Feldman, Robert, 277, 281
Feschotte, Cedric, 338–42
Festschriften, 43
F factor, 229, 234–35
filamentous bacteria, 87
“First Workshop on Archaebacteria, The,” 108–10, 209
fish, 256
Fishlake National Forest, 384
Fitzgerald, Ella, 369
Five Kingdoms (Margulis), 162
5S ribosomal RNA, 61, 68, 79, 137
flagella, 87, 133–34, 135, 151, 162, 190
Fleming, Alexander, 242, 275
fossils, 21, 31, 172, 197, 250, 374
Fox, George, 78, 83-84, 88, 89, 105, 194–95, 366
at archaea workshop, 108–10, 209
background of, 96–97
big tree paper cowritten by, 195–97, 198–201, 201, 202, 208, 334
desire to do theoretical work, 97–98
discover of archaea announced by, 94–95, 98, 101, 194
5S rRNA sequences assembled by, 97
and interest in ratchet model, 97, 100
lab work of, 97–98
lipids studied by, 104–5
methanogen classification papers coauthored by, 93–95, 101
offered job with Woese, 97
RNA extracted by, 83, 89, 93
third kingdom announced by, 194
Woese’s dispute with, 198–200
Franch, John, 81–82
Freeze, Hudson, 86
frogs, 339
fruit flies, 338
Fuchs, Leonhart, 14
Fukusawa, Toshio, 234–35
fungus, 92, 189, 190, 192, 193, 212
HGT and, 256
fusion, 227
Gaia hypothesis, 156–57, 253
Galápagos Archipelago, 4, 5–6
Gamow, George, 47
gas gangrene, 68
gastric ulcers, 264
General Electric Research Laboratory, 50, 367
Generelle Morphologie der Organismen (Haeckel), 177, 178, 179, 181
genes, 39
in cytoplasm, 118–19
question about existence of, 219–20
genetic code:
deciphering of, 37–41, 46, 47
evolution of, 46–49, 52, 320
Woese and Goldenfeld’s paper on origin of, 329–30
Genetic Code, The (Woese), 48, 366
genetic diseases, 42
genetic engineering, 293
genetic modification, 360–61
“Genetic Transfer and Bacterial Taxonomy” (Jones and Sneath), 249–50
genomes:
of bacteria, 252–53
of chloroplasts, 152, 293–94
human, 265–67, 275, 336
of mitochondria, 152, 293–94
palindromes in, 360
genome sequencing, 306, 311–12
geology, 23–24
Germany, 31, 103, 108
germline, 260, 261–62, 360
giraffes, 18–19
Göbel, Ulf B., 318, 324
God Delusion, The (Dawkins), 305
Goethe, Johann Wolfgang von, 167, 168, 181
Gogarten, Peter, 280, 284, 289–91, 297, 302, 311
Gold, Larry, 367–68, 370, 386
Goldenfeld, Nigel, 328–31, 334, 345, 378, 383, 386
gonads, 115
gonorrhea, 87, 245
Gould, Stephen Jay, 161, 282
grafting, 272
Gray, Michael W., 148–50, 153, 155
Great Britain, 108
green algae, 118–19, 121, 158
Greenland, 69
Gressel, Jonathan, 120
Griffith, Fred, xiii, xvi, 215
background of, 215–16
transformation of pneumococcus discovered by, 216–18, 219, 222, 226
Grigsby, Steve, 241–42
groves, 383–84
gum bacteria, 326
gum disease, 318, 324
Haeckel, Ernst, xiv, 188
background of, 167–70
book sent to Darwin by, 165–66
death of wife of, 174–75, 176
“natural laws” discovered by, 176–77, 184
natural selection lectures of, 172–73, 174
radiolaria studied by, 165–66, 171–72
religious views of, 175
trees of life of, 166, 172–73, 175, 177–79, 180, 181, 182, 183, 184, 186, 205, 210
Whittaker influenced by, 187
Haemophilus influenzae, 242, 275, 281
Haldane, J. B. S., 117
halophiles, 10, 104–5, 106, 362
Woese’s fingerprinting of, 105–6, 107–8
head lice, 261
Heidmann, Thierry, 350, 351–56, 357–58, 359
Helicobacter pylori, 264
hemoglobin, 40–41, 43, 52
hemoglobinuria, 87
Henslow, John Stevens, 3–4
hereditary continuity, 26, 28, 38, 91
heredity, see also horizontal gene transfer; infective heredity
