Page numbers followed by an “f” indicate figures.
Action
belief, desire, and, 243–244
decisive, 335–337
effective, xxiv, xxv, 304, 347, 368
guides to, 157–164 (see also Instinct; Reason)
overlapping representation of and perception of, 166
Adaptation, 127, 128. See also Extended phenotypes; specific topics
fitness and, 18, 160, 262, 273, 276
imprecision of, 128
scope of the term, 273
vs. teleonomy, 195 (see also Teleonomy)
Adaptationism, xii, xx, 219, 371, 375
Panglossian, 272
“Adaptationist program,” 219
Adaptationists, 219–222, 225, 232
adaptationist narratives and, 372
natural selection and, 220, 221, 232, 272, 273
novelty and, 220
and positive and negative selection, 272–273
structuralists (vs. functionalists) and, 213, 227, 272–273
Günter Wagner and, 213, 219–221
Adaptedness, 195
Adaptive explanations of internal conflict, 128–129
Adaptive function
ultimate cause as, 200 (see also Ultimate causes)
Adaptive innovation, unit of, 61
Adenosine triphosphate (ATP), 325
Adenosylcobalamin (vitamin B12), 325
Adipose tissue. See Brown adipose tissue
Adrenergic receptors, 107–108
Agency, language of, 17
Aition and aitia, 235. See also Aristotelian causes
Allele frequency, 75
fitness and, 75, 113–114, 252, 253
functional vs. nonfunctional, 76
maternal and paternal, 49, 113
nucleotides and, 99
phenotypic effects and, 99, 113, 253
selective sweeps and, 75–76
silent, 49
silent locus and, 113
Allelic recombination, 43
Allelic substitutions, 253.255
“Allelomorphs,” 55
Allosteric macromolecules, 322
Allosteric mechanisms, 336
Allostery, 326–327
concept and nature of, 326
Altruism, 386. See also Benevolence/benevolent motives
DNA and, 57
genes and, 57
mutations and, 296–297
nucleotides and, 264, 327, 328, 348, 349
polypeptides and, 249, 254, 327
proteins and, 57, 230, 243, 249, 296–297, 327, 328, 348
Amundson, Ron, 277–278
Analogues, 204
Anatomists, functional, 277–278
Angelman syndrome, 117–121
Anti-anti-Shine-Dalgarno (SD) sequence, 325
Anti-Shine-Dalgarno (SD) sequence, 325
conformations and, 326, 335, 336, 343
ligands and, 322, 328–329, 331, 335–336, 343
riboswitches and, 322, 324–326, 329, 335, 336
ribozymes and, 322–324
Archetypes
Darwin on, 206–207
replaced by ancestors, 207, 212
Aristotelian causes (aitia), four categories of, xxi, xxii, 187, 199, 201, 205, 229, 235–236, 265, 269, 373. See also Aristotle: on causes; specific categories of causes
Aristotelian pluralism, 235
Aristotle
Thomas Aquinas and, 185–186, 233
on causes, 13, 184–186, 233, 250 (see also Aristotelian causes; Final causes: Aristotle and)
eidos, 241
psuche, 353
teleology, 194
Asymmetries of relatedness, 50, 138–139, 245
Augustine of Hippo, v
Autocatalysis, 96–98. See also Catalysts
Automata, 105. See also Robots; specific topics
cellular, 106
communication and, 103
genes as, 102–104
heat-generating (see Brown adipocytes)
higher-level, 102–103, 105, 106
lower-level/simple, 102–104, 279
interactions between, 102
meaning of information for, 279 (see also Information; Interpretation(s); Meaning)
nature of, 102–103
organism-level/organismal, 102, 108, 121, 279–280
proteins as, 102–107
Automaton. See Automata
Bacillus clausii, 325
Bacon, Francis, 1–4, 187, 235, 359
barren virgins and, 359
final causes and, 3–5, 7, 8, 11, 235
Queen Elizabeth and, 1–2
Bacteria, 29–30, 51, 323, 325. See also specific species
plasmids and, 29–31
Bacterial chromosomes, 29–32, 51
Bacterial recombination, 49, 51
Badcock, Crespi, 120–121
“Barren virgins,” 2
final causes as, 1, 4, 8, 9, 11, 12
Basil (Ocimum basilicum), 275, 276
Bateson, Gregory, 246–247
Bathtub, parable of the, 310–313
Behavioral ecology, 109–110
Belief, desire, and action (C. S. Peirce’s trinity), 243–244
Benevolence/benevolent motives, 176. See also Altruism; Morality
self-interest and, 176 (see also Self-interest)
selfish gene(s) and, 60, 61, 87, 160 (see also Selfish gene(s))
sympathy and, 165
B-group vitamins, 324, 325. See also TPP
Binary choices, 325
reducing complexities to, 261, 263
Biotype, 55
Bird, A. P., 39
Borges, Jorge Luis, 339
Bowler, Peter, 13–14
Braitenberg’s Law, xii–xv
Braitenburg, Valentino, xii–xv
Brown adipocytes, 107, 108, 116, 117
Brown adipose tissue, 107, 116
Brücke, Ernst Theodor von, 15, 359
Bryant, William Cullen, 345
Butterfly effect, 312
Cadherins, 35
Capacities of a system, 277–278
Capsid proteins, 230
Carranza, Venustiano, 300–301
Cassidy, S. B., 117
Catalysis, RNA and, 321–323, 326, 331
Catalysts, genes as, 21–22, 77, 96–98
Causal models, 285n
Causation, 158, 185, 192–193, 195, 235, 237, 267, 351, 373. See also Interpretation(s): causes and
chains of efficient (see Efficient causation)
defined, 247
as difference making, 247, 309, 310, 351 (see also Difference making and mechanisms)
information and, 247
natural selection and, xxiii–xxiv
type vs. token, 230 (see also Token causation)
“Cause”
concepts of, 235
terminology, 235
uses and connotations of the term, 269
Cause and effect, distinctions between, 237. See also Chickens and eggs
“Cause and Effect in Biology” (Mayr), 191, 192. See also Mayr, Ernst
Causes. See also Aristotelian causes; Efficient causes; Final causes; Interpretation(s): causes and; Teleology
Aristotle on, 13, 184–186, 233, 250
Cause-talk vs. function-talk, 199
Chance, 127–128, 375, 376. See also Randomness
Chapman, John, 188
Character identity
character states and, 213–214, 216
Günter Wagner on, 213–214, 216, 230
Character Identity Networks (ChINs), 214, 230
Characters and states, 211–215
Character states, 215
character identity and, 213–214, 216
Günter Wagner on, 213–214, 216
Chickens. See Eggs
Chickens and eggs, xxiv–xxv, 8, 236–237, 255, 284, 319
Chimerism, 35–37
Choice, 132, 249–250, 315, 349–350. See also Decisions
captures information, 269
degrees of freedom and, 250, 315
nature of, 250
nature’s “choices,” 284
Chromosomes
recombination and, 32, 40, 51, 68, 85–86
Clade selection, 227
Communication, 109–110
Shannon’s fundamental problem of, 306
Compassion. See Sympathy
Competition, 177
Competition and conflict. See also Cooperation
within- and between-group, 176–177
Conditions of Existence, law of the, 231
Conflicting interests of maternal and paternal genes, 141
Conflicting preferences, 132, 133, 138, 140, 149, 159. See also Conflict(s)
Conflict resolution, 113, 176–177
Conflict(s). See also Conflicting preferences; Intragenomic conflicts
Conflict(s) (cont.)
