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The Tangled Tree

Page 51

by David Quammen


  On the Origin of Species (Darwin), 25, 29, 31, 32–33, 114, 165, 166, 171, 173, 184, 202, 345

  opossums, 339

  organelles, 115–16, 124

  Origin of Eukaryotic Cells (Margulis), 123, 136, 139, 148, 273

  Origins of Order, The (Kauffman), 331

  Origins of Sex (Margulis and Sagan), 158

  Osborn, Henry Fairfield, 185

  Owen, Richard, 187

  oxygen, 40–41, 52, 78, 88, 95, 101, 116, 131

  P-32 (radioactive phosphorus), 63, 67–68, 78, 93, 105, 140, 144, 196

  Pääbo, Svante, 382, 384

  Pace, Bernadette, 320

  Pace, John K., II, 339, 340, 341–42

  Pace, Norman R., 137, 138, 319–23, 324, 327, 366, 368, 376, 386

  palindrome, 359–60

  Panama-Pacific International Exposition, 272

  Panisset, Maurice, 252, 253, 255

  parasites, 341

  parthenogenesis, 258–59, 261

  Pasteur, Louis, 72, 73

  patterns, 328

  Pauling, Linus, xiv, 60

  on chemical paleogenetics, 42–45, 56, 113, 344

  penicillin, 228, 232, 242, 244

  Pennisi, Elizabeth, 276–77, 281, 282

  peptides, 300

  peptidoglycan, 76

  absent in certain methanogens, 104

  periodontitis, 318

  Petri, Julius, 252

  phenol, 68

  Philosophie Zoologique (Lamarck), 18, 20

  phosphorus, radioactive (P-32), 63, 67–68, 78, 93, 105, 140, 144, 196

  photosynthesis, 88, 116, 126, 128–29, 158

  phyla, 375

  “Phylogenetic Classification and the Universal Tree” (Doolittle), 283–86, 287

  phylogenetics, 175, 177, 192, 204–7, 206, 210

  phylogenomics, 332–33

  “Phylogeny of Procaryotes” (Fox et al.), 198–201, 201, 220

  Pictet, François Jules, 34

  pigs, 232

  Piper, Debra, 334, 378–79, 384–85, 386

  pistola, Volta’s, 90

  placenta, 357

  placental tissue, 352, 354–56

  placozoans, 192

  Plant and Its Life, The (Schleiden), 167

  plant-animal hybrids, 158

  plants, 92, 188, 189, 190, 193, 212

  HGT and, 255, 294

  Linnaeus’s classification of, 15–16

  plasmids, 238, 245, 249, 255–56, 363

  Plaut, Walter, 118, 119–20, 121

  plesiosaurs, 33

  Plutarch, 308

  pneumococcus, 216–18, 219, 222, 223

  Pneumococcus pneumoniae, 226, 252

  pneumonia, 87

  Poland, 232

  Pollard, Ernest, 329

  pollen, 114, 119

  polyphyletic taxa, 192–93

  Poor Laws, 27

  population growth, 26–27, 28, 29

  Porton Down, 240–47, 275

  Portuguese man-o’-war, 383

  Prigogine, Ilya, 330–31

  Principles of Geology (Lyell), 23–24

  Proceedings of the National Academy of Sciences (PNAS), 94–95, 99, 101, 144–45, 157

  Prochlorococcus, 88

  Prochlorococcus marinus, 86

  progenote, 205–7, 206, 300

  prokaryotes, 78

  category declared meaningless, 200, 287, 290

  eukaryotes vs., 50–51, 75–76, 77, 115, 139

  Woese and Kandler’s desire to get rid of term, 211

  proteins, x, 44, 47, 220

  DNA translated into, 38–39, 41, 47–48, 51–52

  and evolution of prokaryotes, 51

  “fingerprinting” of, 43, 56

  formed from amino acids, 38–39, 47, 53, 57, 100, 220, 281, 300

  individual trees for, 281

  ratchet model of production of, 97, 100

  in Reciprocating Ratchet Mechanism, 100

  in ribosomes, 54, 60

  RNA converted to, 53–55, 54

  sequencing of, 40–41, 51, 55

  protein taxonomy, 40–41, 46, 306, 344

  see also molecular phylogenetics

  Protista, 179, 187, 189, 190, 193

  argument over definition of, 191–92

  protists, 92, 190

  protozoans, 192

  Pseudomonas, 263–64

  Public Health England, 240, 241, 242

  quince, 272

  rabbits, 355

  radical transformation, xi, xiii, 13, 72–73

  radiolaria, 165, 166, 168, 171–72, 179

  Reciprocating Ratchet Mechanism, 100

  recombination, 227, 258

  red alga, 142

  reefs, 7–8

  reproduction, 5, 26

  reticulate evolution, 255

  retroviruses, 351–56, 357–58, 382

  R factor (resistance transfer factor), 235, 239, 245

  rheas, 6

  rheumatic fever, 88

  Rhodnius prolixus, 341

  ribosomal RNA (rRNA), 58, 59, 148, 153, 321, 368

  Doolittle’s work on transcription from DNA, 137, 138, 142, 153

  Fox’s extraction of, 98, 196

  Luehrsen’s extraction of, 67–68, 78–79, 105

  in mitochondria, 149, 150

  Woese’s reading of, 54–55, 60–65, 78–80, 82, 88–89, 90, 93, 153–54, 195, 196, 202–3, 205, 206, 276, 283–84, 298, 318, 322–23

