426, 527, 530, 623, 625, 691 statistical fields, 145-186 self-replication, 531, 537, 619 steady state, 193, 301, 539, 590, 627, 637 self-similar, 258-9, 283 steepest descent, 208, 211, 325, 597 selfish, 604, 615-9 Sterling’s approximation, 45, 46, 53, 79, 151, 218, 728 semantics. See language, linguistics stimuli. See experiment sensory-motor system, 253, 298, 324, 328, 394, 412, 809 stochastic systems, 38, 131, 192 sensory processing, 296, 299, 328, 338, 411 Stokes’ law, 487, 507, 511, 515, 520-1, 667 separation of time scales. See scale storage capacity. See memory—capacity Shakespeare, 11, 303 stress, 391, 396 Shannon, 214 string (character), 215, 544 Sherrington-Kirkpatrick spin glass, 172 subconscious mind, 329, 393, 411-6 sickle-cell allele, 607 subdivision, 60, 61f, 92, 296, 328-370, 395, 404, 407, Sierpinski gasket, 259 461, 529, 619, 623, 774, 791, 823. See hierarchy sigmoidal, 299, 323-4 biological brain, 337 signal-processing, 299, 411. See sensory processing creativity and, 406-8 848 Inde x dissociation, 374-6, 388, 392, 407 truth, 689 dynamics, 374 truth table, 236 generalization and, 403-404 Turing machine, 243-251, 622, 713, 715, 766 language, 340-5 Turing patterns, 648, 652 object recognition and, 394-6 Turing test, 777 partial, 338, 340, 342, 347 two-level system . See two-state system time scale, 461-5, 471 two-spin system, 432-435 vision, 338-340 two-state system, 95-108, 146, 177, 182, 195, 212-3, substrings, 229 273, 427, 430, 483, 529, 543, 555, 577-8 substructure, 6, 367. See subdivision superorganism, 618, 699, 783-7 United States, 799, 821-2 superposition, 40 universal Turing machine, 247, 706 superstition, 257 universality, 1-2, 257, 278, 288, 512, 531, 689-90, 710, surface properties, 92, 455 714. See also computer switch, 299 UP , 146 symmetry, 137, 277, 300, 435, 563, 650 symmetry breaking, 153, 611 Van der Waals bonds, 423, 524 synapses, 11, 296-8, 388, 399, 622, 773 variation, 254. See also mutation, life synchronous, 300, 306, 349, 577, 632 velocity, 20, 52-56, 75, 187, 446, 486, 648 Verlet, 187 θ-point, 478, 503-5, 509-10, 518 vigilance test, 387, 391 tautology, 238, 563 virial coefficient, 504 technology, 799, 804, 817, 824 viscosity, 105, 486 telomere shortening, 687 vision, 298, 329, 338-40, 391, 394, 411, 693, 773 temperature, 10, 58-9, 63, 64, 68, 89, 131, 317, 457, 459, computational, 395 486, 489, 533, 550, 552, 638 volume, 58-60, 62, 64 theoretical biology, 688 voluntary motor control, 414 theorem, 238 voting. See cellular automaton—majority rule thermal equilibrium, 58. See also equilibrium thermal length scale, 79 thermal motion, 486 wall, 75 thermal reservoir, 58, 69-70, 84, 95-7, 191, 198, 476, war, 618, 789, 794, 821 489 washboard potential, 111, 446-8 thermodynamics, 10, 58-66, 192, 479, 489, 533, 579, wave equation, 140 703, 716 wavelength, 273, 484 first law, 59, 61 weather, 366 principles/assumptions, 89-95 well. See energy second law, 59, 62-3, 533 water, 86-7, 89-90, 179, 183, 429 zeroth law , 59 will (consciousness), 413 thermodynamic limit, 66, 94, 439, 465, 637, 743 Wilson, 393 time scale. See scale Wolfram, 120 trait. See evolution, life, genome, phenome worlds, external and internal, 406, 408 transformational grammar, 340 work (mechanical) 58, 62, 83, 393 transition, 102, 182, 191, 203. See also phase transition, freezing transition XOR, 399-403 coherent, 432 transition probability, 39, 192, 489 zebra, 626, 678 tree (like), 89, 263-7, 284-5, 625, 678 zero temperature, 186, 302 triangular lattice, 162 Zimm relaxation, 483, 485-8 , 502, 510-1, 515 true(T), 236 zygotes, 538 Index 849