Life's Greatest Secret
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of using metaphors 313
xeno-nucleic acids (XNAs) 275, 285
Darwin, Charles 138, 216, 260
data storage using DNA 271–2
Davidson, Eric 243
Davies, David 274
de Broglie, Louis 82
de Latil, Pierre 82
de Souza, Francis 236
de Valera, Éamon 11
de Vries, Hugo 3
deamination of cytosine 290
decibans 26
Delbrück, Max
George Gamow and 32–3, 113
at mathematical problems symposium 175
models of DNA replication 163–4, 227
Nobel Prize 215
phage course 151, 183
as ‘phage group’ member 60, 63, 65
reaction to Avery’s discoveries 63, 65–6
reaction to cybernetics 83
reaction to Matthaei’s discoveries 183, 186
reaction to the α-helix 95
reaction to What is life? 17–18
at Royaumont 203
Three-Man Paper contribution 5–6
virus studies 8
Watson letters to 97–8, 112
see also phage group; Three-Man Paper
Delbucco, Renato 252
Denisovans 241–2
‘derepression of repression’ 257
‘Determinism and free will’ according to Schrödinger 16
diamond code (Gamow) 114–16, 115f, 118, 120, 122
dideoxy sequencing 228
differentiation
epigenetic effects 256
regulator genes and 169, 171
directed mutation 283
DNA (deoxyribonucleic acid)
A, B, C and Z forms 98–101, 103–6, 273–4
advantages over RNA 290–1
assumed invariability 7, 43, 46, 94
coding on complementary strands 200, 212
crystal structure 100, 104–5
cytosine methylation 256–9
decisive X-ray work 96–106
defined 317
different names for 35n
direct action by repressors on 158–9
discovery, as nuclein 15
doubts over biological specificity 42, 47, 60, 64, 70, 106
early X-ray work 54, 91–4
electron micrographs 103
evidence of genes as composed of DNA 35, 43, 50, 56, 67, 93
first use of the abbreviation 56
genes duplication and 111
‘junk DNA’ 247–9, 299
mapping segments 248
model structures for 99, 103, 106–7, 107f
non-coding 141, 222, 232, 246
non-functional 262
numbering of sugars and strands 212
quantities in species and in germ cells 60, 69, 90
reading direction 200, 212–13
rejection of direct template role 121–2
support for genes as composed of 52, 56, 61–2, 91
synthetic DNA 267–8
transforming principle as 41, 46–7, 54–5
in viral reproduction 67–9
DNA → RNA → protein sequence 72, 116, 140, 251
DNA amplification 229–30, 233, 278
DNA fingerprinting 230–1
DNA polymerases 229–30
DNA replication models 163–4
DNA sequencing
of extinct species 240–1
models of 163–4
nanopore sequencing 236
next-generation sequencing 234–6
Sanger’s method 228
shotgun sequencing 232
see also genome sequencing
Dobzhansky, Theodosius 38–9
Dochez, Alphonse 36
dodder 271
dogs, relatedness 239, 239n
domains of life 238–9
Donohue, Jerry 106, 109
double helix
A, B, C and Z forms 98–101, 103–6, 273–4
discovery, representations of 90
error-correction mechanisms 290
gene duplication via 111–12
major and minor grooves 273
Stern’s DNA+protein helix 71
Watson and Crick’s final model 106–7, 107f
The Double Helix, by Jim Watson 105, 108
Doudna, Jennifer 283–4
Dounce, Alexander 72, 116, 140, 214
Drosophila
Beadle’s experiments on 9–10
codon bias in 294–5
Dscam gene 223
dunce gene 302
genetic engineering of 280
genome 231, 233
histone modification in 257
Morgan’s experiments on 4
nongenetic transmission of information 255
drug therapy and genomic variation 236–7
Dscam gene 223
Dubarle, Dominique 77
Dutch famine, 1944–45 257–8
E
E. coli
cell-free protein synthesis 177–9, 183–4, 191
control of pyrimidine synthesis 154
demonstration of colinearity 213
DNA replication studies 163–4
genetically recoding 284
transformation in 51–2, 56, 61, 63, 279
unnatural base pairing 213
Eck, Richard 200–1
Eddy, Sean 248
eggs, quantities of DNA in 60
electrochemical gradients 287
electron microscopy 66, 103
electrophoresis
in DNA fingerprinting 230–1
A and S forms of haemoglobin 126–7
in Sanger sequencing 228
Elias, Pete 147–8
embryogenesis 256, 258
ENCODE (Encyclopaedia of DNA Elements) project 247–8, 296
endonucleases, Cas9 282–3
enhancer regions 243
entropy
information and 27–8, 30, 75, 78
Maxwell’s Demon and 27–8, 30
‘negative entropy’ (negentropy) 12, 18, 75–6, 78, 202
environmental effects
inbred mouse behaviour 304
‘parity thesis’ 303
enzymes
defined 317
DNA functioning as 55
gene relation to 10–11, 87
inducible enzymes 153–7, 168–9, 175, 177, 307
RNA functioning as 288
superiority of proteins over RNA 291
