The Tangled Tree

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The Tangled Tree Page 49

by David Quammen


  Zinder, Norton D., and Joshua Lederberg. 1952. “Genetic Exchange in Salmonella.” Journal of Bacteriology 64 (5).

  Zuckerkandl, Emile, and Linus Pauling. 1965a. “Evolutionary Divergence and Convergence in Proteins.” In Evolving Genes and Proteins: A Symposium.” Edited by Vernon Bryson and Henry J. Vogel. New York: Academic Press.

  ____. 1965b. “Molecules as Documents of Evolutionary History.” Journal of Theoretical Biology 8 (2).

  Index

  A note about the index: The pages referenced in this index refer to the page numbers in the print edition. Clicking on a page number will take you to the ebook location that corresponds to the beginning of that page in the print edition. For a comprehensive list of locations of any word or phrase, use your reading system’s search function.

  Page numbers in italics refer to illustrations.

  Academic Press, 123

  Acinetobacter, 263

  Acinetobacter baumannii, 88

  acne, 87

  acrylamide, 63, 68

  adaptation, 176

  adenosine triphosphate (ATP), 116, 131, 148

  aerobic bacteria, 116

  Africa, 127

  Agassiz, Louis, 34

  Agrobacterium tumefaciens, 154–55

  AIDS, 156, 159, 237, 352

  Alexander, Leone, 117

  Alexander, Morris, 117

  algae, 75–76, 192

  chloroplasts of, 118, 119

  Alliance for the Prudent Use of Antibiotics (APUA), 237, 238

  Allmers, Hermann, 169–70

  Alm, Eric J., 325–26, 327

  alpha-proteobacteria, 155

  Alu, 338

  American Academy of Arts and Sciences, 159

  American Society for Microbiology, 237

  amino acids:

  proteins formed by, 38–39, 47, 53, 57, 100, 220, 281, 300

  in Reciprocating Ratchet Mechanism, 100

  ammonites, 33

  amobae, 76, 179

  amphibians, 182

  Anacystis nidulans, 154

  Anderson, Ephraim S., 248–49, 255

  animals, 92, 188, 189, 190, 193, 212

  HGT in, 255, 257–59, 261–64

  Linnaeus’s classification of, 15

  Antarctica, 85–86

  anthrax, 87

  Antibiotic Paradox, The (Levy), 238–39

  antibiotic-resistant bacteria, 238, 249, 264, 325

  from before antibiotics, 244–45

  HGT and, xi, 88, 231–35, 236, 239, 245–46, 247

  plasmids and, 238, 245, 249

  antibiotics, 88, 216, 222–23

  antibodies, 364

  antimicrobials, 232

  antiserum therapy, 216

  Apologetics Press, 305

  arbre botanique, 13, 14

  archaea, 92, 105, 194–95, 200, 287, 309

  cell walls of, 208

  concept of “species” in, 251, 381

  discovery and identification of, x, xi, xii–xiii, 94–95, 98, 99–102, 194, 327

  eocytes’ relation to, 203

  German workshop on, 108–10, 209

  halophiles classified as, 106

  HGT as rampant phenomenon among, 284, 294, 297–98

  in humans, 317

  importance of, xiv

  molecular phylogenetics of, 279

  naming of, 209–12

  novel lineages, 311

  and origin of eukaryotes, 375–76

  in popular press, 100–101

  resistance to idea of, 101–2, 103

  sequencing of, 275–76, 280–81, 282

  Woese and Kandler’s paper on, 208, 209–12

  Archives Research Center, 81–82

  Aristotle, 10–11, 13, 179, 182, 283, 380

  aspen trees, 383–84

  asthma, 316

  At Home in the Universe (Kauffman), 331

  Atkin, Isobel, 240–41, 242

  atmosphere, 95

  Augier, Augustin, xiv, 13, 14, 16

  Avery, Oswald, xiii, xvi, 220, 242

  background of, 221–22

  transformation work of, 222, 223, 224, 284, 344

  Avery, Roy, 224

  bacillary dysentery, 232

  bacilli, 87

  Bacillus anthracis, 251–52

  Bacillus infernus, 85–86

  Bacillus subtilis, 252

  bacteria, 68, 73, 92, 105, 179, 192, 195, 200, 212, 231, 287, 308

  aggregation of, 87–88

  Alm’s sequencing of, 325–26, 327

  antibiotic-resistant see antibiotic-resistant bacteria

  cladistics and, 249–50

  classification of, 48–49, 61–65, 72–73, 74–77, 78–79, 83, 87, 249–50, 251–54

  concept of “species” in, 251, 252, 330, 381

  considered plants, 73

  diversity of, 85

  evolution of, 50

  films formed by, 88

  gene sequences of, 240, 276, 280–81, 293

  HGT as rampant phenomenon among, 284, 294, 297–98

  horizontal gene transfer among, see horizontal gene transfer (HGT)

