Arrival of the Fittest: Solving Evolution's Greatest Puzzle (46 page)

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

Planck, Max, 197

plants

carbon fixation, 199

chemical defense molecules, 75–76

globins and nitrogen fixation, 122–23

Mendel’s experiments on, 12

photosynthesis, 50

regulation circuits and leaf shape, 155–56

Plato/Platonic worldview, 9–10, 34–35, 219–20

polymerase, 138–40

population genetics, 18–19

population genomics, 30

primordial soup/warm ponds hypothesis of life’s origins, 39–40, 48–49

proteins and amino acids

beta-galactosidase (beta-gal), 138–41

bicoid, 147–48

biomass building blocks, 59, 64–65, 69, 83–84, 101

cell division, 57–58

crystallins, 3–4, 143–44, 177–78

distalless, 154–55

DNA copying errors, 117, 120

engrailed, 148–49

enzymes and catalysts, 22–23, 48, 62

fish antifreeze proteins, 107, 111, 179

function-specific shapes, 25, 108–11, 138

genotype networks and neighborhoods, 124–27, 131–35

heat-induced vibrations and oscillations, 110

hemoglobin and globins, 112, 120–24

hypercube organization of genotype texts, 115–16

innovation and multiple solutions to problems, 111, 114, 117–19, 122, 126, 131–35

in interstellar space, 40–41, 47, 56

KNOX, 156

lysozyme, 173–74

molecular meaning, 83–84, 116–17

number and types of, 3–4, 108, 115, 117, 120, 127

in organism’s phenotype, 23, 26

Pax6 protein, 143–46

peptide bonds, 205

primary, secondary, and tertiary structures, 109–10

robustness, 173–75, 189

self-organizing folds in predictable patterns, 62–63, 109, 122–24

silent mutations and redundant genetic codes, 27–28

small modifications of amino acids, 111–14

Sonic hedgehog protein, 200

spontaneous change in shape, 139

synthesis of, 24–25

in theory of life’s origins, 39–40

purposeless genes, 171–73, 189

radioactivity, 2

Raman, Karthik, 212–15

Redi, Francesco, 36–37

redundant genes, 171–73, 189

regulation of genes.
See
gene regulation and regulation circuits

Reidhaar-Olson, John, 118–19

Reinitz, John, 150–51

replication

cell division, 57–58

DNA replication and copying errors, 42–43, 117, 120

error catastrophe, 45–46, 174

Game of Life computer model, 217–18

as life’s first innovator, 42–48

regulation of, 58

RNA replicase, 44–46, 54

viruses, 42

reptiles, 9–10, 153

ribozymes, 130, 132, 181–82

RNA.
See also specific molecular processes

autocatalysis, 54–55

biomass building blocks, 59

as catalyst, 43–44, 59

Eigen’s paradox, 46

innovability, 127–28, 130–35, 185–86

recombination standards, 205

regulated growth, 58

replicase, 44–46, 54

replication error catastrophe, 45–46, 174

secondary structure and meaning, 128–29

stickiness of bases, 44–45

uracil, 59

robotics, 195, 210–11

robustness

duplicate genes, 171–73, 189

in genotype networks, 173–75, 194

genotypic disorder, 169–70, 175, 179, 186

innovability and, 174–75, 186, 194

invariance of phenotype despite genotypic change, 170–71, 174–75

metabolic complexity or simplicity in relation to, 186–87, 191–93

neutral mutations, 179–82

viability in changed environment, 170, 188–94

Rodrigues, João, 96–97

Rowan, William, 202

Rutherford, Ernest, 1–2

Saccharomyces cerevisiae
, 171–72

Saint-Hilaire, Etienne Geoffroy, 8

saltationist (Mendelist) school of evolutionary biology, 16–17, 19

Sanger, Frederick, 114

Sauer, Robert, 118–19

Schrödinger, Erwin, 169

Schultes, Erik, 130–31

Schumpeter, Joseph, 201

Schuster, Peter, 128–29

self-organization

biological membranes, 55–57

cell division, 57–58

genotype networks, 175–76, 194

in origin of life, 54–55, 63, 66

protein folds, 62–63, 109, 122–24

secondary structure of RNA, 129

throughout universe, 57, 176

sexual reproduction, 76–77

silent mutations, 27–28

simplicity, 187–88, 191–93, 215–16

snakes, 9–10, 153

Sonic hedgehog protein, 200

space, organic molecules in, 40–41

Sphingobium chlorophenolicum
, 72–73

spontaneous generation, 36–38

spontaneous mutations, 76–77

standards

in human technology, 205–7

universal laws of nature, 63–65, 204–5, 215–16