Darwin's Doubt

by Stephen C. Meyer

  competition for survival, 10–11

  Complex Adaptations in Evolving Populations (Frazzetta), 232

  Comte, August, 19–20

  conditional probability, 201

  convergent evolution, 133–34

  Conway Morris, Simon, 75, 113, 291, 357

  Cooper, Alan, 84

  cooption model of protein evolution, 249–54

  coordinated mutations: chloroquine complexity cluster (CCC), 247–49; complex adaptations explained by, 237–41; cooption model of protein evolution, 249–54

  Coyne, Jerry, 100, 115, 116, 124, 317

  “creationist” label, 401

  creative intelligence, 100

  Crick, Francis, 159, 160fig, 166, 168, 187, 236, 339, 385, 400

  Current Biology, 291

  Cuvier, Georges, 19

  cytoskeletons, 277–79

  Darwin, Charles: countering Paley’s watch-to-watchmaker design argument, 37–38; explanation for discontinuity found in fossil record, 6, 17–18, 23–24, 379, 381; Galápagos Islands trip by, 21; growing anomaly and failure to explain Cambrian explosion, 8fig–10, 13–17, 18–24fig, 34–44, 50–52, 69, 71–76, 286–87; Lyell’s influence on, 348–49; on natural selection requiring favorable variations, 264; photograph of, 7fig; ten children of, 118; uniformitarian method used by, 391–92, 393. See also On the Origin of Species (Darwin)

  Darwin, Emma, 118

  Darwin and Modern Science (Bateson), 237

  “Darwinian Alchemy: Human Genes from Noncoding RNA” (Genome Research), 220

  Darwinian evolutionary theory: Agassiz’s challenge to the, 8fig–10, 13–17, 18–24fig, 69, 379, 381; apparent design suggested by, 338–40; Burgess Shale’s Cambrian explosion features challenging the, 34–44; China’s Chengjiang fossils challenging the, 50–52, 71–76; comparing neo-Darwinism with, 104; comparing punctuated equilibrium’s tree of life with traditional one of, 141fig; Darwin’s Dilemma documentary challenging, 77–78, 96; Darwin’s explanation for discontinuity issue of, 6, 17–18, 23–24, 99; discontinuity of fossil record challenge to, 8fig–10, 13–17, 18–24fig, 69, 101, 379, 381; growing anomaly and failure to explain Cambrian explosion, 8fig–10, 13–17, 18–24fig, 34–44, 50–52, 69, 71–76, 286–87; introducing natural selection idea of, 3, 5–6, 10–11; introducing universal common ancestry idea of, 3–5, 12–13, 36fig, 41–42fig; Lamarckian mechanisms role in, 329–30; theory of blended inheritance favored by, 155–57; Whittington’s analysis challenging Walcott’s solution for, 52–54. See also artifact hypothesis; evolutionary biology; neo-Darwinism

  Darwin’s Cambrian dilemma display (Sam Noble Science Museum), 96–97

  Darwin’s Dilemma (documentary film), 77–79, 96

  daughter cells, 258, 278

  Davidson, Eric, 57, 265, 267, 269, 270, 319–20, 355, 357, 363–64

  Dawkins, Richard, 40–41, 98, 115, 117, 124, 148, 176, 185–86, 207, 339, 358–59, 361, 392, 409, 411

  Dawkins’ Shakespearean “Methinks it is like a weasel” phrase experiment, 185–86

  deductive argument, 343–44

  deep-divergence hypothesis: common descent of all animal forms assumption of, 110–11; description of the, 100, 101; fossil record bringing reasonable doubt to, 105; gene sequencing studies bringing reasonable doubt to, 105–8; molecular clock analysis used in, 102fig–3, 121; questionable assumptions of, 109–10; “shmoo-like” catch–22 of the, 111–13; Wray study (1990s) argument for, 103–4

  degree of difference: deep-divergence explanation on missing fossils, 100, 101; description and assumptions about, 100; Wray study (1990s) on the, 103–4. See also universal common ancestry

  demarcation: arguments against intelligent design using, 389–90; criteria of, 386–87; general problem of, 387–89

  “The Demise of the Demarcation Problem” (Laudan), 388

  de novo origination, 213fig, 217, 219–21

  Denton, Michael, 178, 179, 180

  design: CD-ROM technology, 378; distinctive hallmarks of, 380fig; looking for evidence of Cambrian explosion, 351–52, 371–78. See also intelligent design

  developmental genetic toolkit, 300–305

  Devonian period fossils, 14

  dGRNs (developmental gene regulatory networks): as Cambrian explosion evidence, 363–66; Davidson’s findings on principle of constraints in building, 268; as dependent on preexisting cell structures, 825; difficulty to alter without damaging regulation ability, 319–20; principle of constraints for engineering new, 268–69; research being conducted on, 264–68; Strongylocentrotus purpuratus (purple sea urchin), 266fig, 267–68