of impulses, 129–130
internal/intrapersonal, 127–129
“system,” 128
Conformational change, 105, 324, 335
aptamers and, 326, 335, 336, 343
DNA sequences and, 77
ligands and, 331, 332, 335, 336, 343
riboswitches and, 324, 332, 335
Conformity
cultural, 355
Consciousness, 319, 363, 364–367. See also Subjective awareness
contents of, 365–367
Derrida and, 318–319
etymology of the term, 364
and the material world, 367
Cooperation, 21. See also Competition and conflict; Iterated prisoner’s dilemmas
competition and, 176
evolution of, 176
green beard effect and, 27, 34
Copying. See also Gene copies and copying
Cosmides, Leda, 28–29
Creationists, 374
Creativity and natural selection, xxviii, 338–340, 343–345
Crystallins, 214–215, 222, 231
Cultural elements of morality, 179–181
Cultural replicators. See Memes
Culture. See also specific topics
memes and, 45, 53–54, 63, 65, 67
Cummins, Robert, 278
Cytoplasmic commons, managing a, 27–28
Cytoplasmic conflict, 44
comparative embryology and, 12–13
on final causes, xi, 8–9, 14, 206
Asa Gray and, 12–13
T. H. Huxley and, 9–10
marriage of form and function, 13
misinterpretations of, 338
on natural selection, 343
On the Origin of Species by Means of Natural Selection, xi, 9, 13–14, 207, 266
on purpose in nature, 158
on rudimentary organs, 381
on selection and sources of variability, 223
serial homology and, 206–209
teleology, morphology, and, xi, 9–12, 231
thought experiment/metaphor of old springs, wheels, and pulleys, 223, 271
understanding of hereditary material, 158
use of metaphor, 207–208, 223, 252, 271
Darwin, Erasmus, 188
Darwinian account of the origins of meaning, 374
Darwinian final causes, 268
Darwinian hermeneutics. See Hermeneutics
Darwinian information, concepts of, 268
Darwinian nuptials, 8–12
“Darwinian paranoia,” xii
Darwinian revolution, 15–16. See also specific topics
Darwinism, 268
creationists and religious fundamentalists on, 374
criticism, critics, and dislike of, 338, 375, 376
Charles Hodge on, 338
human nature and, 374
Darwinized final causes, 199. See also Final causes
Darwin’s demon (natural selection), 250, 255–260, 269. See also Natural selection
David Copperfield (Dickens), 388
Dawkins, Richard, 69, 71. See also Selfish Gene
centrality of inscription and, 318
Derrida and, 318
evolutionary genes and, 85
The Extended Phenotype, 19–20
on genes, 17, 20, 26, 54, 59–61, 63, 68, 82, 87, 101
genetic autonomy and, 101
on inclusive fitness, 19–20
on natural selection (and selfishness), 18–20, 53, 59–60, 67
thought experiment, 26
Dawkinsian genes, 68
Death, 354
Decisions. See also Choice; Indecision
types of, 125–126
Decisive action, 335–337. See also Indecision
Definitions of words, 197, 217–218, 260, 274, 383–387, 389–390. See also Meanings of words
heterogeneity vs. uniformity in, 74
natural selection and evolution of, 74
Degrees of freedom, 281, 312, 324, 335, 357–358, 376
complexity and, xvi
Delbrück, Max, 241
Demons, 250, 255, 258–260, 269
Dennett, Daniel, 45, 276, 279–280, 310, 319
De novo mutation, 352
Derrida, Jacques, 317–320
consciousness and, 318–319
deconstructing, 318–320
Daniel Dennett and, 319
François Jacob and, 320
metaphysics of absence, 232, 390
Of Grammatology, 318
belief and, 243–244
Desired conduct, 306
Determined stance, 349
cultural, 355
Developmental systems theory, 74, 75, 92–96
adaptation and, 93
differences and, 95
gene-selectionism and, 93, 95, 96, 261–262
on the role of genes, 74, 92–94, 121, 262
Developmental vs. evolutionary questions, 263
Development and transmission, conceptual separation of axes of, 262–263
Diarrhea, causes of, 188
Diachronic. See Synchronic and diachronic.
Dichotomies, 197–198, 263, 308. See also Binary choices
Dickens, Charles, 388
Dickie, George, 206
Dictyostelium caveatum, 36
Dictyostelium discoideum, 36
Difference. See also Hermeneutic circle; Sameness and difference
demystified, 246–250
information and, xiv
nature of, 246
Difference-made, 282
Difference-maker, 281–282
Difference making and mechanisms, 308–310. See also under Causation
“Difference that makes a difference,” 281–282
Dilthey, Wilhelm, 361–364, 384
DNA. See also specific topics
copying of, 23, 27–28, 37, 238
evolutionary genes and, 82–83, 85, 254
informational genes and, 61, 92, 242
interpretation and, 242, 295–296, 347
messenger RNA (mRNA) and, 31, 88, 238–239, 245, 249, 295, 296
nucleotides and, 92, 248, 254, 327
protein(s) and, 57, 85, 245, 249, 296, 297, 347
recombination and, 60, 82, 83, 254
RNA polymerases and, 238, 245, 248, 294–296, 347
DNA polymerases, 88, 239, 295–297, 347
nature of, 294
RNA polymerases and, 28, 295–297, 347
capsid proteins encoded by, 230
conformations adopted by, 77
effects, 78
genes and, 23, 57, 60–61, 67, 78, 82, 103
homologous, 32, 210 (see also Homologous chromosomes)
information contained in, 243
meaning extracted from, 244
nucleotides and, 248, 327, 328
polymerases and, 295
replication, 39
RNA and, 77, 103, 244, 248, 295, 328, 340
rRNA and, 328
Downhill synthesis, xiii
Du Bois-Reymond, Emil, 15
Eckardt, Heinrich von, 300–301
Eckermann, Johann Peter, 190
Effective action, xxiv, xxv, 304, 347, 368
Effects of genes. See Gene’s effects
Efficient causation, 199
chains of, 186
Efficient causes, 157, 230, 268, 351, 354. See also Aristotelian causes
doctrine of, 7
environmental differences acting as, 352
and evolutionary change, 198
final causes and, xxi, 2, 4–5, 185, 190, 199–201, 235, 236, 268, 284, 350
formal causes and, xxi, 2, 235, 236, 350, 351
genes and, 261
Efficient causes (cont.)
