Darwin's Doubt
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Figure 14.2: Diagram drawn by Ray Braun based on PowerPoint slides developed by Michael Keas.
Figure 14.3a: Drawn by Joseph Condeelis. Copyright © Discovery Institute 2013. Used with permission.
Figure 14.3b: Courtesy of The Company of Biologists. Source: Figure 1B from Smyth, J. T., DeHaven, W. I., Bird, G. S., and Putney, J. W., “Role of the microtubule cytoskeleton in the function of the store-operated Ca2+ channel activator STIM1,” Journal of Cell Science, 120 (November 1, 2007): 3762–71. Used with permission.
Figure 15.1: Photograph of Stuart Kauffman courtesy of User: Teemu Rajala Wikimedia Commons CC BY 3.0. Used with permission; usage not intended to imply endorsement by the author/licensor of the work.
Figure 15.2: Drawing of DPMs by Ray Braun based on information from Table 1, Stuart A. Newman and Ramray Bhat, “Dynamical patterning modules: physico-genetic determinants of morphological development and evolution,” Physical Biology, 5 (1): 1–14 (April 9, 2008); Figure 11.1, Stuart A. Newman, “Dynamical Patterning Modules,” in Evolution: The Extended Synthesis, 294, Massimo Pigliucci and Gerd B. Muller eds. (The MIT Press, 2010); Stuart A. Newman, “Physico-Genetic Determinants in the Evolution of Development,” Science, 338 (October 12, 2012): 217–19.
Figure 16.1: Drawn by Ray Braun and Paul Nelson.
Figure 16.2: Copyright 2007 National Academy of Sciences, U.S.A. Figure 1, Prud’homme, B., Gompel, N., and Carroll, S. B., “Emerging principles of regulatory evolution,” Proceedings of the National Academy of Sciences (PNAS), USA, 104 (May 15, 2007): 8605–12. Use of PNAS material does not imply any endorsement by PNAS or the National Academy of Sciences or the authors. Used with permission.
Figure 16.3: Reprinted from Current Biology, 11, Starling, E. B., and Cohen, S. M., “Limb development: Getting down to the ground state,” R1025–R1027, Figure 1, Copyright 2001, with permission from Elsevier.
Figure 17.1: Photograph of Charles Thaxton courtesy of Charles Thaxton. Used with permission.
Figure 17.2: Drawing by Ray Braun based on information from Grotzinger, J., Jordan, T. H., Press, F., Siever, R. Understanding Earth, 32–33, 5th ed., New York: W. H. Freeman, 2007; Cox., A., and Hart, R. B. Plate Tectonics: How It Works, 19, Cambridge, MA: Blackwell Science, 1986; Lowrie, W. Fundamentals of Geophysics, 18–19, Cambridge, UK: Cambridge University Press, 1997.
Figure 17.3: Drawing by Ray Braun based on information from Sober, E., Reconstructing the Past, 4–5. Cambridge, MA: MIT Press, 1988.
Figure 18.1: Photograph of Douglas Erwin courtesy of Robyn Wishna UPHOTOCornell University. Used with permission.
Figure 18.2: Drawn by Ray Braun based on information from Figure 2:2, Meyer, S. C., Minnich, S., Moneymaker, J., Nelson, P. A., and Seelke, R. Explore Evolution: The Arguments for and Against Neo-Darwinism, 44. Melbourne and London: Hill House, 2007.
Figure 18.3: Photograph of transistors courtesy of iStockphoto.com/ S230. © iStockphoto.com/ S230. Used with permission.
Figure 18.4: Diagram drawn by Ray Braun based on information from Figure 2, Nelson, P., and Wells, J., “Homology in Biology: Problem for Naturalistic Science and Prospect for Intelligent Design.” In Darwinism, Design and Public Education, 317, edited by John Angus Campbell and Stephen C. Meyer, 303–322. East Lansing, MI: Michigan State University Press, 2003.