  Ribosomes (book), 368

  ribosomes, 52–55, 54, 368

  evolution of, 206

  ratchet model by, 97, 100

  RNA maturation in production of, 138

  structure of, 203, 281

  universal utility of, 205

  Richards, Robert J., 167, 170, 174, 175, 177

  Ridley, Matt, 40, 52

  Ripley, Robert, 272

  Ris, Hans, 118, 119–20, 121, 133

  RNA, x, 40

  alphabet of, 61

  catalogs of, 64–65, 78, 92, 94, 106, 136, 140, 142, 149–50, 195, 196, 203, 371

  converted to proteins, 53–55, 54

  and evolution of prokaryotes, 51

  fingerprinting of, 59, 60, 69, 82, 83, 90

  messenger, 52, 54, 108

  recognition of role of, 47

  replication of, 320

  ribosomal, see ribosomal RNA

  sequencing of, 51, 55, 56, 57, 59, 63, 143, 274

  structural, 53–55

  transfer, see transfer RNA (tRNA)

  viral, 57

  in vitro replication of, 143

  RNA Biology, 370

  RNA maturation, 137, 138

  RNA polymerase, 108

  RNA Tie Club, 47

  RNA-world, 300–301, 331, 368

  Roberts, Jodie, 241–43, 246

  Rockefeller Institute, 220, 222, 230

  Rocky Mountain spotted fever, 155

  Romer, Alfred S., 186

  Rose, Michael, 303

  rotifers, 256–59

  Royal Society, 317–18

  rumen fluid, 93

  Russell, Bertrand, 43

  Russell, Julie, 241, 247

  Russian Academy of Natural Sciences, 159

  Rutherford, Ernest, 329

  Sagan, Carl, 114, 117–18, 120, 121–22

  Sagan, Dorion, 118, 120

  Sagan, Jeremy, 120

  Sagan, Lynn see Margulis, Lynn

  St. Hilaire, Geoffroy, 18

  Salmonella, 248

  Salmonella typhimurium, 228

  Salzberg, Steven L., 266–67, 336

  Sanger, Frederick, xiv, 55, 60, 137, 345

  background of, 56–57

  bovine insulin amino acids sequenced by, 51, 57

  DNA sequenced by, 154

  and sequencing of RNA, 56, 57, 59, 63, 143

  Sapp, Jan, 48, 107, 125, 127, 129, 130, 204, 288, 386

  proposed book with Woese, 346–47, 348, 349

  scale of natural being, 11–12, 19–20, 19

  scarlet fever, 87


  Schiller, Friedrich, 167, 168

  Schimper, Andreas, 126–27

  Schleicher, August, 177

  Schleiden, Matthias, 167

  Science, 48, 189, 256, 262, 267, 275, 276, 282–83, 285, 288, 303, 307, 359, 370

  Scientific American, 208, 288, 289, 308

  sea urchins, 256

  Sedgwick, Adam, 34

  Selfish Gene, The (Dawkins), 305, 340

  self-organization, 331

  September 11, 2001, terrorist attacks of, 156, 159

  serotype 2A, 244

  Sethe, Anna, 168–69, 170, 174–75, 176

  sex, 227, 229–30, 258

  invention of, 134–35

  Shigella dysenteriae, 233–34, 235, 252

  Shigella flexneri, 243–44, 246

  Ship of Theseus problem, 308

  sickle cell anemia, 42, 43

  sinus infections, 87

  16S rRNA, 137, 200

  complete sequence of, 145–46

  as molecular clock, 61, 63, 64, 67, 78, 79, 83, 92, 103, 145, 154, 195, 205, 212, 274, 281, 287–88, 306, 318, 321, 324, 325, 327, 331, 375

  skin bacteria, 326

  skin infections, 87

  Sneath, Peter, 249–50

  Society for Evolutionary Protistology, 192

  Society for Experimental Biology, 40

  Society of German Natural Scientists, 172

  Sogin, Mitchell, 57–59, 97, 140, 144, 210

  ribosomal RNA read by, 62–63, 64

  RNA fingerprinting by, 59, 60, 320–21

  talent for lab work of, 58–59, 60, 68

  Solomon Islands, 244–45

  Sonea, Sorin, 252, 253, 255, 284, 383

  special-creation hypothesis, 4, 5, 13, 18, 24–25

  species:

  assumed stability of, 4, 5, 13, 18, 24–25, 251

  of bacteria, 72, 330

  blurring of concept of, 251, 252, 330, 380, 381

  sperm, 114, 119, 151, 260, 261

  Spiegelman, Sol, 57, 58–59, 143, 144, 319

  Spiegelman, Will, 144

  spinach, 152

  spirochetes, 87, 134–35, 136, 151, 160

  sponges, 192

  spontaneous generation, 19, 73

  spore germination, 58, 73

  Stammbaum, 173

  Stammbaum der Organismen, 178–79, 184

  Stammbaum der Säugethiere, 178

  Stammbaum der Wirbelthiere, 178

  Stanier, Roger, 75, 76, 77, 85, 102, 109, 115, 138, 139, 189, 190, 210

  Staphylococcus, 87–88, 232, 245

  Staphylococcus aureus, xi, 87–88

  methicillin-resistant, xi, 88, 232, 245

  vancomycin-resistant, 245–46

  Stetter, Karl, 107–8

  Stettiner Zeitung, 173

  strep throat, 87

  Streptococcus, 88

  Streptococcus pneumoniae, 216, 242

  structural RNA, 53–55

  structural transition, 328

  Subglacial Lake Whillans, 85–86

  sulfa drugs, 222–23, 233–34

  Sulfolobus, 104

  sulfur, 86, 87, 88

  superorganism, 253–54, 383

  symbiogenesis, 126–28, 130, 132, 133, 273, 312

  see also endosymbiosis

  symbionticism, 132–33

  see also endosymbiosis

  symbiosis:

  as alleged origin of species, 158, 202

  origin of term, 126

  see also endosymbiosis

  Symbiosis in Cell Evolution (Margulis), 136

  Symbioticism and the Origin of Species (Wallin), 132–33

  syncytin, 354–56, 357–58

  syncytin-2, 354, 356, 382

  syncytin-Opo1, 355

  syncytiotrophoblast, 354

  syphilis, 87, 134, 302, 318

  Systema Naturae (Linnaeus), 15, 74

  Takano, 236

  Tatum, Art, 369, 370

  Tatum, Edward L., 227–28

  tenrec, 339–40

  tetracycline, 238

  thermoacidophiles, 109

  thermophiles, 86

  Thermoplasma, 104

  Thermus aquaticus, 86, 321–22

  Thiomargarita namibiensis, 86–87

  Thomas, Lewis, 161

  Thompson, Jerry, 365–66

  Thompson, William, Lord Kelvin, 329

  tortoises, 5–6

  Tournefort, Joseph Pitton de, 16

  “Towards a Natural System of Organisms” (Woese and Kandler), 209–12

  toxic shock syndrome, 87

  transduction, 227, 229, 230

  and antibiotic-resistant bacteria, 231, 235

  transfer RNA (tRNA), 148

  transformation, 230

  Avery’s work on, 222, 223, 224–25, 284, 344

  DNA and, 224–25

  gradual see evolution

  of pneumococcus, 216–18, 219, 222, 223

  radical, xi, xiii, 13, 72–73

  see also horizontal gene transfer (HGT)

  transforming principle, 222

  translation apparatus, 52, 53

  transposable elements, 336–42

  “Tree of Life, The” (blog), 267

  “Tree of One Percent, The” (Martin), 297–98

  tree(s) of life:

  bacteria mischaracterized on, 73, 308–9

  as beyond Darwinian theory, 346

  “big tree,” 195–97, 198–201, 201, 202, 205, 208, 274, 298, 334

  Brown’s work on, 279

  changing meaning of, 17, 19–20

  complicated by HGT, 250, 256, 272, 279, 284, 288, 297–301, 299, 306, 327–28, 380

  controversy over image of, 307–8

  Darwin’s conception of, 6, 7, 8–9, 8, 25, 32–34, 33, 256, 303, 305, 308, 309

  Doolittle’s correction of, xv, 284–86, 285

  Fox’s drawing of, 94

  of Haeckel, 166, 172–73, 175, 177–79, 180, 181, 182, 183, 184, 186, 205, 210

  Hitchcock’s, 21–22, 23, 24–25, 32

  Lamarck’s, 19–20, 19

  Margulis’s, of eukaryotes, 141, 162, 273

  Martin’s recognition of complexity of, 297–98, 299, 302

  Merezhkowsky’s, 273

  methanogens on, 71

  of mid-20th-century paleontologists and biologists, 185

  of mitochondria and bacteria, 155

  New Scientist’s take on, 302–4, 305

  origin and history of idea of, 10–11, 12–14

  of proteins, 281

  16S rRNA’s importance in, 61

  of Whittaker, 189–90, 190, 205

  Woese and Kandler’s paper on archaea in, 208, 209–12, 211, 283-84

  Woese’s quest for a universal, 48-49

  in Zuckerkandl and Pauling’s paper, 44–45

  see also ladder of life

  Treponema pallidum, 302, 318

  treponemes, 318

  trilobites, 33

  tumors, 263, 352

  typhoid, 248

  typhus, 155

  ulcerative colitis, 316

  ulcers, 264

  Ultra-Low Temperature Storage Facility (ULTSF), 241

  undulipodia, 135, 136, 160, 162, 273

  United Press International, 101

  United States, 108, 232, 245

  universal phylogenetic tree, 274, 298–301, 327–28

  “Uprooting the Tree of Life” (Doolittle), xv

  Urbana, Ill., xii, xiii, 46, 50, 57, 90, 93, 96–97, 101, 103, 139–40, 143–44, 146, 187, 194–96, 210, 334–35

  vaccination, 363

  vagina, 326

  vanA, 245, 246

  vancomycin, 245–46

  vancomycin-resistant Staphylococcus aureus (VRSA), 245–46

  van Niel, C. B., 75, 76, 77, 85, 102, 109, 189

  variation, 26, 28, 29, 91, 92, 158, 258

  Varsol, 64, 140, 142

  Venter, J. Craig, 260–61, 274–76, 282, 336, 344

  Vertebrate Paleontology (Romer), 186

  Vetsigian, Kali
n, 329, 330

  Vietnam, 232

  viral RNA, 57

  viruses, 229, 363

  in humans, 317

  selfish DNA carried by, 341, 349

  vitamins, 104

  volcanism, 24

  Volta, Alessandro, 90

  von Humboldt, Alexander, 12, 167

  Vossbrinck, Carl, 370–73

  Wallace, Alfred Russel, 29–30, 181, 305, 345, 380

  Wallin, Ivan E., 118, 121, 131–33, 136, 202, 293

  Washington Post, 95, 101, 262, 375–76

  Watanabe, Tsutomu, xiv, 231, 234–35, 236, 237–38, 243, 245, 249, 252

  Watson, James, 39, 109, 344

  DNA structure discovered by, 37, 38, 39, 344

  waxes, 104

  Wedgwood, Caroline, 169

  Wedgwood, Josiah, III, 169

  Weismann, August, xiv, 117, 260

  Weismann barrier, 260

  Welles, Orson, 365

  wheat, 148, 149–50, 151

  Wheelis, Mark L., 210–11, 274, 280

  white blood cells, 357, 364

  Whitehead Institute for Biomedical Research, 266

  Whittaker, Robert H., 186–90, 190, 194, 210

  in dispute over definition of Protista, 191–92

  on polyphyletic taxa, 192–93, 205

  whole-genome shotgun sequencing, 274–75

  Williamson, Donald I., 157

  Wilson, E. B., 121, 124

  Wilson, Edward O., 159, 161, 343

  Woese, Carl, xv, xvi, 46–47, 69, 79-80, 83-84, 104, 108, 136, 139, 140, 142, 144–45, 147, 148, 193, 276–77, 280, 318, 319, 375

  at archaea workshop, 108–10, 209

  attempt to reconcile HGT and universal phylogenetic tree, 298–301, 327–28

  bacteria classified by, 74–75, 77, 78–79, 83

  “big tree” of, 195–97, 198–201, 201, 202, 205, 208, 274, 298, 334

  complex dynamic systems studied by, 328–29

  discovery of archaea announced by, xii–xiii, 94–95, 98, 99–102, 194, 327, 366

  disdain for Darwin, 331, 335, 345–48, 366, 370, 373

  Doolittle aided by, 139–40, 143, 144–46, 288

  Doolittle’s break in friendship with, 287–89

  and evolution of genetic code, 46–49, 329–30

  and evolution of prokaryotes, 50, 51, 57

  and exobiology, 99, 120

  files of, 81

  Fox offered job by, 97

  Fox’s dispute with, 198–200

  Gold’s friendship with, 367–68, 370

  gruffness of, 332, 335, 343, 345, 347, 367

  halophiles fingerprinted by, 105–6, 107–8

  on holistic problems of evolution, 344–45

  honors and awards received by, 343–44

  illness and death of, 65, 365, 374, 377–79, 385–86

  invited to Germany, 108

  and Lake’s naming of eocytes, 203–4

  lipids studied by, 104, 105

  Luehrsen mentored by, 66–67

  Margulis criticized by, 114, 161–62

  memorial symposium for, 96

  on methanogens not being bacteria, 89, 90

  methanogens classified by, 88–89, 92–95, 107

 

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