  in humans, 315, 316–17

  and idea of individuality, 330–31, 380, 382–83

  lack of nuclei in, 190

  lactic acid, 88

  as large portion of microbes, 71

  lithotrophic, 88

  location of, 85–86

  molecular phylogenetics of, 279

  ribosomes in, 53

  shapes of, 48, 86–87, 88

  size of, 86–87

  small genome of, 252–53

  as superorganism, 253–54, 383

  taxonomy of, 197

  total mass of, 86

  transformation of, xiii

  transposable elements in, 338

  bacterial spores, 58

  bacterial taxonomy, 71–72

  Bacteroides thetaiotaomicron, 316

  Baker, Chet, 368

  Baker, Kate S., 244, 246

  Balch, Bill, 324

  at archaea workshop, 108–10

  methanogen growing technique of, 78, 83, 84, 93

  molecular papers coauthored by, 93–95, 103

  Bapteste, Eric, 304

  bdelloids, 257–59

  Beagle, HMS, 3–4, 7, 24, 30, 167, 341

  Bergey, David Hendricks, 74

  Bergey’s Manual of Determinative Bacteriology, 74, 75, 109

  Beyond God and Darwin (Woese and Sapp), 346–47

  Bible, 10, 13, 24

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

  biochemical signaling, 104

  biofilms, 88

  biogenetic law, 177, 184

  bioinformatics, 98, 263, 266–67

  “Biology’s Next Revolution” (Goldenfeld and Woese), 330–31, 383

  biophysics, 196

  Bishop, David, 57, 59, 143–44

  blepharitis, 87

  blood infections, 87

  blue-green algae see cyanobacteria

  Blyth, Edward, 345

  Bonen, Linda, 64–65, 66, 93, 139–40, 142, 144–45, 147, 150, 160, 288

  big tree paper coauthored by, 198

  mitochondrial endosymbiosis confirmed by, 147–48, 149

  Bonnet, Charles, 11, 12, 182

  Borneo, 245

  bovine insulin, 51, 57

  Bowler, Peter J., 184

  Brazil, 232

  Brenner, Sydney, 40

  ribosome’s function discovered by, 52–53

  brewer’s yeast, 256, 275

  Brock, Thomas, 86, 104, 321–22

  Bronn, Heinrich Georg, 177, 178

  Broughton-Alcock, William, 243–44, 246

  Brown, James R., 279, 280–81

  butterflies, 157

  Cable, Ernest, 243–44, 246–47

  Cameroon, 127

  Canada, 108

  cancer, 263–64, 316

  caused by retroviruses, 352

  experiments on, 367

  Cancer Genome Atlas, 263 />
  “Can Genes Jump Between Eukaryotic Species,” 256

  carbohydrates, 38, 220

  Carl XVI Gustav, King, 343

  Carl R. Woese Institute for Genomic Biology, 96, 386

  Carl Woese Papers, 81–82, 347

  catastrophism, 24

  caterpillars, 157

  cattle, 232

  Cavendish Laboratory, 329

  celiac disease, 316

  Cell in Development and Heredity, The, 121

  cells, origin of, 300

  cell-to-cell fusion, 355

  cellular slime mold, 383

  cell walls, 103–5, 300–301

  of archaea, 208

  Centers for Disease Control and Prevention, U.S., 246

  centrioles, 116, 133–34, 135, 136

  Chadwick, James, 329

  Chagas disease, 341–42

  chaos, 74, 330–31

  Chardin, Pierre Teilhard de, 191, 193