  Dickinsonia fossil, 80fig, 81, 82, 83, 86, 88

  Dill, Ken, 183

  discontinuity of fossil record: Agassiz’s challenge to Darwin’s theory using, 8fig–10, 13–17, 18–24fig, 69, 379, 381; of Cambrian period fossils in Wales, 13–14; Darwin’s explanation for, 6, 17–18, 23–24, 99; deep-divergence hypothesis to explain, 101. See also fossil record

  Discovery Institute, 50

  Distal-less Hox gene), 321

  DNA: Axe’s experiments on protein natural selection and, 187–200, 202–8; Cambrian explosion of new genetic information, 161–64; combinatorics used to calculate mutations in, 172–83; complexity characterizing information in, 306–9; Crick’s sequence hypothesis on, 159, 169, 177; de novo origin of new genes in Drosophila melanogaster from noncoding, 220–21; double helix structure of, 159; ENCODE project study of genome and, 400–402; functional information contained in, 164, 168, 178–84, 187–200, 202–8, 274–75; information and genetic variations of, 159–61fig; junk, 402; mechanisms for generating gene duplicates in, 198–200; minimally required for complex single-celled organisms, 163; model showing nucleotide bases along sugar-phosphate molecule, 161fig; natural genetic engineering understanding of, 332–35; neo-Lamarckian theory on, 330–32; organismal form and function determined by, 274–75; Shannon information contained in, 164–68, 274, 275. See also epigenetic information; gene sequences; gene sequencing; genetic mutations

  Doushantuo Phosphorite formation (Maotianshan Shale), 64, 66–68, 90

  Dover, Kitzmiller v., 211, 221

  Drosophila melanogaster (fruit flies): base pairs of the, 163; de novo origin of genes from noncoding DNA, 220–21; epigenetic information role in embryo development in, 279–80; examples of deleterious macromutations of, 260, 261fig; germ-cell formation in, 129fig; Heidelberg screens experiment on, 255–57; Hox genes causing fatal mutations in, 318–19; “morphogens” influencing embryological development in, 260–61; ontogeny studies using model system of, 258; study of a gene that codes for histone protein in, 222; Ultrabithorax gene in, 261–62. See also morphological change

  Drosophila simulans, 222

  Dupree, A. Hunter, 19

  Durrett, Rick, 249, 253

  dynamical patterning modules (DPMs), 301fig–2, 303–4

  Easter Island “Moais,” 396fig

  Ecdysozoa hypothesis, 122–23fig, 124

  Eden, Murray, 169–70fig, 171, 175, 176, 177, 178, 179, 183, 186

  The Edge of Evolution (Behe), 242, 247, 249

  Ediacaran Hills site (Australia): debate over Vernanimalcula fossil of, 89, 90, 91fig–96; Ediacaran fauna and Vendian radiation, 79–81; evidence of mini-explosion of organisms, 78, 86–88; exotic fossils as plausible ancestors to Cambrian animal forms, 88–92; significance of findings of, 81–86; trace fossils of, 81, 85–86

  Ediacaran period, 79

  Ehrlich, Paul, 234

  Eldonia fossils, 64

  Eldredge, Niles, 293, 314; photograph of, 137fig; theory of punctuated equilibrium contributions by, 136–52

  Elsberry, Wesley R., 210–11, 221

  embryos: Chengjiang embryo sponge fossils, 66–68, 67fig; dGRNs (developmental gene regulatory networks) role in development of, 264–69, 285, 319–20, 363–66; early-acting bodyplan mutations in, 259–64; epigenetic information role in development of, 279–80; how microtubules influence development of, 277–79; Kauffman on genes generating
“pathways of differentiation” in, 294–95; role of genes and proteins in development of, 258–59; studies indicating the DNA is required to complete development of, 271–72. See also animal development

  ENCODE project, 400–402

  epigenesis germ-cell mode, 129fig, 130fig

  epigenetic information: cell differentiation role of, 276–77; challenge posed to neo-Darwinism by, 281–82; chemically blocking transcription of DNA into RNA, 271; cytoskeleton, 277–79; description and function of, 275–77; early experiments revealing, 271–72; hierarchical organization of, 364–66; issues to consider for inheritance of, 286; making the case against “gene-centric” using, 282–84; mutations of, 285–86; order vs. complexity of, 305–9; Origination of Organismal Form essays on, 272–73; in patterns of proteins in cell membranes, 279–81, 305; self-organization models on, 295–97; sugar molecule, 280–81, 282–83. See also DNA; genetic information; information