Figure 18.5: Diagram drawn by Ray Braun based on PowerPoint slides developed by Michael Keas.
Figure 18.6: Diagram drawn by Ray Braun based on PowerPoint slides developed by Michael Keas.
Figure 18.7: Diagram drawn by Ray Braun based on PowerPoint slides developed by Michael Keas.
Figure 19.1: Photograph of Richard Sternberg courtesy of Laszlo Bencze. Used with Permission.
Figure 19.2: Photograph of Moais courtesy of iStockphoto/Think-stock. Used with permission.
Figure 20.1: Photograph of trilobite fossil at Burgess Shale courtesy of Michael Melford NATIONAL GEOGRAPHIC IMAGE COLLECTION Getty Images. Used with permission.
Figure 20.2a: Photograph of Stephen C. Meyer and family copyright © 2013 Stephen C. Meyer.
Figure 20.2b: Photograph of mountainside near Burgess Shale copyright © 2013 Stephen C. Meyer.
Index
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Page references followed by fig indicate an illustration.
abductive inference: definition of, 343; inductive and deductive arguments, 343–44; plausibility of, 345. See also causal adequacy
Abegg, Adam, 327–28
Agassiz, Louis: belief in a creative intelligence by, 100; “Evolution and the Permanence of Type” by, 11; extensive fossil specimens collected by, 21; German idealism and cosmic philosophy of, 18–19, 20; on incomplete fossil record challenging Darwin’s theory by, 8fig–10, 17, 18–24fig, 69, 379, 381; photograph of, 7fig
allopatric speciation process: allowing for rapid fixation of preexisting traits, 146–47; theory of punctuated equilibrium and, 139–42
Altenberg 16, 291–92, 293, 313
American Association for the Advancement of Science (AAAS), 385
amino-acid sequences: combinatorial inflation problem applied to proteins, 173–74fig, 181fig; forming polypeptide chain, 190fig; ratio of functional to nonfunctional, 178–79; responses to Sauer’s experiment on, 180–84, 187–89, 192–94; Sauer’s experiments on, 180–83, 187–89, 192–94; technologies for calculating functional, 180–83. See also proteins
“Anarchist’s Manifesto” (Nelson), 370
anatomical characteristics: analysis of animal life histories using, 125–32; “Coelomata” hypothesis based on analysis of, 122
animal development: dGRNs (developmental gene regulatory networks) required for, 264–69, 285, 319–20, 363–66; epigenetic information required to complete, 271–87; dynamical patterning modules (DPMs) role during, 301fig–2, 303–4; early-acting bodyplan mutations and embryonic lethals, 259–64; Hox genes expressed after the beginning of, 319–20; ontogeny studies on, 258–69; principle of constraints and, 268–69; self-organizational models on, 293–310; three challenges to neo-Darwinism posed by, 262–64; understanding the Cambrian explosion in context of engineering, 270. See also body plans; embryos; genetic information; genetic mutations; organisms
animal life histories: analysis of anatomical characteristics of different, 125–32; attempts to confirm evolutionary phylogenies, 121–25; conflicting molecular data, 119–21; fundamental difficulties with phylogenetic reconstruction of, 132–33; molecular homologies studies on, 121–25
animal phyla: chart showing representatives in the fossil record, 32fig; debate over Vernanimalcula fossil as bilaterian ancestor, 89, 90, 91fig–96; description of, 31; diagrams representing, 24fig; Ediacaran mini-explosion of fauna and, 86–88; Metazoan, 104, 107, 126–27, 128fig; “morphological space” between, 70–71; Precambrian-era, 81–92; rapid divergence of specifically genetic evidence, 121; representatives of major animal groups, 33fig; selection of incompatible phylogenetic trees representing, 131fig; stasis or persistent morphological isolation evidence in Cambrian fossil record, 375–78; statistical paleontology casting doubt on animal tree of life, 69–71; Vernanimalcula bilaterian shape, 89, 90, 91fig–96. See also bilaterian phyla; Cambrian phyla (animal groups); intermediate animal life forms; organisms; phylogenetic classification
