The Mysterious World of the Human Genome
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HERV–K115 212, 223, 236, 288
HERV–K116 223
HERV–W group 166, 170
MSRV–HERV–W 170
see also retroviruses
human genome
amount of protein-coding genes (20,500) discovered in human genome sequencing 129–6, 170–1, 174
DNA breakdown of 129–30, 195–6
DNA discovered 14–35, 36, 53
DNA extrapolation to proteins first explored 92–111, 131–5
DNA structure discovered 38–49, 50–8, 59–91, 92, 93, 95, 112, 113
epigenetics and 172–96 see also epigenetics
genetic engineering/genomic creativity and 292–304
genomic level evolution of 172–84
HERVs and see HERVs
human origins and migrations and 197–291
mapping of 120–3, 124–36, 170, 193, 281, 293
mutations and see mutations
natural selection and 137–45 see also natural selection
number of genes in common with other organisms 130, 281–2
percentage of retroviral DNA in 162
symbiosis and 146–55 see also symbiosis
uniqueness of each 283–91
unknown 50 percent of, explanation for 135–6, 170–1, 189, 193–6
virus symbiosis with 159–71 see also retrovirus and virus
whole genome sequencing, increase in number of 287–8
see also under individual components of human genome
Human Genome Project, The 122–3, 124–30, 168, 245
human origins and migrations 197–291
African origins of Homo sapiens 211–24, 226–42, 248, 249–50, 256, 259–61, 267, 276, 288, 290, 301
autosomes and 212, 241
common ancestors 200, 210–24, 248, 259, 260, 265–6, 274, 275, 276, 277, 290, 291
extraction and assessment of ancient DNA, advances in 226, 229, 234, 236, 243–7, 250, 257, 258, 260, 268, 274, 276, 277
first evolutionary emergence of modern humans 226, 243–80, 289–91
haplotypes/haplogroups and 200–3, 204, 205, 206–9, 211–12, 213–14, 218–19, 220, 222, 223, 224, 229, 239–40, 289–90
HERV distribution and 212–13, 222–4, 236, 288
hominids and 228, 235, 244, 248
hominins and 233, 244, 248, 249, 275–6, 277, 278
Homo erectus and 248–50, 251, 252, 259, 260, 277, 290
Homo floresiensis and 248
Homo heidelbergensis and 251, 252, 259–60, 278
human evolutionary tree/species evolution and 248–56, 257–80
hunter-gatherers 215, 216, 233, 267, 270, 271
Ice Ages/climate and 197, 198–9, 221, 233–4, 235, 236, 238–40, 251, 252, 253, 266, 267–8, 271
Last Glacial Maximum (“LGM”) and 239–40, 271
loss of diversity and near-extinction event 221–4
Major Histocompatability Complex (MHC) and 221, 283–4, 301
mitochondrial DNA and 203–9, 212–24, 237, 240, 250, 257, 258, 260, 273–4, 275–6, 278, 279, 282, 288–9
MSRY and 239–40
“multi-regional theory” and 249–50
Neanderthal evolution and see Neanderthals
radiocarbon dating and 208, 226–7, 228, 229, 231, 232, 236
Richard III and 207–9
sites of excavation and fossil names see under individual site location/name
SNPs (“single nucleotide polymorphisms”) (“snip”) and 198–201, 203–7, 211–15, 219, 241, 258, 274, 284, 285, 289, 301
whole genome sequencing and 288–91
Human Proteome Project 168
hummingbird 149–50, 160
Huntington's disease 108, 109, 141–2, 188, 300
Huxley, Julian: Evolution: The Modern Synthesis 14, 15, 139
Huxley, Thomas Henry 137, 139
hybridization
genomic creativity and 145, 178
human ancestry and 235–6, 261–2, 265–80, 288, 293, 299, 301
viruses and 157
hydrogen bond 65–7, 76, 81, 86, 87, 88, 104, 191, 199
Iberia 239, 255, 257
Ibsen, Joy (née Brown) 209
Ibsen, Michael 209
Ice Ages 197, 198–9, 221, 234, 235, 236, 239, 240
identical twins (“monozygotic twins”) 2, 172–3, 182–3, 283, 284, 286
India 222
Indiana University, Bloomington 40–1, 43–4, 57
Institute for Advanced Studies, Dublin 38