of genotypes, phenotypes as, 238
material causes and, xxi, xxii, xxv, 2, 16, 235, 236
natural selection and, 236, 253
nature of, xxi
phenotypic differences and, 228
proximate causes and, 190, 199, 200
purpose and, xxii, 7, 201, 236
ultimate causes and, 184–185, 190, 199, 200
Effort and volition, 125–126
Eggs. See Chickens
Eimer, Theodor, 14
Electrical circuitry, analogy of, 221
Eliot, T. S., 332
Elizabeth I, 1–2
Embryology, 12–15
Embryos, 278
Emotional responses, repertoire of, 175
Empathy. See Sympathy
Endometrium, 222
Ends, 156, 157, 206, 313, 369, 374. See also Means and ends; Telos
culture and, 174
final causes and, 7, 186, 201, 262, 269
genes and, 20, 73, 108, 130, 134, 159, 255, 370
interpretations and, 251, 289–290
natural selection and, xxvi, 269, 376–377
propaganda and, 64
proximate, 161, 186, 243, 251, 255, 262, 263
“Ends justify the means,” 376–377
Environment, 269
phenotype and, 76, 78–81, 93, 94, 99, 203, 228, 246, 252, 257, 261, 262
restriction, 31
E pluribus unum (“Out of many, one”), 121–123
Equilibrium. See also Linkage disequilibrium; Selective equilibrium
Escherichia coli (E. coli), 37, 39. See also thiM
Ethics. See Morality
“Ethics of care,” 172
Eukaryotes, 51, 52, 84, 216–217. See also Slime mold
clade of, 216
replication, 37–38
Eukaryotic alliance, 43–45
features of, 38
Eukaryotic genomes, 238
Eukaryotic recombination, 51, 52
Euphemisms, 389
Evolution
goal/purpose, 194
meanings and uses of the term, 13, 208
Evolutionary biology, xvi, 126. See also specific topics
adaptationist explanations within, 374–375
criticisms of, 192
functional biology, functional biologists, and, 192–194
Geisteswissenschaften and, 371
Ernst Mayr and, 158, 183, 192–197
Adam Smith and, 183
Evolutionary bricolage, 329, 348
Evolutionary causes. See also Ultimate causes
defined, 201
vs. proximate causes, 193–194, 198, 201
Evolutionary genes, 82–86, 254, 255
asexual genotypes as, 258
chromosomes and, 82–86
defined, 254
gene pools and, 86
sexual eukaryotes and, 84
Evolutionary narratives, 371. See also Narratives
Evolutionary questions
vs. developmental questions, 263
vs. ontogenetic questions, 93
Evolutionary stable strategy (ESS), 149, 150
Evolutionary synthesis, 13
Evolutionary theory, xix. See also specific topics
causes of disagreement within, 272, 343
developmental biology and, 14
mathematics and, xix
defined, 223
Explanation
four kinds of, 158
two domains of, 262
understanding and, 361–362, 384–385
Expression, axis of, 262
Extended Phenotype, The (Dawkins), 19–20
Extended phenotypes, 20, 79, 99, 119, 245
Eyes (vertebrate), lens of, 214–215
Factor VIII protein, 296–297
Final causes, xxiii, 206, 269, 279, 351, 367, 373. See also Aristotelian causes; Utility
Thomas Aquinas on, 186
Aristotle and, xi, xxi, 13, 235, 250
Francis Bacon and, 3–5, 7, 8, 11, 235
as barren virgins (irrelevant to practical inquiry), 1, 4, 8, 9, 11, 12
Darwinian, 268
Darwinized, 199
Descartes on, 4
George Dickie on, 206
efficient causes and, xxi, 4–5, 199–201, 235, 236, 268, 284, 350
exclusion from scientific explanation, 5
explanation and, 251
formal causes and, 236, 269, 350–353
form and, 6
and functions, 250–255
genes and, xxiii–xxiv, 79, 228–229, 252
God and, 4, 157, 158, 186–187, 200, 206
homology and, 206
natural selection and, xxiii, 9, 10, 279
nature and, xxii–xxiii, 16, 200
nature of, xxi, xxv, 3, 12, 200
physics, physiology, and, 7
proximate causes and, 185–188, 190, 199
psuche, soma, and, 353
rejection of, xxi, xxv, 3–4, 11, 14–16, 187, 205, 235–236
role in the physical domain, 3
Spinoza’s objection to, xxii–xxiii, 187
teleology and, xxi, 9, 11, 79, 158, 262
ultimate causes and, 184–187, 190, 199, 200
Final type of decision, 125
First-person image/first-person representation, 165–169, 171
First-person sympathy, 165–166
defined, 165
reflected, 168–170
Fisher, Ronald, 267, 344–345, 356
Fitness, 47, 176. See also Inclusive fitness
adaptation and, 18, 160, 262, 273, 276
alleles and, 75, 113–114, 252, 253
genes and, 18, 22, 28, 46–48, 59, 75, 81–82, 135, 138, 160–161
heritability and, 81–82
memetic, 55
modularity and, 226
natural selection and, 82, 126, 135, 163, 164
passion(s) and, 160–164
patrilineal and matrilineal, 113–114
plasmids and, 30
positive and negative selection and, 272, 273
reason and, 131, 161, 163, 176
reproductive, 59
two routes of promoting, 138
Force, conservation of (for living things), 15
Form. See also Form and function
nature of, 354
Formal causes, xxii, 228–232, 350–352
final causes and, 236, 269, 350–353
information and, 241–246
Form and function, 5–8
marriage of, 13
Freedom, degrees of. See Degrees of freedom
Free will/free choice, 315, 349–350. See also Choice
“Function,” 278. See also Form and function
as an intentional term, 283
“casual role” concept of, 277
defined, 277
meanings of the term, 275–277
Functional analysis, goal of, 277
Functional biology (and functional biologists), 192–194, 196
vs. evolutionary biology, 192–194, 371
Functionalism and structuralism, 212–213, 231, 232, 371
Functionalist narratives, 371. See also Narratives
Functions
as adaptations of genes, 79
as (not) causes, 263
Function-talk vs. cause-talk, 199
Gag proteins, 239
Games, evolutionary theory of, 22
Gametic fusion, 38, 40, 44, 52
Geisteswissenschaften, 371
Gender, 2, 386–389. See also Maternal and paternal genes
meanings and scope of the term, 386–389
sex and, 388–389 (see also Sex)
Gender roles, 58
“Gene”
definitions and meanings of the term, 23, 56–60, 67, 68, 73, 74, 82, 88, 265–266