animal tree of life: Cambrian explosion and, 12–13; comparing actual animal phyla pattern to one using Darwin’s, 24fig; conflicting histories of anatomical characteristics, 119–32; convergent evolution invoked for, 133–34; Darwin’s argument on similar anatomical structure of distinct organisms, 99fig–101; Darwin’s evolutionary, 3–5, 41–42fig; examining possibility of Precambrian and Cambrian, 117–32; iconic image and representation of Darwin’s, 114–17; lack of convergent evidence supporting, 135; statistical paleontology analysis failure to support, 69–71. See also Cambrian phyla (animal groups); evolutionary biology; unive
rsal common ancestry
Anomalocaris fossils, 38–39fig, 53, 60, 62
Antennapedia mutant, 318–19fig
Archives of Natural History journal, 114
Aris-Brosou, Stéphane, 106
Arkarua fossil, 89fig, 90
arthropods: exoskeleton of, 60–61; onychophorans once proposed as ancestors of, 60
Arthur, Wallace, 275, 312
artifact hypothesis: contemporary versions of, 57–62, 105; other versions of the, 56–57; statistical paleontology failure to support, 69–71; Walcott’s conception of, 46–47, 49, 52, 55, 56. See also Darwinian evolutionary theory; Lipalian interval hypothesis; Walcott, Charles Doolittle
Asher, Robert, 392, 393, 394, 397, 398
At Home in the Universe: The Search for the Laws of Self-Organization and Complexity (Kauffman), 297–98
Atkins, Peter, 115
Atlantic Monthly, 11
ATP, 280
Axe, Douglas, 185, 186fig–89, 191–95, 196, 198–200, 202–8, 226, 229, 235, 250–51, 253, 254, 327–28
Ayala, Francisco, 107
Babcock, Loren, 83
Bateson, William, 18, 237
Behe, Michael, 184, 240, 241fig, 242–43, 244–49, 253
Bengtson, Stefan, 90–91, 92
Berlinski, David, 362
bilaterian phyla: Coelomata hypothesis on three classifications of, 122, 123fig, 124; Ecdysozoa hypothesis on three classifications of, 122–23fig, 124; Vernanimalcula as possible ancestor of, 89, 90, 91fig–96. See also animal phyla
Biological Society of Washington, 384–85
Biological Theory (journal), 125
Birket-Smith, Sven Jorgen, 82
Blanco, Francisco, 197
blended inheritance theory, 156–57
The Blind Watchmaker (Dawkins), 176, 185–86
body plans: dGRNs (developmental gene regulatory networks) role in, 264–69, 285, 319–20, 363–66; DNA epigenetic information required for animal development and, 271–87; embryonic lethals and early-acting mutations, 259–64; Heidelberg screens experiments on Drosophila melanogaster (fruit flies), 255–57; Kauffman on self-organizational process of, 295; neo-Darwinian failure to explain generation of new genes and proteins for, 257; self-organizational to explain origin of, 300–302. See also animal development; genetic mutations
Bottjer, David J., 90, 91–92
bottom-up pattern: Burgess Shale’s top-down pattern contradicting Darwin’s, 39–44; Cambrian top-down pattern contradicting punctuated equilibrium’s, 142–44fig; Chengjiang fauna fossil top-down pattern contradicting Darwin’s, 74–76; neo-Darwinism’s, 144fig, 145–46, 371. See also top-down pattern
Bowring, Samuel, 73
Brachiopod internal anatomy fossil, 8fig, 10
brachiopods, 8, 10, 59–61
Bradley, Walter, 341
Brenner, Sidney, 187, 275–76
Britten, Roy, 265
Bromham, Lindell, 106
Budd, Graham, 85, 90–91, 96, 291
Burgess Shale Geoscience Foundation, 405
