Darwin's Doubt

by Stephen C. Meyer

  Marshall, Jessica. “Proteins Made to Order.” Nature News, November 7, 2012. http://www.nature.com/news/proteins-made-to-order–1.11767.

  Marshall, Wallace F., and Joel L. Rosenbaum. “Are There Nucleic Acids in the Centrosome?” Current Topics in Developmental Biology 49 (2000): 187–205.

  Masui, Y., A. Forer, and A. M. Zimmerman. “Induction of Cleavage in Nucleated and Enucleated Frog Eggs by Injection of Isolated Sea-Urchin Mitotic Apparatus.” Journal of Cell Science 31 (1978): 117–35. http://jcs.biologists.org/content/31/1/117.long (accessed October 30, 2012).

  Mattick, John S., and Michael J. Gagen. “The Evolution of Controlled Multitasked Gene Networks: The Role of Introns and Other Noncoding RNAs in the Development of Complex Organisms.” Molecular Biology and Evolution 18 (2001): 1611–30.

  Mattick, J. S., and I. V. Makunin. “Small Regulatory RNAs in Mammals.” Human Molecular Genetics 14 (2005): R121–32.

  ——— . “Noncoding RNA.” Human Molecular Genetics 15 (2006): R17–R29.

  Matz, Mikhail V., Tamara M. Frank, N. Justin Marshall, Edith A. Widder, and Sönke Johnsen. “Giant Deep-Sea Protist Produces Bilaterian-like Traces.” Current Biology 18 (December 9, 2008): 1849–54.

  Matzke, Nicholas J. “The Edge of Creationism.” Trends in Ecology and Evolution 22 (2007): 566–67.

  Matzke, Nicholas J., and Paul R. Gross. “Analyzing Critical Analysis: The Fallback Antievolutionist Strategy.” In Not in Our Classrooms: Why Intelligent Design Is Wrong for Our Schools, edited by E. C. Scott and G. Branch, 28–56. Boston: Beacon, 2006.

  Maynard Smith, John. “Natural Selection and the Concept of a Protein Space.” Nature 225 (1970): 563–64.

  ——— . “Darwinism Stays Unpunctured.” Nature 330 (1987): 516.

  Mayr, Ernst. Foreword. In Darwinism Defended: A Guide to the Evolution Controversies, edited by M. Ruse, xi–xii. Reading, MA: Addison-Wesley, 1982.

  Mayr, Ernst, and William B. Provine. The Evolutionary Synthesis: Perspectives on the Unification of Biology. Cambridge, MA: Harvard Univ. Press, 1998.

  Mazur, Suzan. The Altenberg 16: An Exposé of the Evolution Industry. Berkeley, CA; North Atlantic Books, 2010.

  McCall, G. J. H. “The Vendian (Ediacaran) in the Geological Record: Enigmas in Geology’s Prelude to the Cambrian Explosion.” Earth-Science Reviews 77 (2006): 1–229.

  McDonald, John F. “The Molecular Basis of Adaptation: A Critical Review of Relevant Ideas and Observations.” Annual Review of Ecology and Systematics 14 (1983): 77–102.

  McGinnis, William, and Michael Kurziora. “The Molecular Architects of Body Design.” Scientific American 270 (1994): 58–66.

  McKenzie, Richard W., and Mark D. Brennan. “The Two Small Introns of the Drosophila affinidisjuncta Adh Gene Are Required for Normal Transcription.” Nucleic Acids Research 24 (1996): 3635–42.

  McMenamin, M. A. S. “Ediacaran Biota from Sonora, Mexico.” Proceedings of the National Academy of Sciences USA 93 (1996): 4990–93.

  ——— . The Garden of Ediacara: Discovering the First Complex Life. New York: Columbia Univ. Press, 1998.

  ——— . The Evolution of the Noösphere. New York: American Teilhard Association for the Future of Man, 2001.

  ——— . “Spriggina Is a Trilobitoid Ecdysozoan.” Geological Society of America Abstracts with Programs 35 (2003): 105–6.

  ——— . “Harry Blackmore Whittington, 1916–2010.” Geoscientist 20 (2010): 5.

  ——— . “Fossil Chitons and Monomorphichnus from the Ediacaran Clemente Formation, Sonora, Mexico.” Geological Society of America Abstracts with Programs 43 (2011): 87.

