Thaxton, Charles, Walter L. Bradley, and Roger L. Olsen. The Mystery of Life’s Origin: Reassessing Current Theories. New York: Philosophical Library, 1984.
Theissen, Günter. “The Proper Place of Hopeful Monsters in Evolutionary Biology,” Theory in Biosciences 124 (2006): 349–69.
——— . “Saltational Evolution: Hopeful Monsters Are Here to Stay,” Theory in Biosciences 128 (2009): 43–51.
Theobald, Douglas. “Punctuated Equilibrium.” In International Encyclopedia of the Social Sciences, 2nd ed., 6: 629–31. Detroit: Macmillan Library Reference, 2008.
——— . “29+ Evidences for Macroevolution.” http://www.talkorigins.org/faqs/comdesc/section1.html (accessed October 31, 2012).
Thomson, K. S. “Macroevolution: The Morphological Problem.” American Zoologist 32 (1992): 106–12.
Todd, Scott C. “A View from Kansas on That Evolution Debate.” Nature 401 (1999): 423.
Tremblay, A., M. Jasin, and P. Chartrand. “A Double-Strand Break in a Chromosomal LINE Element Can Be Repaired by Gene Conversion with Various Endogenous LINE Elements in Mouse Cells.” Molecular and Cellular Biology 20 (2000): 54–60.
Tyndall, John. “The Parallel Roads of Glen Roy.” In Fragments of Science: A Series of Detached Essays, Addresses, and Reviews. Vol. 1. New York: Appleton, 1915.
Ulam, Stanislaw M. “How to Formulate Mathematically Problems of Rate of Evolution.” In Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, edited by P. S. Moorhead and M. M. Kaplan, 21–33. Wistar Institute Symposium Monograph No. 5. New York: Liss, 1967.
University of California at Berkeley Museum of Paleontology. “Brachiopoda.” http://www.ucmp.berkeley.edu/brachiopoda/brachiopodamm.html.
Uversky, Vladimir N., and Keith Dunker. “Understanding Protein Non-Folding.” Biochimica at Biophysica Acta 1804 (2010): 1231–64.
Valentine, James W. “Fossil Record of the Origin of Bauplan and Its Implications.” In Patterns and Processes in the History of Life, edited by D. M. Raup and D. Jablonski, 209–22. Berlin: Springer-Verlag, 1986.
——— . “Late Precambrian Bilaterians: Grades and Clades.” In Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson, edited by W. M. Fitch and F. J. Ayala, 87–107. Washington, DC: National Academy Press, 1995.
——— . “Why No New Phyla After the Cambrian? Genome and Ecospace Hypotheses Revisited.” Palaios 10 (1995): 190–94.
——— . “Prelude to the Cambrian Explosion.” Annual Review of Earth and Planetary Sciences 30 (2002): 285–306.
——— . On the Origin of Phyla. Chicago: Univ. of Chicago Press, 2004.
Valentine, James W., and Douglas H. Erwin. “Interpreting Great Developmental Experiments: The Fossil Record.” In Development as an Evolutionary Process, edited by R. A. Raff and E. C. Raff, 71–107. New York: Liss, 1987.
Valentine, James W., Douglas H. Erwin, and David Jablonski. “Developmental Evolution of Metazoan Body Plans: The Fossil Evidence.” Developmental Biology 173 (1996): 373–81.
Valentine, James W., David Jablonski, and Douglas H. Erwin. “Fossils, Molecules and Embryos: New Perspectives on the Cambrian Explosion.” Development 126 (1999): 851–59.
Van de Lagemaat, L. N., J. R. Landry, D. L. Mager, and P. Medstrand. “Transposable Elements in Mammals Promote Regulatory Variation and Diversification of Genes with Specialized Functions.” Trends in Genetics 19 (2003): 530–36.
Van Valen, Leigh. “Similar, but Not Homologous.” Nature 305 (1983): 664.
——— . “How Do Major Evolutionary Changes Occur?” Evolutionary Theory 8 (1988): 173–76.
Vedantam, Shankar. “Eden and Evolution.” Washington Post, February 5, 2006.
