Darwin’s Black Box

Michael J. Behe
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Table of Contents

A-B-C-D metabolic pathway, 150-56
Abiotic syntheses, 155
Abzymes, 202
Accelerin, 83, 88
Activated antihemophilic factor, 88
Activation unit, 133
Adenine (A), 265, 267
synthesis of, 149-50, 152-53
ADP, 157, 158
Aggression, threats of, 117-20
Alberts, Bruce, 115, 152
Aliens, intelligent design and, 248-49
Allegiance to science, 234-35, 251
Amine, 260-61
Amino acids

antibodies and, 120
as building blocks of proteins, 11, 52-53, 89, 142, 260-62
categories of, 261
chains, 52, 142-43
codons designating, 269
in origin-of-life research, 167, 169-70
properties of different, 52
references to, biochemical, 52
sequences, 89 structure of, 260-62

Ammonia, 146-48, 150
AMP biosynthesis, 142, 143-44
A-B-C-D metabolic pathway and, 150-56

Darwinian evolution and, 150-56, 159, 160-61 described, 145-49
intelligent design and, 207-8
molecules involved in, 143-44
regulation of, 157-58, 159
failure of, 159-60
summarized, 149

Amphiphilic molecules, 256
Annual Review of Biochemistry (ARB) book series, 114
Antennapedia, 41
Anthropic principle, 246-47
Antibodies, 120-36

amino acids and, 120
B cells, 122-24, 127
binding site of, 120-22
clonal selection and, 124-26
complement pathway and, 132-36
function of, 120
genes of, in DNA, 122, 127
helper T ceils, 123
increasing, 129
intelligent design and, 202-3
limitations of, 131 -32
plasma cells, 124
proteins and, 127
RNA and, 128

Antibody diversity, 127-32
Antihemophilic factor, 84, 89, 96
a2-Antiplasmin, 88, 89
Antithrombin, 87, 95
Aquinas, Thomas, 243
Aristotle, 7, 8
Armstong, Frank, 182, 183 Arrestin, 21
Artificial objects, intelligent design inferred for, 195-96
Artwork, intelligent design in, 194-95
Aspartic acid, 148
Atoms, 143, 259-62
ATP, 63, 64, 145, 146, 157, 158
Authority, knowledge gained from, 184
Auto-catalytic, blood clotting as, 83

Backbone, protein, 262
Background radiation, 245
Bacteria, DNA of, 268
Bacterial flagellum, 65, 70-73, 257
Bacteriophages, 271-72
Bacteriorhodopsin, 284n18
Baltimore, David, 136-37
Bases, 265
B cells, 122-24, 127
Big Bang theory, 27-28, 244-45, 246, 247, 248, 251-52
Binding site of antibody, 120-22
Biochemical design, 193, 199-208.
See also Intelligent design examples of, 199-202
Biochemical principles, 255-76

of cells and membranes, 255-59
of DNA, 268-76
regulation, 271 -72
replication, 274-76
transcription, 268-71
translation, 273-74
of lipids, 268
of nucleic acids, 265-68
of polysaccharides, 268
of proteins, 259-65

Biochemicals, designing new, 202
Biochemistry

Darwinian evolution and, challenge to, 3, 15,22
defined, 3
early study of, 11-13
of immune system, 126-30
inculturation into
Darwinian evolutionary view in, 179-83
intelligent design and, 193,199-208
difficulty in distinguishing, 205-8
macroevolution and, 14-15
microevolution and, 14-15, 202
molecular machines and, 4-5, 51-52, 130, 157
molecular phenomenon and, x
multicellular structures and, 46
mutation in, 40-41
neo-Darwinism and, 24-25, 26
progress since mid-1950s, x, 3, 4
spontaneous generation and, 23-24
textbooks, 180-83
of vision, 18-22

Biology

evolutionary synthesis (Neo-Darwinism) in, 24-25
micro level of, 8-10
spontaneous generation theory and, 23-24