  ——— . “Teilhard de Chardin’s Legacy in Science.” In The Legacy of Teilhard de Chardin, edited by J. Salmon and J. Farina, 33–45. Mahwah, NJ: Paulist Press, 2011.

  McMenamin, M. A. S., and D. L. S. McMenamin. The Emergence of Animals: The Cambrian Breakthrough. New York: Columbia Univ. Press, 1990.

  Medstrand, P., J.-R. Landry, and D. L. Mager, “Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans.” Journal of Biological Chemistry 276 (2001): 1896–903.

  Merhej, Vicky, and Didier Raoult. “Rhizome of Life, Catastrophes, Sequence Exchanges, Gene Creations, and Giant Viruses: How Microbial Genomics Challenges Darwin.” Frontiers in Cellular and Infectious Microbiology 2, no. 113 (2012).

  Meyer, Stephen C. “Of Clues and Causes: A Methodological Interpretation of Origin of Life Studies.” Ph.D. dissertation, Cambridge University, 1990.

  ——— . “A Scopes Trial for the ’90s.” Wall Street Journal, December 6, 1993, A14.

  ——— . “Laws, Causes and Facts: A Response to Professor Ruse.” In Darwinism: Science or Philosophy? edited by J. Buell and V. Hearn, 29–40. Dallas: Foundation for Thought and Ethics, 1994.

  ——— . “The Methodological Equivalence of Design and Descent.” In The Creation Hypothesis: Scientific Evidence for Intelligent Design, edited by J. P. Moreland, 67–112. Downer’s Grove, IL: InterVarsity Press, 1994.

  ——— . “The Nature of Historical Science and the Demarcation of Design and Descent.” In Facets of Faith and Science. Vol. 4, Interpreting God’s Action in the World, 91–130. Washington, DC: Univ. Press of America, 1996.

  ——— . “The Demarcation of Science and Religion.” In The History of Science and Religion in the Western Tradition: An Encyclopedia, edited by G. B. Ferngren, 17–23. New York: Garland, 2000.

  ——— . “The Scientific Status of Intelligent Design: The Methodological Equivalence of Naturalistic and Non-Naturalistic Origins Theories.” In Science and Evidence for Design in the Universe, The Proceedings of the Wethersfield Institute, 151–212. San Francisco: Ignatius, 2000.

  ——— . “The Origin of Biological Information and the Higher Taxonomic Categories,” Proceedings of the Biological Society of Washington 117 (2004): 213–39.

  ——— . “The Origin of Biological Information and the Higher Taxonomic Categories.” In Darwin’s Nemesis: Phillip Johnson and the Intelligent Design Movement, edited by W. A. Dembski, 174–213. Downers Grove, IL: InterVarsity, 2006.

  ——— . Signature in the Cell: DNA and the Evidence for Intelligent Design. San Francisco: HarperOne, 2009.

  ——— . “Sauce for the Goose: Intelligent Design, Scientific Methodology, and the Demarcation Problem.” In Nature of Nature: Examining the Role of Naturalism in Science, edited by B. L. Gordon and W. A. Dembski, 95–131. Wilmington, DE: ISI Books, 2011.

  Meyer, Stephen C., Scott Minnich, Jonathan Moneymaker, Paul A. Nelson, and Ralph Seelke. Explore Evolution: The Arguments for and Against Neo-Darwinism. Melbourne and London: Hill House, 2007.

  Meyer, Stephen C., Marcus Ross, Paul Nelson, and Paul Chien. “The Cambrian Explosion: Biology’s Big Bang.” In Darwinism, Design and Public Education, edited by J. A. Campbell and S. C. Meyer, 323–402. East Lansing: Michigan State Univ. Press, 2003.

  Michel, Bénédicte. “After 30 Years, the Bacterial SOS Response Still Surprises Us.” PLoS Biology 3 (2005): 1174–76.

  Miklos, George L. G. “Emergence of Organizational Complexities During Metazoan Evolution: Perspectives from Molecular Biology, Palaeontology and Neo-Darwinism.” Memoirs of the Association of Australasian Palaeontologists 15 (1993): 7–41.

