Page numbers in italics refer to illustrations. Boldface page numbers refer to plates.
Acanthostega, 185–87
Adaptive Coloration in Animals (Cott), 221, 223–24
Adler, Lou, 292
African Game Trails (Roosevelt), 222–23
Agouti protein, 230, 231, 235, 237
agriculture, 301
Akanthokera kaputensis, 152, 152
Alfonseca, Antonio, 48–49
algae, 140
Alpert, Herb, 292
alpha-melanocyte-stimulating hormone (MSH), 230, 231, 236
Altiparmak, Turkey, 49 amino acids, 58, 62, 64, 230, 232, 274
analogical resemblance (mimicry), 198–200, 199, 218–19, 290–92
animal architecture, 17–35, 18, 129
building blocks of, 19–25
diversity and, 26–27
genome and, 34–35
homology and, 29–33
modular design and, 21–27, 22, 27, 28, 29, 34
polarity and, 33–34
thematic variation and, 25–27, 28
variety and, 17–19
Animal Kingdom, 33
Aniridia gene, 67
antibody proteins, 120
ants, 3
brain of, 265–66
see also humans; primates; specific species
Aphorisms and Reflections (T. Huxley), 5–6
Apterous proteins, 175–76, 179
aquatic nymphs, 177
arthropods, 4, 33, 69, 105, 126–28, 138, 141, 159, 161, 179, 184, 286–87, 288
evolution of, 150–54, 151, 156, 170, 171, 181
limb evolution of, 171–75, 172 173, 185
repeated structures of, 26
artificial selection, 216
Athenaeum, 254
At Home in the Universe (Kauffman), 197
At the Water’s Edge (Zimmer), 184
Augustine, Saint, 301
A. africanus, 259
autopods, 185
evolution of, 187–88
Averof, Michalis, 156, 175, 179
Aysheaia, 148–49, 148, 150–51, 153, 174
A. pedunculata, 22
gene logic in, 60
genetic on-off switch of, 59–60
see also Escherichia coli
barnacles, 156
Barry, Dave, 69
basal cell carcinoma, 78
Bates, Henry Walter, 2, 3, 196, 197–200, 207, 303
Batesian mimicry, 198–200, 199, 290–91
Bateson, William, 25–26, 33, 34–35, 46, 200
bats, 149–50, 169, 188, 189, 190, 194–95, 288, 290
Battus philenor (pipevine swallowtail), 218, 8j
BBC, 46
Beagle, 2
Beethoven, Ludwig van, 14
Behe, Michael, 298–99
Belize, 3
beta-galactosidase enzyme, 55–56, 58–59, 59
Bible-Science Association, 299
Bicyclus:
B. anynana, 206, 210, 212–17, 8f, 8i
B. safitza, 216
bilaterians, see Urbilateria
evolution as foundation of, 294
revolution in, see evolutionary developmental biology
biramous limbs, 171–75, 172, 173
birds, 104, 159, 160, 161, 163, 169, 275, 288, 290
wing evolution in, 188, 189, 190
Biston betularia (peppered moth), 135, 226–27, 228
Bithorax, 50
Bithorax Complex, 61
Black, Lewis, 10
blastopore, 141
blastula, 85
boas, 190
Boleyn, Anne, 48
Bone Morphogenetic Proteins (BMPs), 124, 125, 188, 4w
book lungs, 171
brachiopods, 146
Broca’s area in, 262, 264–65, 274
cognitive ability and, 261–62
embryonic development and, 99–100
FOXP2 gene and, 276
handedness and, 265
jaw musculature and size of, 273
physical areas of, 262, 262, 264, 264
previous structures in evolution of, 263, 264
speech, language and, 264–65
Brakefield, Paul, 212–16
Bridges, Calvin, 50
British Columbia, 138
Britten, Roy, 271
Broca, Paul, 263
Broca’s area, 262, 264–65, 274
Brunetti, Craig, 210
Burgess Shale:
Cambrian arthropods of, 147
Cambrian lobopodians of, 148
Chengjiang fauna and, 146, 158–60
fossils of, 21, 137–39, 146–49
trilobites of, 136