Biomolecules, 260
Black box

black box within, 8-9
cell as, 9-10, 15
computer as, 6-7
defined, 6
human mind’s response to, 23
of vision, 16-18,22

Blind Watchmaker, The (Dawkins), 33, 213, 217, 249
Blood circulation, 7-8
Blood clotting, 77-97

auto-catalytic characteristic of, 83
as cascade system, 81-85, 87, 96, 97
controlling, 87-89
Darwinian evolution and, 89-93
criticism of, 93-97
Doolittle’s explanation of, 90-97, 177
inadequacy of, 93-97
flow of blood and, 78
function of, 86
health problems caused by defective, 89
intelligent design and, 199-201, 204-5
irreducible complexity of, 78, 86, 96-97, 218
precision required for, 78-79
proteins in, 79-81, 90, 94-97, 199-200
Rube Goldberg machine and, 85-86, 97
ship canal analogy to, 87
simple systems of, 86-87
triggering 85
yin and yang scenario of, 92-93

Blood plasma, 79
Blood vessels, 86
Bloom, Allan, 153
Blueprint for a Cell (de Duve), 155
Bluster, knowledge based on, 185, 186
Bombardier beetle, evolution of, 31-36, 47
Bryan, William Jennings, 236
Bubble universe theory, 246
Building blocks of cells, l 42-61.

See also AMP biosynthesis described 142-44
steps in constructing, 145-49

C1 proteins, 132-33, 135-36
C2 protein, 133-34
C3 convertase, 134
C3 protein, 133, 134, 135
C4 protein, 133, 134, 135
C5 convertase, 134
C5 protein, 135
Calcium ions, 21
“Cambrian explosion,” 27
Campbell, John Angus, 284n 7
Carbon, 260-61
Carbon dioxide, 147
y-Carboxyglutamate residues (Gla), 83-84, 135
Carboxylic acid group, 260-61
Cargo delivery systems, problems of; 101
Cascade system

blood clotting as, 81-85, 87, 96, 97
complement pathway as, 135

Causes of Molecular Evolution, The (Gillespie), 179
Cavalier-Smith, 1, 69, 70
Cech, Thomas, 171
Cell(s), 255-59

B, 122-24, 127
biochemical principles, 255-59
as black box, 9-10, 15
building blocks of, 142-61. See also AMP biosynthesis
Darwinian evolution and, 160-61
described, 142-44
steps in constructing, 145-49
complexity of, intracellular transport and, 101-3
as dynamic systems, 103, 113
eukaryotic, 102, 188, 257-59, 268, 270
helperT, 123
intelligent design and, 232-33
molecular machines and, 5
nucleus of, 9, 10, 102, 258
parts of, 102
plant, 259
plasma, 124 prokaryotic, 257,270, 271
DNA replication in, 274-76
DNA translation in, 273-74
Schleiden and Schwann’s research on, 9
size of organism and, 255-56
structure of, 256-59

Cell membranes, 205-6, 255-59
Cell theory of life, 9
Cell wall, 257
cGMP 20-21
Chauvinism, scientific, 234-35, 251
Chemical bond, 260
Chemistry of life.
See Biochemistry
Chlorophyll, 259
Chloroplast, 259
Christmas factor, 84, 85, 89, 90, 95
Ciliary membrane, 59
Cilium, 59-73

described 59
evolution of, efforts to model, 66-70, 73
flagellum compared to, 70-72
intelligent design and, 204
irreducible complexity and, 66-67, 72-73
proteins in, 72
research literature on, 68-70
separation from cells, 63-64
structure of, 59-62
workings of, 62-66

11-Cis-retinal, 18, 21, 38, 84
Clathrin proteins, 108
Clonal selection, 124-26
Closing of the American Mind, The (Bloom), 153
Coagulation of blood. See Blood clotting
Codons, 269
Cold Spring Harbor Laboratories, meetings sponsored by, 179
Collagen, 52
Comparative immunology, 136
Complement pathway, 132-36
Complex biochemical systems.

