The Mysterious World of the Human Genome
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Bernal, John Desmond 53–4, 83, 84, 90
beta-globin 97–8, 107, 133–4, 141
bidirectional transcripts 194
Biological Journal of the Linnean Society 145
Birkbeck college, Biomolecular Research Laboratory 83–4, 90–1
Blair, Tony 124
Blombos Cave, South Africa 227–8
BNC2 (gene) 269
Boivin, André 95
Bonnet, Marie Louise 31–2
Boule, Marcellin 262
Bragg, Sir William Lawrence 51–2, 53, 54–5, 56, 64, 67, 68–9, 84, 86, 89
Bragg, Sir William Henry 51, 52, 53–4, 68
Bragg's Law 52, 89
Branson, Herman 68
BRCA 1 and BRCA 110, 188, 297
Brenner, Sydney 96–7, 114, 115, 118, 185, 186, 294
Briggs, Adrian 247
British Museum 231
Broad Institute 268
Broca's area 254, 263
Bronowski, Jacob 121
The Ascent of Man 1
The Identity of Man 1
Brown, Wesley M. 214
Caenorhabditis elegans (round worm) 114–15, 185, 186–7
California Institute of Technology (Caltech) 41, 57, 67–8, 121
Cambridge University 32–3, 48, 51–5, 56, 57, 58, 60, 62, 63, 64, 65, 68, 70, 75, 76, 78–9, 82, 86, 90, 91, 97, 114, 121, 222, 237 see also under individual laboratory or college name
cancer 16
bladder cancer 195
bone cancer 195
bowel cancer 141
brain cancer 195
breast cancer 110, 111, 141, 188, 195, 297, 300
colon cancer 110, 111, 195
genetic engineering and 295, 297, 300
HERVs and 167, 170
kidney cancer 141
lncRNAs and 194–5, 294
lung cancer 111, 195
methylation patterns and 178–9
mutations and 107, 109, 110–11, 141, 188
ovarian cancer 90, 188, 297, 300
prostate cancer 195
research 128
skin cancer 141
somatic mutations and 141
Cann, Rebecca L. 213–14
Carbon-14 dating 236
Carrel, Dr. Alexis 6
Cartagena Protocol on Biosafety, 2000 299
Cavalli, Sforza, Professor Luigi Luca 210, 211, 288
Genes, Peoples and Languages 211
Cavendish, Henry 51
Cavendish Laboratory, Cambridge University 51–5, 57, 58, 60, 62, 63, 64, 65, 68, 78–9, 82, 86, 90, 114
cave paintings 254–5
CD+T helper lymphocyte 160
CD4 160, 161
Celera Genomics 123, 124, 125, 126, 127–8, 302, 303
cell
division (mitosis) 140–1, 186, 190–1
DNA amount within 94–5, 113, 173
eukaryotic 114
germ cell 7, 8, 9, 10, 106, 107, 109, 162, 174, 198–9, 200, 205, 218, 283, 304
nuclear genome within see nuclear genome
pluripotent (“stem”) cells 115–16, 168, 172, 183, 194
programmed cell death (apoptosis) 153, 185–9, 260
regeneration and repair 260
RNA, variation of amount within 94–5
symbioses and 151, 152–4, 282
totipotent 115
viruses and 156–69
zygote and see zygote
CFTR (cystic fibrosis transmembrane regulator gene) 108
Chargaff, Erwin 35, 79–81, 86, 92
Chase, Martha 27–8, 34, 36, 53
chemical bonds 65, 66–8, 71, 79, 81, 104
Chetverikov, Sergei Sergeevich 140
chloroplasts 151, 152
chromosomes
autosomes 107, 108, 114, 189, 212, 241
Avery's discovery of DNA and 44
bacterial transfer of DNA and 99–100
chromosome 3 223
chromosome 4 141, 142
chromosome 6 179–82, 283–4
chromosome 7 108, 165
chromosome 8 223
chromosome 19 223
common male ancestor and 218–21
Crick and Watson's discovery of structure of DNA and 55, 93, 98
discovery of 8–9
genotypes and 295
haplotypes/haplogroups and 200–1, 204, 205, 206–7, 211–12, 218–19, 220, 222, 223, 224, 229, 239–40, 289–90
homologous sexual recombination 9
Hox genes and 116, 117
lncRNAs (long non-coding RNAs) and 191–3
Major Histocompatability Complex (MHC) and 179, 180–4, 269 283–4, 301
meiosis 283
MSRY (male specific region) of Y chromosome 218, 239–40
mutation and 107, 108–9, 141–2, 200, 211, 241 see also mutations and Snips
