Darwin's Doubt

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Darwin's Doubt Page 66

by Stephen C. Meyer


  inductive argument, 343, 344

  information: hierarchical layering or arrangement of, 276fig; self-organization issue of order vs., 305–9; Shannon information theory, 164–68, 274. See also epigenetic information; functional information

  insect wing coloration mutations, 316fig, 317

  intelligent design: abductive inference arguments for, 344–45; applied to Cambrian explosion, 351–52, 353–81; theological implications of, 410–13; author’s story on examining, 340–43; commonalities with neo-Darwinism, 392; Cambrian explosion mystery solution, 378–81; attempt to define as unscientific by AAAS, 385; demarcation arguments against, 389–90; distinctive features of Cambrian explosion design evidence for, 380fig; early arguments supporting, 338–40; firestorm around Smithsonian’s NMNH journal article on, 209–11; introducing, 337–40; New Atheists attacks against, 409–10, 412; answers to new objections to scientific status of, 392–98; reasons to regard as scientific theory, 391–92; arbitrary “rules of science” over seeking truth of, 398–400; Sternberg case controversy over, 384–85; what is at stake for honest consideration of, 404–13. See also design

  intermediate animal life forms: lack of Cambrian explosion evidence for, 34–38; “morphological space” between, 70–71; statistical paleontology failing to find evidence of, 69–71; Wray study (1990s) explanation for missing, 103–4. See also animal phyla; universal common ancestry

  “Interpreting Great Developmental Experiments: The Fossil Record” (Erwin and Valentine), 143

  “The Invisible Man” (Chesterton), 382–83

  Jablonka, Eva, 330, 331–32

  Jablonski, David, 83–84, 106, 107, 109, 110, 124

  James, William, 20–21

  Jensen, Sören, 85, 96

  John, Bernard, 259

  Jones, Judge John E., 211

  Journal of Molecular Biology, 209

  Jukes, Thomas, 173

  junk DNA, 402

  Kauffman, Stuart, 293–300, 305, 309, 310

  Kendrew, John, 187

  Kimberella mollusk, 81, 82, 86

  King, Jack, 173

  Kirschner, Marc, 292

  Kitzmiller v. Dover, 211, 221

  Knoll, Andrew, 84, 104

  Kumar, Sudhir, 106

  Küppers, Bernd-Olaf, 361

  Kuziora, Michael, 318

  Laboratory for Molecular Biology (LMB), 187

  Lamarckism, mechanisms of, 329–30

  Lande, Russell, 149

  The Language of God (Collins), 410, 411

  lateral gene transfer, 213fig, 217, 218, 219

  Laudan, Larry, 388

  Leibniz, Gottfried Wilhelm, 387

  Levinton, Jeffrey S., 57, 103, 148–49

  Lewin, Roger, 41

  Lewontin, Richard, 171, 339, 386

  LexA (DNA-binding protein), 333

  Li, Wen-Hsiung, 240–41

  Lincoln, Abraham, 368–69fig, 370

  Lipalian interval hypothesis, 46. See also artifact hypothesis

  Lipton, Peter, 348

  Long, Manyuan, 211, 214, 216, 220, 221–23, 226

  Longfellow, Henry Wadsworth, 18

  lumping classification approach, 47–48, 55

  Lurie, Edward, 18, 19, 21, 22

  Lyell, Charles, 348–49, 392

  Lynch, Michael, 321–29

  macromutations: description of, 11; Goldschmidt’s argument for, 311; Gould’s argument for, 311, 312; neo-Darwinist rejection of, 312

  magnetic seafloor stripe pattern explanation, 346–48

  Maley, Laura, 124

  Mangold, Hilda, 271, 273, 275

  Maotianshan Shale site (China): Cambrian explosion fossils from fauna of, 62–64, 65fig, 73–76; discovery of the, 50–52; Doushantuo Phosphorite formation of, 64, 66–68, 90; top-down pattern observed at, 74–75

  Maresca, Bruno, 125

  Marrella splendens fossils, 29, 30fig, 38, 48, 53, 60, 62

  Marshall, Charles R., 57–58, 124

  Martin, William, 107

  materialistic causes, 394

  “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution” conference (1966), 170–77, 187

  Matzke, Nicholas, 210–11, 221

  Maynard Smith, John, 237–39, 240

  Mayr, Ernst, 171, 339

  McDiarmid, Roy, 384

  McDonald, John F., 262, 315

  McGinnis, William, 318

  McMenamin, Dianna, 68

  McMenamin, Mark, 68, 83

  McNiven, Mark, 284

  Medawar, Sir Peter, 171

  Mendel, Gregor, 156–57, 236

  Mendelian genetics, 156–59

  “A Merciful Death for the ‘Earliest Bilaterian,’ Vernanimalcula” (Bengtson and colleagues), 91–92