See also Blood clotting; Building blocks of cells; Immune system; Intracellular transport; Irreducible complexity formation of
complexity theory on, 29-30, 189-92, 203
by cooperation and symbiosis, 188-89, 192, 203
lack of detailed explanation of, 176
time in history of, 227-28
form of, 198-99
function of, 196
intelligent design of.
See Intelligent design perturbations of, 190
science and, x

Complexity theory, 29-30, 189-92, 203
Computers as black boxes, 6-7
Conceptual precursor, 43-45
Convertin, 84-85
Cooperation and symbiosis, 188-89, 192, 203
Cooperativity, 206-7
Copernicus, 252
Covalent bond, 260
Cox, Michael, 181
Coyne, Jerry, 29
Creationism, 5, 33, 237.
See also Religion
Creighton, Thomas, 151-52
Crick, Francis H.C., 12, 185, 224, 248-49
Cro protein, 272
C-terminal end, 262
Cycling universe theory, 246
Cytidine (C), 265
Cytoplasm, 257, 258
Cytosine, 267
Cytoskeleton, 259

Darrow, Clarence, 236
Darwin, Charles, ix-x, xi, 3-6, 14-18, 24, 173, 250-51, 252
Darwinian evolution (gradualism)

acceptance of, 30
alternatives to, 188-92, 203.
See also Intelligent design
AMP biosynthesis and, 150-56, 159, 160-61
biochemistry and challenge to, 3, 15, 22
blood clotting and, 89-93
criticism of, 93-97
bombardier beetle and, 31-36, 47
cilium and, 66-68, 73
creationism and, 5, 33, 237
Dawkin’s support of, 33-34, 36-39
described, 3-4
of gated transport, 109
immune system and, 124-26, 136-39
as inadequate framework for under standing origin of complex biochemical system, 176
irreducible complexity and, 39-4 110-11, 160, 177
limits of, 3-6, 26-30, 141-42
macroevolution, 14-15
metabolic pathways challenging, 150-56, 159, 160-61
microevolution, 14-15, 202
minimal function and, 45-46
molecular evolution research and, 176, 177, 179-80, 186, 18,
inculturation into evolutionary view and, 179-83
natural selection and, x, 3-4, 5, 28 39, 45
neo-Darwinism, 24-25, 26
physical vs. conceptual precursors and, 43-45
rejection of, 26-30
vesicular transport and, 116
vision and, 16-18, 38

Darwin’s Dangerous Idea (Dennett), 250
Dawkins, Richard, 33-34, 36-39, 46-47,48, 203, 213, 217, 219, 220, 249-51
de Duve, Christian, 155, 156
Dennett, Daniel, 221, 250
Deoxynucleotides, 274
Deoxyribonucleic acid.
See DNA Deoxyribose, 265
Design.
See Intelligent design
Devlin, Thomas, 182-83
Diabetes, 138-39, 159
Dialogues Concerning Natural Religion (Hume), 217
Dickerson, Richard, 238-43
Digestive enzymes, 81
Diogenes, 210, 222, 227
DNA, 268-76

antibody genes in, 122, 127
biochemical principles of, 268-76
regulation, 271-72
replication, 274-76
transcription, 268-71
translation, 273-74
change in, 40-41
intelligent design and, 202-3
“interrupted,” 127
location of, 258
nucleotides of, 142,265, 267
pseudogenes and, 225-26
RNA polymerase and, 270-71
sequencing, 175
splicing and rearrangement of, 89-90, 127-30
structure of cellular, 266-68

DnaA, DnaB, and DnaC proteins, 275
DNA polymerase, 75-76

I (Pol 1), 274
II (Pol 11), 275
III (Pol 111), 275

Doolittle, Russell, 90-97, 177
Doppler shift, 244
Dose, Klaus, 168
Duplication of genes, 89, 94
Dynein, 60, 62, 63-64, 66
Dyson, Freeman, 224