  Miller, Kenneth R. “Falling over the Edge: Review of The Edge of Evolution, by Michael Behe.” Nature 447 (2007): 1055–56.

  Mintz, Leigh W. Historical Geology: The Science of a Dynamic Earth. 2nd ed. Columbus, OH: Merrill, 1977.

  Moczek, Armin P. “On the Origins of Novelty in Development and Evolution.” BioEssays 30 (2008): 432–47.

  ——— . “The Nature of Nurture and the Future of Evodevo: Toward a Theory of Developmental Evolution.” Integrative and Comparative Biology 52 (2012): 108–19.

  Monastersky, Richard. “Siberian Rocks Clock Biological Big Bang.” Science News 144 (1993): 148.

  ——— . “Ancient Animal Sheds False Identity.” Scien
ce News 152 (1997): 32.

  ——— . “Society Disowns Paper Attacking Darwinism.” Chronicle of Higher Education 51, no. 5 (2004): A16.

  Mondal, T., M. Rasmussen, G. K. Pandey, A. Isaksson, and C. Kanduri. “Characterization of the RNA Content of Chromatin.” Genome Research 20 (2010): 899–907.

  Monteys, A. M., R. M. Spengler, J. Wan, L. Tecedor, K. A. Lennox, Y. Xing, and B. L. Davidson. “Structure and Activity of Putative Intronic miRNA Promoters.” RNA 16 (2010): 495–505.

  Morrish, T. A., N. Gilbert, J. S. Myers, B. J. Vincent, T. D. Stamato, G. E. Taccioli, M. A. Batzer, and J. V. Moran. “DNA Repair Mediated by Endonuclease-Independent LINE–1 Retrotransposition.” Nature Genetics 31 (2002): 159–65.

  Moss, Lenny. What Genes Can’t Do. Cambridge, MA: MIT Press, 2004.

  Müller, Dietmar R., Walter R. Roest, Jean-Yves Royer, Lisa M. Gahagan, and John G. Sclater. “Digital Isochrons of the World’s Ocean Floor.” Journal of Geophysical Research 102 (1997): 3211–14.

  Müller, Gerd B. “Homology: The Evolution of Morphological Organization.” In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by G. B. Müller and S. A. Newman, 51–69. Cambridge, MA: MIT Press, 2003.

  Müller, Gerd B., and Stuart A. Newman. “Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory.” In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by G. B. Müller and S. A. Newman, 3–10. Cambridge, MA: MIT Press, 2003.

  Muller, H. J. “Artificial Transmutation of the Gene.” Science 66 (1927): 84–87.

  Muller, K. J., D. Bonn, and A. Zakharov. “ ‘Orsten’ Type Phosphatized Soft-Integument Preservation and a New Record from the Middle Cambrian Kuonamka Formation in Siberia.” Neues Jahrbuch für Geologie und Paläontologie, Monatshefte 197 (1995): 101–18.

  Mura, M., P. Murcia, M. Caporale, T. E. Spencer, K. Nagashima, A. Rein, and M. Palmarini. “Late Viral Interference Induced by Transdominant Gag of an Endogenous Retrovirus.” Proceedings of the National Academy of Sciences USA 101 (2004): 11117–22.

  Murchison, Roderick Impey. Siluria: The History of the Oldest Known Rocks Containing Organic Remains. London: John Murray, 1854.

  Murphy, Nancey. “Phillip Johnson on Trial: A Critique of His Critique of Darwin.” Perspectives on Science and Christian Faith 45 (1993): 26–36.

  Nanney, D. L. “The Ciliates and the Cytoplasm.” Journal of Heredity 74 (1983): 163–70.

  Nardi, F., G. Spinsanti, J. L. Boore, A. Carapelli, R. Dallai, and F. Frati. “Hexapod Origins: Monophyletic or Paraphyletic?” Science 299 (2003): 1887–89.

  ——— . “Response to Comment on ‘Hexapod Origins: Monophyletic or Paraphyletic?’ ” Science 301 (2003): 1482.

  Nash, J. Madeleine. “When Life Exploded.” Time 146 (1995): 66–74.

  National Academy of Sciences. Teaching About Evolution and the Nature of Science. Washington DC: National Academy Press, 1998.

  National Ocean Industries Association. “About NOIA.” http://www.noia.org/website/article.asp?id-51 (accessed March 29, 2013).