history and etymology of the term, 54, 55
Gene copies and copying, xx, xxiii, 25, 62, 91, 111, 112, 117, 136–138, 262–263. See also Copying; Copying fidelity
Gene networks/regulatory networks, 213, 222, 230, 272. See also Character Identity Networks
Gene polymorphism. See Polymorphism
Genes, 121, 134–137. See also Evolutionary genes; specific topics
as countable, 82–86
Richard Dawkins on, 17, 20, 26, 54, 59–61, 63, 68, 82, 87, 101
developmental systems theory on the role of, 74, 92–94, 121, 262
as dispensable, 81–82
ends and, 20, 73, 108, 130, 134, 159, 255, 370
final causes and, xxiii–xxiv, 79, 228–229, 252
fitness and, 18, 22, 28, 46–48, 59, 75, 81–82, 135, 138, 160–161
genomes and, 39, 43, 68–69, 80, 86, 136, 182, 215, 221, 222, 228, 262, 314, 328
kinds of, 23–25
“learn” the hard way, 161
of maternal vs. paternal origin, 110–111, 138–140
nature of, 59, 98–99, 134, 354
“responsibility” for their effects, 252–253
as special, 96–99
Gene’s effects, xxiii, xxiv, 75, 76, 79, 111, 252. See also Genes; Phenotypes; specific topics
defined, 75
Gene-selectionism, 74. See also Multilevel selection theory
developmental systems and, 93, 95, 96, 261–262
multilevel selection theory and, 73–74, 88, 91
strengths and weaknesses, 83–84, 95
Gene-selectionists, 19, 20, 24, 74, 88, 95
vs. hierarchical-selectionists, 60
Gene selfishness. See Selfish gene(s)
Gene’s functions, 78–79
defined, 252–253
and gene’s side effects, 78
Genetic boundaries of an organism, 51. See also Linkage disequilibrium: species boundaries and
Genetic information. See also Information
inheritance of, between generations, 262
Genetic material, xxxii, 84. See also specific topics
Gene tokens. See Tokens
Genome rearrangement, 210
Genomes, 38, 136, 229. See also Intragenomic conflicts
chromosomes and, 37, 46, 86, 210
evolution and, 128, 226, 228, 231–232, 243
genes and, 39, 43, 68–69, 80, 86, 136, 182, 215, 221, 222, 228, 262, 314, 328
information in, 242–243
maternal and paternal, 146, 314
natural selection and, xxvi, 223, 262, 295
nature of, 43, 68, 110, 231–232
genomes as texts, 264–267, 295, 296
nucleic acid sequence, 224
organisms interpreting their, 296
organization of meanings within, 265
pieces/“factions”/“parties” of, 152, 259
plastid, 45
reciprocity within, 150
recombination and, 68, 80, 259
retrotransposons and, 238–239
sexual, 68–69
single-stranded, 90f
Genomic imprinting. See Imprinting, genomic
Genomic parasites, 220
alleles and, 254
clonal reproduction and, 258
Wilhelm Johannsen and, 54–56, 65
Genotypes (cont.)
memes and, 65–66
phenotypes and, 54, 65, 66, 78, 100, 210, 237, 238, 245, 261, 263
sexual and asexual, 258
GlcN6P (glucosamine-6-phosphate), 323, 324, 326, 327
GlmS aptamers, 324
GlmS riboswitches, 323, 324, 327
GlmS ribozymes, 326
Glucosamine-6-phosphate (GlcN6P), 323, 324, 326, 327
Glucosamine-6-phosphate riboswitch ribozyme. See GlmS ribozymes
Glucose-6-phosphate (G6P), 324
Goal-directedness and goal-directed behaviors, 13, 14, 194, 195, 262
“Goal-directed” vs. “purposive,” 195
Goals, 160
diachronic vs. synchronic, 224
evolutionary, 198
moral, 166
ultimate (see Ultimate goals)
working together to achieve common, 40, 51, 108
God, 4
as cause of things, 186–187
Descartes on, 4
final causes and, 4, 157, 158, 186–187, 200, 206
nature and, 4, 5, 186–187, 200, 264
Spinoza on, 186–187
Godfrey-Smith, Peter, 83–85
Goethe, Johann Wolfgang von, 8, 190, 191
“Good of the gene,” 20, 253–255
“Good of the group” (and “good of the species”), 18, 24, 60
“Good of the organism,” 20, 251, 255
Gould, Stephen Jay, 273, 371–372
Gray, Asa, 11–12
Green beard effect, 26–27, 31, 34–35, 42
linkage disequilibrium and, 34–35, 42
Groups. See also “Good of the group”; Social groups
genes and, 60, 73 (see also Genes: groups of; Social groups)
David Wilson on, 18
Group selection, 18
Haeckel, Ernst, 10
Haidt, Jonathan, 178
Haldane, J. B. S., 110–111
Half-siblings, 50, 111–113, 115, 138, 141, 145, 147, 148
Hamilton, William D., 111, 258
Haplotype, 43
Heat generation. See Thermogenesis
Held, Virginia, 172
Helmholtz, Hermann, 15
Hermeneutic circle, 122, 361, 362, 367, 382, 384
Hermeneutics, 360–363
Hierarchical selection, 18–19. See also Multilevel selection theory
Hierarchies
causes and, 186
genes and, 18, 23, 24 (see also Multilevel selection theory)
Histidine, 296–297
Historical kinds, 91–92, 100, 386
Historical narratives, 370–372. See also Narratives
Hodge, Charles, 338–339
Homogenous bodies, 189. See also Homogeny
Homogeny, 208
Homologous capsid proteins, 230
Homologous chromosomes, 27, 209. See also Alleles; Homologous DNA sequences
Homologous DNA sequences, 32, 210
Homologous genes, 210
Homologous organs and body parts, 207, 214. See also Homologous structures
Homologous parts in disparate organisms, identification of, 218
Homologous similarities vs. analogous similarities, 204
Homologous structures, 206. See also Homologous organs and body parts
Homologs, 213
defined, 211–213
morphological, 210 (see also Morphological homology)
origin, 219
serial, 217
Günter Wagner on, 212, 213, 216, 217, 219
Homology, 214
Miles Berkeley on, 206
definitions and meanings of the term, 204, 206
and the doctrine of final causes, 206
morphological, 210–213
terminology, 208
toward a genetic concept of, 208–211
types of, 204, 206–207 (see also Serial homology)
Homology, Genes, and Evolutionary Innovation (Wagner), 212–220, 229, 230
definitions in, 217–218
Homology concepts, 218
Homoplasy
homogeny and, 208
nature of, 208
How come?