Venema, D. R. “Seeking a Signature.” Perspectives on Science and Christian Faith 62 (2010): 276–83.
Vermeij, Geerat J. “Animal Origins.” Science 25 (1996): 525–26.
Von Sternberg, Richard. “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System.” Annals of the New York Academy of Sciences 981 (2002): 154–88.
Von Sternberg, Richard, and James A. Shapiro. “How Repeated Retroelements Format Genome Function.” Cytogenetic and Genome Research 110 (2005): 108–16.
Vorzimmer, P. “Charles Darwin and Blending Inheritance.” Isis 54 (1963): 371–90.
Waddington, Conrad. “The Epigenotype.” Endeavour 1 (1942): 18–20.
Waggoner, B. M. “Phylogenetic Hypotheses of the Relationships of Arthropods to Precambrian and Cambrian Problematic Fossil Taxa.” Systematic Biology 45 (1996): 190–222.
Wagner, Andreas. “The Molecular Origins of Evolutionary Innovations.” Trends in Genetics 27 (2011): 397–410.
Wagner, G. P. “What Is the Promise of Developmental Evolution? Part II: A Causal Explanation of Evolutionary Innovations May Be Impossible.” Journal of Experimental Zoology (Molecular and Developmental Evolution) 291 (2001): 305–9.
Wagner, G. P., and P. F. Stadler. “Quasi-Independence, Homology and the Unity of Type: A Topological Theory of Characters.” Journal of Theoretical Biology 220 (2003): 505–27.
Walcott, Charles Doolittle. “Cambrian Geology and Paleontology II: Abrupt Appearance of the Cambrian Fauna on the North American Continent.” Smithsonian Miscellaneous Collections 57 (1910): 1–16.
Wallace, Bruce. “Adaptation, Neo-Darwinian Tautology, and Population Fitness: A Reply.” Evolutionary Biology 17 (1984): 59–71.
Wang, Daniel Y. C., Sudhir Kumar, and S. Blair Hedges. “Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi.” Proceedings of the Royal Society of London B 266 (1999): 163–71.
Wang, E. T., R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. F. Kingsmore, G. P. Schroth, and C. B. Burge. “Alternative Isoform Regulation in Human Tissue Transcriptomes.” Nature 456 (2008): 470–76.
Wang, Wen, Frédéric Brunet, Eviatar Nevo, and Manyuan Long. “Origin of Sphinx, a Young Chimeric RNA Gene in Drosophila melanogaster.” Proceedings of the National Academy of Sciences USA 99 (2002): 4448–53.
Ward, Peter. On Methuselah’s Trail: Living Fossils and the Great Extinctions. New York: Freeman, 1992.
——— . Out of Thin Air: Dinosaurs, Birds, and Earth’s Ancient Atmosphere. Washington, DC: Joseph Henry Press, 2006.
Watanabe T., et al. “Endogenous siRNAs from Naturally Formed dsRNAs Regulate Transcripts in Mouse Oocytes.” Nature 453 (2008): 539–43.
Webster, Gerry, and Brian Goodwin. Form and Transformation: Generative and Relational Principles in Biology. Cambridge: Cambridge Univ. Press, 1996.
Welch, John J., Eric Fontanillas, and Lindell Bromham. “Molecular Dates for the ‘Cambrian Explosion’: The Influence of Prior Assumptions.” Systematic Biology 54 (2005): 672–78.
Wells, Jonathan. “Making Sense of Biology: The Evidence for Development by Design.” In Signs of Intelligence: Understanding Intelligent Design. edited by J. Kushiner and W. A. Dembski, 118–27. Grand Rapids, MI: Brazos, 2001.
Wen, Y., L. Zheng, L. Qu, F. J. Ayala, and Z. Lun. “Pseudogenes Are Not Pseudo Any More.” RNA Biology 9 (2012): 27–32.
West, John G. Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science. Wilmington, DE: ISI Books, 2007.
Whewell, William. “Lyell’s Principles of Geology.” British Critic 9 (1830): 180–206.
Whitehead, Alfred North. Science and the Modern World. New York: Macmillan, 1926.
Whitfield, John. “Biological Theory: Postmodern Evolution?” Nature 455 (2008): 281–84.