Institute of Archaeology and Ethnography, Akademgorodok, Russia 275
integrase 160
introns 132, 133, 134, 135, 187, 190, 194
J1c2c (mitochondrial haplotype) 209
Jablonka, Eva 172
Jacob, François 99–100, 101
Jeffreys, Alec 285–7
Johannsen, Wilhelm 7–8
Journal of Experimental Medicine 22–3
Judson, Horace Freeland 18, 26, 35, 55, 74, 81, 92
The Eighth Day of Creation 197
Kalckar, Herman 45, 55–6, 60
Kebara cave, Palestine 235
Kendrew, John 53, 54, 57, 58, 60, 61, 80, 89
Kenya 248
keratin 64, 269
Khorana, Gobind 98
King's College, London: Medical Research Council Biophysics Unit 45, 46, 47, 48–9, 58, 70, 72–6, 77, 82, 83, 84, 85, 86, 88, 90
Klug, Aaron 72–3, 84, 91
Koch, Robert 10–11, 14, 15
“Koch's postulates” 10–11
Krause, Johannes 273–4, 275
Ksar Akil rock-shelter, Lebanon 228, 230–3
Laboratoire Central des Services Chimique de l’Etat, Paris 71
Lagar Velho, Portugal 257
Lake Turkana, Kenya 248
Lamb, Marion J. 172
Langley, Philippa 208
language
human evolution and 215, 253–5, 260
Neanderthal 254–5
Larsson, Erik 167, 168
Last Glacial Maximum (“LGM”) 239, 271
LCA (last common ancestor) 219, 290
Leakey, Richard 248
Leber's hereditary optic neuropathy 155
Lederberg, Joshua 99
Lee, Rosalind 185
Leiden University, Netherlands 231, 272
Le Page, Michael 125
Levant 233, 236
Levene, Phoebus Aaron 18, 79, 80
Libby, William F. 225–6, 227, 228–9
LINEs (virus-like entity) 164, 170, 195
lin-14 (gene) 185
Linnaean system 10, 247–8
Linnaeus, Carl 167
Luria, Salvador 41–4, 57–8, 60, 63
Lwoff, André Michel 99, 101
Lyon, Mary F. 189–90
MacLeod, Colin 21, 22–3, 29, 36
Maddox, Brenda 71, 74, 75
Major Histocompatability Complex (MHC) and 179, 180–4, 221–2, 269, 283–4, 301
Mallet, Dr. Francois 165
Manhattan Project 47, 49, 229
Margulis, Lynn 146, 152, 282
Marler, Peter 254
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 243, 244, 258, 260, 268, 273–5
Maxwell, James Clerk 51
Mayr, Ernst 139
McCarty, Maclyn 21–3, 25, 26, 29, 36
McClintock, Barbara 8–9, 55, 140
McCoy, Dr. John M. 164–5
Medical Research Council 47, 72, 97
Mediterranean 230, 233, 236, 255, 289
meiosis 283
Melanesians 269, 277
Mellars, Sir Paul 222, 227, 230, 237, 264–5, 271
Mello, Craig C. 186, 187
Mendel, Gregor 7, 8, 15, 24, 106, 109, 139, 153, 162, 204
meningitis 12–13, 19, 20, 300
Mering, Jacques 71–2
MESH (mutation, epigenetics, symbiosis and hybridization) 145
methylation 163, 175, 176–9, 180, 182, 183, 191, 247
methyl chemical groups
176, 181, 247
methyltransferase, DNA– 176
Mezmaiskaya Cave, Caucasus 268
Middle Awash, Ethiopia 224
Middle East 217, 228, 249, 251, 258
Miescher, Johann Friedrich 17
Ministry of Health, London 12–13, 16
Mirsky, Alfred E. 25, 26
Mithen, Steven 265
mitochondria 152–5, 162, 194, 200–7, 209, 211, 212–19, 224, 237, 240, 250, 257–9, 260, 273–6, 278, 279, 282, 288–9
haplotypes/haplogroups and 200–7, 209, 211–15, 219, 237–8, 240, 250, 258, 274, 289
mitochondrial disease 154–5
“mitochondrial Eve” 215–17, 220
mitochondrial genome 153–4, 203–4, 205, 211–13, 216, 218, 219, 257–9, 274, 275, 279, 288–9
mitochondrial lncRNAs 194
mitochondrial snips see SNPs (“single nucleotide polymorphisms”) (“snip”)
nuclear genome and see nuclear genome
paleontology, use of mitochondrial genetics in 200–7, 209, 211–15, 219, 237–8, 240, 250, 258, 274, 289
symbiotic origin of (SET) 152–5, 205–6
mitosis (cell division) 140–1, 186, 190–1
“Modern Human Superiority Complex, the” 272–3
molecular biology 37, 53, 94, 96, 97, 120, 122, 167, 168, 184, 185
molecular clock 144, 213, 214, 219, 223
Monaco, Anthony 254
Monod, Jacques 99, 101
Morgan, Thomas Hunt 8, 93, 126, 140