vs. how?, 198
vs. what for?, 193–195, 197, 200, 201
How? vs. why?, 158, 190, 191, 193, 200
Humanists
physicalists and, 375
Humanities, 359
science and, x, xxv, xxvii, 263, 360, 370, 373, 374
Human uniqueness, 349, 357, 374–376
Hume, David, xxiv
Hypoxia, 227
Ideas, 134–135, 266. See also Memes
“good,” 135
IGF1R and IGF2R, 114–115
IGF2 (insulin-like growth factor 2), 49, 114–115
Imitation, 161
Immediate causes, 187, 193, 235, 349–350. See also Proximate causes
Imprinted genes, 77, 103, 113, 145–146, 390
and brain development and function, 140
gene’s parental origin and the effects of, 111
influence on broad behavioral tendencies and personality traits, 141
loudest-voice-prevails and, 116
molecular functions, 151
nature of, 140
and Prader-Willi and Angleman syndromes, 117–118
Imprinting, genomic, 390
absence of, 113
and the altercation of generations, 47–50
defined, 111
gene dosage and phenotypic difference made by, 116
and kinship, 110–112
nature of, 139–140
and nonshivering thermogenesis in brown adipocytes, 116–117
Impulses, 126, 128–130, 152. See also Instinct
conflicts of, 129–130
control over, 58
deciding between contradictory, 130
reason and, 130
Inclusive fitness, 22
natural selection and, 19–20, 126
Richard Dawkins on, 19–20
Indecision, 286
pathological, 133
Indeterminacy, 266, 267. See also Uncertainty
of interpretation, 265–267
of translation, 265
Individuation and reproduction, antagonism between, 189
Inductive reasoning, natural selection as, xxiv
Infinite monkey theorem, 338
Information. See also Genetic information; Meaning; Unit of information
causation and, 247
formal causes and, 241–246
integration of, 286n
mutual, 244–245
and meaning, 302–305
unit of, 247
Informational genes
and the construction of organisms, 104
copies, 25
defined, 192
material genes and, 23–24, 61, 242, 362–363
nature of, 24, 91, 92, 123, 242, 351, 362
strategic genes and, 24, 25, 92
Information theory and meaning, 305–308
Innovation. See also Novelty; Recombination
vs. adaptation, 219
Instinct. See also Impulses
adaptation and, 131
Darwin and, 338
as guide to action, 131, 156, 160–161
ideas and, 135
reason and, 130, 131, 161, 176
Insulin-like growth factor 2 (IGF2), 49, 114–115
“Intelligent design,” 65
Intentionality
of natural selection, xxv, 280, 285
secondary, 285
Intentional language, 200, 280
function and, 283
incentives hiding, 369
interpretation and, xxv, 283, 289–292, 382
meaning and, 283, 294, 315, 381–382, 384
telegraphing one’s, 298–302
Intention(s) (cont.)
understanding, 381–382, 384–385
Interludes (morality plays), 271
Interpretation(s), 231, 273, 282–283, 287, 304, 308, 314, 320, 347, 348, 357, 366, 370, 387. See also Hermeneutics; Meaning; Semantic information; Semantic problems; Zimmermann telegram
causes and, 191, 193, 199–201, 248, 285n, 309–310, 334, 349–350, 352
choice, decision making, and, 315, 323, 348–351, 354–355, 391
conceptions of, 360–361
continuity between simplest and most complex forms of, 376
difference and, 245, 281–282, 310
freedom of, 385
genes, genetics, and, 251, 252, 261, 263, 294–297, 314, 315, 348–349, 351–355
humanism, humanists, and, 370, 374
indeterminacy of, 244, 265–267 (see also Uncertainty)
information and, 106, 243–245, 248, 281–288, 292, 296, 301, 302, 310, 354, 355, 367, 384
intention and, xxv, 243–244, 283, 289–292, 297, 302
of interpretations, 289–293, 391
learning and, 348–349
nature of, 285–286, 286f, 289–290, 292
objective, 288
organisms and, 246, 296, 348, 357, 363, 368
as recursive process, 360
ribosomes and, 248, 295–297, 347
RNA and, 242, 245–246, 248–249, 295–296, 347–348
semantics and, 273
of synchrony, 334
teleology of, 282–285
of texts, 257, 263, 266, 267, 290–296, 308, 315, 318, 320, 359–361, 382–385, 391
understanding and, 315, 362, 363, 382, 384–385
Interpretative mechanisms, 368, 383
Interpreters. See also Interpretation(s)
vs. tools, 323
Intragenomic conflicts, 20, 22, 28–29, 69, 110, 111, 152, 182
sources of, 110–111
Iterated prisoner’s dilemmas (IPDs), 149–150
Jacob, François, xiv–xv
James, King, 1–3
James, William, 125–126, 129–130, 183
on inheritance, 55
Kant, Immanuel, 231, 261, 263, 368
Keverne, Barry, 140–141
Kidneys, 217
Kin-altruism, xv
Kingsley, Charles, 190
genomic imprinting and, 110–112
green beard effect and, 26, 27
Lactate dehydrogenase A (LDH-A), 215
Lactate dehydrogenase B (LDH-B), 215
Language, xx, 255, 382. See also Angelman syndrome; Definitions of words
of agency and purpose, 17
basis, 120
children and, 121
diversity and beauty of, xxi
evolutionary biology, evolutionary biologists, and, 198–199, 201
functionalist, 213
genetics and, 121
imprecision of, 265
interpretation and, 265, 381–383
meaning and, xx, 74, 266, 381 (see also Meanings of words; Semantics)
“motor theories” of the evolution of, 120
nature of, 55
origin, xxi
teleological, xxv, 79, 184, 198, 201, 250–251
Language centers of brain, 121
Language development, 121
cause and culpability in Germanic, 235
evolution, xx
nature of, 386
Langue, 382
Lankester, E. Ray, 208–209
Lauder, George, 277–278
Learning, 161
Life, meanings of, 313–315
Life and Opinions of Tristram Shandy, Gentleman, The (Sterne), 233
Ligands, 331
aptamers and, 322, 328–329, 331, 335–336, 343