Whitman, W. B., D. C. Coleman, and W. J. Wiebe. “Prokaryotes: The Unseen Majority.” Proceedings of the National Academy of Sciences USA 95 (1998): 6578–83.
Wieschaus, Eric. “From Molecular Patterns to Morphogenesis: The Lessons from Drosophila.” Nobel lecture, December 8, 1995.
Wiley, E. O., and Bruce S. Lieberman. Phylogenetics: Theory and Practice of Phylogenetic Systematics. New York:
Wiley-Blackwell, 2011.
Willey, Basil. “Darwin’s Place in the History of Thought.” In Darwinism and the Study of Society, edited by M. Banton, 15. Chicago: Quadrangle, 1961.
Willmer, Pat G., and Peter W. H. Holland. “Modern Approaches to Metazoan Relationships.” Journal of Zoology (London) 224 (1991): 689–94.
Wills, M. A., S. Gerber, M. Ruta, and M. Hughes. “The Disparity of Priapulid, Archaeopriapulid and Palaeoscolecid Worms in the Light of New Data.” Journal of Evolutionary Biology 25 (2012): 2056–76.
Wilson, T. E., U. Grawunder, and M. R. Liebe. “Yeast DNA Ligase IV Mediates NonHomologous DNA End Joining.” Nature 388 (1997): 495–98.
Withgott, Jay. “John Maynard Smith Dies.” Science, April 20, 2004. http://news.sciencemag.org/sciencenow/2004/04/20–01.html.
Wimsatt, William C. “Generativity, Entrenchment, Evolution, and Innateness: Philosophy, Evolutionary Biology, and Conceptual Foundations of Science.” In Where Biology Meets Psychology: Philosophical Essays, edited by V. G. Hardcastle, 139–79. Cabridge, MA: MIT Press, 1999.
Wimsatt, William C., and J. C. Schank. “Generative Entrenchment, Modularity and Evolvability: When Genic Selection Meets the Whole Organism.” In Modularity in Development and Evolution, edited by G. Schlosser and G. Wagner, 359–94. Chicago: Univ. of Chicago Press, 2004.
Wolf, Yuri I., Igor B. Rogozin, and Eugene V. Koonin. “Coelomata and Not Ecdysozoa: Evidence from Genome-wide Phylogenetic Analysis.” Genome Research 14 (2004): 29–36.
Wolfe, Stephen L. Molecular and Cellular Biology. Belmont, CA: Wadsworth, 1993.
Wolfram, Stephen. A New Kind of Science. Champaign, IL: Wolfram Media, 2002.
World Net Daily. “Intelligent Design Torpedoes Tenure.” World Net Daily, May 19, 2007.
Wray, Gregory A., Jeffrey S. Levinton, and Leo H. Shapiro. “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla.” Science 274 (1996): 568–73.
Wu, Dong-Dong, David M. Irwin, and Ya-Ping Zhang. “De Novo Origin of Human Protein-Coding Genes.” PLoS Genetics 7 (2011): e1002379.
Xiao, S., A. H. Knoll, J. D. Schiffbauer, C. Zhou, and X. Yuan. “Comment on ‘Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists.’ ” Science 335 (2012): 1169.
Xun, Gu. “Early Metazoan Divergence Was About 830 Million Years Ago,” Journal of Molecular Evolution 47 (1998): 369–71.
Yochelson, Ellis L. Charles Doolittle Walcott, Paleontologist. Kent, OH: Kent State Univ. Press, 1998.
Yockey, Hubert P. “On the Information Content of Cytochrome C.” Journal of Theoretical Biology 67, no. 3 (1977): 345–76.
——— . “A Calculation of the Probability of Spontaneous Biogenesis by Information Theory.” Journal of Theoretical Biology 67 (1977): 377–98.
——— . Information Theory and Molecular Biology. Cambridge: Cambridge Univ. Press, 1992.
Youngren, K. K., et al. “The Ter mutation in the Dead End Gene Causes Germ Cell Loss and Testicular Germ Cell Tumours.” Nature 435 (2005): 360–64.