Enzyme, Antigen and Virus: A Study of Macromolecular Pattern in Action, by Macfarlane Burnet 134–5, 139, 141, 146–7
Enzyme Cybernetics book project 159
Ephrussi, Boris
Drosophila experiments 9–10
spoof letter on cybernetics 87–8, 88f, 111, 159
on whether DNA encodes amino acids 124–6, 128
Ephrussi-Taylor, Harriett 62–3, 310
as Harriett Taylor 51, 55, 59, 69
epigenetic effects 256–9
equations, readers’ tolerance of 73–4, 77–8, 83
error-avoidance in genetic codes 293
error-correction mechanisms 290–1
Escherichia coli see E. coli
eukaryotes
acquisition of mitochondria 224
colinearity absent from 221–2
enhancer regions in 243
evolution of code variations 227
evolution of introns with 222–3
genetic information in 300–1
horizontal gene transfer 271
loss of domain status 238–9
mechanism of protein synthesis in xi
numbers of genomes sequenced 237
evolution
and the genetic code 214–15, 226–7, 239
insights from genome sequencing 235, 239–42
insights from proteins 140–1
The Major Transitions in Evolution (book) 299
palaeogenomics 240–1
rethinking the domains 238–9
>
role of epigenetics 261
Timetree database 239
‘Extrapolation, interpolation, and smoothing of stationary time series with engineering applications’ (Yellow Peril document) 24–5, 27, 30
eye colour in Drosophila 4, 9–10
F
Farzadfard, Fahim 272
FASEB (Federation of American Societies for Experimental Biology) meetings 177, 179–80
Feedback Mechanisms and Circular Causal Systems in Biology and the Social Sciences meeting 29
feedback systems
in acoustics, gunnery and biology 22–3
as circular causality 23, 29
neglected by Shannon 78
see also negative feedback
Feig, Larry 255
Festetics, Count Emmerich 2
Feynman, Dick 117
Fire, Andrew 283
Fischer, Emil 189n
Fisher, R(onald) A(ylmer) 77
Fox, George 238
Fraenkel-Conrat, Heinz 132, 174, 180–1
frame-shift mutations 223
Franklin, Rosalind
DNA helical structure 104–6
DNA images from 98–101, 103–6
reaction to double helix model 107–8
recruitment 95–6
relations with Wilkins 96, 98–9, 101, 107–8
Fraser, Bruce and Mary 94, 106
Freeland, Stephen 293
Freymann, Enriques 74, 77
funding of biological research 217, 312
Furberg, Sven 92, 94, 103
G
G-quadruplex DNA 274
β-galactosidase 152–3, 156, 158, 160, 165
game theory 28
Gamow, George
attempts to meet Watson and Crick 114, 116
character and influence 113–14, 117–18, 217
friendship with Delbrück 32, 113
genetic code contributions 113–24, 174, 213, 292
at Oak Ridge symposium 142–3, 146
physics of living matter conference 32, 113
Scientific American article 119
Garrod, Archibald 11
Gelsinger, Jessie 282
genes
acting as templates 72
alleged to be nucleoproteins 42–3, 91
assumed to be proteins 6–9, 49
coinage of the term 3
complementary replication of DNA 101, 109
control of protein synthesis 131
definitions of 161, 244
discovery of ‘split genes’ 221, 223, 243
as DNA 35, 50, 56, 61–2, 67, 93
horizontal gene transfer 270–1
identifying within DNA sequences 238
mapping chromosome locations 4–5
mutations affecting protein product 127–8
as nucleic acids 47, 91
as nucleic acids, opposition 43, 56, 70, 131–2
number of human protein-coding genes 242, 244
repression of activity 156–9, 257
Schrödinger’s view of 15–17, 80, 113, 170–1
self-reproducing automata as a model 32, 80
speculations on the nature of 5–8, 161–2, 216, 312
structural and regulator
distinguished 160, 168–70
unchanging character 12
viewed as information 112, 159, 168, 177, 300–4, 306–8
viruses, possible relationship to 8, 32
gene duplication 101, 109, 111–12
‘gene-enzyme relationship’
Kalmus on 87
‘one gene, one enzyme hypothesis’ 10–11, 160, 204, 244
von Neumann on 32
gene expression
determined within the genome 170
mRNA untranslated regions and 297
‘gene for’ something claims 302
gene silencing
epigenetic effects 256
heritable, in Arabidopsis 259
gene splicing (RNA splicing) 222–3, 300, 302
gene therapy 282–3
genetics
century of 3
conservatism of geneticists 63, 65
Shannon on gene spreading 25–6
genetic cancers 257
genetic code
absence from an RNA world 288
code within a code 296–7
Crick, on the general nature of 193, 197
Crick, on the origins of 292–3
CRISPR editing 282–5
degeneracy/redundancy idea 121, 193–4, 199, 208, 212–13, 301
first successes in reading 174, 181–2, 185
Gamow’s attempts to crack 113
information theory approach 143–6, 148
