Scientific American journal, 92
Scudder, Samuel, 20
Sedgwick, Adam, 13–14, 15
self-organizational models: on epigenetic information, 295–97; failure to provide vera causa (true cause), 309–10; on genetic information, 297–99; Kauffman proposal on the Cambrian explosion using, 299–300; Kauffman’s system of interconnected lights, 298–99; order vs. information dilemma of, 305–9; origin of body plans explained by, 300–302; overview of the, 293–95; presupposing developmental genetic toolkit, 300–305
Sepkoski, David, 138, 150
Sepkoski, Jack, 41
sequence hypothesis, 159, 169, 177
Shannon, Claude, 164
Shannon information theory, 164–68, 274, 275
Shapiro, James, 332–35, 402
Shapiro, Leo H., 57, 103
Shu, D. G., 75
Signature in the Cell (Meyer), 359–60, 389, 391, 392, 402
Silurian period. See Cambrian period
Simpson, George Gaylord, 61
Slatkin, Montgomery, 149
Smith, Andrew, 109
Smith, William, 15
Smithsonian’s National Museum of Natural History (NMNH), 209–11, 384
Snoke, David, 240, 241, 244–47, 253
soft-bodied fossil representatives, 57–62, 105
species selection, eliminating less fit species, 147, 148
Spemann, Hans, 271, 273, 275
spliceosomes, 323–24
sponges: Chengjiang embryo fossils, 66–68, 67fig; Ediacaran mini-explosion producing, 86–88; morphological studies on monophyletic nature of, 125
Spriggina fossil, 80fig, 81, 82–83, 88
St. Johnston, Daniel, 256
Stanley, Steven, 137, 141, 147, 314
statistical paleontology: casting more doubt on artifact hypothesis, 69–71, 105; Darwin’s tree of life inconsistency with findings of, 69–71; theory of punctuated equilibrium questions raised by, 145–46
Sternberg, Richard, 210, 384fig, 385, 402
stromatolite fossils, 58fig
Strongylocentrotus purpuratus (purple sea urchin), 266fig, 267–68
The Structure of Evolutionary Theory (Gould), 149, 150
sugar molecules, 280–81, 282–83
Syvanen, Michael, 120
Szathmáry, Eörs, 320, 362
TalkReason.org, 210–11
TFs (transcription factors), 258–59
Thaxton, Charles, 341fig–42
Theobald, Douglas, 122
theory of blended inheritance, 155–57
theory of gene regulation for higher cells, 265–68
theory of punctuated equilibrium (“punk eek”): “allopatric speciation” process used in, 139–42; Cambrian top-down pattern contradicting the bottom-up pattern of, 142–43; the fossil record problem for, 142–45; history of life depicted by the, 141fig; initial interest and then decline of, 149–51; origins and development of the, 137–39
Thomson, Keith Stewart, 259, 286
TIME magazine, 50
Todd, Scott, 402–3
top-down pattern: of Chengjiang fauna fossil, 74–76; found at Burgess Shale site, 39–44; Precambrian-Cambrian fossil record, 371–73, 374fig, 375; punctuated equilibrium history of life contradicted by Cambrian, 142–44fig. See also bottom-up pattern
trace fossils (Ediacaran Hills site), 81, 85–86
traits: allopatric speciation allowing for rapid fixation of preexisting, 146–47; analysis of anatomical, 125–32; “long periods of stasis” bringing about new, 147; Mendel’s experiments with factors and genes for, 157; species selection eliminating undesirable, 147, 148; theory of blended inheritance on, 155–57. See also genetic mutations
transfer of mobile genetic units, 213fig, 217, 218–19
transistor (general purpose), 368fig
The Tree of Life, 110
tree of life. See animal tree of life
Trends in Ecology and Evolution journal, 119
Trends in Genetics journal, 107
Triassic period fossils, 14
trilobite fossils: anatomy, 9fig, 10; Burgess Shale site, 405fig
TRs (transcriptional regulators), 258–59
tubulin subunits, 277–78fig
Turing, Alan, 295–96
“20+ Evidences for Macroevolution” (Theobald), 122
Ulam, Stanislaw, 171, 177
Ultrabithorax gene (fruit fly), 261–62
Understanding Bioinformatics, 110
uniformitarian principles, 391–92, 393
