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
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
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
sucrase enzyme, 62–63
systems biology, 162, 218–19
Szostak, Jack, 57, 58, 118
technological innovation
access to nature’s libraries, 69–70, 117, 220–21
adaptation of old technologies for new uses, 199–200
Boolean logic functions and logic gates, 207–15
complexity and simplicity, 215–16
design for changing environments, 189
digital circuit networks, 212–15
evolutionary algorithms mirroring biological evolution, 202–4
exaptation, 200
failures and attachment to wrong ideas, 196–97
ingenuity, 204–5
machine learning, 211–12
modular robots, 195, 210–11
multiple origins of inventions and solutions to problems, 198–99
new combinations of old technologies, 200–201
parallels with biological innovation, 196–202, 212–16
populations of innovators, 197–98
standards, 205–7
trial and error, 196, 198
Tegmark, Max, 220
texts, genotype. See genotype networks
tidal pool theory of life’s origin, 49
toxins, microbial metabolization of, 72–74
transcriptional regulators, 138–40
traveling salesman problem, 202–3
truth tables, 208–9
Tsiantis, Miltos, 156
Unger, Franz, 8
universal library concept, 67–69, 87–89
universal standards, 63–65, 204–5, 215–16
uracil, 59
van Helmont, Jan Baptista, 36
van Leeuwenhoek, Antonie, 37
Venter, Craig, 29–30
vesicles, 55–57
viruses, 42, 79, 119
vitalism, 22
volcanoes, underwater, 49–51
Vrba, Elizabeth, 200
Waddington, C. H., 171
Wagner, Andreas, and research team
comparison of phenotypes among bacterial organisms, 81–83
on complexity and robustness, 193
on diversity of genotype neighborhoods, 103–5
laboratory evolution study on RNA ribozyme, 132–35
laboratory facilities and research goal, 5, 95–97
on metabolic gen
otype networks, 97–101
on organization of digital circuit libraries, 212–15
on regulation circuits, 158, 162–66
warm ponds/primordial soup hypothesis of life’s origins, 39–40, 48–49
Watson, James, 24, 43
Whitehead, Alfred North, 9
Wigner, Eugene, 220
Wittgenstein, Ludwig, 220
Wright, Sewall, 18, 218
YaMoR (Yet another Modular Robot), 195, 210–11
yeasts
fermentation by, 22
gene duplications and robustness, 171–73, 189
regulation circuits, 166–67
young earth creationism, 8–9