Ectodermal glands, 31, 32
Eddington, A.S., 244
Einstein, Albert, 243-44, 246, 252
Eldredge, Niles, 27
Electrically charged amino acids, 261
Electrical machines, 4-5
Electron, 260, 261
discovery of, 10
Electron microscopy, structures revealed with, 10, 59-62, 71, 79
Elements, 260
Elongation factor Tu (EF-Tu), 273
Endler, John, 29
Endoplasmic reticulum (ER), 102, 107,258
Energy pellets, 145, 148, 153, 157
Enhancers (DNA sequences), 270
Enzyme catalysts, 52

AMP biosynthesis and, 145-49, 157-58
blood clotting cascade and, 81, 83-84, 87
in bombardier beetle, 31, 32- 33

Eukaryotes, 102, 188, 257-59, 268. 270
Evolution, defined, x-xi.
See also Darwinian evolution (gradualism); Molecular evolution research
Evolutionary synthesis, 24-25
Evolution at the Molecular Level (Selander, Clark, and Whittam). 179
Extrinsic pathway, 84-85
Eye. See Vision

Fibrin, 80, 81-82, 87, 88, 95
Fibrinogen, 79-81, 82, 86, 87, 95
Fibrin stabilizing factor (FSF), 88, 89
Fischer, Emil, 11
Flagellin, 71
Flagellin filament, 71
Flagellum, bacterial, 65, 70-73, 257
Formate, 146, 153
Formic acid, 146
Fossil record, 22, 27
Founder effects, 229
Fox, Sidney, 170
Function of system, intelligent design and, 196, 204-5
Futuyma, Douglas, 225, 226

Galen, 7-8
Galileo, 9, 252
Gamow, George, 268
Gated transport, 108, 109, 110
GDP, 19-20, 157, 158 Gene(s), 269.

See also DNA; RNA antibody, 122, 127
duplicated, 89, 94
insulin, 201
introns in, 175
mutations of, 40-41, 89, 127, 202
pseudogenes, 225-26, 227, 228
regulation of, 271-72
replication of, 274-76
split, 89-90
transcription of, 268-71
translation of, 273-74

Gene flow, 229
Genetic drift, 229
Genetic information, coding of, 268-69
Gesner, Conrad, 8
Gillespie, John, 178-79
Gla (y-Carboxyglutamate) residues, 83-84, 135
Glutamate (Glu) residues, 83-84
Glutamine, 145, 147
Glycine, 145-46
GMP 157, 158
Goldschmidt, Richard, 26-27, 40
Golgi apparatus, 102, 107-8, 258
Gould, Stephen Jay, 27-28, 228-29
Gradual evolution. See Darwinian evolution (gradualism)
Grew, Nehemiah, 9
GTE: 20, 157, 158
Guanine (G), 265, 267
Guanylate cyclase, 21
Gyrase, 275

Haeckel, Ernst, 24, 101-2
Hageman factor, 84, 85
Harvey, William, 8
Hawking, Stephen, 246
a-Helix, 264
Helper T cell, 123
Hemoglobin, 11, 174, 206-7, 225
Hemophilia, 89
Heparin, 87
Hexokinase, 52
Hippocrates, 7
History, science and, 235-37,251
Hitching, Francis, 33, 36-39, 46-47
HMK (protein), 84
Ho, Mae-Wan, 28
Hooke, Robert, 9
Hook protein, 71
“Hopeful monster” theory, 27, 40, 96
Hoppe-Seyler, Ernst, 11
Horowitz, N.H., 154-55, 160
Hoyle, Fred, 244-45, 246
Hubble, Edwin, 244
Hume, David, 217-19
Huxley, Thomas Henry, 235-36
Hydrocarbon amino acids, 261
Hydrogen, 260, 261
Hydrogen bonds, 264, 266-68
Hydrogen cyanide, 150
Hydrogen peroxide, 31, 32,34, 35-36, 47
Hydrophilic regions of molecules, 256
Hydrophobic regions of molecules, 256
Hydroquinone, 31, 32, 34, 35, 36, 47