Burgess Shale site (Canada): Anomalocaris fossils of, 53, 60, 62; artifact hypothesis used to explain, 46–47, 49, 52, 55, 56, 105; author’s hike with son up to, 404–8, 412–13; Cambrian explosion features challenging Darwinism, 34–44; Cambrian period diversity preserved at, 44–46; discovery of, 26, 27fig–28; Hallucigenia sparsa fossils of, 29, 30fig, 38, 53; lumping classification approach to, 47–48, 55; Marrella splendens fossils of, 29, 30fig, 38, 48, 53, 60, 62; Nectocaris fossils of, 53, 54fig; Opabinia fossils of, 36, 37fig, 38, 52–53; seafloor fossils of, 54–56; soft-bodied representatives found at, 61–62; top-down pattern evidenced at, 39–44; trilobite fossil found at, 405fig; variety of fossils found at the, 28–34; Whittington’s analysis of, 52–54fig; Wiwaxia fossils of, 53, 62. See also Cambrian period fossils; fossil record; Walcott, Charles Doolittle
Caenorhabditis elegans, 258, 267
Cambrian explosion: Chengjiang fauna fossils from, 62–64, 65fig, 73–76; Darwin’s growing anomaly and failure to explain, 8fig–10, 13–17, 18–24fig, 34–44, 50–52, 69, 71–76, 286–87; deep-divergence hypothesis explanation for the, 100, 101–13; evidence redefining the narrow geological time of, 72fig–74; examining the deep-divergence hypothesis used to dispute, 100, 101–13; features of, 34–44; firestorm around Smithsonian’s NMNH journal article on, 209–11; fossils establishing a “fuse” for, 78; how Axe’s experiments bear on problems for neo-Darwinian explanations of, 205–7; intelligent design applied to, 351–52, 353–81; Kauffman’s self-organizational proposal on, 299–300; neo-Darwinism’s failure to explain, 257, 286–87; new genetic information arising during, 161–64; serious and important questions raised by the, 411–13; statistical paleontology on pattern of, 69–71; theory of punctuated equilibrium attempt to provide explanation of, 137–52; the tree of life and, 12–13; understood in context of engineering animal development, 270; Walcott’s Burgess Shale’s fossil record of, 31, 33–34. See also Cambrian phyla (animal groups)
The Cambrian Explosion (Valentine and Erwin), 69
Cambrian explosion features: completely novel animal forms, 34, 38–39fig; radical differences before more minor, small-scale diversification, 34, 39–44; sudden appearance and missing intermediates, 34–38
Cambrian explosion mystery: as acknowledged by Darwin, 23; as noted by Agassiz, 17, 24; as made more acute by Burgess fauna, 34–44; as made more acute by Chinese fossils, 62–69, 74–76; Cambrian information explosion providing evidence on, 161–64, 358–63; considering intelligent design as solution to, 378–81; dGRNs (developmental gene regulatory networks) role in solving the, 363–66; distinctive features of design evidence in, 380fig; examining evidence of design, 351–52; looking for evidence of design in the fossil record, 371–78; organismal and informational context considered in the, 366–71; profile of the suspect in, 354–56; profiling a cause of the, 356–58; stasis or persistent morphological isolation evidence, 375–78; top-down pattern of fossil evidence, 39–44, 74–76, 142–44fig, 371–73, 374fig, 375
The Cambrian Fossils of Chengjiang, China (Hou), 63
Cambrian information explosion, 161–64, 358–63
Cambrian period fossils: Agassiz’s challenge to Darwin using record of, 8fig–10, 17, 18–24fig, 69; Chengjiang discoveries (China), 62–64,