  Nature editors. “Life on Land.” Nature 492 (2012): 153–54.

  Nelson, Paul, and Jonathan Wells. “Homology in Biology: Problem for Naturalistic Science and Prospect for Intelligent Design.” In Darwinism, Design and Public Education, edited by J. A. Campbell and S. C. Meyer, 303–22. East Lansing: Michigan State Univ. Press, 2003.

  Newman, Stuart. “The Developmental Genetic Toolkit and the Molecular Homology-Analogy Paradox.” Biological Theory 1 (2006): 12–16.

  ——— . “Dynamical Patterning Modules.” In Evolution: The Extended Synthesis, edited by M. Pigliucci and G. B. Müller, 281–306. Cambridge, MA: MIT Press, 2010.

  ——— . “Animal Egg as Evolutionary Innovation: A Solution to the ‘Embryonic Hourglass’ Puzzle.” Journal of Experimental Zoology B: Molecular and Developmental Evolution 314 (2011): 467–83.

  Newman, Stuart, and Ramray Bhat. “Dynamical Patterning Modules: Physico-Genetic Determinants of Morphological Development and Evolution.” Physical Biology 5 (2008): 015008.

  Newton, Isaac. Newton’s Principia. Translated by Andrew Motte (1686). Translation revised by Florian Cajori. Berkeley, CA: Univ. of California Press, 1934.

  Nielsen, Claus. Animal Evolution: Interrelationships of the Living Phyla. Oxford: Oxford Univ. Press, 2001.

  Nijhout, H. F. “Metaphors and the Role of Genes in Development.” BioEssays 12 (1990): 441–46.

  Nikoh, Naruo, et al. “An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks.” Journal of Molecular Evolution 45 (1997): 97–106.

  Nilsen, Timothy W. “The Spliceosome: The Most Complex Macromolecular Machine in the Cell?” BioEssays 25 (2003): 1147–49.

  Nurminsky, D. I., M. V. Nurminskaya, D. De Aguiar, and D. L. Hartl. “Selective Sweep of a Newly Evolved Sperm-Specific Gene in Drosophila.” Nature 396 (1998): 572–75.

  Nüsslein-Volhard, C., and E. Wieschaus. “Mutations Affecting Segment Number and Polarity in Drosophila.” Nature 287 (1980): 795–801.

  O’Brien, L. J., and J.-B. Caron. “A New Stalked Filter-Feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada.” PLoS One 7 (2012): 1–21.

  Ohno, S. “The Notion of the Cambrian Pananimalia Genome.” Proceedings of the National Academy of Sciences USA 93 (1996): 8475–78.

  Oliveri, Paola, and Eric H. Davidson. “Built to Run, Not Fail.” Science 315 (2007): 1510–11.

  Oliveri, Paola, Qiang Tu, and Eric H. Davidson. “Global Regulatory Logic for Specification of an Embryonic Cell Lineage.” Proceedings of the National Academy of Sciences USA 105 (2008): 5955–62.

  Oosthoek, Jan. “The Parallel Roads of Glen Roy and Forestry.” Environmental History Resources. http://www.eh-resources.org/roy.html.

  Oreskes, Naomi. “From Continental Drift to Plate Tectonics.” In Plate Tectonics: An Insider’s History of the Modern Theory of the Earth, edited by N. Oreskes, 3–30. Boulder, CO: Westview, 2003.

  Orgel, L. E., and F. H. Crick. “Selfish DNA: The Ultimate Parasite.” Nature 284 (1980): 604–7.

  Orr, H. Allen. “The Genetic Theory of Adaptation: A Brief History.” Nature Reviews Genetics 6 (2005): 119–27.

  Osigus, Hans-Jürgen, Michael Eitel, and Bernd Schierwater. “Chasing the Urmetazoon: Striking a Blow for Quality Data?” Molecular Phylogenetics and Evolution 66 (2013): 551–57.

  Ou, Q., J. Liu, D. Shu, J. Han, Z. Zhang, X. Wan, and Q. Lei. “A Rare Onychophoran-Like Lobopodian from the Lower Cambrian Chengjiang Lagerstätte, Southwestern China, and Its Phylogenetic Implications.” Journal of Paleontology 85 (2011): 587–94.