  Charpentier, Emmanuelle, 364

  chemical paleogenetics, 42–43, 44–45, 46, 93, 113, 344

  see also molecular phylogenetics

  Chicago Tribune, 101

  chicken, 232

  chimpanzees, 382

  China, 232

  China, William Edward, 185

  chloroform, 68

  chloroplasts, 118, 190

  coining of term, 127

  DNA in, 118–19, 121

  Doolittle and Bonen’s work on origins of, 140, 142, 144–45

  in endosymbiosis, 116, 119, 121, 144–45, 147, 151, 153, 158, 200, 273, 284, 293

  genome of, 152, 293–94

  Merezhkowsky’s belief in symbiogenesis of, 126, 127–28, 130, 133, 273

  cholera, 87

  cholesterol, 104

  chromosomes, 219, 220

  in nucleus, 119

  cilia, 133–34, 135, 257

  ciliates, 179

  Citizen Kane (film), 365–66

  cladistics, 249–50

  Clark, Michael, 261, 262

  Clemens, Frederic, 187

  Clinton, Bill, 159, 161, 343

  Clostridium difficile, 316–17

  Clostridium perfringens, 68

  clown fish, 126

  Cohn, Ferdinand Julius, xiv, 109, 249

  bacteria classified by, 72–73, 74, 75, 87, 102, 251, 252

  Collins, Francis, 266

  comparative genome studies, 332, 333

  complex dynamic systems, 328–29

  complexity theory, 330–31, 384

  compound 05865, 245

  “Concept of a Bacterium, The” (Stanier and van Niel), 76, 77

  congenital defects, 360

  conjugation, 226, 227, 228, 229, 230

  and drug-resistant bacteria, 231, 234, 235

  convergence, 191

  by endosymbiosis, 193

  Copeland, Herbert F., 185–86, 187–88, 189, 210

  coral, 7–8

  cows, 93

  Coyne, Jerry, 304–5, 307

  creationism, creationists, 305, 306, 346

  Crick, Francis, xiv, 44, 59, 100, 109, 137, 345

  DNA discovered by, 37, 38, 39, 344

  and evolution of prokaryotes, 50, 51, 57

  measuring genealogical relationships by, 37, 40–41, 197, 220, 306, 344

  Nobel received by, 344

  on origin and deciphering of genetic code, 39–41, 47, 320, 329

  and reading of ribosomal RNA, 54–55

  and translation of DNA into proteins, 40–41, 51–52, 53, 54

  CRISPR, 359–64

  Crohn’s disease, 316

  crustaceans, 261

  crystal growth, 328

  Cunningham, Scott, 149–50

  Current Biology, 345

  cyanobacteria (blue-green algae), 76, 88, 116, 119, 137–39, 145, 151, 153, 154, 192

  cyanophytes, 127

  cytochrome c, 51

  cytoplasm, 118–19, 127, 142

  cytoplasmic inheritance, 119, 120–21

  Dairy Science, Department of, 93

  Darwin, Charles, 3–6, 77, 91, 117, 123, 132, 158, 167, 169, 253, 259, 291, 312, 381, 384-85

  Beagle journey of, 3–4, 7, 24, 30, 167, 341

  Die Radiolarien read by, 165–66

  first inkling of evolution of, 5–6, 26

  on heredity, 219

  natural selection formulated by, 27–28, 29, 30–31, 132–33, 172, 174, 176, 181, 202, 303, 383

  notebooks of, 3, 5–6, 7, 8, 26, 27, 28, 29, 33, 308, 341

  tree of life conception of, 6, 7, 8–9, 8, 25, 32–34, 33, 48, 256, 303, 305, 308, 309