butterflies, 2, 3, 8, 34, 47, 69, 104, 135, 178, 182, 289, 305
hind wings of, 183–84
larval development in, 206–7
melanism in, 218–19
mimicry in, 198–200, 199, 218–19, 291–92
serially repeated design and, 23–24, 24, 25
see also specific species
butterfly wings, 200–217, 287, 8a–8k
coloration of, 204–5
Dll gene and, 208–10, 209, 214–17, 217
eyespot development in, 43–44, 45, 207
eyespot evolution in, 212–16
eyespot mutation in, 215–16
eyespot variation in, 212–16
hind, 183–84
larval development and, 206–7
modular subdivisions of, 202
natural selection and eyespots in, 214–15, 216
new genetic switches and, 208–10
patterns in, 200–203, 207–8, 214–17, 217
role of eyespots in, 205–6
tool kit genes and, 207–9
buttonhead gene, 75
Caitee (author’s niece), 250
Camarasaurus, 20
Cambrian Explosion, 12, 64, 131
animals existing prior to, 140–45, 140
arthropod evolution in, 150–54, 151, 156
complexity and diversity of, 164–65
geologic boundary of, 145–46
Hox genes and biology of, 153–57, 155
questions raised by, 138–39
vertebrate evolution in, 157–63, 158, 162
Cambrian period, 11, 138, 141–42, 144, 153–54, 159, 165, 295
camels, 27
Canadaspis perfecta, 147
cancer, 78
Carroll, Lewis, 37
cats, 49
cave art, 303
cells, 45
communication among, 74
differential function in, 60
“knowing” by, 89–90
lateral inhibition process in, 105
melanocyte, 238
selective protein production in, 54–55
specialization of, 54–55
centipedes, 26, 69, 153, 154–57, 155, 163, 173
cephalochordates, 157, 158, 159–61
cerebellum, 100
cetaceans, 193
see also dolphins; whales Chaetodipus intermedius (rock pocket mouse), 233–34, 234, 246, 290
Chance and Necessity (Le Hasard et la Nécessité) (Monod), 60, 197, 290
Charcharadon megalodon, 18, 19
Charles VIII, king of France, 48
cheetahs, 3
chelicerates, 179
“Chemical Basis of Morphogenesis, The” (Turing), 123
chemotherapy, 78
chickens, 49, 101, 105, 161, 163
embryo development in, 42–43, 43, 44, 45, 103
chimpanzees, 10, 79, 250, 262, 268, 271, 273, 275
human’s shared DNA with, 250–51
skull maturation in, 266–67
chordates, 138, 146, 157–58, 158
“chronospecies,” 256
Churchill, Winston, 48
Clapton, Eric, 11
cleaner shrimp, 155
coelacanth, 160
Cohen, Stephen, 175
concentration gradient, 45
Cooke, Sam, 292
cosmology, 110
creationism, 296–301
crickets, 184
crustaceans, 69, 153, 156–57, 170–71, 172, 173, 175, 289
cyclopia, 38–39
in humans, 77–78
cyclops, mythology of, 38–40, 39
Cyclops, The (film), 36
Damen, Wim, 179
dark energy, 110
Darwin, Charles, ix–x, 2, 3, 5–6, 13, 135, 145, 170, 194, 198, 200, 239, 249, 250–53, 281–83, 284, 285, 289, 293, 296, 297–98, 303
Darwin’s Black Box: The Biochemical Challenge to Evolution (Behe), 298–99
Dave (author’s friend), 37–38
Davidson, Eric, 271
Democritus, 290
De Robertis, Eddy, 143
Descent of Man, The (Darwin), 5, 249
Desert hedgehog gene, 76–77
development, x
differences in scale and, 24
diversity and, 10–12
embryo interactions and, 40–41
homeodomains and, 70–71
mosaic pattern evolution of, 266–68
Devonian period, 184
Dickinsonia costatala, 140
dinosaurs, 20, 21, 150, 161, 190, 287, 295
Distal-less (Dll) gene, 69–71, 96, 211
butterfly eyespots and, 208–10, 209, 214–17, 217
in early evolution, 143–45