HERV-L, 352
History of Animals (Aristotle), 10–11
History of Creation, The (Haeckel), 181
Hitchcock, Edward, xiv, 17, 22–23
Darwin read by, 34
trees of life of, 21–23, 23, 24–25, 32
HIV, 156
HIV-1, 352
Hogg, John, 187
Homo neanderthalensis, 381–82
Hooker, Joseph, 30
horizontal gene transfer (HGT):
Alm’s study in bacteria of, 325–26
and antibiotic-resistant bacteria, 231–35, 236, 239, 245–46, 247
attempt to reconcile with universal phylogenetic tree, 298–301, 327–28
of bdelloids, 257–59
between major bacteria lineages, 302
as beyond Darwinian theory, 346
and blurring of concept of species, 251, 252, 254, 380, 381
and cladistics, 250
coining of term, 255
in creatures other than bacteria, 255–56, 261–64, 284, 288–89, 293–96
Doolittle’s seminal paper on, xv, 283–86, 287
Doolittle’s skepticism of, 278–79
in E. coli, 284
eukaryotes and, 273, 276, 284, 297–98
four ways of understanding, 290–91
HTT as subcategory of, 341
implications for evolution of, 248, 255, 302–6, 330–31
microbes protected by CRISP-cas from, 364
microbiome and new insights into, 325–26
MRSA produced by, xi, 88, 232
in nongermline human cells, 263–64, 265–68, 336
as rampant phenomenon, 284, 288–91, 294–96, 297–98, 302–4, 307, 329–30
recognition of, x–xi
and small bacteria genome, 253
three cardinal mechanisms of, 226–27, 230
tree of life complicated by, 250, 256, 272, 279, 284, 288, 297–301, 299, 306, 327–28, 380
in Woese and Sapp’s unfinished book, 349
in yeast, 294
see also endosymbiosis; transformation
horizontal transposon transfer (HTT), 341
Hotopp, Julie Dunning, 260, 261, 262–64, 302
human, junk DNA in, 336–38
human endogenous retroviruses (HERVs), 352
human genome, sequencing of, 265–67, 275, 336
Human Genome Project, 260–61, 267, 274
humans, 182, 184
ancestry of, x
bacteria in, 315, 316–17
as eukaryotes, 76
HGT in, 263–64, 265–68, 336
hybridizing with Neanderthals, 381–82
identity of, 312
as top of tree of life, 11, 22
Hutcherson, Bobby, 368
Hutchins, Robert Maynard, 117
Hutchinson, G. Evelyn, 161
Huxley, Thomas H., 165
hydrothermal vents, 86
hypertrophic cardiomyopathy (HCM), 361
ichthyosaurs, 33
I Contain Multitudes, 317
Ideonella sakaiensis, 88
Illinois, University of, 332
immunology, 332
impetigo, 88
India, 232
individuals, 330–31, 380, 382–84
infections, 87
and transposons, 341
infective heredity, xi, xiii, 230, 231, 266
influenza pandemic of 1918–19, 216
inheritance, 176, 202, 233, 380
inheritance of acquired traits, 18–19, 184
inosculation, 272
insects, 260, 261
Institute for Genomic Biology (IGB), 334, 377, 378, 379
Institute for Genomic Research (TIGR), 260–61, 266, 275, 276
International Human Genome Sequencing Consortium, 265–67, 275, 336, 337
Introduction to Physiological Chemistry, 228
“Is Something Wrong with the Tree of Life?” (Martin), 297
Jablonski, David, 282
Jacob, François, 100
at archaea conference, 109
Japan, 108, 232, 233–34, 245
Jena, University, 172
Johns Hopkins University, 275
Jones, Dorothy, 249–50
Journal of Experimental Medicine, 225
Journal of Molecular Evolution, 92–93, 363
Journal of Theoretical Biology, 44, 113–14, 122
junk DNA, 336–42
Kandler, Otto, 103–4, 107, 274
at archaea workshop, 109, 209
paper on archaea coauthored by, 208, 209–12, 280
Kauffman, Stuart, 330–31
Keeling Atoll, 7–8
Kelvin, Lord, 329
kingdoms:
five, 186, 187–88, 189–90, 192, 193, 205
fourth, 188–89, 193