universal common ancestry: Burgess Shale’s failure to support, 36fig; Cambrian explosion and tree of life of, 12–13; conflicting gene evidence on the timing of, 105–6; convergent evolution invoked for, 133–34; Darwin’s theory of evolution on pattern of, 3–5; deep-divergence hypothesis argument for, 100, 101–13; Long’s inferred common ancestral gene of, 214–15; molecular clock analysis argument for, 102fig–3, 121; sequencing DNA to attempt to prove, 100–101; “shmoo-like” catch–22 of the assumption of, 111–13; similar anatomical structures evidence of, 99fig–100. See also animal tree of life; degree of difference; intermediate animal life forms
universal metamorphism hypothesis, 57
Valentine, James, 41, 59, 69, 83–84, 90, 106, 107, 109, 110, 124, 143–44, 151, 162, 163, 292, 355–56
Vendian period, 79
vera causa (true cause) principle: causal adequacy criteria of, 348; Darwin’s argument using criterion of, 216–17; description of, 309; materialistic causes compared to, 394; only known cause, 349–51; self-organization “natural magic” versus, 309–10. See also hypotheses; science
Vernanimalcula fossil, 89, 90, 91fig–96
Waggoner, Benjamin, 81
“Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett and Schmidt), 249
waiting times: neutral or nonadaptive evolutionary theory on, 327–29; population genetics models calculating, 240–42
Walcott, Charles Doolittle: Burgess Shale discovery of, 26, 26–29, 34, 40, 48–49, 52; lumping approach favored by, 47–48, 55; other versions of artifact hypothesis by, 56–62, 105; Whittington’s analysis undercutting solution offered by, 52–54. See also artifact hypothesis; Burgess Shale site (Canada)
“Walcott, the Burgess Shale and Rumours of a Post-Darwinian World” (Morris), 291
Wallace, Bruce, 260
Wall Street Journal, 385
Wang, Daniel, 106
Waptia arthropods, 60, 65fig
Ward, Peter, 11
Warrawoona Group fossils (Australia), 58
watch-to-watchmaker design argument, 37–38
Watson, James, 159, 160fig, 166, 187, 236
Wegener, Alfred, 346
Wells, Jonathan, 77, 92, 273fig, 370
Whittington, Harry, 52–54
Wieschaus, Eric, 255–56, 257fig, 260, 270, 315
Willmer, Pat, 132
Wistar Institute conference (1966), 170–77, 187
Wiwaxia fossils, 53, 62
“word salad” explanations, 227–29
Wray, Gregory A., 57, 103
Yang, Ziheng, 106
Yockey, Hubert, 180–81, 308
Yunnanozoon lividum, 74–75
Zhou, Gui-Qing, 59, 61, 63
Zuckerkandl, Emile, 121, 122, 125
Acknowledgments
Though I am not a biologist, but a philosopher of biology, I have the good fortune of overseeing an interdisciplinary scientific research effort that gives me a bird’s-eye view on some cutting-edge discoveries and insights coming from some exceptional scientists. With that in mind, I would like to thank my colleagues at the Discovery Institute and Biologic Institute, in particular Paul Nelson, Douglas Axe, Jonathan Wells, Michael Behe, Ann Gauger, Richard Sternberg, Paul Chien, and Casey Luskin—whose research has made the argument of this book possible. I would especially like to acknowledge Paul Nelson for his assistance writing Chapters 6 and 13, expanded versions of which we pla
n to publish jointly as technical articles. In addition, Casey Luskin, Discovery research coordinator, has repeatedly gone above and beyond the call of duty in his commitment to, and skillful work on, this book. I’d also like to acknowledge the two anonymous biologists and two paleontologists who gave such careful attention to improving the scientific rigor and accuracy of the manuscript during the peer-review process. I would also like to express my thanks to Paul Chien, Marcus Ross, and Paul Nelson for the research they did in support of our 2003 article “The Cambrian Explosion: Biology’s Big Bang,” which provided a scaffolding for the argument developed here in a much expanded form.