Cambrian period fossils (continued) 65fig, 71–76; Darwin’s Cambrian dilemma display (Sam Noble Science Museum) on, 96–97; Darwin’s Dilemma documentary challenging Darwin’s theory based on, 77–79; Darwin’s explanation for discontinuity of, 6, 17–18, 23–24; Darwin’s theory challenged by evidence of, 6–17; discontinuity evidence found in Wales, 13–14; examining the deep-divergence hypothesis to explain discontinuity of, 100, 101–13; looking for evidence of design in the, 371–78; punctuated equilibrium’s bottom-down pattern contradicted by top-down pattern of, 142–44fig; stasis or persistent morphological isolation evidence in, 375–78; top-down pattern of, 39–44, 74–76, 142–44fig, 371–73, 374fig, 375. See also Burgess Shale site (Canada); fossil record
Cambrian phyla (animal groups): Brachiopod internal anatomy fossil, 8fig, 10; chart showing representatives of, 32fig; diagrams representing, 24fig; Ediacaran Hills exotic fossils as possible ancestors to, 88–92; examining the possibility of tree of, 117–32; fossil record showing soft and hard body parts, 57–62, 105; how Axe’s experiments bear on problems for neo-Darwinian explanations of, 205–7; “morphological space” between, 70–71; representatives of, 33fig; soft-bodied representatives, 59–60, 105; statistical paleontology casting doubt on Darwin’s tree of life, 69–71; Trilobite anatomy fossil, 9fig, 10. See also animal phyla; animal tree of life; Cambrian explosion
Cambrian radiation duration, 88
Cambrian strata: Agassiz’s challenge to Darwin using lack of fossil evidence, 8fig–10, 17, 18–24fig, 69; Darwin’s explanation for discontinuity evidence in, 6, 17–18, 23–24; discontinuity evidence found in Wales, 13–14; geological time of Cambrian explosion evidenced in, 72fig–74; ra
diometric dating of zircon crystals in Siberia, 71–72fig
Carroll, Sean B., 84, 120, 121, 312, 314, 317, 368
causal adequacy: criteria of, 348; only known cause issue of, 349–51; problem of retrodiction in testing, 349, 350fig; Signature in the Cell proposed explanations for biological information, 359–60; vera causa (true cause) principle of, 216–17, 309–10. See also abductive inference
CD-ROM technology, 378
cell differentiation: description of, 258–59; epigenetic information role in, 276–77; self-organization models on, 294–95, 297–99; theory gene regulation for higher cells for, 265–68
cells: biological complexity scale as measure in different organism, 162fig; cytoskeletons of eukaryotic, 277–79; daughter, 258, 278; dGRNs (developmental gene regulatory networks) influencing development of, 264–69, 285, 319–20, 363–66; DNA minimally required for complex single-celled organisms, 163; epigenetic information in patterns of proteins in cell membranes, 279–81, 305; epigenesis germ-cell mode, 129fig, 130fig; primordial germ cells (PGCs), 127, 129fig; studies on ontogeny process of, 258–59; theory of gene regulation for higher cells, 265–68
Chamberlain, Thomas, 346
change hypothesis, 201–2
Charlesworth, Brian, 149
Charnia fossil, 80fig, 81, 82, 88
Chen, J. Y., 50, 51fig, 52, 59, 61, 63, 66, 67, 72, 76, 406
Chengjiang discoveries (China): Cambrian conundrum of the, 71–74; Cambrian explosion fossils from fauna of, 62–64, 65fig, 73–76; story of the discovery, 50–52; top-down pattern observed at, 74–76
Chesterton, G. K., 382, 385
Cheungkongella ancestralis, 75
Chien, Paul, 64, 66–67, 88, 406
chloroquine complexity cluster (CCC), 247–48
choanoflagellates, 161–62
Christian theology, 410–13
Chronicle of Higher Education, 210
cis-regulatory elements (CREs), 316, 317
Coelomata hypothesis, 122, 123fig, 124
Collins, Francis, 410, 411, 412
combinatorial inflation problem, 173–74fig, 181fig
combinatorics: used to calculate DNA mutations, 172–83; description of, 172; looking for the functional sequences solution, 178–79; problem of combinatorial inflation, 173–74fig, 181fig