conformations and, 331, 332, 335, 336, 343
natural selection and, 326, 329
riboswitches and, 323, 325, 332, 336
Linkage disequilibrium, 46, 83, 254
definition and nature of, 83, 85, 86
DNA blocks defined by strong, 85
green beard effects and, 34–35, 42
recombination and, 40–42, 85–86, 254
species boundaries and, 86
Loss-of-function mutations, 76, 253–255
Loudest-voice-prevails, 113–116, 146, 147
Ludwig, Carl, 15
Luther, Martin, 349–350
“Machine,” organismal
parts of, acting at cross purposes in pursuit of conflicting agendas, 108
Maintenance of existing function, 272
Marmosets, 36–37
Marx, Karl, xi
Maternal and paternal genes
conflicting interests of, 141
relatedness asymmetry between, 50
reversed roles of, 145
Mathematics and evolutionary theory, xix, 328, 330
Matrilineal kinship, 141
Matter in motion, xxi, xxii, xxv
Maxwell, James Clerk, 255
Mayr, Ernst
evolutionary (vs. functional) biology and, 183, 192–197, 371
on evolutionary causes, 193–194, 201
on historical explanation in biology, 184
on historical narratives, 371
on how come? vs. what for?, 193–195, 197, 200, 201
on how? vs. why?, 158, 190, 191, 193, 200
on immediate vs. historical causes, 197
“political motivations,” 192
on proximate causes, 158, 183, 191–194, 200, 201, 334
on proximate How? explanations vs. ultimate Why? explanations, 158, 191
teleology and, 190–196
on ultimate causes, 158, 183, 191–195, 197, 200, 201, 334
vitalism and, 192
McCosh, James, 206
Meaning, 374. See also Semantics
automata and, 279 (see also Information; Interpretation(s))
information and, 243–245, 285–288, 302–305 (see also Information theory and meaning)
intention and, 283, 294, 315, 381–382, 384
interpretation and, xx, xxv, xxvii, 243–245, 265, 269, 281–288, 292–297, 302–306, 308, 310, 314, 318, 343, 355, 360, 362, 364, 373–374, 381–382, 384, 389, 391 (see also Hermeneutics)
of life, 313–315
as metaphor, 391
“Meaning”
as an intentional term, 283
definitions, xxv, 285, 288, 303–305
Meanings of words, 274, 383–385, 389–390. See also Definitions of words; Semantics
Means and ends, 73, 157, 159, 161, 165, 251, 358, 370. See also Ends
natural selection and, 236, 376–377
“the ends justify the means,” 376–377
Mechanism(s). See also Difference making and mechanisms
vs. adaptive function, 184, 197, 200
explanations of mechanisms vs. explanations of mechanisms’ evolution, 183
reduction to, 14–16
vs. subjective experience, 153
“Mechanistic revolution,” 15
Meiosis, 47
Meiotic segregation, 27, 38, 52
Meiotic vs. bacterial recombination, 40
Meme complexes, 69
Memes, 21, 45, 53–55, 63, 65–67, 69–70
adaptations of, 69
adaptive features, 65
culture and, 45, 53–54, 63, 65, 67
Richard Dawkins on, 53, 63, 67, 134
etymology of the term, 53
forms of, 67
ideas and, 134
nervous system and, 67
phenotypes, genotypes, and, 65–66
propaganda and, 63–66
Memetic fitness, 55
Memetic propagation, 135. See also Memes: propaganda and
Memetic recombination, 57
Memetics, 65–66
Memetic shift, 19
Memetic transmission, 56, 63–67
Mendelian genetics, 14
Mendelian inheritance, rules of, 68–69
Mendelian probabilities, 47
Mendelism, 54–56
Mendel’s demon, 258–259
Mesonephros, 217
Messenger RNA (mRNA), 31, 322–328, 347
DNA and, 31, 88, 238–239, 245, 249, 295, 296
nucleotides and, 328
proteins and, 16, 62, 88, 105, 238–239, 245, 249, 254, 294–296, 322, 323, 325
ribosomes and, 239, 294–296, 347
RNA polymerases and, 295, 296, 347
transcription and, 31, 116, 245, 249, 295, 296
translation of, 31, 105, 238–239, 245, 294, 295
Metanephros, 217
Metaphors, xi–xxi, 98, 223, 224, 259. See also Natural selection: metaphor of
agential, 98
consciousness and, 367
Darwin’s use of, 207–208, 223, 252, 271
of information, 241
interpretation and, 292, 364, 366, 391
meaning and, 269, 318, 391 (see also Meaning)
signifiers and, 391
Metaphysics
Bacon on physics and, 2–4, 235
causes in, 235
Methylase, 31
Methylation, 77
Minicircles, 31
Misinterpretation, 265–267. See also Interpretation(s)
Mitochondria, 20, 31, 43–45, 107
Mitochondrial genes, 44, 45, 136
Mitochondrial genome, 86
Mitochondrial membrane, 107, 108
Modern synthesis, 13
Modularity and evolvability, 224–228
Monod, Jacques, 326
Moral codes, 181
Moral concepts, 180
Moral goals, 166
Morality, 174
cultural elements, 179–181
instinctive elements, 175–177
rational elements, 177–179
responsibility, 182
Adam Smith on moral sentiments, xvi, 155–157, 164, 171, 172, 174, 177–179, 182, 183
Morality plays, 271
Morphological characters, 213, 216
Morphological features, 211, 272
Morphological homology, 210–213
Morphologists, 13, 207, 211, 231
final causes and, 8
functional, 276
comparative, 230
Motion, matter in, xxi, xxii, xxv
Motivation. See Psychological motivation
Mullahy, John H., 191–192
Muller, Hermann, 96–97, 340–344
Multilevel selection theory, 18–19, 73–75, 88, 89, 91
“Mutation” (Bryant), 345
Mutation(s), 39, 41, 65, 76, 229, 253–255, 284, 311, 328, 333, 337, 340, 352, 363
adaptationists and, 220, 272–273
aptness and, 341
causal history behind each, 267
de novo, 352
directional, 341
Ronald Fisher on, 344
and genetic novelty, 24, 61, 78
natural selection and, 284, 329, 340, 341, 343
nature of, 100, 257–258, 278, 341, 344
Mutation(s) (cont.)