prokaryotes and 9–10
retroviruses and 162, 163, 164, 165, 166, 167, 206–7, 222–3
Schrödinger's What Is Life? and 39–40
sequencing of entire human genome and 120, 122, 126, 127, 129, 132
Snips and 200, 211, 241 see also SNPs (“single nucleotide polymorphisms”) (“snips”)
VNTR and 286–7
X-inactivation in female embryos 189–91
Church, Dr. George M. 295
chymotrypsin 22
Cicero 147
clades 201, 240
Clinton, Bill 124
Clovis culture 197–8, 207
co-evolution 158, 160
Coghlan, Andy 125
Cold Spring Harbor Laboratory, New York 131, 274
Collins, Francis 124, 127, 128
color blindness 109, 190
Columbia University 79, 93, 263
Columnea plant 149–50
“Complex I deficiency” 154–5
Corey, Robert 68
Corsica 289
covalent bond 65–6, 67, 102, 176
cranberry bog bacillus 19
creative genomics 293–4
creativity
creative genomics 293–4
Crick-Watson discovery of structure of DNA and 63–4, 69, 88, 90
DNA and 3
genomic 145, 175, 178, 282, 293, 304
hybrid 266
Neanderthal 270
personality and scientific 20, 30–1
Crichton, Michael: Jurassic Park 243
Crick, Francis 34, 71, 74
Avery's discovery of DNA and 53, 55
background 52
Brenner and see Brenner, Sydney
Cavendish Laboratory and see Cavendish Laboratory, Cambridge
character 54–5, 64–5
Chargaff and 80–1, 86
DNA extrapolation to proteins, investigates 93–4, 95–8, 114
Franklin and 74, 76–8, 84, 85
Gamow and 95–6
Griffith and 78–9, 86, 97
Pauling's paper on structure of DNA and 82–3, 85
“perfect biological principle” and 79
RNA Tie Club and 96, 97
Schrödinger's inspires 40, 52, 52, 91, 93, 125
second paper on genetic implications of the structure of DNA, 1953 88
structure of DNA, investigation into and discovery of 34, 40, 53, 55, 59, 60, 54–6, 58, 61–5, 68, 69–70, 74, 76–91, 92, 93, 94, 99, 102, 103, 112
Watson and 40, 55–6, 58, 60, 61–5, 69
What Is Life? and 52–3
“What Mad Pursuit” (ad-hoc seminar) 54–5
Wilkins and 47, 75–6, 83
Crick, Michael 62
Crick, Odile 62
cyanobacteria 151–2, 206, 282
cystic fibrosis 108, 109, 300
cytoplasm 94, 95, 131, 134, 152, 153, 165, 187, 203–4
cytosine 17–18, 69, 77, 80, 81, 87, 94, 102, 142, 176, 177, 178, 181, 191, 199, 247
“D” root (haplogroup) 201
D4h3a (haplogroup) 202, 207
Daily Telegraph 124, 281
Dale, Sir Henry 33
Danube River 230
Darwin, Charles 7, 12, 14, 15, 31, 37, 41, 90, 130, 137–9, 144, 145, 146–7, 247–8, 281, 282, 283, 291, 298
Darwinism 41–2, 144
Dawkins, Richard: The Selfish Gene 146–7
Dawson, M. H. 15–16
deacetylase HDAC11 182
Deichmann, Uti 24
Delbruck, Max 26, 39, 41–2, 43, 44, 57–8, 63, 92, 96
Denisovan man (Denisova hominins) 248, 276–8, 279, 288, 301
Department of Agriculture, US. (USDA) 299
Department of Energy, US. 122
Derevianko, Anatoly 273, 275
De Valera, Eamon 38–9
developmental pathway 117–18
Diamond, Jared 262
disease 8, 10–11, 12–13, 20, 97–8, 106–11, 112, 120, 134–55, 160, 161, 164, 167, 169, 170, 175, 188, 190, 192, 195, 212–15, 242, 256, 261, 264, 269, 270, 271, 284, 289, 294–7, 298, 300–2 see also under individual disease name
Dmanisi, Georgia 249
DNA (deoxyribonucleic acid) 3
anti-sense 105–6, 177, 194, 199
cDNA (complementary DNA) 193
coding triplets, search for 94–9
codons 98–9, 106–7, 191
constancy 25
correspondence of number of genes to number of proteins 93, 130, 131–5
discovered by Avery, 1944 14–35, 36
discovery confirmed by Hershey and Chase's experiment with bacteriophage, 1951 27–8, 34, 36, 53
epigenetics and see epigenetics
exons and 132, 133, 134, 135, 142, 187, 190, 193