Icarus (journal), 248
I-cell disease, 113-14
Ideas, simple, 209-10
Imaginary time, 246
Immune system, 117-39

aggression and, threats of, 118-20
antibody diversity and, 127-28, 130-32
biochemistry of, 126-30
clonal selection and, 124-26
complement pathway and, 132-36
Darwinian evolution and, 124-26, 136-39
drawbacks to, 138-39
health problems from defects in, 136
irreducible complexity of, 130-31, 135, 139
protein binding and, 124-25
research literature on, 136-38
skin and, 119
workings of, 120-24

Immunoglobulins, 137
IMP, 148, 158
Imperfection argument against intelligent design, 222-25
Inculturation into Darwinian evolutionary view of world, 179-83
Initiation factors, 273
Insulin, 201
Integrase, 272
Intelligent design, 187-253

aliens and, 248-49
AMP synthesis and, 207-8
antibodies and, 202-3
arguments against chauvinist, 234-35, 251
historical, 235-37, 251
of Hume, 217-19
imperfection, 222-25
philosophical, 237-45, 251
religious, 245-48
sentimental, 210-11, 243-45
of Sober, 217-21
useless feature, 225-27
artificial objects and, 195-96
artwork end, 194-95
biochemical design, 193, 199-208
difficulty in detecting design, cases of, 205-8
examples of, 199-202
new biochemicals, 202
blood clotting and, 199-201, 204-5
cells and, 232-33
cilium and, 204
complexity of world and, 228-30
Dawkins’s view of, 213
defined, 193
designer and, 196-97, 224, 248, 249, 251
detection of, 192-96, 205-8
evolution and, 228-29
examples of, 192-94
form of system and, 198-99
function of systems and, 196, 204-5
future research on, 230-31
inferences to, 194-98
insulin gene and, 201
intracellular transport and, 204-5
mechanical objects and, 195
microevolution and, 202
natural components and, 195
nature and, laws of, 203-4
origin-of-life question and, 169, 252-53
ouija board analogy of, 219-21
Paley’s view of, 211-15
refutation of, 215-16
pre-Darwinian ideas of, 210- 16
proteins and, 202
science and, 230-31, 233
simple ideas and, 209-10
in social situation, 194
time in history of, 227-28
time travel and, 249

Interleukin, 123
Intermediate filaments, 259
Intracellular transport, 98-116

complexity of cell and, 101-3
health problems from defective, 113-14
intelligent design and, 204-5
irreducible complexity of, 109, 110-13, 115-16
measles epidemic scenario and, 98-101, 113
methods
gated, 108, 109, 110
transmembrane, 108-9
vesicular, 109-10, 114-15, 116
process, 107-8
of proteins, 103
space probe analogy and, 103-7

intrinsic pathway, 84-85
Introns, 175
Invertebrate classification, 7
lon charnel, 21
Irreducible complexity, 39-40, 42-45.

See also Complex biochemical systems
of blood clotting, 78, 86, 96 97, 218
of cilium, 66-67, 72-73
conceptual precursor and, 43-45
Darwinian evolution and, 39-45, 110-11, 160, 177
defined, 39
determining, 42-45
of flagellum, 72, 73
of immune system, 130-31, 135, 139
of intracellular transport, 109, 110-13, 115-16
minimal function and, 46
of mousetrap, 42, 47
physical precursor and, 43-45
as problem for Darwinism, 160, 177
of Rube Goldberg machine, 76, 86, 218