negative selection and, 220, 278
positive selection and, 272
randomness, 257, 329, 341 (see also Random mutation(s))
repeat-induced point, 38–39
retrotransposition and, 239
selection and, 64–65, 75–76, 220, 232, 239, 252, 253, 257–258
synonymous vs. nonsynonymous, 297
TPP (thiamin pyrophosphate) and, 341, 342f
transposition and, 239
Myxococcus, 33–35
Nabi, Isidore, 94n1
Narratives, 234, 370–372. See also Texts; specific topics
Natural kinds, 211, 212, 216–218
Natural selection, 127. See also Darwin’s demon
adaptationists and, 220, 221, 232, 272, 273
alleles and, 253
aspects of, 272
creativity of, 338–340, 343–345
“the ends justify the means” and, 376–377
final causes and, xxiii, 9, 10, 279
fitness and, 82, 126, 135, 163, 164
genomes and, xxvi, 223, 262, 295
grounding of function by recent utility and, 278
intentionality of, xxv, 280, 285
and means and ends, 236, 376–377
metaphor of, 16, 252, 270, 362
monkeys, typewriters, and, 338–340
mutation and, 284, 329, 340, 341, 343
nature of, xxiv, xxvi, 73, 252, 253, 270, 284
phenotypes and, 78, 94, 95, 98, 99, 252
and the power of selection, 343
products of, 270
as a purposeless process, xi, 78, 270
as a recursive process, xxiii, 236, 261
subset selection and, 257, 284
teleology and, 201, 283–284, 339
Günter Wagner and, 214, 219–221
Natural transformation, 32
adaptation and, 272–273
costs, 225
deleterious mutations and, 220, 252, 272
functional and structural constraints and, 272–273
maintains useful order, 278
nature of, 272
older features maintained by, 232, 272
positive selection and, 220, 232, 253, 272–273, 279
Neurons, 106, 107, 136, 165, 246, 348
Neurospora crassa, 38–39
Niche construction, 99
Nietzsche, Friedrich Wilhelm, 363, 373, 387
Nominalism, 218
Nominal kinds, 216–218
Nonshivering thermogenesis, 106–107, 115–117
control of, 115–117
Nonsynonymous mutations, 297
Noradrenergic neurons, 107
Novel functions, 224, 272, 329
Novelty, 219
defined, 213–214
evolutionary processes leading to, 199
mutation and genetic, 24, 61, 78
Günter Wagner on adaptation and, 213–214, 219–220
Nucleic acids, 121, 123, 211, 224, 230
Nucleotide aptamers, 328–329
Nucleotide difference, 99
Nucleotides, 254, 255, 349. See also Ribonucleotides; Single-nucleotide polymorphisms
amino acids and, 264, 327, 348, 349
DNA sequences and, 248, 327, 328
phenotypic effects and, 99
polymerases and, 248
retrotransposition and, 239
RNA and, 248, 324, 327, 329, 348
RNA sequences and, 248, 327, 329, 330
Nucleotide sequences, 240, 264
Objective interpretation of information, 288
Objective phenomena, 368–370
Objectivity, 368
On the Origin of Species by Means of Natural Selection (Darwin), xi, 9, 13–14, 207, 266
Ontogenetic mechanisms, developmental systems theory and, 262
Ontogenetic vs. evolutionary questions, 93
Ontogenetic vs. phylogenetic explanations, 263
Ontogenetic vs. phylogenetic questions, 208
“Organism,” etymology of the term, 357
Organisms, 108, 357–358. See also specific topics
genes and, 122–123
nature of, 20–21
“Original” function of a conserved feature, search for the, 274
“Original” meaning, 274
Origin of Species. See On the Origin of Species by Means of Natural Selection
Origin recognition complex (ORC), 38
Orthogenesis, 14
Owen, Richard, 7–8, 204–205, 207–208
Pangene, 54
Panglossian Paradigm, xii
Parasites, genomic, 220
Parts to wholes, relation of, 122, 231, 360–363
fitness and, 160–164
intuitions as coming from, 177
nature of, 163
preferences and, 160–161
and preservation of society, 157
reason and, 130, 157, 161, 162
telos and, 160
Paternity
multiple, 115–116
Peirce, C. S., 243–244, 259–260
Peptides. See also Polypeptides
Phenomena, 365–366
objective, 368–370
Phenotype(s), 118, 195, 198. See also Adaptation; Gene’s effects
changes in, 333
creation of, 262
Richard Dawkins and, 19, 20, 68
and the environment, 76, 78–81, 93, 94, 99, 203, 228, 246, 252, 257, 261, 262
extended, 19–20, 79, 99, 119, 245
genes and, 75–82, 93, 94, 98, 237, 252, 257, 262–263 (see also Strategic genes: phenotype(s) and)
genotypes and, 54, 65, 66, 78, 100, 210, 237, 238, 245, 261, 263
Wilhelm Johannsen on, 54, 55, 65
memes and, 66
methylation and, 77
natural selection and, 78, 94, 95, 98, 99, 252
overview, 75–77
scope of the term, 76
Phenotypic development and genetic inheritance, 80
Phenotypic difference, 100
genes and, 57–58, 86, 117, 228
imprinting and, 117
evolution and, 87
genotypic difference and, 237
informational genes and, 25
nature gene’s functions and purpose, 158
nucleotides and, 99
strategic genes and, 24–26, 62, 89, 91
Phyllodes, 211
Physical causation, 158, 193, 237, 373
Physical causes, 158, 188, 190, 191, 201, 234
Physics, 311–312, 328. See also Thermodynamics
Bacon on metaphysics and, 2–4, 235
causes in, 2–4, 7, 14, 95, 235
Pittendrigh, Colin, 255
Placenta, 222
Plasmids, 29–32
bacteria and, 29–31
defined, 29
viruses and, 30–32
Plastids, 43–45
Plato, footnote to, 241n1
Poet, natural selection as a, 340, 343
Pol protein, 239
Polymers, 104, 294. See also DNA polymerases; RNA polymerases
Polymorphism
genetic, 150
single-nucleotide, 244
Polypeptides, 248, 249, 254, 327
Positive selection, 227, 243, 272–273, 279
negative selection and, 220, 232, 253, 272–273, 279
Posterior vs. prior causes, 185
Potential and the actual, the, 330–331
Poulton, Edward, 190
Prader-Willi syndrome, 117–119
Preadipocyte factor-1, 116
Preferences, 160–161, 257, 281, 308, 321, 323. See also Conflicting preferences; Morality
Kenneth Arrow on, 132
nature of, 308
Prior causes, 185–187
Prisoner’s dilemma. See Iterated prisoner’s dilemmas
Private self, 169–170
