Arrival of the Fittest: Solving Evolution's Greatest Puzzle (44 page)

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Evolution: The Triumph of an Idea
. New York: HarperCollins, 2001.

The page numbers in this index refer to the printed version of this book. To find the corresponding locations in the text of this digital version, please use the “search” function on your e-reader. Note that not all terms may be searchable.

adenosine triphosphate (ATP), 64–65, 118

alcoholdehydrogenase gene, 27–28

algorithms, evolutionary, 202–4

alleles, 18

Alon, Uri, 140

Altman, Sidney, 43–44

amino acids.
See
proteins and amino acids

amphiphilic lipid molecules, 55–56

Anaximander, 8

antibiotic resistance, 113, 192

antifreeze proteins, 107, 111, 178–79

aphids, 189–91

Arctic cod, 107, 111, 178–79

Arthur, W. Brian, 201

ATP (adenosine triphosphate), 64–65, 118

autocatalysis, 54–55, 56, 66

Avery, Oswald, 23–24

Backus, John, 196

bacteria.
See
microbes

bar-headed goose, 112, 120, 197

Bartel, David, 130–31

beta-galactosidase (beta-gal) protein, 138–41

bicoid protein, 147–48

biochemistry, 22–23

BioCyc database, 70

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

birds

bar-headed goose, 112, 120, 197

evolutionary exaptation of feathers, 200

peregrine falcon, 2–3

Boolean logic functions and logic gates, 207–15

Boreogadus saida
(Arctic cod), 107, 111, 178–79

Buchner, Eduard, 22–23

Buchnera aphidicola
, 190–93

building blocks of life, 59, 64–65, 69, 83–84, 101

Burkholderia xenovorans
, 73

Cambrian explosion, 196

canalization.
See
robustness

carbon fixation, 199

Carroll, Lewis, 187–88

catalysts, 22–23, 48, 62–63

Cech, Thomas, 43–44

Celera Genomics, 29

cell division, 57–58

chemosynthesis, 50

Christian theology, 9

circuits.
See
gene regulation and regulation circuits

citric acid cycle, 53–54, 56, 60

combinatorial innovation, 66, 72–73, 75, 83, 102, 200–201

complexity

phenotypes, 22, 31, 33–34, 37–38, 71, 84–88

regulation circuits, 142, 145–46, 150–51, 188

robustness and, 186–87, 191–93

technological innovation, 215

computers and computation.
See also
technological innovation

Boolean logic functions and logic gates, 207–15

evolutionary algorithms, 202–4

Game of Life self-replication model, 217–18

machine learning, 211–12

in modern biological research, 31–32, 95

mutation, 202–3, 213

conservation of innovations, 3, 5, 14–15, 176–79

Conway, John, 217

co-option of earlier innovations for new purposes, 153, 154, 178, 200

Crick, Francis, 24, 43

crystallins, 3–4, 143–44, 177–78

Cuvier, Georges, 9–10

Darwin, Charles

on adaptation of organs to new purposes, 200

on common ancestry of all life, 10

ignorance of causes of new variations, 14, 21

ignorance of heritability, 11

on limitations inherent in natural selection theory, 177

on mathematics, 218

natural selection theory, 1–2, 4–5, 11, 14

publication of
The Origin of Species
, 7, 8, 12, 22, 23

warm-pond hypothesis of origin of life, 39, 48–49

databases of metabolic information, 69–70, 117, 220–21

deep-ocean volcanoes, 49–51

Dekel, Erez, 140

developmental biology, 142

de Vries, Hugo, 13, 15

digital electronics, 207–12

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

distalless protein, 154–55

DNA.
See also specific molecular processes

biomass building blocks, 59

components existing in interstellar space, 40

copying errors, 117, 120

duplicate genes, 172–73, 189

energy required for replication, 46–47

horizontal gene transfer and gene deletion, 78–80

Human Genome Project, 29–30

as information repository, 43, 59

in molecular evolutionary biology, 27

molecular structure of, 23–24

in organism’s genome, 29

polymerase transcription enzyme, 138–40

recombination standards, 205

replication process, 42–43

sequencing technology, 29–30

silent mutations, 27–28

Dobzhansky, Theodosius, 11

Drosophila melanogaster
(fruit flies)

alcoholdehydrogenase gene, 27–28

computer simulator, 151

Pax6 gene, 146

regulation circuits, 147–50

duplicate genes, 172–73, 189

earth, age of, 1–2

E. coli. See
Escherichia coli

Edison, Thomas, 196

Eigen, Manfred/Eigen’s paradox, 45–46

Einstein, Albert, 20

embryology, 21–22

embryonic development

fruit flies, 147–51

Hox code expression, 153

humans, 149–50

endosymbiotic mutualism, 190–91

energy storage molecules, 64–65

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