  Erwin, Douglas, 41, 69, 73, 81, 83–84, 104, 106, 107, 109, 110, 124, 143–44, 151, 292, 319, 354–55fig, 356, 357

  ethyl methane sulphonate (EMS), 255

  eukaryotic organisms: choanoflagellates, 161–62; cytoskeletons of, 277–79; spliceosomes of, 323–24; transposons (“jumping genes”) of, 219

  “Evidence for a Clade of Nematodes, Arthropods and Other Moulting Animals” (Nature journal), 122–23

  evo-devo theory, 314–15, 316

  Evolution and Belief (Asher), 392

  “Evolution and the Permanence of Type” (Agassiz), 11

  evolutionary biology: Altenberg 16 exploring the future of, 291–92, 293, 313; Darwin’s argument on similar anatomical structure of distinct organisms, 99fig–101; degree of difference concept of, 100, 101; evo-devo theory of, 314–15, 316; forensic nature of, 98–99; homology concept of, 100; how new models deviate from neo-Darwinism, 313fig–35; impasse reached by modern, 337; natural genetic engineering, 332–35; neo-Lamarckism, 329–32; neutral or nonadaptive evolutionary theory, 321–29; “phylogenetically informative” data chosen or cherry picked by, 108; self-organizational theories, 293–310; sequencing DNA to reconstruct evolutionary relationships of species, 100–101; theory of punctuated equilibrium of, 137–52. See also animal tree of life; Darwinian evolutionary theory; neo-Darwinism; science

  Evolution journal, 317

  exon shuffling, 213fig, 217, 218, 219, 223–27

  Explore Evolution, 315–17

  Extavour, Cassandra, 129

  fauna: Chengjiang evidence of Cambrian explosion, 62–64, 65fig, 71–76; Ediacaran Hills site of Precambrian, 79–81, 80fig–86; Ediacaran mini-explosion of organisms and, 78, 86–88; top-down pattern of Chengjiang, 74–76

  Fedonkin, Mikhail, 81

  Fersht, Alan, 187, 192

  Fisher, R. A., 260

  Foote, Michael, 69–70, 145, 146

  Fortey, Richard, 84

  fossil record: chart showing when representatives of animal phyla appear in, 32fig; deep-divergence explanation for fossils missing from, 100, 101; deep-divergence hypothesis challenged by gene sequencing and, 105–13; Ediacaran Hills site (Australia), 78–92; geological timescale, 15, 16fig; Hox genes in the, 318; Ordovician period, 14fig; Paleozoic period, 14; theory of punctuated equilibrium (“punk eek”) problem with, 142–45; Triassic period, 14. See also Burgess Shale site (Canada); Cambrian period fossils; discontinuity of fossil record; Precambrian-Cambrian fossil record

  fossil succession phenomenon, 15–17

  Franklin, Harold, 275

  Frazzetta, Tom, 230–31, 232–33, 234, 235, 237

  fruit flies. See Drosophila melanogaster

  functional information: amino-acid sequences ratio of nonfunctional to, 178–79; Axe’s experiments on protein natural selection and, 187–200, 202–8; description of, 164, 168; DNA inclusion of, 274–75; genes under selection pressure and, 197fig; Sauer’s experiments on amino-acid sequence, 180–84, 187–89, 192–94; technologies to calculate, 180–83. See also gene sequences; genetic information; information

  Fuxianhuia protensa arthropods, 60

  Gabius, Hans-Joachim, 281

  Galápagos Islands, 21

  Gates, Bill, 359

  Gauger, Ann, 226, 250fig–51, 253

  Gegenbauer, Carl, 21

  gene duplication, 213fig, 217, 218, 219

  gene expression: Hox genes coordination in, 285, 287, 314–15, 314–21; TFs (transcription factors) role in, 258–59; theory of gene regulation for higher cells, 265–68; TRs (transcriptional regulators) role in, 258–59

  gene fission/fusion, 213fig, 217, 219

  genes: animal development and role of proteins and, 258–59; dGRNs (developmental gene regulatory networks), 264–69, 285, 319–20, 363–66; different structures when used in different animals, 367fig; homeotic (Hox), 285, 287, 314–15; Long’s inferred common ancestral, 214–15; mutational mechanisms of, 213fig, 216–19; neo-Darwinian failure to explain generation of new, 257; ORFans, 215–16; organismal and informational context consideration of, 363–71

  gene sequences: Axe’s experiments on protein natural selection and, 187–200, 202–8; combinatorics to calculate possible mutations, 172–83; depiction of how gene duplication and subsequent gene evolution may occur, 214fig; importance of protein folds in, 189–92; Long’s inferred common ancestral, 214–15; mechanisms for DNA generating duplicate, 198–200; problem of combinatorial inflation, 173–74fig, 181fig; “purifying selection” of, 195; under selection pressure, 197fig. See also DNA; functional information