Ingram’s work on mutant haemoglobin and 128
last codon read 213
mathematical approaches 115–16, 143, 174–5, 201
non-canonical codes 224–6
nonsense codes 199
one-to-one correspondence 199
possibility of overlap 121–4, 193, 200
press coverage 174, 197
reductionist approach 227
Royaumont colloquium session 202–3
and Schrödinger’s code-script idea 19
as a scientific revolution 309–10
as strictly a cipher 110n
transcription factor binding and 296
whether a triplet code 116–17, 179, 192–4, 201, 205–6, 209
whether universal 174, 195, 204, 209, 224–6
see also coding problem; protein synthesis
‘genetic constitution of man’ 84
genetic diseases
alkaptonuria 11
directed mutation and 283
genetic cancers 257
Huntington’s disease 231, 304
sickle-cell anaemia 126–7, 132, 165, 304
genetic drift 226, 262
genetic engineering 269, 271, 279–81
genetic fingerprinting 230–1
genetic fossils 244
genetic manipulation, foreseen 171
‘genetical information’
carried by nucleic acid bases 111, 297
copying between DNA and XNA 275
specifying protein amino acid sequences 129, 132
genetically modified (GM) organisms
genetically recoding 284
plants 269–71
Genetics and the Origin of Species, by Dobzhansky 38
genomes
determining gene expression 170
size of human 232, 234
size of mitochondrial 224–5
size variations 237, 246
genome sequencing
annotation problem 238
automation 310
costs 235
data volumes 237, 272
first genomes sequenced 229
100,000 genomes project 236
insights into evolution 235, 240–1
see also DNA sequencing; human genomes
genomics 238
genomic imprinting 248
genomic recording 272
George, Frank 147
germ line
discovery 3, 260
gene therapy 282
removal of methylation 257
Gilbert, Wally 221–2, 228, 279, 310
Glass, Bentley 131
Gleick, James 84
goats expressing spider silk 269
Godfrey-Smith, Peter 301
Golomb, Solomon 175, 202
Gosling, Raymond 93–4, 96–7, 99, 103–5
Griffith, Fred 36–9, 44
Griffith, J. S. 178
Gros, François 177–8, 204
Grunberg-Manago, Marianne 210, 310
guanine see purines
Gulland, Masson
on DNA variability 54, 62, 64
on hydrogen bonding in DNA 58, 92, 106
H
H-bomb 86
haemoglobin
crystal structure 105
A and S forms 126–9
Haldane, J. B. S. 7, 17, 74, 80–1, 84, 86
Hapsburg lip 12
Hartley, Ralph 27
Harvey, William 2
Hawking, Stephen 73
Heaton, Norma 210, 310
helical structures
the α-helix 95, 97, 100, 105
DNA as 58, 70–1, 94, 99–101, 104–5
triple helix models 99–100, 104, 106
X-ray signature of 102, 106
see also double helix
Heppel, Leon 176, 180
herbicides and GM crops 270
heredity
concept of the gene 3
genetic code and views of 312
inheritance of acquired characteristics 138, 260
patterns of, in humans 2
Schrödinger’s code-script and 13
see also genes
Herriott, Roger 66–7
Hershey, Al 60, 65–70, 215
Hertwig, Oscar 3
Hinshelwood, Sir Cyril 71–2, 114, 214
hippo 239
Hiroshima 18, 28–9, 75, 86, 89, 151
histones, epigenetic marks 257
Hitler, Adolph
Mrs Norbert Wiener and 21
Schrödinger and 11
Hoagland, Mahlon 134–5
Holliger, Philipp 274–5
Homo floresiensis 242n
horizontal gene transfer 270–1, 284
Hotchkiss, Rollin 38, 59–60, 65, 68, 197
RNA world hypothesis 289
human beings
On the human use of …, by Norbert Wiener 83, 268
information content 84
number of anticodons 211
patterns of heredity 2
human brain, computer parallels 30–1
Human Genome Project 231–2
human genomes
base pair frequency 295
ENCODE project 247–8, 296
evolutionary insights 239–42
information content 85
mass sequencing 236
number of protein-encoding genes 242, 244
proportion of transposons 245
variability of 234
100,000 genomes project 236
Huntington’s disease 231, 304
Hurst, Laurence 293
Hurwitz, Jerry 183, 187–8
Hutchinson, G. Evelyn 29
hydrogen bomb 86
hydrogen bonding between DNA bases 58, 92, 101, 106
hydrophobicity and codon structure 292
hydrothermal vents 287
I
Illumina Inc. 236
immune response
codon variants 225
Neanderthal genes and 241
to pneumococci 35
RNA incorporation idea 140
inducible enzymes 153–7
information
absent from Schrödinger’s views 19
bits as units 27, 144
communication as variable information 25
content of living things and genomes 84–5, 148, 298
Crick and Burnet on possible transfers 135, 138–40
entropy and 27–8, 30, 75, 151
evolutionary, from protein comparisons 140–1
‘genetical information’ carried by DNA bases 111, 132
human conversation example 144–5