third see archaea
“Kingdoms of the Living World, The” (Whittaker), 187–88
kissing bugs, 341
Koch, Robert, 72, 252
Koonin, Eugene, 298–99, 302, 311
Krubsack, John, 271–72, 310, 384
Kruif, Paul de, 11
lactic acid bacteria, 88
ladder of life, 11–12, 19–20, 19, 182
see also tree(s) of life
Lake, James, 203–4, 210, 284
Lamarck, Cornelie, 18
Lamarck, Jean-Baptiste, xiv, 17–18, 21, 34, 345
Lamarckism, 18–19
Lander, Eric S., 266, 267
language evolution, 177
La Suisse, 129, 130
lateral gene transfer, see horizontal gene transfer (HGT)
Lavoisier, Antoine-Laurent, 17
law of correlative adaption, 176
Lawrence, Jeffrey, 289–91, 297, 311
Lawton, Graham, 303–4, 305
Lebanon Daily News, 101
Lederberg, Esther, 229, 231
Lederberg, Joshua, xiii, xvi, 161, 227–28, 230, 231, 284, 315
Leeuwenhoeck, Antoni von, 11–12, 72, 74, 77, 256, 315, 317–18, 366
leptospirosis, 134
Levy, Jay, 237
Levy, Stuart B., 236–38, 245
Lewin, Harris, 332–35, 343–44, 377
lichen, 126
Life of Theseus (Plutarch), 308
Linnaeus, Carl, xiv, 14–15, 48, 74, 205, 283, 380–81
Linnean Society, 31
lipids, 38, 104
Lister, Joseph, 72
lithotrophic bacteria, 88
livestock, 232
Lokiarchaeota, 375–76
Lovelock, James, 157, 253
Luehrsen, Ken, 66–67, 68–69, 97
radioactive RNA extracted by, 67–68, 78–79, 105
Luria, Salvador, 102, 109, 366
Lyell, Charles, 23–24, 25, 30–31
Lyme disease, 87, 134, 157, 159–60
Lyons, Eric, 305
Lyons, Richard D., 100–101
McCarty, Maclyn, 224, 225
McClintock, Barbara, xiii, 337–38, 344
MacLeod, Colin, 222, 223–24, 225
Magrum, Linda, 93, 97, 105–6, 196
big tree paper coauthored by, 198
Malay Archipelago, 29, 31
Malthus, Thomas, 27
Margulis, Lynn, xiii–xiv, xv, xvi, 131, 148, 190, 193, 194, 202, 210, 288
awards and accolades received by, 159, 160–61
background of, 117–18
controversial views of, 156–58, 159–60, 253
cytoplasmic inheritance studied by, 120–21
in dispute over definition of Protista, 191–92
endosymbiosis suggested by, xiv, 113–14, 115–16, 118, 122–23, 124, 133, 134–37, 142, 144, 147, 149, 150, 151, 160, 162, 191, 273, 293, 312
on polyphyletic taxa, 192–93, 205
Sagan’s relationship with, 114, 117–18, 120, 121–22
tree of life of, 141, 162, 273
Woese’s criticism of, 114, 161–62
Margulis, Thomas N., 114, 122, 156, 160
Margulis, Zachary, 122
Mariana Trench, 85
mariner, 328
marine sediments, 375
Marinobacter salarius, 88
marsupials, 355
Martin, William F., 267, 288, 289, 303, 311, 376, 384
endosymbiosis studied by, 292–96
HGT’s importance in tree of life recognized by, 284-85, 287, 297–98, 299, 302
tree of life of, 284–85
Maryland, University of, 262–64
maternal inheritance, 119
Max Planck Institute for Biochemistry, 107
Maxwell, James Clerk, 329
Mayr, Ernst, 160–61, 381
Medical Research Council (MRC), 39–40, 137
meiosis, 114, 115, 135
membranes, 104
Mendel, Gregor, 117, 119, 158, 305
meningitis, 87
Merezhkowsky, Constantin, 118, 124–30, 131, 133, 136, 142
symbiogenesis idea of, 119, 121, 126, 127–28, 130, 132, 133, 273, 292, 293, 312
messenger RNA, 52, 54, 108
Meszoly, Laslo, 139, 141
metabolism, 281
metagenomics, 325
methane, 68, 90, 101, 108, 275
Methanobacterium ruminantium, 70, 71, 93
Methanobacterium thermoautotrophicum, 93, 101
Methanococcus jannaschii, 275–76
methanogens, 68–70, 83–84, 109, 324
cell walls of, 103–5
classification of, 71–72, 78–79, 88–89, 90, 91–95, 103, 107
fingerprinting of, 88–89, 90, 91–95, 107