  gene sequencing: deep-divergence hypothesis challenged by fossil record and, 105–13; deep-divergence hypothesis examined by, 100, 101, 103–4; molecular clock analysis of, 102fig–3, 121; questionable assumptions of, 109–10. See also DNA

  genetic information: arguments against a “gene-centric” view of, 282–84; connecting process control and regulation over, 186–87; depiction of how gene duplication and subsequent gene evolution may occur, 214fig; difficulty of explaining the origin of complex adaptations to, 237–39; errors in hypothetical scenarios for origins or mutations of, 211–14; exon shuffling hypothesis on creating, 213fig, 217, 218, 219, 223–27; hierarchical organization of, 364–66; mutational mechanisms assuming preexisting, 213fig, 216–27; population genetics and the origin of, 235–37; scientific debate over origins of new, 209–11; self-organization models on, 297–99; “word salad” explanations for, 227–29. See also animal development; epigenetic information; functional information

  genetic mutations: Antennapedia, 318–19fig; argument that new proteins require multiple improbable, 244–47; attempt to reconcile Darwinian theory with Mendelian genetics, 158–59; Axe’s experiments on protein natural selection and, 187–200, 202–8; cis-regulatory elements (CREs) theory of, 316–17; combinatorics used to calculate, 172–83; cooption model of protein evolution, 249–54; coordinated chloroquine complexity cluster (CCC), 247–49; difficulty of explaining the origin of complex adaptations, 237–39; DNA genetic variation and, 159–61; embryonic lethals and early-acting bodyplan, 259–64; epigenetic information, 285–86; exploring the process of, 169–70; the “great Darwinian paradox” of, 262, 315, 317; Hox genes considered in, 317–21; insect wing coloration, 316fig, 317; looking for the functional sequences solution, 178–79; multiple coordinated mutations required for complex adaptations, 240–41; mutational mechanisms of gene, 213fig, 216–21; population genetics models to explain, 233–44fig; responses to Sauer’s experiments on amino-acid sequences, 180–84, 187–89, 192–94; “sweet spot” for, 246fig; various types due to different mechanisms, 213fig; “waiting times” for, 240–42, 327–29; Wistar Institute conference (1966) on mechanisms of, 170–77, 187; “word salad” explanations for, 227–29; X-ray-induced, 157–58. See also animal development; body plans; DNA; natural selection; traits

  Genome Biology journal, 400

  Genome Research journal, 220, 400

  genomes: ENCODE project study of, 400–402; Heidelberg screens experiments of, 255–57fig; transposons (“jumping genes”) of eukary
otic, 219

  geologic timescale, 15, 16fig

  Gerhart, John, 292

  germ-cell formation modes: epigenesis, 129fig, 130fig; overview of, 127, 129; preformation, 129fig, 130fig

  Gettysburg Address (Lincoln), 368–69fig, 370

  Gilbert, Scott, 287, 314

  Gillespie, Neal, 21

  Gishlick, Alan, 210–11, 221

  Glaessner, Martin, 82–83

  The God Delusion (Dawkins), 409, 411

  God Is Not Great (Hitchens), 409

  “God of the Gaps” objection, 392

  Goldschmidt, Richard, 311

  Gompel, Nicolas, 317

  Goodwin, Brian, 275

  Gould, Stephen Jay, 15–16, 28–29, 39, 48, 54, 57, 231, 293, 311, 312, 314, 344, 368; photograph of, 137fig; theory of punctuated equilibrium contributions by, 136–52

  Graur, Dan, 107

  Gray, Asa, 18

  “great Darwinian paradox,” 262, 315, 317

  Gross, Paul, 211

  Haeckel, Ernst, 4, 18

  Haikouella lanceolata, 74

  Haikouichthys ercaicunensis, 75fig

  Hallucigenia sparsa fossils, 29, 30fig, 38, 53

  Harvey, Ethel, 271

  Hedges, S. Blair, 106

  Heidelberg screens experiments, 255–57fig

  Hennig, Willi, 44

  heritability of variations, 10

  histones, 107–8

  Hitchens, Christopher, 409

  Hoekstra, Hopi, 317

  Holland, Peter, 132

  Holm, Richard, 234

  Hood, Leroy, 359

  Hooker, Joseph, 18

  Hou, Xian-Guang, 62–63

  Hox genes: considering mutation role of, 317–21; Distal-less, 321; evo-devo theorists on, 314–15; in the fossil record, 318; possible harmful effects of, 318–19; regulatory function of, 285, 287, 318

  Huxley, Julian, 158–59

  Huxley, T. H., 18, 158

  hydrophobic core, 192

  Hyman, Libbie, 122

  hypotheses: abductive inference basis for developing, 343–45; method of multiple competing, 346–49; problem of retrodiction in testing, 349, 350fig. See also specific hypothesis; vera causa (true cause) principle