Private texts, 382–383
Prokaryotic firm, 27–28
Prolactin (PRL), 221
Propaganda, 63–66
Proper functions, 282
Protein-coding genes, 39, 57–59
Protein(s), 107, 108, 114–117, 239
allosteric, 326, 348 (see also Allostery)
amino acids and, 57, 230, 243, 249, 296–297, 327, 328, 348
as automata, 102–107
“behavioral flexibility,” 105
cadherins, 35
capsid, 230
DNA and, 57, 85, 245, 249, 296, 297, 347
DNA-binding, 32
factor VIII, 296–297
genes and, 76, 102–105, 116, 242, 254, 296 (see also Protein-coding genes)
housekeeping functions of organisms are performed by, 104
lens, 214
messenger RNA (mRNA) and, 16, 62, 88, 105, 238–239, 245, 249, 254, 294–296, 322, 323, 325
mRNA and, 16, 88, 105, 238–239, 245, 249, 254, 294–296, 322, 323, 325
nature of, 104
nonsynonymous mutations and, 297
photons and, 105
rhodopsin, 105
ribosomes and, 244–246, 249, 294–297, 325, 347
RNA and, 16, 62, 239, 246, 249, 324, 326–328, 337, 347, 348
Proximate causes, 95, 185, 186, 337. See also under Mayr, Ernst; Ultimate causes
vs. evolutionary causes, 193–194, 198, 201
final causes and, 185–188, 190, 199
God as proximate cause, 186
Ernst Mayr on, 158, 183, 191, 200, 201, 334
in medicine, 187–188
vs. remote causes, 185–188, 194, 350
Herbert Spencer on, 189–190
“Proximate,” definition and etymology of the term, 185
Proximate ends, 161, 186, 243, 251, 255, 262, 263
Proximate explanations vs. evolutionary explanations, 198
Proximate mechanisms, 113
Proximate telos, 160
Proximate–ultimate distinction, 196–201. See under Mayr, Ernst; Ultimate causes
Psuche (soul), 353
Psychological motivation, 158–160, 163–164, 176. See also Benevolence/benevolent motives; Self-interest; Selfishness
vs. evolutionary function, 159–160
Psychologists, evolutionary, 58–59
Public self, 170
Pulleys, old springs, wheels and (slightly altered), xxviii, 10, 223, 271–272, 276
Punishment, 133, 157, 180–182, 387
Purpose, 17. See also Teleology; Telos; Utilitarian purposes
efficient causes and, xxii, 7, 201, 236
Purpose in nature, naturalistic account of the appearance of, 158
Purposeless algorithm, natural selection as a, xi, 78, 270
“Purposive” vs. “goal-directed,” 195
Random mutation(s), 65, 257, 329, 341
Randomness. See also Chance; Mendel’s demon
critics of Darwinism and, 338–339
and selection, 256, 257, 338–339
Random variation(s), 329, 338, 375, 376. See also Chance
Rationalization, 178
Reason, 130. See also Morality: rational elements
Adam Smith on, 157
adaptation and, 131
fitness and, 131, 161, 163, 176
as guide to action, 131, 156, 162–163
instinct and, 130, 131, 161, 176
nature of, 131
passion and, 130, 157, 161, 162
Reason (cont.)
telos of, 162
utility and, 162, 176, 178, 179
Reciprocal altruism, 386
Reciprocal representation, 245
Reciprocity, 153
direct vs. indirect, 171–172
within the genome, 150
second-person sympathy and direct, 165–168
third-person sympathy and indirect, 165, 170–172
Recombinant-progeny hypothesis, 32
Recombination, genetic, 29, 40–43, 52, 254, 266, 329. See also Bacterial recombination
allelic, 43
chromosomes and, 32, 40, 51, 68, 85–86
coreplicons and, 51
creates relatives, 52
genes and, 29, 41, 51, 52, 57, 60, 68, 82, 85–86
“hot spots” of, 83
linkage disequilibrium and, 40–42, 85–86, 254
memetic, 57
nature of, 32
suppression of, 85–86
first-, second-, and third-level, 166, 168, 169
interpretation and, 245, 284, 360
reproductive, 284
Recursive processes, xiv, 230, 231, 237, 284, 360. See also Natural selection: as a recursive process
Recursive representation, 241, 242, 269, 270
of mutable replicators, 258
Reddy, Vasudevi, 172
Reductionism. See under Mechanism(s)
Reflected first-person sympathy, 168–170
Reflections, 156. See also Self-reflection; Sympathy
upon reflections, 156
Reflexes, conditioned, 285
Reflexions upon our self-image, 156
Regulatory networks. See Gene networks/regulatory networks
Relatedness, asymmetries of, 50, 138–139, 245
Relatives, 138–139
Remote causes, 185–189, 191, 193–194
defined, 187
Repeat-induced point mutation (RIP), 38–39
Replication, 269
Replicators, 23, 61, 78, 98–99, 104, 144, 242, 245, 252. See also under Memes
DNA- and RNA-based, 27
mutation and, 258
natural selection and, 252, 257
recursive selection of mutable, 258
Reproduction, clonal. See Clonal reproduction
Reproduction, sexual. See Sexual reproduction
Retrorecursion, 238–241
Retrotransposition, 239–240
Retrotransposons, 238–241, 264
Retroviruses, 222–223
Reuses old materials for new purposes, xxvi, 223, 266
Rhodopsin (gene), 104–105
Ribosomal RNA (rRNA), 295
choice of amino acid by, 250
glycine and, 248
interpretation and, 248, 295–297, 347
methionine and, 249
protein and, 244–246, 249, 294–297, 325, 347
translation and, 239, 245–246, 248, 249, 294
Riboswitches, 325, 329, 332, 343, 364
acting in tandem, 325
aptamers and, 322, 324, 326, 329, 335, 336
conformations and, 324, 332, 335
defined, 322
ligands and, 323
mRNA and, 323
ribozymes and, 322–323
thiamin pyrophosphate (TPP), 324, 327, 336, 337
aptamers and, 322–324
B-group vitamins and, 324
defined, 322
mRNA and, 326–327
nature of, 323
riboswitches and, 322–323
RNA. See also Messenger RNA; Riboswitches; specific topics
amino acids and, 249, 328, 348
aptamers and, 322, 325, 329, 335
catalysis and, 321–323, 326, 331
RNA (cont.)
conformations and, 324, 330, 331
DNA and, 27–28
interpretations and, 242, 245–246, 248–249, 295–296, 347–348
protein and, 16, 62, 239, 246, 249, 324, 326–328, 337, 347, 348
TPP (thiamin pyrophosphate) and, 324–327
DNA and, 238, 245, 248, 294–296, 347
DNA polymerases and, 28, 295–297, 347
interpretation and, 248