new kingdom discovered to include, 89, 90, 91–92
shapes of, 69
on tree of life, 71
methicillin-resistant Staphylococcus aureus (MRSA), xi, 88, 232, 245
mice, 354–55
Microbe Hunters (de Kruif), 11
microbes, 71-72, 202
Microbiology and Molecular Biology Reviews, 344
microbiome, 315–16
changeability of, 316
and new insights into HGT, 325–26
research in, 316–17
Micro-Cosmos (Margulis and Sagan), 158
microscopy, 115, 118, 119, 132, 135–36, 217
microsomal particles, 52
see also ribosomes
Miles (cat), 369
mitochondria, 190, 294, 375, 383
in endosymbiosis, 116, 121, 147–48, 151, 152–54, 158, 160, 200, 273, 284, 293–94, 295, 349, 375
genomes of, 152, 293–94
passed through egg, 151
progenitor of, 153–55
rRNA of, 149, 150
Wallin’s theory on cells’ capture of, 131–32
wheat, 148, 149–50, 151
“Mitochondrial Origins” (Woese et al.), 153–55
mitosis, 114–15, 135, 190
Mitrocoma annae, 176
mockingbirds, 3–4
Modern Synthesis (neo-Darwinism), 158, 305
Mojica, Francisco, 362
–64
“molecular clock,” 44–45
molecular phylogenetics, 40–41, 46, 51, 371
Balch et al.’s paper on, 93
and Brown’s work on tree of life, 279
see also chemical paleogenetics; protein taxonomy
molecular sequencing, 46, 136, 197, 200, 203
“Molecules as Documents of Evolutionary History” (Pauling and Zuckerkandl), 44
Moneres, 179, 182, 187, 189, 190, 190, 204–5
monism, 175, 176
Monod, Jacques, 100, 109
Morgan, Thomas Hunt, 219–20
morphology, 168
“Mosaic Bacterial Chromosomes: A Challenge En Route to a Tree of Genomes” (Martin), 284–85, 297
mouse leukemia, 352
M. thermoautotrophicum, 93, 101
Müller, Johannes, 168, 170, 171
Mulligan, Gerry, 369
Mushroom Spring, 86
mutations, 43, 158, 202, 233, 234, 258, 264, 360
Mycoplasma hominis, 87
Myers, Paul, 305
Namibia, 87
National Academy of Sciences, 159, 208–9
National Aeronautics and Space Administration, 99, 108
National Collection of Type Cultures (NCTC), 240, 241, 247
National Institutes of Health, 263
National Science Foundation, 99, 108
natural selection, 92, 233
Darwin’s formulation of, 27–28, 29, 30–31, 132–33, 172, 174, 176, 181, 202, 303, 383
Haeckel’s lecture on, 172–73
rejection of, 19
Wallace’s formulation of, 29–30
Natural System, 208, 209–12, 211
Nature, 38, 48, 106, 133, 144, 204, 228, 266, 330, 361, 363, 370, 376
NCTC1, 243–44, 247
Neanderthals, 381–82
necrosis, 68
Neisseria gonorrhoeae, 87
nematode worms, 261, 262, 276
neo-Darwinism, 158, 305, 381
neo-Lamarckism, 19
Netherlands, 108
net of life, 280
neutron, 329
New Bacteriology, A (Panisset), 252
“New Biology for a New Century, A” (Woese), 344, 364
“New Concepts of Kingdoms of Organisms” (Whittaker), 189, 192
New England Journal of Medicine, 238
New Foundations of Evolution, The (Sapp), 211, 346
New Scientist, 302–4, 305–6, 307
New York Times, 100–102, 195, 262, 267, 378
Noller, Harry, 368–70
Non-Darwinian Revolution, The (Bowler), 184
Norris Geyser Basin, 86
nuclear weapons, 43, 44
nuclei, 190
nucleic acids, 38, 220
nucleotides, 38, 300
numerical taxonomy, 249
obesity, 316
Occupational Safety and Health Administration (OSHA), 60
O’Connor, Flannery, 191, 193
Octopus Spring, 322–23, 324
Olsen, Gary, 276, 343
“On Protein Synthesis” (Crick), 40, 51
“On the Broad Classification of Organisms” (Whittaker), 189
“On the Origin of Mitosing Cells” (Margulis), 114, 115–16, 122, 123, 132, 133
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