  Metazoan canonical tree, 126–27, 128fig

  Metazoan phyla, 104, 107

  method of multiple working hypotheses, 346–49

  methodological naturalism, 19–20, 384–86

  Meyer, Jamie, 404–8, 406fig, 412–13

  Meyer, Stephen C.: anti-uniformitarianism of, 393; hiking up to Burgess Shale, 404–8, 412–13; his story on examining intelligent design, 340–43; photograph with son, 406fig; Signature in the Cell by, 359–60, 389, 391, 392, 402

  “Meyer’s Hopeless Monster” (Gishlick, Matzke, and Elsberry), 210–11

  microtubule associated proteins (MAPs), 282–84

  microtubules, 277–79

  Miklos, George, 259, 287

  Miller, Kenneth, 211, 221

  Molecular Biology and Evolution journal, 109

  molecular clock analysis, 102fig–3, 121

  “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla” (Wary, Levinton, and Shapiro), 103–4

  Molecular Evolution (Li), 240–41

  molecular homologies studies, 121–25

  Moran, Laurence A., 401

  Morgan, T. H., 259–60

  morphological change: Cambrian fossil record showing persistent morphological isolation, 375–78; Darwin’s theory of descent with, 99–100; Explore Evolution textbook discussion of, 315–16; “morphogens” molecules critical for, 260–61; neo-Darwinian evolutionary estimates on, 87–88; pentadactyl limb five-digit pattern example of, 99fig; statistical paleontology failure to fill missing “space” of, 70. See also Drosophila melanogaster (fruit flies)

  morphological space, statistical paleontology failure to fill, 70

  Müller, Gerd, 272

  Muller, Hermann, 157–58

  Murchison, Roderick Impey, 13

  mutations. See genetic mutations

  The Mystery of Life’s Origin (Thaxton, Olsen, and Bradley), 341

  National Center for Science Education (NCSE), 315–17

  National Museum of Natural History (NMNH) [Smithsonian Institution], 209–11, 384

  natural genetic engineering, 332–35

  “natural magic,” 309–10

  natural selection: Axe’s conclusion that protein folds are preserved by, 199–200, 202–8; Axe’s experiments on protein mutation and, 187–200, 202–8; Cambrian fossil evidence challenging idea of, 8fig–10, 18–24fig; Darwin on favorable variations required for, 264; Darwin’s theory of evolution on, 3; Dawkins’ Shakespearean “Methinks it is like a weasel” phrase experiment on, 185–86; description of process of, 5–6; DNA genetic variation and, 159–61fig; three discrete elements driving, 10–11; as understood by neo-Darwinism, 194. See also genetic mutations

  Nature journal, 122, 125, 210, 400, 402–3

  Nature Reviews Genetics, 211, 239

  Nectocaris fossils, 53, 54fig

  Nelson, Paul, 262–63fig, 317, 368–70

  neo-Darwinism: apparent design arguments offered by, 338–39; artifact hypothesis of, 46–47, 49, 52, 55–62, 69–71, 105; bottom-up pattern of, 144fig, 145–46, 371; challenged posed by epigenetic information for, 281–82; combinatorics used to calculate DNA mutations, 172–73; commonalities of intelligent design and, 392; comparing orthodox Darwinian point of view with, 104; cooption mo
del of protein evolution, 249–54; estimates on morphological change by, 87–88; examining the deep-divergence hypothesis of, 100, 101–13; failure to explain Cambrian explosion by, 257, 286–87; focus on mathematical modeling by, 230–35; how Axe’s experiments on proteins are problematic for, 187–200, 202–8; how new evolutionary models deviate from tenets of, 313fig, 314–35; macromutations rejected by, 312; “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution” conference (1996) on, 170–77; natural selection as understood by, 194; problem of anatomical peculiarities for, 230–33; punctuated equilibrium’s bottom-up pattern similar to, 144fig; responses to Sauer’s experiment, 180–84, 187–89, 192–94; as synthesis of Mendelian genetics with Darwinian theory, 158–59; theory of punctuated equilibrium (“punk eek”), 137–52; three challenges posed by animal development to, 262–64; three core claims or pillars of, 292–93; Wells’ argument against animal body plans being adequately explained by, 273–74. See also Darwinian evolutionary theory; evolutionary biology; New Synthesis; “The Origin of New Genes: Glimpses from the Young and Old” (Long and colleagues)

  neo-Darwinism math: population genetics models of, 233–54; to solve problem of anatomical peculiarities, 230–33

  neo-Lamarckism, 329–32

  Neoproterozic era, 110

  neutral or nonadaptive evolutionary theory: critique of, 323–26; overview of, 321–23; on waiting times, 327–29

