Life's Greatest Secret

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Life's Greatest Secret Page 48

by Matthew Cobb


  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
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  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

 

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