Mount Toba, Sumatra 222
Mousterian culture 263
Moyzis, Robert 241
MRC Molecular Biology Laboratory, Cambridge 97, 114
MRCA (most recent common ancestor) 219–20
MS (multiple sclerosis) 169–70
MSRY (male specific region) of Y chromosome 218, 239–40
Muller, Hermann J. 25, 26, 41, 44, 93, 140
Mullis, Kary 246
“multi-regional theory” 214, 249–50
muscular dystrophy 109, 135
mutation
autosomes and 107, 108
concept/discovery of 13–15, 25, 41, 44, 105–7, 137–40
disease and 107–11, 112, 115, 120, 134–55, 190, 212–15 see also under individual disease name
dominant gene mutation 107, 108, 141–2
error in the nucleotide sequence 104–6
evolution of Homo sapiens and 198–201, 203–7, 211–15, 219, 241, 258, 274, 284, 285, 289, 301
FOXP2 and 254
frame-shift mutation 106–7
frequency for whole genomes 284–5
gene therapy and see gene therapy
genetic symbiosis and 150–1
genomic creativity and 145
haplotypes/haplogroups and 198–201, 203–7, 211–15, 219, 241, 258, 274, 284, 285, 289, 301
LCA/MRCA and 200–1, 215, 216, 219
mitochondrial disease and 153–5, 212–15 see also mitochondria
mutational clock 258
natural selection and 137–45
Neanderthal 258, 260
point mutation 105–7, 199
recessive gene mutation 107–9, 141, 190
retroviruses and 157, 161, 163, 164, 166–7, 223 see also retroviruses
sex-linked recessive mutant gene 108–9
single-gene disorders and 109
SNPs 198–201, 203–7, 211–15, 219, 241, 258, 274, 284, 285, 289, 301
somatic mutations 140–1
structure of DNA discovery and 97–9, 100, 105–6
X-ray induced gene 25, 44
Mycobacterium tuberculosis (tuberculosis germ) 10
Mycoplasma genitalium genome 303–4
myelin 169–70
National Academy of Sciences, US 122
National Human Genome Research Institute, US 171
National Institutes of Health (NIH), US 111, 122, 125, 126, 299
National Research Council Fellowship, US 6, 44, 56, 60
Native Americans 197, 198, 202–3, 207
Natural History Museum, London 138, 198, 220, 259
natural selection 14–15, 37–8, 90, 117, 137–45, 149, 151, 153, 160, 166, 169, 199–200, 213, 241, 266, 281, 283, 284, 286, 293, 298, 304
Nature 84, 88–9, 127, 128, 170, 197–8, 220, 275, 278–9
Neanderthal (Homo neanderthalensis) 228, 229, 230–8, 247, 248, 250–6, 257–80, 288, 290, 301
Near East 228, 230, 233, 234, 235–6, 288
near-extinction event, loss of human diversity and 221–4
neo-Darwinism and 144
Neolithic era 240
New Guinea 221, 261
New Scientist 125
New York University 252
School of Medicine 21
Nirenberg, Marshall 98, 125
nitrogen cycle 150
Nobel Prize 24, 25, 26, 29, 32, 33, 34–5, 38, 41, 43, 51, 65, 67, 69, 75, 76, 90, 91, 101, 121, 132, 135, 185, 187, 229, 243, 249
Norrish, Professor R. G. W. 75
North Africa 236
nuclear genome 121, 153–4, 160, 162, 188, 189, 203, 204, 205, 206, 207, 214, 218, 250, 257, 258–9, 260, 261, 268, 273, 275, 276, 277, 288, 289
nucleic acid 17–18, 79
obesity, methylation and 179
Ochoa, Severo 98
Olby, Robert 26
Old Man of Shanidar 264
oligodendrocyte (brain cell) 169
organ development, genetic regulation of 185
Orgel, Leslie 97
Ötzi, the Tyrolean Iceman 289
ovum 9, 37, 106, 107, 168, 172, 177, 198–9, 204, 284
Owen, Sir Richard 138–9
Oxford Radiocarbon Accelerator Unit 226, 231, 232
Oxford University 96, 146, 185, 226–7, 231, 232, 254
oxygen 52, 57, 66, 67, 68, 97–8, 151–2, 153, 154, 203, 206, 278, 282
Pääbo, Svante 243, 244, 246, 247, 250, 256, 258, 260, 265, 267, 268, 270, 273, 274, 275, 276, 278, 279, 280, 289–90
Pakendorf, Brigitte 218
Paleolithic era 202, 229, 230, 232, 240, 255
“pangene” 7
paper chromatography 80
Pasteur, Louis 11
Pasteur Institute 99, 113