Journal of Molecular Evolution (JME) 165-77, 238

background of, 165-66
detailed models missing from, 176-77
mathematical models for evolution in, 173-74
origin-of-life research in, 166-73
sequence comparison research in, 174-75, 284-85n18

Joyce, Gerald, ] 71-72, 202
Juvenile diabetes, 138-39

Kallikrein 84
Kaplan, Martin, 29
Kauffman, Stuart, 29-30, 155-56. 178, 189-92
Kendrew, J. C., 12
Khorana, H. Gobind, 269
Killer proteins, 135
Knowledge of molecular evolution, bases of, 183-86
Kornberg, Arthur, 274
Kumura, Motoo, 178

Laudan, Larry, 287n3
Leeuwenhoek Anton van, 9, 13
Lehninger, Albert, 180-81, 182
Lenses, scientific use of, 8-9
Lesch-Nyhan syndrome, 159
Liebig, Justus von, 11
Life Itself (Crick), 248
Light-sensitive spot of eye, 37-38, 46
Linkage, 229
Linnaeus, C, 8
Lipid bilayer, 256-57
Lipids, 268
Lysogenic cycle, 271, 272
Lysosomes, 102, 107-8, 113-14,258
Lytic cycle, 271, 272

McDonald, John, 28
Macroevolution, 14-15
Maddox, John, 250
Magainins, 119
Malpighi, M., 9
Mannose-6-phosphate (M6P), 108
Manufacturing machines, 5
Margulis, Lynn, 26, 70, 188-89
Masked proteins, 135
Mathematical models for evolution, 173-74
Maxwell, J.C., 251
Measles epidemic scenario, 98-101, 113
Mechanical objects, intelligent design inferred for 195
Meiotic drive, 229
Membranes.
See Cell membranes Messenger RNA (mRNA), 107, 266, 273-74
Metabolic pathway, 150-61

A-B-C-D, 150-56
regulation of, 157-58, 159
failure of, 159-60

Metabolism, 11
Metarhodopsin, 21
Metarhodopsin 11, 19-20
MHC protein, 123
Microevolution, 14-15, 202
Microfilaments, 259
Microscope electron microscopy, 10, 59-62, 71, 79 limits of, 10
Microtubules, 59-62, 64, 66, 67, 259
Miklos, George, 28
Miller, Kenneth, 222-23, 225-26, 227, 228, 239
Miller, Stanley, 150,166-67, 169
Mims, Forrest, 237
Minimal function, 45-46, 130-31
Mitochondria, 10,26, 102-3, 188-89, 258
Mitotic spindle, 259
Mivart, St. George, 30
Molecular Biology of the Cell (Alberta, Watson, et al), 115, 152
Molecular clock theory, 174
Molecular evolution research books of, 178-79

Darwinian evolution and, 176, 177, 179-80, 186, 187
inculturation into, 179-83
in Journal of Molecular Evolution, 165-77
background of, 165-66
detailed models missing from, 176-77
mathematical models for evolution, 173-74
origin-of-life research, 166-73
sequence comparison research, 174-75, 284-85n 18
knowledge of molecular evolution, bases of, 183-86
Proceedings of the National Academy of Sciences, 177-78
“publish or perish” proverb and, 186

Molecular machines, 4-5, 51 -52, 130, 157
Molecules amphiphilic, 256

in AMP synthesis, 143-44
biomolecules, 260
in cell membranes, 205-6
defined, 260
hydrophilic regions of, 256
hydrophobic regions of, 256
magainins, 119
new, making, 143
polar, 261
science and molecular phenomenon, ix-xi

Motor proteins, 62, 67-68
Mt. Rushmore, intelligent design of, 198, 227
Mousetrap, irreducible complexity of 42, 47
mRNA (Messenger RNA), 107,266 273-74
Multiple sclerosis, 138
Mutations, 40-41, 89, 127, 202
complexity theory and, 190
Myoglobin, 12, 207