  “New Atheism,” 409–10, 412

  Newman, Stuart, 272, 275, 300–305

  New Scientist journal, 119, 120

  New Synthesis, 158–59. See also neo-Darwinism

  Newton, Isaac, 387–88

  New York Review of Books, 385–86

  Nijhout, Fred, 275

  Nikoh Naruo, 106

  Nüsslein-Volhard, Christiane, 255–56, 257fig, 260, 270, 315

  Ohno, Susumu, 191

  Olsen, Roger, 341

  only known cause, 349–51

  On the Origin of Species (Darwin): Agassiz’s challenge using the fossil record, 8fig–10, 17, 18–24fig, 69; Centennial celebration of publishing, 158–59; criticism regarding accurate tree of life goal of, 120; apparent design in living organisms argument in, 338; expressing concerns over Cambrian period in, 7; growing anomaly of arguments set forth in, 286–87; on Lamarckian mechanisms, 330; “The Mutual Affinities of Organic Beings” on similar anatomical structures of distinct organisms, 99fig–100; natural selection introduced in, 3, 5–6; uniformitarian principles used in, 391–92, 393; universal common ancestry introduced in, 3–5; vera causa (true cause) criterion arguments made by, 216–17. See also Darwin, Charles

  ontogeny studies: on dGRNs (developmental gene regulatory networks), 264–69, 285, 319–20, 363–66; on early-acting bodyplan mutations and embryonic lethals, 259–64; on principle of constraints, 268–69; on role of genes and proteins in animal development, 258–59

  onychophorans (velvet worms), 60

  Opabinia fossil, 36, 37fig, 38, 52–53

  Opitz, John, 287

  Ordivician period fossils, 14fig

  The O’Reilly Factor (TV news show), 210

  ORFan genes, 215–16

  organismal form and function, 274–75

  organisms: biological complexity scale as measure in cell types of different, 162fig; Cambrian explosion fossils of, 78; Cambrian explosion of DNA information and new, 161–64; Darwin’s argument on similar anatomical structure of distinct, 99fig–101; DNA information required for form and function of, 274–75; Ediacaran mini-explosion of, 78, 86–88; estimated DNA required for minimally complex single-celled, 163; eukaryotic, 161–62, 219, 277–79, 323–24; ontogeny studies on development of embryos into mature, 258–69. See also animal development; animal phyla

  Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology (Müller and Newman), 272–73

  “The Origin of New Genes: Glimpses from the Young and Old” (Long and colleagues): common ancestor gene inferred in, 211–15; controversy over, 211; on exon shuffling, 213fig, 217, 218, 219, 223–27; failure to explain origin of new protein folds, 221–27; ORFans genes unexplained by, 215–16; on plausibility of mutational processes, 216–21. See also neo-Darwinism

  The Origins of Order: Self-Organization and Selection in Evolution (Kauffman), 293–94, 297

  Orr, H. Allen, 239

  Owen, Richard, 100

  Paleobiology journal, 150

  Paley, William, 38

  parallel roads of Glen Roy, 22, 23fig

  Parvancorina fossil, 89

  Pauling, Linus, 121, 122, 125

  Peirce, C. S., 343

  pentadactyl limb five-digit pattern, 99fig

  People’s Daily (Chinese Communist party newspaper), 64

  Perutz, Max, 187

  Peterson, Kevin, 87, 109

  Phacops rana, 136–37

  phyla (animal groups). See animal phyla

  phylogenetic classification: description of, 31, 33; phylogenetic inference assumptions, 132–33; selection of incompatible phylogenetic trees, 131fig. See also animal phyla

  Pigliucci, Massimo, 330

  PLoS Genetics journal, 220

  Polanyi, Michael, 341

  population genetics models: attempting to explain origin of complex adaptations, 237–41; on chloroquine complexity cluster (CCC) coordinated mutations, 247–49; cooption model of protein evolution, 249–54; description and functions of, 233–34; the origin of genetic information and, 235–37; Powerball lottery game used to understand, 242–44fig; “waiting times” calculated using, 240–42

  positivism scientific approach, 20

  post-Darwinian models: evo-devo theory, 314–15; how new models deviate from tenets of neo-Darwinism, 313fig, 314–35; natural genetic engineering, 332–35; neo-Lamarckism, 329–32; neutral or nonadaptive evolutionary theory, 321–29; self-organizational theories, 293–310