extraction techniques 21–2, 25, 26, 28, 29, 226, 244, 246, 247, 250, 257, 258, 260, 268, 274, 276, 277
extrapolation to proteins first explored 92–111, 112–23
fingerprinting 285–7
GACT (guanine, adenine, cytosine, thymine) bases 17–18, 77, 93, 94, 95
genetics engineering/creative genomics and 292–304
genomic level evolution and 172–85
human ancestry and 197–291
introns and 132, 133, 134, 135, 187, 190
junk 164, 170
mutations of see mutations
natural selection and see natural selection
number of protein-coding genes in human genome and 130–1, 135
profiling 285
promoter sequences 100, 113, 134, 141–2, 165, 169, 176–7, 183, 191, 193, 194, 207
questions over the discovery of 24–9
recombinant 294, 299
RNA and see RNA
sense strand 177, 186, 191, 194, 199
sequencing of 120–3, 124–36, 167, 198, 202, 246–7, 258, 270–1, 278, 284–5, 287, 288–9, 302
splicing 130–5, 87
structure discovered by Crick and Watson, 1953 38–49, 50–8, 59–91, 92, 93, 95, 112, 113
sugar—deoxyribose 94, 102
symbiosis and see symbiosis
tetranucleotide hypothesis and 18, 79, 80
up-stream regulatory elements 134
viruses and see viruses
DNA-methyltransferase 176
Dobzhansky, Theodosius 140
Domagk, Dr. Gerhard 20
Donohue, Jerry 86–7
Douka, Dr. Katerina 226–38
Down's syndrome 109
Dubos, René Jules 5–7, 10, 14, 15, 16–17, 19–21, 22, 23, 29–30, 31, 32, 33, 34
Dutton, Professor Gordon N. 145
dystrophin 134–5
East Africa 211, 212, 222
Edge (website) 244
Edqvist, Dr. Per-Henrik 167, 168
Egbert (skeleton fossil) 231–3
Egypt 244
electron microscope, invention of 42
electron spin resonance 234, 236
Elmer, Perkin 126
embryo/embryogenesis 2, 8, 37, 40, 109–10, 113–19, 120, 143, 164, 167–8, 172–3, 174, 178, 183, 189, 190–1, 194, 284, 294, 297, 304
ENCODE “Encyclopedia of DNA coding elements” 171
Environmental Protection Agency (EPA) 299
enzymes 19, 22, 25, 26, 54, 93, 104, 117, 119, 143, 157, 158, 159, 160, 165, 182, 247
EPAS1 (gene) 277–8
epigenetics 116, 118–19, 120, 145, 157, 163, 164, 172, 173–84, 187, 189, 191, 192, 194, 236, 247, 282, 283, 285, 286, 293–4, 295, 296, 297, 301
discovery of 96–106, 113–16
epigenetic mark 182–3
epigenetic silencing 163, 176–7, 183, 186, 189, 192
epigenetic system 173–84
epigenome and 175, 183, 295, 302
evolutionary potential 175, 178, 182–3
four epigenetic control systems 175–84
genetic engineering and 293, 294, 295, 296, 297
genomic creativity and 175, 178
histone modification and 175, 180–3, 191
Hox genes and see Hox genes
imprinting 192
lncRNAs and 192, 194
LTRs and 164
meiosis and 283
methylation and 163, 175, 176–9, 180, 181, 182, 183, 191, 247
mutation location and 285
non-coding RNAs and 173–4, 175, 183–4, 185–96, 236, 266
puberty and 118–19
RNAi and 187–9
tandem repeats and 286
Escherichia coli—E. coli 99, 121
Es Skhul cave site, Mount Carmel, Palestine 228, 234–5
ESTs 302
Ethelruda (fossil) 232, 233
Ethiopia 220–1, 224
eugenics 110, 297
eukaryotes 9–10, 114, 135, 141
Eurasia, human ancestry/migration patterns and 202–3, 214, 217, 228, 229, 230, 234, 235, 236, 237, 238, 239, 248, 249, 251, 256, 259, 261, 264–6, 269, 271, 272
Europe: human ancestry/migration patterns and 143, 144, 197–8, 200–1, 202, 211, 212, 217–18, 224, 226, 227, 228, 229, 230, 236, 237, 238, 239–41, 249, 251, 253, 256, 258, 260, 261, 262, 264–5, 267, 269, 271–2, 277, 288, 289, 299–300, 301
evolution
continuing 301–2
Darwin and theory of see Darwin, Charles
genomic level 172–84
see also under individual area of evolution
evolutionary biologists 11–12, 37, 140, 198, 251