fruit fly development and, 116–17, 8c-8d
in limb-building, 174–75
in spiders, 179
animal architecture and, 26–27
in Cambrian Explosion, 165
development and, 10–12
in evolution, 168–70
Modern Synthesis and, 286–88
modularity of design and, 26–27, 28, 286
DNA (deoxyribonucleic acid), x, 35, 51, 61, 91, 107, 130, 225, 273, 276
brain development and, 100
dark matter in, 108, 110–11, 112
embryo development and, 94–95, 97–98
as genetic switches, 59–60
homeobox sequence of, 62–63
human sequence of, 268–69
junk, 112
in Modern Synthesis, 284–85
of Neanderthals, 260–61
protein code and, 11–12
regulatory, 12
signature sequences of, 115–16, 118–22
transcription process of, 57–58, 58
translation process of, 58, 58
universal nature of, 53–54
see also genes; genetic switches
dogs, 235
donkeys, 239
larva of, 192
Drosophila:
D. biarmipes, 242
D. melanogaster, see fruit fly
ducks, 103
dugong, 19
Duke University, 200–201
Earth, 140
echinoderms, 34, 34, 141, 143, 146, 160
Eldredge, Niles, 7
embryology, 5–7, 10, 13, 40–45, 134, 283, 284, 294
homeotic mutants and, 50–51, 51
reductionism in, 82–84
bone development in, 103
brain development in, 99–100
chemicals affecting, 39–40
chicken, 42–43, 43, 44, 45, 103
coordination system of, 92–93, 96–97
gastrulation and, 84–86, 88, 97, 99
geography and geometry of, 89–94, 92–93, 163–64
Hox gene clusters in, 66
mammal pattern evolution and, 240–42, 241
mouth formation in, 141
organ and limb building in, 95–96, 102–4
organizers of, 40–45
pattern regularity in, 140–5, 104
serially repeated modules in, 95–98
shifting Hox gene zones in, 153–57, 155, 161, 162
somite formation in, 100–101
endoderm, 84
Engrailed protein, 210, 216–17
beta-galactosidase enzyme production in, 55–56, 58–59, 59
number of genes of, 60
ethanol, 77–78
Evidence as to Man’s Place in Nature (T. Huxley), 5, 254
evolution, 112, 122, 126, 130–31, 134, 137–66
of arthropods, 150–54, 151, 156, 170, 171, 181
of autopods, 187–88
in Cambrian Explosion, 138–45, 164–65
cell types and, 160–61
of color patterns, 218–19
creationism and, 296–301
of dark coloration, see melanism
definition of, 5
of different larval and adult forms, 178
diversity in, 168–70
Ediacaran fauna and, 140–45, 140
embryological approach to, 294–95
of eyes, 70
as foundation of biology, 294
of genes, 150–53
genetic switches and, 122, 126, 130–31, 139, 163–64
homologous genes and, 71–72
Hox gene shifts and, 153–67, 155, 158, 162, 163–64
human, 254–57, 254–57, 266–68, 270–71, 276–79
of human jaw muscles, 271–72, 272
Lewis hypothesis and, 150
of limbs and appendages, see limbs, evolution of
of melanism, 230–32
modularity and, 194–95
multifunctionality of, 194
parallel, 187
of patterns, see mammals, pattern evolution in
preexisting structures in, 168–71, 194
public understanding of, 292–94
punctuated equilibria and, 7–8
redundancy and, 194
repetitive body design in, 168–71
as “reproducible,” 193
serial homologs and, 29
specialization in, 168–71
of spiders, 179–80
teaching of, 292–98
as variation in number and kind, 25–27, 28
of vertebrates, 157–63, 158, 162, 169, 170
see also Modern Synthesis
Evolution: The Modern Synthesis (J. Huxley), 7
