engrailed protein, 148–49
environmental change
adaptive solutions to, 11, 14–15
fuel innovations, 85–87, 88
gene activation or repression in response to, 141
organism flexibility and robustness, 61–62, 85–86, 173–75, 188–94
enzymes. See also proteins and amino acids
function of, 22, 48, 62
innovation and creation of novel enzymes, 111–12, 114
in makeup of phenotype, 23
optimal temperature for, 110
as self-assembling macromolecules, 62–63
error catastrophe, 45–46, 174
Escherichia coli
dissimilarity of strains, 80, 82
gene regulation, 137–41, 166
genome size, 29
multiple glucose metabolisms, 97–98
robustness to changing environments, 61–62, 84, 87, 188, 191, 192
synthesis of essential biomass molecules, 61, 70, 97
essentialism, 9–10, 34–35
Eupodophis snake, 10
evo-devo (evolutionary developmental biology), 21–22
evolution. See innovability and innovation; natural selection
evolutionary science. See also Darwin, Charles
additive nature of theories, 28
algorithms in computational technology, 202–4
evolutionary biology, 28
evolutionary developmental biology, 21–22
gradualist versus mutationist schools, 16–17, 19
pre-Darwinian theories, 8
theories counter to evolution, 8–10
exaptation, 200
expression of genes. See gene regulation and regulation circuits
Falco peregrinus, 2–3
fermentation, 22
Ferrada, Evandro, 125–26
fish
antifreeze proteins, 107, 111, 179
coelacanth, 28
Fisher, R. A., 18, 218
Freedman, Richard, 206
fruit flies. See Drosophila melanogaster
fuel innovations, 85–87, 88
Galápagos Islands, 49–51
Galilei, Galileo, 220
Game of Life self-replication computer model, 217–18
gene knockout technology, 171–73
gene regulation and regulation circuits
beta-galactosidase (beta-gal) expression, 138–41
biological cost of gene expression, 140–41
cascades of regulators, 144
circuit equilibrium gene expression pattern, 146
circuit library and genotype texts, 157–60
complexity of, 142, 145–46, 150–51, 188
in developmental biology, 142
distalless expression, 154–55
diversity of biological forms and functions, 137, 142–43, 147, 151–52
in embryonic development, 147–50
engrailed expression, 148–49
expressed genes, 136
genotype network, 164–68, 182–85
Hox circuits, 152–54
hypercube organization of circuit library, 159
innovation and new expression codes, 142, 147, 152–56, 166–68
KNOX expression, 156
meaningful texts, 159–60
mechanism of gene expression, 108, 136, 138–40
multiplicity of regulators, 143–44
mutations, 137, 161–62, 166, 168
number of expression patterns, 160–61, 162
polymerase transcription enzyme, 138–40
regulated genes, 136
repression or activation in response to environment, 141
robustness, 174–75
transcriptional regulators, 138–40
genetics, population, 18–19
gene transfer and gene deletion, 78–80, 92, 94
genome, human, 29–30
genomics, population, 30
genotype networks
disorder, 169–70, 175, 179, 186
diversity of neighborhoods, 92, 102–5, 125–27, 129, 167
hypercube organization of texts, 89–92, 115–16, 159
mapping of, 34–35, 93–95, 97–101, 124, 126
in metabolism, 92, 99–105, 125–27
neutral change, 179–82
organizational principles facilitating innovation, 94–95, 99–102, 125, 131–35, 170, 181–86
parallels between biological and technological processes, 196–202, 212–16
in proteins, 124–27, 131–35
in regulation circuits, 164–68, 182–85
robustness, 173–75, 194
self-organization, 175–76, 194
genotype versus phenotype, 13