Zamora, S., R. Gozalo, and E. Linñán. “Middle Cambrian Gogiid Echinoderms from Northeast Spain: Taxonomy, Palaeoecology, and Palaeogeographic Implications.” Acta Palaeontologica Polonica 54 (2009): 253–65.
Zhang, Jianzhi, David M. Webb, and Ondrej Podlaha. “Accelerated Protein Evolution and Origins of Human-Specific Features: FOXP2 as an Example.” Genetics 162 (2002): 1825–35.
Zhang, Jianzhi, Y. P. Zhang, and H. F. Rosenberg. “Adaptive Evolution of a Duplicated Pancreatic Ribonuclease Gene in a Leaf-Eating Monkey.” Nature Genetics 30, no. 4 (2002): 411–15.
Zhang, Z., et al. “A Sclerite-Bearing Stem Group Entoproct from the Early Cambrian and Its Implications.” Scientific Reports 3 (2013): 1066.
Zhen, Ying, M. Aardema, E. M. Medina, M. Schumer, and P. Andolfatto. “Parallel Molecular Evolution in an Herbivore Community.” Science 337 (2012): 1634–37.
Zheng, Jie, Igor B. Rogozin, Eugene V. Koonin, and Teresa M. Przytycka. “Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation.” Molecular Biology and Evolution 24 (2007): 2583–92.
Zvelebil, Marketa, and Jeremy O. Baum. Understanding Bioinformatics. New York: Garland Science, 2008.
Zuckerkandl, Emile, and Linus Pauling. “Evolutionary Divergence and Convergence in Proteins.” In Evolving Genes and Proteins, edited by B. Bryson and H. Vogel, 97–166. New York: Academic, 1965.
Credits and Permissions
The inclusion of any figures, illustrations, photographs, diagrams, charts, or other types of images in this book should not be construed as an endorsement of the ideas and arguments contained in this book on the part of any copyright holders or creators of those images, other than the author of the book himself.
Illustrations © 2013 Ray Braun, Seattle, WA.
Cover photograph: Courtesy Chen, J. Y., G. Q. Zhou, M. Y. Zhu, and K. Y. Yeh. The Chengjiang Biota—A Unique Window of the Cambrian Explosion. Taichung, Taiwan: National Museum of Natural Science (1996), 149, Figure 186. Used by permission.
Cover: Photograph of trilobite fossil courtesy of J. Y. Chen. Source: Figure 186, Chen, J. Y., Zhou, G. Q., Zhu, M. Y., and Yeh, K. Y. The Chengjiang Biota—A Unique Window of the Cambrian Explosion, 149. Taichung, Taiwan: National Museum of Natural Science, 1996. Used with permission.
Figure 1.1: Tree of life image from Ernst Haeckel, Volume II of Generelle Morphologie (1866). Public Domain.
Figure 1.2a: Louis Agassiz photograph courtesy of Wikimedia Commons. Public Domain.
Figure 1.2b: Charles Darwin photograph courtesy of Wikimedia Commons. Original photograph taken by Henry Maull and John Fox. Public Domain.
Figure 1.3a: Drawing of brachiopod by Ray Braun based on information from Figure 18, Brusca, R. C., and Brusca, G. J. Invertebrates, 794. Sunderland, MA: Sinauer Associates, 1990; Figure 7.55, Mintz, L. W. Historical Geology: The Science of a Dynamic Earth, 130. 2nd ed. Columbus, Charles E. Merrill Publishing, 1977.
Figure 1.3b: Brachiopod fossil photograph showing internal remains courtesy of Paul Chien. Used with permission.
Figure 1.3c: Brachiopod fossil photograph © Colin Keates DK Limited Corbis. Used with permission.
Figure 1.4a: Drawing of trilobite by Ray Braun based on information from “Fossil Groups,” University of Bristol, http://palaeo.gly.bris.ac.uk/palaeofiles/fossilgroups/trilobites/page2.htm.
Figure 1.4b: Trilobite fossil photograph courtesy of Illustra Media. Used with permission.
Figure 1.5: Drawing of tetracoral by Ray Braun based on information from “Convergence,” http://www.znam.bg/com/action/showArticle;jsessionid=FA17A83CDA0EC25151F6B80869F07E49?encID=790&article=2059773460.