“Evolution and Tinkering” (Jacob), 194
evolutionary developmental biology (Evo Devo), x, 8–10, 13, 134–35, 139, 143, 145, 164, 204, 288–89, 291
see also Modern Synthesis
faint little ball gene, 75
Fauris menado, 203
fer-de-lance, 3
fetal alcohol syndrome, 78
FGF8 signaling protein, 102, 4r
finches, 295
fish, 79
limb evolution in, 185–87, 186, 190, 191–92
fitness, concept of, 245
fleas, 289
Flintstones, The, 293
forebrain, 99–100
fossils, fossil record, ix–x, 6, 18, 31, 134, 171, 193, 278, 284, 294
analyzing, 19–20
of Burgess Shale, 137–39
of Chengjiang fauna, 146, 158–60
of Ediacaran fauna, 141–45, 141
fin to limb transition in, 185
of human ancestors, 252–56, 253–54, 258, 258, 267, 278
limb evolution and, 176–77, 185
mammals in, 149–50
modular design demonstrated by, 20, 21
FOXP2
French, Vernon, 214
frogs, 41, 64, 66, 80, 99, 161
embryo development of, 84–86, 85, 89
vertebrae of, 47
Fromm, Erich, 250
fruit fly (Drosophila melanogaster), 8–9, 49–51, 74, 114, 117, 120, 152, 154, 207, 208
bristle patterns of, 201
Dll gene and, 116–17
embryonic development in, 86, 87, 89, 91–98, 4a-4x
genetic switches of, 122–23
genome of, 108
homeobox of, 64–65
homeotic (Hox) genes and proteins of, 61–64, 62, 65, 66, 4d, 4j, 4n, 4p
homeotic mutations in, 50–51, 51
life cycle of, 87
mutant genes of, 75–76
wing formation in, 96–98, 4g-4j
galactose, 55
Galant, Ron, 204
Galapagos finches, x, 135, 226, 295
Galapagos Islands, 303–4
Galapagos tortoise, 303–4
galaxies, 111–12
cluster CL0024+1654, 108
Garber, Ted, 151–52
Garcia-Fernandez, Jordi, 159
gastrulation, 84–86, 88, 97, 99
Gates, Julie, 208
GDF (joint-making) family of genes, 188
geese, 161
gene logic, 59–60
genes, x, 8, 9, 56–57, 57, 90–91, 268
Antennapedia Complex of, 61, 63
Bithorax Complex of, 61
cloning technology and, 61
evolution of, 150–53
homologous, 71–72
Lewis hypothesis and, 150
paradox of shared, 78–79
pigmentation, 242–44
and sequence similarity among species, 64–65, 69–71, 78–79
speech, 274–76
“tool kit” paradox and 10–12
for wing building, 207–8
see also specific genes
genetic switches, 111–31
for Agouti gene, 237
butterfly eyespots and, 208–10, 217, 217
circuits and networks of, 128–30, 129
combinatorial logic of, 118–20
in E. coli, 112–13
evolution and, 122, 126, 130–31, 139, 163–64
of fruit flies, 122–23
gene expression and, 112–14, 113, 115, 116, 117, 121, 126–28, 128
hormones and, 215
Hox genes and, 126–28, 128, 163–64
in human evolution, 270–71
insect wing evolution and, 178
as integrators of positional information, 114–15
Modern Synthesis and, 287, 291
modular construction of, 126–27
pattern formation and, 122–23
pigmentation genes and, 242–44
regulatory function of, 114–16
sharing of, 125
signature DNA sequences and, 115–16, 118–22, 125
tool kit paradox and, 130–31
versatility of, 123–24, 130–31
animal architecture and, 34–35
dark matter of, 108, 110–11, 112
Gilbert, Scott, 298–99
glucose, 55
Goethe, Johann Wolfgang von, 296, 297
Gould, Stephen Jay, 7–8, 48, 72, 138, 148–49, 173, 237
grasshoppers, 184
Gray, Asa, 284
Grenier, Jen, 151–52
hagfish, 158
Haikouichthys ercaicunensis, 158–59, 158
Hall, Stephen, 83–84
Harper, Charles, 298
Harrison, Ross, 17
