Darwin's Doubt
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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