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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