Harvard Museum of Comparative Zoology, 200
Hasard et la Nécessité, Le (Chance and Necessity) (Monod), 60, 197, 290
Haught, John, 300–301
Heliconius butterflies, 3
hemoglobin, 54–55
Hendrix, Jimi, 1
Henry VIII, king of England, 48
heredity, 6
Herr, Christopher, xiv
Hill, Andrew, 258
hindbrain, 99–100
Holland, Peter, 159
homeobox, 64–65
homeotic (Hox) genes, 61–65, 62, 66, 70–71, 72, 73, 79, 139, 150, 291
in brain development, 100
in Cambrian period evolution, 153–57, 155
early development and, 94–95, 97–98
in early evolution, 143–45
in embryos, 66
in fruit flies, 61–64, 62, 65, 66, 4d, 4j, 4n, 4p
genetic switches and, 126–28, 128, 163–64
insect wing evolution and, 178–79
in limb development, 103–4, 182, 184
in Modern Synthesis, 286–87
mutation of, 187
shifting zones of, 153–57, 155, 158, 162
snake limblessness and, 191
somite formation and, 101
in vertebrate evolution, 157–63, 158, 162
homeotic variants, 46
hominids, hominins:
evolutionary tree of, 255
hominin evolution and, 249–79
use of terms, 255
see also humans
H. habilis, 257
H. neanderthalensis, 253, 253, 260–61
H. sapiens, see humans
homology, 29–33
Hooker, J. D., 296–97
“hopeful monster,” 291
horseshoe crabs, 173, 179–80, 181
house mouse, 237
“How the Leopard Got His Spots” (Kipling), 221–22
Hox genes, see homeotic genes
humans (Homo sapiens), 13, 103, 253, 253, 256, 257, 259, 260–61, 301
anatomical asymmetry in, 265
bipedalism in, 251, 257–59, 278
brain-body size ratios in, 259–60, 259
brain cortex of, 262
cell types of, 160–61
cyclopedia in, 77–78
development of, fertilized egg in, 86–87
digital variation in, 48–51, 49, 50, 51, 77
DNA sequence of, 268–69
evolution of, 254–57, 254–55, 266–68, 270–71, 276–79
features of, 251–52
in fossil record, 252–56, 253, 258, 258, 267, 278
genetic switches and evolution of, 270–71
jaw muscle evolution in, 271–74, 272
junk DNA of, 112
mosaic pattern in evolution of, 266–68, 278
mouse genome and, 269–70
Neanderthal’s coexistence with, 260–61
population growth and, 301–2
shared DNA of, 9–10, 250–51, 268–70
skull mutation in, 266–67
somite formation in, 101
Humboldt, Alexander von, 2
Huxley, Julian, 7
Huxley, Thomas H., 5–6, 252–53, 254, 293, 304–5
hybridization, 239–40
immune systems, 120
Indian hedgehog gene, 76–77
Industrial Revolution, 301
insects, 29–30, 153, 157, 163, 171, 173, 242, 288, 289
Hox gene proteins and, 127
melanism in, 226, see also peppered moth
Jacob, François, 56, 58–59, 60, 105, 194, 271, 289
jaguars, 3, 135, 229, 229, 234
Jenny (orangutan), 249–50
Johnson, Donald, 258
John Templeton Foundation, 297 “junk” DNA, 112
Jurassic period, 21
Just So Stories (Kipling), 14
Kakadu National Park, 303
kangaroos, 104
Kauffman, Stuart, 197
Kenya Wildlife Service, 239
Keys, David, 214
Kimberella, 142
King, Mary Claire, 271
Kipling, Rudyard, 14, 111, 212, 222
knirps gene, 75
Knoll, Andy, 140
Krox 20 gene, 4n
Krüppel gene, 75
Kukalova-Peck, Jarmilla, 176
lac repressor protein, 59–60, 59, 63, 112
ladybird beetles, 226
Laetoli, Tanzania, 257–58
Langeland, Jim, 178
large ground finch, 304
Late Devonian period, 185, 187
lateral inhibition, process of, 104–5
Laughon, Allen, 63
leaf-cutter ants, 3
Leakey, Mary, 258