Gilfillan, S. Colum, 201
glass lizard, 10
globins, 112, 120–24
Goldschmidt, Richard, 17
Gould, Stephen Jay, 180, 200
gradualist school of evolutionary biology, 16
Hadean Eon, 38–39
Haldane, J. B. S., 18, 39
hammerhead ribozyme, 181–82
Hay, Angela, 156
Hayden, Eric, 132–34
hemoglobin and globins, 112, 120–24
heritability and inheritance
blending of traits, 16
fitness, 20
Mendelian principles for, 12–13, 16
on molecular level, 23–24
in natural selection process, 4, 11, 42
preservation of innovations, 11, 15
Hersey, George, 206
horizontal gene transfer and gene deletion, 78–80, 92, 94
Hox (homeobox) circuits, 152–54
Hoyle, Fred, 197
Human Genome Project, 29–30
humans
alcohol tolerance, 27
brain proteins and Alzheimer’s disease, 110
duplicate enzymes, 189
genome, 29–30
ingenuity, 205–7
lactose digestion, 136–37
lens of eye, 177–78
Mendelian traits, 13
metabolic shortcomings, 77–78
regulation circuits, 143–46, 149–50, 152–53
Huxley, Julian, 19
hydrothermal vents, 49–52, 55, 57
hypercube representation of genotype networks, 89–92, 115–16, 159
Ibn Khaldun, 8
inheritance. See heritability and inheritance
innovability and innovation. See also gene regulation and regulation circuits; metabolism; proteins and amino acids
basic principles and themes, 66
Cambrian explosion, 196
combinatorial function, 66, 72–73, 75, 83, 102, 200–201
conservation function of natural selection, 3, 5, 14–15, 176–79
co-option of earlier innovations for new purposes, 153, 154, 178, 200
through genotype networks, 92, 94–95, 99–102, 125, 131–35, 170, 181–86
genotypic disorder, 169–70, 175, 179, 186
heritability of innovations, 11, 15
incremental steps, 3, 111–14, 117, 123–24, 161–62, 178–79
multiple solutions to similar problems, 118–19, 170, 199
neutral change, 179–82
parallels between biological and technological innovation, 196–202, 212–16
by populations of evolving organisms, 18–19, 77, 101–5, 117, 161, 175
innovation, technological. See technological innovation
insects
aphids, 189–91
fruit flies, 27–28, 146, 147–51
globin proteins of, 123–24
peppered moth, 17–18
interstellar space, organic molecules in, 40–41, 47, 56
Isalan, Mark, 166
Jacob, François, 137
Johannsen, Wilhelm Ludvig, 13
Johnson, Stephen, 199
Keefe, Anthony, 118
&nb
sp; Kelvin, Lord (William Thomson), 197
Kimura, Motoo, 180
knockout technology, 171–73
KNOX protein, 156
Kreitman, Martin, 27–28
Kyoto Encyclopedia of Genes and Genomes, 69–70
lactose digestion, 136–40
Lamarck, Jean-Baptiste, 8
Leydig cells, 149
libraries of genotype texts. See genotype networks
life, building blocks of, 59, 64–65, 69, 83–84, 101
life, origin of
autocatalysis and self-organization, 55, 62–63
basic requirements and principles, 42, 66
citric acid cycle, 53–54
first microbes, 39, 52
hydrothermal vents, 49–52, 55, 57
interstellar organic molecules, 40–41, 47, 56
lipid molecules and membranes, 55–57
primordial soup/warm ponds hypothesis, 39–40, 48–49
replication, 42–48
single common ancestor of modern life, 10, 63–65
spontaneous generation, 36–38
tidal pool hypothesis, 49
Linnaeus, Carl, 9–10
lipid molecules and membranes, 55–57
logic functions and logic gates, 207–15
lysozyme protein, 173–74
machine learning, 211–12
mapping of genotype networks, 34–35, 93–95, 97–101, 124, 126
Martin, Olivier, 163–64
Marvell, Andrew, 4
mathematics, 31–32, 180, 218–20
Mayr, Ernst, 10
meaning, phenotypic, 83–84, 116–17