In addition, I deeply appreciate the work of our Discovery Institute writers and editors—Jonathan Witt, David Klinghoffer, Bruce Chapman, and Elaine Meyer—who have made this manuscript infinitely more readable. Jonathan Witt deserves special mention for helping me to launch this project and for his help developing story elements and ideas. I’d like to thank my assistant Andrew McDiarmid for his diligent work on the bibliography and managing the flow of information. And Ray Braun cannot be thanked enough for his beautiful artwork. Finally, I’d like to express my gratitude to the good people at Harper: Lisa Zuniga for her exceptional coordination and skill in moving the book through the production process; Ann Moru for her expert copyediting; and to my senior editor Roger Freet for his vision, patience, and uncommon strategic guidance.
Photographic Insert
Plate 1. Mt. Maotian, near Chengjiang, China. The famous Chengjiang fossil site was discovered near the top of this mountain. Courtesy Illustra Media (all).
Plate 2. The original discovery site of the first Chengjiang fossils. Today this area is a preserve.
Plate 3. Looking down from Mt. Maotian, with the large Fuxian Lake in the distant foreground.
Plate 4. The opabinid Jianfengia multisegmentalis. Courtesy Paul Chien. Unless otherwise noted, all fossils shown on this and subsequent color pages are from the Maotianshan Shale near Chengjiang, China.
Plate 5. A fossilized comb jelly (a ctenophore). Species: Maotianoascus octonarius. Courtesy J. Y. Chen.
Plates 6 & 7. Priapulid worms of the species Maotianshania cylindrica. Courtesy Paul Chien and Illustra Media.
Plate 8. A lobopodian “worm with legs” of the genus Microdictyon.
Plate 9. Another lobopod worm. Species: Microdictyon sinicum.
Plate 10. Luolishania longicruris, a rare lobopod of the Maotianshan Shale.
Plate 11. The extinct and enigmatic Vetulicolia, thought to represent either an arthropod, a tunicate-like urochordate, or a distinct phylum. Courtesy Illustra Media (all).
Plates 12 & 13. Two specimens of the arthropod Leanchoilia. The top specimen shows its distinctive long frontal whiplike appendages.
Plate 14. Chengjiangocaris longiformis (below), a rare arthropod known only from the Chengjiang biota. Courtesy Illustra Media (all).
Two fossils from the dark-colored Burgess Shale, near the town of Field in British Columbia, Canada. Note the contrast in color to the fossils from the honey-colored Maotianshan Shale depicted on the previous and subsequent pages.
Plate 15. A fossil of the arthropod Marrella from the Burgess Shale. Courtesy Illustra Media.
Plate 16 (below). The shrimp-like arthropod Waptia. Courtesy Illustra Media.
Plate 17. The arthropod Fuxianhuia protensa. Note its exquisitely preserved eyes, antennae, segmented body, and forked tail. Courtesy Illustra Media.
Plate 18. A fossil of the arthropod Waptia, from the honey-colored Maotianshan Shale. Courtesy Paul Chien.
Plate 19. A fossil of an Anomalocaris, whose large eyes and jaws made it the fiercest predator in the Cambrian seas. Some reached a length of one meter. Courtesy J. Y. Chen.
Plates 20–22. A montage of beautifully preserved trilobites from the Maotianshan Shale, including a specimen of Eoredlichia intermedia (left). Courtesy Illustra Media (all).
Plate 23. A specimen of the trilobite Kuanyangia pustulosa from the Maotianshan Shale near Chengjiang, China. Courtesy Illustra Media.
Copyright
DARWIN’S DOUBT: The Explosive Origin of Animal Life and the Case for Intelligent Design. Copyright © 2013 by Stephen C. Meyer. All rights reserved under International and Pan-American Copyright Conventions. By payment of the required fees, you have been granted the nonexclusive, nontransferable right to access and read the text of this e-book on-screen. No part of this text may be reproduced, transmitted, downloaded, decompiled, reverse-engineered, or stored in or introduced into any information storage and retrieval system, in any form or by any means, whether electronic or mechanical, now known or hereinafter invented, without the express written permission of HarperCollins e-books.
Illustrations © 2013 Ray Braun, Seattle, WA.
FIRST EDITION
Library of Congress Cataloging-in-Publication Data is available upon request.
ISBN 978–0–06–207147–7
EPub Edition © APRIL 2013 ISBN: 9780062071491
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