“Learning to Fly” (Petty and Lynne), 167
Lennon, John, ix
Lepidoptera, 204
limbic lobe, 262
limbs, evolution of, 70, 171–95
appendage geography and, 181–84, 183
in arthropods, 171–75, 172, 173, 185, 186
autopods and, 187–88
biramous limbs and, 171–75, 172, 173
Dll gene and, 174–75
fin-to-limb transition in, 185
in fish, 185–87, 186, 190, 191–92
fossil record and, 176–77, 185
genetic switches and, 178
gill-to-wing theory and, 175–78
hindwing formation and, 182–83, 183
Hox proteins and, 178–79, 182, 184, 191
in insect wings, 175–79, 177, 181–84, 183
Pitxl gene and, 192–93
proteins needed in, 175–76
serially homologous structures and, 181–84
in snakes, 190–91
in spiders, 179–81, 180, 181, 182
stages of, 174
Ultrabithorax protein in, 183–84
in vertebrates, 184–90, 186, 189, 194–95
winged flight and, 188–91, 189
“Little Wing” (Hendrix), 1
lizards, 191
LMX gene, 102, 4s
lobopodians, 146–49, 148, 159, 171, 174, 180
lobsters, 29–30, 30, 135, 155, 156, 184
locomotion, 33–34 “Lucy” (fossil hominid), 258
Lwoff, André, 56
Lynne, Jeff, 167
McCartney, Paul, ix
McGinnis, Bill, 64
maggot, 5
Majerus, Michael, 227
brain evolution in, 262–63
neocortex of, 262
pattern evolution in, see mammals, pattern evolution in
see also specific species
mammals, pattern evolution in, 237–44
embryonic development and, 240–42, 241
hybridization and, 239–40
natural selection and, 244–46
manatees, 193
Mangold, Hilde, 99
Maoris, 303
Mapping the Next Millennium: The Discovery of New Geographies (Hall), 83
Marcus Aurelius Antoninus, emperor of Rome, 281
Material for the Study of Variation (Bateson), 46, 47
Mauritius, 303
melanism, 226–32, 228, 231, 291
in big cats, 229
in butterflies, 218–19
definition of, 226
evolution of, 230–32
genes involved in, 227, 235–36
in humans, 236
mutations and, 230, 232, 235–36
natural selection and, 234–35
in rock pocket mice, 233–34, 234
melanocortin-1 receptor (MC1R), 230–31, 231, 234
Mendel, Gregor, 6
mice, 5, 29, 49, 64, 65, 67, 68, 79, 103, 105, 130, 161, 163, 187, 268
neocortex of, 269
Microdictyon, 153
midbrain, 99–100
mimicry (analogical resemblance), 198–200, 199, 218–19, 290–92
mites, 179
Modern Synthesis, 6–7, 9, 13, 71–72, 135, 226, 283, 284–92
diversity in, 286–88
DNA in, 284–85
evolutionary process in, 289–90
genetic tool kit in, 285–86, 288
macro- vs. microevolution and, 284, 291
natural selection and, 284, 287, 289–90
novelty and innovation in, 288–91
randomness in, 289–90
variation of existing structures in, 288–91
monkeys, 264
Monod, Jacques, 52, 53, 56, 58–60, 197, 290
morphogenesis, 44
morphogens, 44–45
Morris, Simon Conway, 146
mosasaurs, 31
moths, 204, 226–27, 246, 289, 291, 295
MSH (alpha-melanocyte-stimulating hormone), 230, 231, 236
mutations, mutants, 12, 49, 73–74, 106
in butterfly wing eyespot patterns, 215–16, 8g–8h
of FOXP2 gene, 274–76
in genetic switches, 114, 117–18, 164
in Hox genes, 187
in larva, 76
mammal pattern evolution and, 238, 239
melanism and, 230, 232, 235–36
in Modern Synthesis, 284–85, 290
selection coefficient for making, 245–46
Sonic hedgehog genes and, 76–78
spread in populations, 245–46
striping in mammals and, 238–39
myosin heavy chain 16 (MYH16), 272–74, 275, 277–78