  Pagano, A., M. Castelnuovo, F. Tortelli, R. Ferrari, G. Dieci, and R. Cancedda. “New Small Nuclear RNA Gene-like Transcriptional Units as Sources of Regulatory Transcripts.” PLoS Genetics 3 (2007): e1.

  Palade, George E. “Membrane Biogenesis: An Overview.” Methods in Enzymology 96 (1983): xxix–lv.

  Paley, William. Natural Theology: Or Evidences of the Existence and Attributes of the Deity Collected from the Appearances of Nature. 1802. Reprint, Boston: Gould and Lincoln, 1852.

  Palopoli, Michael, and Nipam Patel. “Neo-Darwinian Developmental Evolution: Can We Bridge the Gap Between Pattern and Process?” Current Opinion in Genetics and Development 6 (1996): 502–8.

  Pandey, R., and M. Mukerji. “From ‘JUNK’ to Just Unexplored Noncoding Knowledge: The Case of Transcribed Alus.” Briefings in Functional Genomics 10 (2011): 294–311.

  Panganiban, G., et al. “The Origin and Evolution of Animal Appendages.” Proceedings of the National Academy of Sciences USA 94 (1997): 5162–66.

  Pardue, M. L., and P. G. DeBaryshe. “Drosophila Telomeres: Two Transposable Elements with Important Roles in Chromosomes.” Genetica 107 (1999): 189–96.

  Parikesit, A. A., P. F. Stadler, and S. J. Prohaska. “Quantitative Comparison of Genomic-W
ide Protein Domain Distributions.” In Lecture Notes in Informatics P–173, edited by D. Schomburg and A. Grote, 93–102. Bonn: Gesellschaft für Informatik, 2010.

  Patterson, Colin, David M. Williams, and Christopher J. Humphries. “Congruence Between Molecular and Morphological Phylogenies.” Annual Review of Ecology and Systematics 24 (1993): 153–88.

  Paulding, Charles A., Maryellen Ruvolo, and Daniel A. Haber. “The Tre2 (USP6) Oncogene Is a Hominoid-Specific Gene.” Proceedings of the National Academy of Sciences USA 100 (2003): 2507–11.

  Peaston, E., A. V. Evsikov, J. H. Graber, W. N. de Vries, A. E. Holbrook, D. Solter, and B. B. Knowles. “Retrotransposons Regulate Host Genes in Mouse Oocytes and Preimplantation Embryos.” Developmental Cell 7 (2004): 597–606.

  Peel, J. S. “A Corset-Like Fossil from the Cambrian Sirius Passet Lagerstätte of North Greenland and Its Implications for Cycloneuralian Evolution.” Journal of Paleontology 84 (2010): 332–40.

  Peifer, Mark, and Welcome Bender. “The Anterobithorax and Bithorax Mutations of the Bithorax Complex.” EMBO Journal 5 (1986): 2293–303. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1167113/pdf/emboj00172–0253.pdf.

  Peirce, Charles S. Collected Papers. Vols. 1–6. Edited by C. Hartshorne and P. Weiss. Cambridge, MA: Harvard Univ. Press, 1931–35.

  ——— . “Abduction and Induction.” In The Philosophy of Peirce, edited by J. Buchler, 150–54. London: Routledge, 1956.

  ——— . Collected Papers, Vols. 7–8. Edited by A. Burks. Cambridge, MA: Harvard Univ. Press, 1958.

  Pellas, Theodore C., B. Ramachandran, M. Duncan, S. S. Pan, M. Marone, and K. Chada. “Germ-Cell Deficient (gcd), an Insertional Mutation Manifested as Infertility in Transgenic Mice.” Proceedings of the National Academy of Sciences USA 88 (1991): 8787–91.

  Peterson, Kevin J., James A. Cotton, James G. Gehling, and Davide Pisani. “The Ediacaran Emergence of Bilaterians: Congruence Between the Genetic and the Geological Fossil Records.” Philosophical Transactions of the Royal Society B (2008): 1435–43.

  Peterson, Kevin J., and Eric H. Davidson. “Regulatory Evolution and the Origin of the Bilaterians.” Proceedings of the National Academy of Sciences USA 97 (2000): 4430–33.