Pauling, Linus vii, 24, 56–7, 64, 65, 67–9, 71, 76, 77, 79, 81, 82, 84, 85, 86, 104
Pauling, Peter 82
PCR (polymerase chain reaction) 246, 287
PE Corporation 126
penicillin 19
“perfect cosmological principle” 79
Personal Genome Project 295–6
personal genomics 294–5
Perutz, Max 51, 52, 53, 54, 55, 57, 58, 60, 62, 63, 68, 69
phage group 41–5, 57–8, 92, 97, 98
phenotype 12, 295
phocomelia 118
photosynthesis 151–2
phylogenetics 248
placental structure and function 115, 165–6, 167, 168–9, 172–3
pluripotent cells 115–16, 168, 172, 183, 194
pneumococci 12–17, 19, 21–2, 23, 25, 29, 33, 35, 300
pneumonia 12–13, 19, 20, 21, 300
polio virus 156, 304
Polynesia 277, 288
polysaccharide 13–14, 17, 19, 21, 22, 25, 33
Pontén, Professor Fredrik 167, 168
Portugal, F. 32, 34, 35
Poznik, G. David 219–20
Prader–Willi syndrome 192, 194
predictive medicine 294, 296
prehistory, the great wilderness of 225, 226, 227, 228
preimplantation genetic diagnosis 109–10, 294, 297
Proceedings of the National Academy of Sciences 82, 97
profiling, DNA 285, 294–5
prokaryotes 9–10
promoter sequences 100, 113, 134, 141–2, 165, 169, 176–7, 183, 191, 193, 194, 207
prontosil 20
proteins 8
DNA discovery and 18–19, 21–2, 25–9, 53, 54, 55
DNA structure discovery and 42, 45, 50, 52, 53, 54, 55, 56–7,
62, 64, 65, 67–9, 72, 79, 81, 89, 91
epigenetics and 173, 174, 176, 179, 180, 181, 182, 183, 186, 187–8, 189, 190, 191, 193, 194
extrapolation of DNA to proteins first explored 92–111, 114, 116, 117
genome sequencing and 119–21, 129–35, 170–1, 174, 284–5
human ancestry and 199, 203, 206, 207, 242, 260–1, 269
mutations in DNA and 140, 142–3, 154, 157, 159, 164
number of protein-coding genes in human genome and 129–35, 170–1, 174, 284–5
one-gene-one-protein maxim, Beadle and Tatum's 93, 130, 131–5
structure of 50, 52, 53–7, 64, 65, 68–9, 79, 81
viruses and 157, 159, 164, 165, 166, 167, 168, 169
X-ray analysis of protein molecules 50, 52, 53–5, 56–7, 64
“Protein Version of the Central Dogma, the” 18
Prx1 (gene) 140
puberty 118–19
purines 18, 102
pyrimidines 18, 102
Qafzeh cave site, Lower Galilee, Palestine 228, 234–5
Qiaomei Fu 273–4
quantum theory/mechanics 38, 39, 65, 67–8, 86
radiocarbon dating 208, 226–7, 228, 229, 231, 232
Ramsey, Margaret 48
Randall, John Turton 47, 50, 72–3, 74, 75, 84–5
recombinant DNA 294, 299
Reich, David 268, 269, 276
retrovirus 16, 101, 155
co-evolution and 158–9
constant change within human genome and 282, 301
endogenous (ERVs) 162–71, 173, 212, 222, 236, 282
epidemic, eastern Australia koala 161–2, 223
epigenetic silencing and 163
exogenous 162, 163, 223–4
human endogenous (HERVs) see human endogenous retroviruses (HERVs)
long terminal repeats (LTRs) and 164, 165, 169, 193, 195, 223
origins of Homo sapiens, distribution of used to locate 212, 222–4, 236, 288, 301
retroviral legacy role in holobiontic evolution of human genome 164–71, 173, 212, 222
RNA based genome 159
symbioses with host 159–62, 222, 223
viral env gene 164, 165, 166
viral loci 162, 163, 164, 165–7, 168, 169
Rhenen, Netherlands 264
Rich, Alex 96
Richard III, King 207–8
Ridley, Matt 97
Riss (Ice Age) 234
RNA (ribonucleic acid) 8
discovery of 17–18
epigenetics and 184, 185–96, 236, 247, 266, 291, 292, 294
GACU structural chemicals (guanine, adenine, cytosine, uracil) 17, 94, 95
lncRNAs (long non-coding RNAs) 191–3
mRNA (messenger RNA) 98, 131, 133, 134, 135, 159, 167, 186, 187, 188, 190, 191, 193
non-coding 173–4, 187–9, 191–6, 199–200, 236, 266
piRNAs (PIWI-interacting RNAs) 189
programmed cell death and 186–9
ribose and 94
ribosomal 187
“RNA gene,” idea of 188