membranes, biological, 55–57
Mendel, Gregor/Mendelism, 12–13, 16–17, 19
Merton, Robert, 198
metabolic information databases, 69–70, 117, 220–21
metabolism
autocatalysis, 54–55, 56, 66
biomass building blocks, 59
catalysts, 62–63, 69
citric acid cycle, 53–54, 56, 60
combinatorial innovation, 66, 72–73, 75, 83, 102
diversity of metabolisms, 81–83
energy storage, 64–65
fuel innovations, 85–87, 88
genotype networks with diverse neighborhoods, 92, 99–105, 124–27
genotype-phenotype mapping, 93–95
horizontal gene transfer and gene deletion, 78–81
hypercube organization of genotype texts, 89–92
innovations forming modern metabolisms, 58–59, 72–76
list representation of genotype information, 70–71
meaningful metabolisms, 71–72, 83–84
mechanisms of innovation, 76–81, 92, 94, 101–2
multiple metabolisms with same meaning, 100–102
number and complexity of phenotypes and innovations, 71, 84–88
origin in hydrothermal vents, 49–53, 55
robustness and environmental change, 85–86, 173–75, 188, 191–94
as series of chemical reactions, 23, 42, 53–54, 60–62, 69
universal library concept, 67–69, 87–89
viability, 83–85
meteorites, 40–41, 47, 56
Methanopyrus kandleri, 51
microbes
antibiotic resistance, 113, 192
carbon fixation, 199
chemosynthesis, 50
diversity of metabolisms among closely related organisms, 81–83
endosymbiotic mutualism, 190–91
in extreme conditions, 51
first life on earth, 39
gene regulation in, 137–41, 166–67
horizontal gene transfer and gene deletion, 78–81
knockout experiments on, 171–72
metabolization of toxins, 72–74
nitrogen fixation, 122
robustness and environmental change, 61–62, 188–89, 190–93
Midoceanic Ridge, 51
Miescher, Friedrich, 23
Miller, Stanley, 39–40, 47
modern synthesis, 19–22, 26–27, 218
modular robots, 195, 210–11
molecular biology, 25
molecular evolutionary biology, 27
Monod, Jacques, 137
montmorillonite, 55, 57
Morgan, Thomas Hunt, 21
Murchison meteorite, 40–41, 56
mutation
DNA copying errors, 117, 120
error catastrophe, 45–46, 174
in evolutionary computation, 202–3, 213
of gene regulators, 161–62
genotypic alterations, 13–14
in Hox genes, 153–54
Mendelists on, 16–17
in natural selection process, 4–5, 14, 202
as nature’s trial and error, 84, 120, 196–97
neutral change, 179–82
in populations, 17–18, 137
scientific study techniques, 34–35, 171–72
silent mutations, 27–28
specialization of duplicate genes, 189
spontaneous mutations, 76–77
mutationist (Mendelist) school of evolutionary biology, 16–17, 19
Muybridge, Eadweard, 7
Mycoplasma pneumoniae, 191
natural selection
conservation of innovations, 3, 5, 14–15, 176–79
Darwin on, 1–2, 4–5, 11, 14
heritability of adaptations, 4, 11, 42
versus Mendelist theory, 16–17
versus neutral change, 179–80
in population genetics, 17–19
Needham, John, 37
networks of genotype texts. See genotype networks
neutral change, 179–82
nitrogen fixation, 122
number theory, 180
Ockham’s razor, 187
Oparin, Alexander, 39
opsins, 3–4, 112–13
origin of life. See life, origin of
Origin of Species, The (Darwin). See Darwin, Charles
parsimony principle, 187
Pasteur, Louis, 22, 37
Pax6 protein, 143–46
pentachlorophenol, 72–73
peppered moth, 17–18
peptide bonds, 205
peptides, 115
peregrine falcon, 2–3
phenotype
complexity of, 22, 31, 33–34, 37–38, 71, 84–88
consistency despite genotypic change, 170–71, 174–75
versus genotype, 13
phenotypic meaning, 83–84, 116–17