  Wallace’s manuscript sent to, 30–31

  Woese’s disdain for, 331, 335, 345–48, 366, 370, 373

  Darwin, Emma Wedgwood, 169

  Darwin, Erasmus (brother), 4, 5

  Darwin, Erasmus (grandfather), 5, 181, 346

  Darwin, Robert, 4–5

  Darwin Conspiracy, The (Davies), 346

  Darwinian Threshold, 301, 306, 329, 384

  Darwin’s Dangerous Idea (Dennett), 302

  Darwin’s Playground, 335

  Davies, Roy, 346

  Dawkins, Richard, 161, 305, 307, 340

  de Bary, Anton, 126

  Deepwater Horizon oil spill, 88

  Delbrück, Max, 109

  delta H, 79–80, 82, 83–84, 89, 93

  Dennett, Daniel, 304–5, 307

  diabetes, 316

  diatoms, 126, 179

  Die Radiolarien (Haeckel), 165–66, 172

  Dioscorides, 13–14

  Discover, 158

  DNA, x, 44

  alphabet of, 37

  in chloroplasts, 118–19, 121

  discovery of, 37, 38, 39, 344

  and evolution of prokaryotes, 51

  HGT and, 261–62, 264

  junk, 336–42

  Sanger’s sequencing of, 154

  sequencing of, 51, 55, 154, 262, 274

  structure of, 220–21

  and transforming principle, 224–25

  as transforming principle of bacteria, xiii

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

  Woese’s study of, 51–52

  DNA fibrils, 119

  dogs, 294–95

  domains, see kingdoms

  Doolittle, Ford, xv–xvi, 143, 144–46, 149, 282-84, 292, 303, 305, 319

  at archaea conference, 108

  belief in “net of life” of, 280

  cyanobacteria work of, 137–39, 145

  endosymbiosis work of, 137, 139–40, 142, 144–45, 153, 283–84

  on genome sequencing of bacteria, 276, 293

  Margulis praised by, 160

  paper on importance of HGT coauthored by, 3–7, 289–91, 297

  philosophical musings of, xv, 307–8, 311

  protein trees constructed by, 281

  skeptical of HGT’s role in history of life, 278–79

  superorganism idea criticized by, 253

  on surplus DNA, 340

  tree of life updated by, 284–86, 285

  Woese’s aid to, 139–40, 143, 144–46, 288

  Woese’s break in friendship with, 287–89

  double membrane, 119

  Doudna, Jennifer, 364

  Drosophila ananassae, 262

  Dupré, John, 304

  dysentery, 87, 233–34, 243–44, 246

  Earthly Paradise, The (Merezhkowsky), 125

  ecology, 177

  eggs, 114, 119, 151, 260, 261–62, 360

  Ehrlich, Paul, 343

  18S rRNA, 61, 78, 274, 287

  Eisen, Jonathan, 267

  electron microscopy, 119, 203

  electrophoresis, xv, 43, 56, 61–63, 64, 106, 368–69

  Elementary Geology (Hitchcock), 24–25, 34

  Eli Lilly, 245

  Elysia viridis, 158

  emergent properties, 330–31, 384

  endogenous retroviruses (ERVs), 352–53, 356

  endosymbiosis:

  as beyond Darwinian theory, 346

&nbs
p; in big tree paper, 200

  centrioles and, 116, 133–34, 135, 136

  chloroplasts in, 116, 119, 121, 144–45, 147, 153, 273, 284, 293–94

  cilia and, 133–34, 135

  composite creatures and, 152

  convergence by, 193

  and DNA in chloroplasts, 119, 121

  Doolittle’s work on, 137, 139–40, 142, 144–45, 153, 283–84

  flagella and, 133–34, 135

  and invention of sex, 134–35

  Margulis’s suggestion of, xiv, 113–14, 115–16, 118, 122, 124, 133, 134–37, 142, 144, 147, 149, 150, 151, 160, 162, 191, 273, 293, 312

  Martin’s introduction to and study of, 292–93

  mitochondria in, 116, 121, 147–48, 151, 152–54, 158, 160, 200, 273, 284, 293–94, 295, 349, 375

  rejection of, 151–53

  Ris and Plaut’s proposal of, 119–20, 121

  see also symbiogenesis; symbionticism; symbiosis

  endosymbiotic gene transfer, 294–96, 298, 303–4

  energy storage, 104

  England, 232, 258

  Enterococcus, 245, 246

  eocytes, 203–4

  episomes, 234–35, 238

  see also plasmids

  Erlandson, Axel, 310–11, 384

  erosion, 24

  ERV-L, 352–53

  erythromycin, 244

  Escherichia, 252

  Escherichia coli, 29, 53, 145, 153, 154, 227–28, 230

  drug-resistant, 234, 235, 245

  genes transferred to brewer’s yeast from, 256

  HGT in, 284

  sequencing of, 362

  Essay on the Principle of Population, An (Malthus), 27

  ethanol, 68

  Ethiopia, 232

  Ettema, Thijs, 311, 375, 376

  Euglena gracilis, 121, 133

  eukaryotes, 78, 92, 105, 212

  centrioles of, 116, 133–34, 135

  cilia of, 133–34, 135

  eocytes’ relation to, 203

  flagella of, 133–34, 135, 190

  genetic isolation of, 253

  HGT and, 273, 276, 284, 297–98

  Margulis’s tree of, 141, 162, 273

  mitosis of, 114, 190

  molecular phylogenetics of, 279

  origins of, 115–16, 122–23, 312, 374–76

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

  sequencing of genomes of, 275, 281, 374–76

  “Everything That Rises Must Converge” (O’Connor), 191

  evolution:

  Darwin’s first inkling of, 5–6, 26

  discovery of archaea as test of, 91–92

  HGT’s implications for, 248, 255, 302–6, 330–31

  holistic problems of, 344–45

  of humans, 173

  speed of, 325

  see also Lamarckism; natural selection

  evolutionary history:

  contingency in, x

  transitions in, ix–x

  exobiology, 99, 120

  extinction:

  catastrophism and, 24

  Darwin on, 7–8, 33

  fats, 104, 220

  fatty acids, 104

 

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