mysids, 155
Nabokov, Vladimir, 200
Nachman, Michael, 234–35
Naroaoia compacta, 146
National Museum of Natural History, 137–38
National Science Board, 293
Naturalism on the River Amazon (Bates), 198
natural selection, x, 7, 46, 72, 170, 198, 218, 219, 225
butterfly wing eyespots and, 214–15, 216
fitness and, 244–46
in mammalian pattern evolution, 242–46
melanism and, 234–35
Modern Synthesis and, 284, 287, 289–90
selective sweep and, 275
in teaching of evolution, 295
Nature, 211, 298
Neanderthals, 253, 253, 260–61
nematode worms, 79
neural crest, 238
New York Times, 211
New Zealand, 303
Nijhout, Fred, 43–44, 46, 201, 207, 208, 210
NK2 gene family, 70
nucleotides, 57
Nüsslein-Volhard, Christiane, 73, 75, 78
Nymphalid butterflies, 202
occipital lobe, 262
Olenoides serratus, 22, 136, 146–47
Ontogeny and Phylogeny (Gould), 7
Onychophora (velvet worms), 149, 150–53, 159, 173
orangutans, 275
Origin of Species, The (Darwin), 5, 6, 170, 198, 239, 254, 281–82, 296
Paabo, Svante, 260–61
pair-rule genes, 94
paper clip, evolution of, 168, 169
Papilio glaucus (tiger swallowtail), 218, 8j
parallel evolution, 187
Parapodia, 69
parietal lobe, 262
Pasteur Institute, 56
patched gene, 4x Patel, Nipam, 156
Pauling, Linus, 271
in early evolution, 143–45
Pensées sur l’Interpretation de la Nature (Diderot), 137
peppered moth (Biston betularia), 135, 226–27, 228
Personal Narrative (Humboldt), 2
Petty, Tom, 167
Pikaia, 157–58
pipevine swallowtail (Battus philenor), 218, 8j
Pitx1 gene, 192–93
planum temporale, 265–66
poison arrow frog, 3
polarity, 33–34
in chicken embryos, 42–43
polydactyly, 48–49, 49, 50, 77, 78
population genetics, 244–45, 294
Poriferans, 142
Precambrian period, 140–42
see also apes; humans
Propylaea (Goethe), 296
proteins, 11, 56, 58, 116, 230, 270
cell production of, 54–55
embryonic development and, 99
homeodomain of, 70–71
in insect wing-building, 175–76
in limb evolution, 175–76
signature DNA sequences and, 118–20
transcription factors and, 74
see also specific proteins
protostomes, 141–43
pterosaurs, 169, 188–90, 189, 194, 288, 290
wing evolution in, 188–90, 189
Pugh, Emerson, 261
punctuated equilibria, 7–8
pythons, 190–91
randomness, 289–90
reductionism, 82–84
regulatory DNA, 12
reptiles, 30, 33, 159, 161, 163
“Revolution 1” (Lennon and McCartney), ix
rhinoceroses, 27
rock art, 303
rock pocket mouse (Chaetodipus intermedius), 233–34, 234, 246, 290
see also mice; rock pocket mouse
Roman Catholic Church, 297, 299
Roosevelt, Kermit, 223
Roosevelt, Theodore, 222–23, 225, 244
Rosenblatt, Roger, 212
Royal Institution, 304
Sahelonthropus tchadensis, 256
Saridaki, Theodora, 179
Sauripteris, 185–87
sawfly, 47
Schaaffhausen, Hermann, 252
Science, 211
science, theology and, 300–301
Scott, Matt, 81–82
sea cow, 19
seals, 169
sea urchins, 34, 34, 69–70, 88, 141, 143
selection coefficients, 245–46
selective sweep, 275
sharks, 19
sharp-beaked ground finch, 304
shavenbaby gene, 75
Shipman, Pat, 188
shrews, 149–50
signaling pathways, 74
signature sequences, 115–16
evolution and, 122
proteins and, 118–20
“situs inversus,” 265
Slack, Jonathan, 65
small eye gene, 67
Smithsonian Institution, 137, 138
snails, 226