National Center for Science Education 236-37
Natural components, intelligent design in system made with 195
Natural selection, x, 3-4, 5, 28, 39, 45
Natural Theology (Paley), 211- 12, 214
Nature, laws of, 203-4
Neck of the Giraffe, The (Hitching), 33, 36-37
Nelson, David, 181
Neo-Darwinism, 24-25, 26
Neutral Theory of Molecular Evolution The (Kimura), 178
Newton, Isaac, 251
Nexin, 60, 62, 63, 64, 66, 68
Nirenberg, Marshall, 269
Nitrogen, 145-47, 148-49
NSF protein, 108
N-terminal end, 262
Nuclear magnetic resonance (NMR) 12-13
Nuclear pores, 258
Nucleic acids, 142, 167-68, 265-68
Nucleoid, 257
Nucleotides, 142-43, 148, 265-66, 267, 268, 270
Nucleus, 9, 10, 102, 258

Ochoa, Severo, 269
Organelles, 258, 259
Orgel, Leslie, 171-72, 224, 248
Origin-of-life question

amino acids in, 167, 169-70
chemical processes and 166-7
factors affecting, 229-30
intelligent design and, 169, 252
Journal of Molecular
Evolution papers on, 166-73
pessimistic reviews of research on 168
RNA research, 171-73
science end, 172-73

Origin of replication, 275
Origin of Species, The (Darwin), 9, 16
Origins: A Skeptic’s Guide to the Creation of Life on Earth (Shapiro), 234
Origins: A Skeptic’s Guide to the Origin of Life (Shapiro), 221
Origins of Order, The (Kauffman), 178
Oro, Juan, 167-68
Ouija board analogy, 219-21
Overton, William, 287n3
Oxygen, 145, 146, 147, 260
binding to hemoglobin, cooperativity and, 206-7

Paley, William, 211-16
Panda’s thumb, Gould on evolution of, 228-29
Pauling, Linus, 174
Penzias (astronomer), 245
Peroxisome, 102
Personal experience, knowledge through, 184
Perspectives on Science and Christian Faith (journal), 238
Perturbations of complex systems, 190
Perultz, Max, 12
Philosophy

intelligent design and, arguments against, 237-45,251
science and, 250-51

Philosophy of Biology (Sober), 217, 220
Phonetic alphabet, creation of, 209-10
Phosphodiesterase, 20, 21
Phosphorus, 145
Photosynthesis, 259
Physical precursor, 43-45
Picosecond, 18-19
Pili1 257
Place-value of numbers, use of, 210
Plant cells, 259
Plant classifications, 8
Plants, designed, 201
Plasma, blood, 79
Plasma cells, 124
Plasma thromboplastin (PTA), 84, 85, 201
Plasmin, 88, 200-201
Plasminogen, 88, 95, 200, 201
Platelets, 86
B-Pleated sheet, 264
Polar amino acids, 261
Pol I (DNA polymerase 1), 274
Pol 11 (DNA polymerase 11), 275
Pol 111 (DNA polymerase 111), 275
Polymers, 142
Polynucleotides, 268
Polypeptides, 262, 268
Polysaccharides, 257, 268
Precursors, physical vs. conceptual, 43-45
Prekallikrein, 84
Pribnow box, 270
Primary structure of protein, 262-64
Proaccelerin, 83, 84, 86
Proceedings of the National Academy of Sciences (PNAS), 154, 177-78
Proconvertin, 84, 90
Proenzymes, 81, 87, 96
Prokaryotes, 257, 270, 271