Figure 1.6: Drawing of geological timescale by Ray Braun based on information from Mintz, L. W. Historical Geology: The Science of a Dynamic Earth, back page. 2nd ed. Columbus, Charles E. Merrill Publishing, 1977; Gradstein, F. M., Ogg, J. G., Schmitz, M. D., Ogg, G. M. The Geological Timescale 2012 Volumes 1 and 2. Elsevier, 2012.
Figure 1.7: Drawing by Sir Thomas Dick-Lauder and published in Tyndall, J., “The Parallel Roads of Glen Roy.” In Fragments of Science: A Series of Detached Essays, Addresses, and Reviews, Volume I. New York: D. Appleton and Company, 1915. Courtesy of Wikimedia Commons. Public Domain.
Figure 1.8: Drawing by Ray Braun based on information from a fossil exhibit that was on display at the California Academy of Sciences in the 1990s.
Figure 2.1: Photograph of the Burgess Shale © Thomas Kitchin & Victoria Hurst/All Canada Photos/Corbis. Used with permission.
Figure 2.2: Photograph of Charles Doolittle Walcott courtesy of Smithsonian Institution Archives. Image #84–16281. Used with permission.
Figure 2.3a: Drawing of Marrella by Ray Braun based on information from Figure 3.12, Gould, S. J. Wonderful Life: The Burgess Shale and the Nature of History, 114. New York: Norton, 1990.
Figure 2.3b: Photograph of Marrella fossil © User: Smith609 (Own Work) Wikimedia C
ommons CC-BY-SA–3.0. Used with permission; usage not intended to imply endorsement by the author/licensor of the work.
Figure 2.4a: Drawing of Hallucigenia by Ray Braun based on information from Figure 14.6, Xianguang, H., Aldridge, R. J., Bergström, J., Siveter, D. J., Siveter, D. J., and Xiang-hong, F. The Cambrian Fossils of Chengjiang, China: The Flowering of Early Animal Life, 88 Oxford: Blackwell Publishing, 2004; Figure 19(b), Conway Morris, S., The Crucible of Creation: The Burgess Shale and the Rise of Animals, 55. Oxford: Oxford University Press, 2000.
Figure 2.4b: Photograph of Hallucigenia fossil courtesy of Smithsonian Institution. Used with permission.
Figures 2.5a, 2.5b, and 2.5c: Chart drawn by Ray Braun based on data compiled from references in Chapter 2, Endnote 5.
Figure 2.6: Diagram drawn by Ray Braun based on information from Figure 1, Meyer, S. C., Ross, M., Nelson, P. and Chien, P. “The Cambrian Explosion: Biology’s Big Bang.” In Darwinism, Design and Public Education, edited by John Angus Campbell and Stephen C. Meyer, 325. East Lansing, MI: Michigan State University Press, 2003. Courtesy of Brian Gage.
Figure 2.7: Diagram drawn by Ray Braun based on original drawing by Art Battson. Courtesy of Art Battson.
Figure 2.8: Diagram drawn by Ray Braun based on Figure 1, Wiester, J., and Dehaan, R. F., “The Cambrian Explosion: The Fossil Record and Intelligent Design.” In Signs of Intelligence: Understanding Intelligent Design, 149. William A. Dembski and James M. Kushiner, eds. Grand Rapids, MI: Brazos Press, 2001. Courtesy also of Art Battson.
Figure 2.9a: Drawing of Opabinia by Ray Braun based on information from Figure 3.21, Gould, S. J. Wonderful Life: The Burgess Shale and the Nature of History, 126. New York: Norton, 1990; Figure 173, Briggs, D., Erwin, D., and Collier, F. The Fossils of the Burgess Shale, 210. Washington: Smithsonian Institution Press, 1994.
Figure 2.9b: Photograph of Opabinia fossil from Walcott, C. D., “Middle Cambrian Branchiopoda, Malacostraca, Trilobita, and Merostomata.” Smithsonian Miscellaneous Collections, Volume 57, Number 6 (Publication 2051), City of Washington, Published by the Smithsonian Institution, March 13, 1912. Public Domain.
Darwin's Doubt Page 62