  Powerball lottery game, 242–44fig

  Precambrian-Cambrian fossil record: Chengjiang discoveries (China), 62–64, 65fig, 71–76; Darwin’s Dilemma documentary challenging Darwin using the, 77–79, 96; diagram showing representation of pattern of, 24fig; examining possibility of tree of animal life from, 117–32; found at the Burgess Shale site, 26, 27fig–28; looking for evidence of design in the, 371–78; puzzling pattern of, 34; sponge fossils, 66–68, 81; statistical paleontology failure to support Darwin’s tree of life in, 69–71; sudden appearance and missing ancestors evidence in, 373, 375; top-down disparity preceding diversity evidence in, 371–73, 374fig, 375. See also fossil record

  Precambrian fossil record: animal phyla of, 81–92; debate over Vernanimalcula as bilaterian ancestor, 89, 90, 91fig–96; Ediacaran Hills site, 79–80fig, 81–92; four main types of fossils found in, 80–81; primitive mollusks, 81; sponge fossils, 66–68, 81; trace fossils, 81, 85–86

  primordial germ cells (PGCs), 127, 129fig

  The Principles of Geology (Lyell), 348

  Proceedings of the Biological Society of Washington journal, 209, 384, 385

  Proceedings of the National Academy of Sciences USA, 106, 192, 316–17

  process control, 186–87

  protein folds: Axe’s conclusion that natural selection preserves, 199–200, 202–8; importance in genetic information producing, 189–92; Long’s failure to explain origin of new, 221–27; protein tertiary structure corresponding to, 189, 190fig; as smallest unit of structural innovation, 191

  proteins: animal development and role of genes and, 258–59; argument that multiple improbable mutations are required for new, 244–47; Axe’s experiments on natural selection and mutation of, 187–200, 202–8; combinatorial inflation problem applied to amino-acid, 173–74fig, 181fig; dynamical patterning modules (DPMs) and role of, 304; epigenetic information in patterns of cell membrane, 279–81, 305; Hox genes role in providing information for building, 320; LexA (DNA-binding protein), 333; MAPs (microtubule associated proteins), 283–84; neo-Darwinian failure to explain generation of new, 257; organismal and inform
ational context consideration of, 363–71; responses to Sauer’s experiment on amino-acid, 180–84, 187–89, 192–94; TFs (transcription factors), 258–59; three levels of structure of, 189, 190fig; TRs (transcriptional regulators), 258–59; under selection pressure, 197fig. See also amino-acid sequences

  Prothero, Donald, 72, 73

  Prud’homme, Benjamin, 317

  “punk eek.” See theory of punctuated equilibrium (“punk eek”)

  Raff, Rudolf, 287, 312, 314

  random variation: competition for survival driving, 10–11; description of, 10; heritability of, 11; macromutations form of, 11

  rank-free classification scheme, 31, 43

  Raymond, Percy, 52

  “Reading the Entrails of Chickens: Molecular Timescales of Evolution and the Illusion of Precision” (Graur and Martin), 107

  Reidhaar-Olson, John, 192

  Retallack, Gregory, 82

  retropositioning mRNA transcripts, 213fig, 217, 218, 219

  reunion hypothesis, 134–35

  RNA: complexity characterizing information in, 306–9; epigenetic information role in function of, 279–80; often treated with DNA as sole repositories of biological information, 275; retropositioning mRNA transcripts, 213fig, 217, 218, 219

  Robinson, Mabel, 18

  Rodin, A. S., 362

  Rokas, Antonis, 120, 121

  Salisbury, Frank, 238

  Sam Noble Science Museum (University of Oklahoma), 77–78, 96–97

  Sanger, Fred, 187

  Sauer, Robert, 180–84, 187–89, 192–94

  Schelling, Friedrich, 19, 320

  Schindewolf, Otto, 311

  Schmidt, Deena, 249, 253

  Schopf, J. William, 58

  Schuchert, Charles, 28, 48

  Schützenberger, Marcel-Paul, 171–72, 176–77

  Schwartz, Jeffrey H., 125, 314, 318

  science: abductive inference basis for developing hypotheses in, 343–45; causal adequacy in, 348–51; demarcation criteria issue of, 386–90; German idealism and cosmic philosophy of, 18–19, 20; method of multiple competing hypotheses in, 346–49; methodological naturalism rule of, 19–20, 384–86; new objections to intelligent design as, 392–98; positivistic view of, 20; reasons to regard intelligent design as, 391–92; truth over “rules” of, 398–400. See also evolutionary biology; vera causa (true cause) principle

  Science journal, 41, 85, 120, 210, 220

 

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