exons 132, 133, 134, 135, 142, 176, 187, 190, 193, 194
Feinbaum, Rhonda 185
fingerprinting, DNA 285–7
Finlayson, Clive 279
Fire, Andrew Z. 186, 187
Fisher, Ronald Aylmer 140
Fisher, Simon 254
Fleming, Alexander 19
Flores, island of 248
Food and Drug Administration (FDA), US 299
454 Life Sciences 246
Foxhall Road, Ipswich, Neanderthal hand axes found at 264
FOXP2 (gene) 254, 260
Francalacci, Paolo 219–20
France 11, 165, 169
GM crops and 300
Homo sapiens ancestry and 230, 237, 238, 239, 255, 255, 263, 264
Human Genome Project and 123, 124
Frank, Albert Bernhard 147, 148
Franklin, Rosalind 36, 47, 58
background 70–2
Biomolecular Research Laboratory, Birkbeck college, move to 83, 84, 90–1
Biophysics Unit, King's College, role at 72–6
character 71–2
Crick and 74, 76
death 90, 91
discovery of structure of DNA, role in 47, 58, 70, 72–8, 82–5, 86, 88, 90
Mering and 71–2
Sayre and 74–6, 78
science and everyday life, on separation of 36
Watson and 43–4, 57, 60–1, 63, 70, 82–3, 84–5
Wilkins and 47, 72–8, 82–5, 90
French, Jennifer C. 237, 271
fruit flies 8, 10, 25, 41, 93, 116, 126, 130, 290
Galapagos islands 138
Gamble, Clive 252
Gamow, George 95–6, 97
Garrod, Archibald E. 93
gene
defin
ition of 7–10
expression 2, 8, 55, 93, 100, 113–14, 117, 120, 131, 134, 165, 166, 167, 168, 170, 173, 174, 175, 178, 188, 190 see also epigenetics
therapy 108, 109, 110, 155, 175, 188, 294, 297
genetic bottlenecks 221–2, 224, 301
genetic engineering 293–300, 302
genetics, birth of discipline 8
genomic creativity (mutation, epigenetics, symbiosis and hybridization) 145, 175, 178, 282, 293, 304
genotype 12, 295–6
Gibraltar, Neanderthal remains in 251
Gibraltar Museum 279
Glasgow Caledonian University 145
GM (genetically modified) 298–300
Gold, Thomas 78–9
Golding, William 262
gonadotrophin-releasing hormone (GnRH) 119
Gosling, Raymond 50, 72, 73, 76, 77, 78, 83, 86, 88, 90
Gravettians 238
Great Apes 165–6, 248, 281
Griffith, Frederick 12–14, 15, 16
Griffith, John 78–9, 86, 97
guanine 17–18, 69, 80, 81, 87, 94, 102, 142, 177, 191
Haemophilus influenza (bacterium) 126
Haldane, John Burdon Sanderson 140
Hamilton, Andrew 186
haplotypes/haplogroups 200–9, 210–21, 223, 236, 239–40, 250, 268–9, 284, 288, 289
Harvard Medical School 268, 276
Harvard University 98, 268
Healy, Bernadine 126–7
Hedges, Professor Robert E. M. 231
hemoglobin 52, 54–5, 57, 68, 69, 97–8, 107, 133–4, 278
hemophilia 108, 190, 300
heredity, principles of 7–15, 17, 18, 24, 25, 29, 33, 34, 36, 37–8, 61–2, 63, 64, 79, 81, 92, 93, 95, 106, 113, 120, 137–45, 153, 162, 178, 182, 184, 196, 204, 265, 283, 292
Herriott, Roger 43
Hershey, Alfred 27–8, 34, 36, 41–2, 43–4, 53, 96
Herto, Ethiopia 220–1
Higham, Thomas F. G. 231
Highfield, Roger 124, 281
histone modification 125, 175, 180–3, 191
HIV-1 157, 159–60, 162, 223
HLA-B (gene) 160
Hodgkin, Dorothy 54
Holloway, Ralph 263
holobiont 148–9
holobiontic genome 151, 153, 155, 159, 162, 164, 205, 222, 266
hominids 244, 248
hominins 228, 233, 234, 235, 244, 248, 249, 275–6, 277, 278
Homo erectus 248–50, 251, 252, 259, 260, 277, 290
Homo floresiensis 248
Homo heidelbergensis 251, 252, 259–60, 278
Hood, Leroy 121
horizontal gene transfer 150–1, 299
Horvitz, Robert 185
Hotchkiss, Rollin 17, 26
Howard Hughes Medical Institute 268
Hox genes 116–18
human endogenous retroviruses (HERVs) 162–70, 173, 212, 222–4, 236, 282, 288
ERV3 166–7, 168
HERV–FRD 166–7, 168–9
HERV–Ks 162, 163, 166, 212, 222–4, 236, 288
HERV–K106 223–4, 236, 288
HERV–K113 212, 223, 236