DNA replication in, 275-76
DNA translation in, 273-74

Promoters (DNA sequences), 270
Proofreading, 274, 275
Proteases, 63 Protein C, 88, 89
Proteinoids, 170
Proteins amino acids as building blocks of, 11, 52-53, 89, 142, 260-62

antibodies and, 127
binding ability of, 124-25
of blood-clotting system, 79-81, 90, 94-97, 199-200
chains, 52
in cilium, 72
in complement system, 132-34
DNA transcription and, 268-71
from duplicated genes, 94
in flagellum, 72-73
folded, 52-53, 262, 264-65
functions of, 52, 53
in hemoglobin, 174, 206
intelligent design of, 202
intracellular transport of, 103
killer, 135
masked, 135
molecular machines and, 51-52
motor, 62, 67-68
RAG, 137
regulatory, 135
single strand binding (SSB), 275
structure of, 259-65
synthesis of, 107-8, 262
workings of, 52-53
x-ray crystallography and, 12

Prothrombin, 81-82, 83-84, 86, 90, 95
Pseudogenes, 225-26, 227,228
PTA (plasma thromboplastin), 84, 85, 201
“Publish or perish” proverb, 186
“Punctuated equilibrium” theory, 27
Purines, 266
Pyrimidines, 266

Quatemary structure of protein, 263, 265
Quinn, Philip, 287n3
Quinone, 31, 32

Radiation, background, 245 RAG proteins, 137
Recognition unit, 133
Regulation of AMP synthesis, 157-58, 159

failure of; 159-60
DNA, 271-72

Regulatory proteins, 135
Relativity, Einstein’s theory of, 243-44
Release factor, 274
Religion creationism and, 5, 33, 237

intelligent design and, arguments against, 245-48
Paley and, 211-16
science and, 235-43, 250-51, 287n3

Replication, DNA, 274-76
Repressor, 272
Rhodopsin, 19, 38, 52, 284nl8
Rhodopsin kinase, 21
Ribonucleotides, 270
Ribose, 265
Ribosomal RNA (rRNA), 266
Ribosomes, 107, 258,273
RNA antibody end, 128

biological classes of, 266
edited and corrected message in, 127
intelligent design and, 202
origin-of-life question and, 171-73
Cech’s research on, 171
Joyce and Orgel’s research on 171-72
skin and, 119

RNA polymerase, 270-71, 273, 276
RNA-world theory, 171-72
rRNA (Ribosomal RNA), 266
Rube Goldberg machine, 74-77, 85-86, 88, 97 218
Rubeola (measles) epidemic scenario 98-101, 113
Ruse, Michael, 221, 287n3

Saunders, Peter, 28
Schleiden, Matthias, 9
Schwann, Theodor, 9
Science

allegiance to, 234-35, 251
complex systems and, x history and, 235-37, 251
intelligent design and, 230-31 233
molecular machines and, 4-5
molecular phenomenon and, ix-xi
origin-of-life question and, 172-73
philosophy and, 250-51
religion and, 235-43, 250-51, 287n3
supernatural explanations and, 243-48, 251-52

Scientific American, 191, 237, 248 249
Scientific method, 242-43
Scopes, John, and Scopes teal, 236
Secondary structure of protein, 263 264
Secretory lobes of beetle, 31, 32
Secretory vesicles, 102
Selective breeding, 202
Sequence comparison research, 174-75, 284-85n 18
Shapiro, Robert, 170, 221, 234
B-Sheet, 264
Side chain, 261
Signal recognition particle (SRP), 107, 112
Singer, Charles, 9
Single strand binding protein (SSB), 275
Skin, protection offered by, 119
Smith, John Maynard, 30, 156
SNAP protein, 108
Sober, Elliot, 217-21
Socrates, 211
Sodium ions, 21
Solar-powered machines, 4
Space probe analogy, 103-7
Spontaneous generation, 23-24
SRP (Signal recognition particle), 107, 112
SSB (Single strand binding protein), 275
Steady-state theory, 245, 246
Stelluti, 9
Stuart factor, 82-87, 89, 90, 95
Supernatural explanations, science and, 243-48, 251-52
Superoxide dismutase, 284n18
Swammerdam, Jan, 9
Swift, Jonathan, 13
Swimming, requirements fo

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