snakes, 27, 101, 135, 171, 185
Hox gene shifts in, 161
limb evolution in, 190–91
somites, 40, 88, 98, 126–28, 238, 4p
formation of, 100–101
Sonic hedgehog gene, 76–78, 102, 105, 191, 4r
speech, 264–65
genes affecting, 274–76
Spemann, Hans, 40–41, 42, 46, 99
spiders, 69, 135, 153, 157, 163, 171, 180, 181, 182
biramous limb design in, 180–81
Dll gene in, 179
evolution of, 179–80
spitz gene, 75
Spriggina flounders, 140
starfish, 34
Stedman, Hansell, 272
Stent, Gunther, 24
Stichophthalma camadeva, 203, 203
Structure of Evolutionary Theory, The (Gould), 72
“survival of the fittest,” 295
swallowtail butterflies, 182, 184
synpolydactyly, 48
Tabin, Cliff, 77
Taenaris macrops, 203
Taking Flight (Shipman), 188
Tasmanian tiger (thylacine), 302, 303
Taylor, Ian, 299
teeth, 31
Tertiary period, 286
tetrapods, 27
digits of, 33
limb structure of, 184–87, 186
thalidomide, 40
theology, science and, 300–301
Thomas Aquinas, Saint, 301
Thoreau, Henry David, 300
threespine stickleback, 191–93, 192, 195, 289
Through the Looking Glass (Carroll), 37
tiger swallowtail (Papilio glaucus) 218, 8j
Time, 212
tinman gene, 70–71
tool kit genes, 103, 106, 109–10, 115
fly embryo development and, 94–96
genetic switches and, 119–20
logic of, 90–91
in Modern Synthesis, 285–86, 288–89
tools, tool use, 257
transcription, of DNA, 57–58
transportation factors, 74, 112
trilobites, x, 22, 136, 144, 146–47, 153, 155, 156, 172, 173, 287, 295
see also specific species
trypsin, 55
Tulerpeton, 186
Turing, Alan, 123
Turkey, 49
Tyranosaurus rex, 104
Ultrabithorax (Ubx) gene, 97–98, 119, 127, 183–84
Van Diemen’s land tiger (thylacine), 302, 303
variation, 7
“hopeful monsters” idea and, 46–48
human digital, 48–51, 49, 50, 51
velvet worms (Onychophora), 149, 150–53, 159, 173
ventral premotor area, 264
of frogs, 47
vertebrates, 4, 65, 88, 286–87, 289
autopod of, 187–88
bone development in, 103
cell types in, 160–61
earliest appearance of, 157–58
embryo development in, 98–99
evolution of, 157–63, 158, 162, 169, 170
evolution of flight and, 188–90, 189
in evolution tree, 141, 142, 158
hedgehog genes of, 76–77
Hox gene in, 126–27, 157–63, 162, 187–88
limb and body part construction in, 102–4
limb evolution in, 184–87, 186, 188–90, 189, 194–95
modular architecture of, 20–21, 26
pattern regularity in, 104–5, 104
polydactyly in, 49
segmentation in, 100–101
somite formation in, 100–101
Victoria, queen of England, 250
Wade, Nicholas, 211
Wallace, Alfred Russel, 2, 3, 198
Waptia fieldensis, 146
Warren, Bob, 151–52
Watson, James, 53
Weatherbee, Scott, 178
Weiss, Paul, 83
Weisskopf, Victor, 14
Wernicke’s area, 262, 262, 265
Whitington, Paul, 151–52
Williston’s Law, 29, 33, 139, 153, 157, 177, 178, 182
Wilson, Allan, 271
genes for building, 207–8
insect, 175–79, 177, 181–84, 183, 207
see also limbs, evolution of
Wonderful Life (Gould), 138, 173
“Wonderful World” (Cooke, Albert and Adler), 292
Wootton, Robin, 176
embryonic development in, 240–42, 241
stripe pattern formulation in, 238–39
stripes as protective coloration for, 223–25, 224, 246
Zimmer, Carl, 184
zone of polarizing activity (ZPA), 42, 44, 45, 4r
Sonic hedgehog gene and, 77
Zuckerkandl, Emile, 271