Arrival of the Fittest: Solving Evolution's Greatest Puzzle (45 page)

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, Mendelian, 12–13

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

butterflies, 154–55

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

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