Darwin's Doubt

by Stephen C. Meyer

  10. Peirce, Collected Papers, 2:372–88; Meyer, “Of Clues and Causes,” 25. See also Whewell, “Lyell’s Principles of Geology”; The Philosophy of the Inductive Sciences.

  11. Peirce, Collected Papers, 2:372–88. See also Fann, Peirce’s Theory of Abduction, 28–34; Whewell, “Lyell’s Principles of Geology”; The Philosophy of the Inductive Sciences.

  12. Gould, “Evolution and the Triumph of Homology,” 61. See also Whewell, “Lyell’s Principles of Geology”; The Philosophy of the Inductive Sciences.

  13. Peirce, “Abduction and Induction,” 150–54.

  14. Chamberlain, “The Method of Multiple Working Hypotheses.”

  15. Conniff, “When Continental Drift Was Considered Pseudoscience.”

  16. Conniff, “When Continental Drift Was Considered Pseudoscience.”

  17. Oreskes, “From Continental Drift to Plate Tectonics,” 12.

  18. Heirtzler, “SeaFloor Spreading”; Hurley, “The Confirmation of Continental Drift”; Vine, “Reversals of Fortune.”

  19. For example, Xavier Le Pichon recalls: “I was progressively forced by the convincing power of the magnetic [data]” (“My Conversion to Plate Tectonics,” 212).

  20. Lipton, Inference to the Best Explanation, 1.

  21. Lipton, Inference to the Best Explanation, 1.

  22. Lyell, Principles of Geology, 75–91.

  23. Kavalovski, “The Vera Causa Principle,” 78–103.

  24. Scriven, “Explanation and Prediction in Evolutionary Theory,” 480; Gallie, “Explanations in History and the Genetic Sciences”; Sober, Reconstructing the Past, 1–5.

  25. Meyer, “Of Clues and Causes,” 96–108.

  Chapter 18: Signs of Design in the Cambrian Explosion

  1. Davidson, “Evolutionary Bioscience as Regulatory Systems Biology,” 35.

  2. Erwin and Davidson, “The Evolution of Hierarchical Gene Regulatory Networks,” 141.

  3. Davidson, “Evolutionary Bioscience as Regulatory Systems Biology,” 6.

  4. Erwin, “Early Introduction of Major Morphological Innovations,” 288.

  5. Erwin, “Early Introduction of Major Morphological Innovations,” 288, emphasis added.

  6. As Erwin puts it: “There is every indication that the range of morphological innovation possible in the Cambrian is simply not possible today” (“The Origin of Body Plans,” 626, emphasis added).

  7. Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe, 327; see also “Evolution: Bringing Molecules into the Fold”; “The Cambrian Explosion of Metazoans.”

  8. Conway Morris, Life’s Solution, 327. See also Conway Morris, “Bringing Molecules into the Fold,” 8.

  9. Shapiro, Evolution.

  10. Dawkins, River Out of Eden, 17.

  11. Hood and Galas, “The Digital Code of DNA.”

  12. Gates, The Road Ahead, 188.

  13. Quastler, The Emergence of Biological Organization, 16.

  14. Of course, the phrase “large amounts of specified information” begs a quantitative question, namely, “How much specified information would the minimally complex cell have to have before it implied design?” In Signature in the Cell, I give and justify a precise quantitative answer to this question. I show that the de novo emergence of 500 or more bits of specified information reliably indicates design. Meyer, Signature in the Cell, 294.

  15. Dawkins, The Blind Watchmaker, 47–49; Küppers, “On the Prior Probability of the Existence of Life”; Scheider, “The Evolution of Biological Information”; Lenski, “The Evolutionary Origin of Complex Features.” For a critique of these genetic algorithms and claims that they simulate the ability of natural selection and random mutation to generate new biological information apart from intelligent activity, see Meyer, Signature in the Cell, 281–95.

  16. Berlinski, “On Assessing Genetic Algorithms.”

  17. Rodin, Szathmáry, and Rodin, “On the Origin of the Genetic Code and tRNA Before Translation,” 2.

  18. Denton, Evolution: A Theory in Crisis, 309–11.

  19. Polanyi, “Life Transcending Physics and Chemistry”; “Life’s Irreducible Structure.”

  20. Oliveri and Davidson, “Built to Run, Not Fail.” All animal embryos, notes Davidson, must “turn on the right regulatory genes in the right place. These genes must also be dynamically locked on; the regulatory state of cells in a given spatial domain must further be made dependent on signaling among them all; the expression of these same regulatory genes must be specifically forbidden anywhere else; and then, on top of all that, specific alternative states must be excluded. These components are of course interlinked… . In the sea urchin embryo, where all of the above are to be found, disarming any one of these subcircuits produces some abnormality in expression” (511; emphasis added).

  21. Davidson, Genomic Regulatory Systems, 54.

  22. “Sameness” (i.e., homology) is determined by nucleotide-sequence conservation within a reading frame.

  23. Newman, “The Developmental Genetic Toolkit and the Molecular Homology-Analogy Paradox,” 12.

  24. Within evolutionary theory, several proposals have attempted to resolve the paradox. Perhaps the most popular modifies the neo-Darwinian definition of the concept of “homology” by preceding it with the adjective “deep,” a verbal slipcover that—if one is cynically inclined—ought to elicit sardonic commentary befitting a late-night comedy sketch. Strictly speaking, we should remember that the neo-Darwinian prediction about genes, phenotypes, and homology was found to be wrong. Nothing wrong ever turned out right by putting the adjective “deep” in front of it.

  25. Carroll, Endless Forms Most Beautiful, 72.

  26. Gould, The Structure of Evolutionary Theory, 1065. Stuart Newman observes: “It came as a big surprise to workers in the fields of evolutionary and developmental biology … that the Drosophila eyeless (ey) gene has extensive DNA similarity to the mouse and human Pax-6 genes” because “evolutionary theory has traditionally held that very long periods of time were needed for natural selection to generate extreme differences in morphological organization.” Yet, he notes, if over long periods of time, natural selection and mutation had produced extensive changes in morphology, it ought to have produced extensive changes in genes as well (“The Developmental Genetic Toolkit and the Molecular Homology-Analogy Paradox,” 12).

  27. Nelson and Wells, “Homology in Biology,” 316.

  28. Nelson and Wells, “Homology in Biology,” 316.

  29. Erwin, “Disparity.” Erwin observes: “The distribution of organic forms is clumpy at any scale from populations to the highest taxonomic categories, and whether considered within clades or within eco-systems. The fossil record provides little support for expectations that the morphological gaps between species or groups of species have increased through time as it might if the gaps were created by extinction of a more homogeneous distribution of morphologies. As the quantitative assessments of morphology have replaced counts of higher taxa as a metric of morphological disparity, numerous studies have demonstrated the rapid construction of morphospace early in evolutionary radiations” (57, emphasis added).

  30. Dembski, “Intelligent Design as a Theory of Technological Evolution”; Savransky, Engineering of Creativity, 8, 24; Bracht, “Inventions, Algorithms, and Biological Design.”

  31. Valentine, “Why No New Phyla After the Cambrian?”; see also Bergström, “Ideas on Early Animal Evolution.” Bergström comments: “There is absolutely no sign of convergence between phyla as we follow them backwards to the Early Cambrian. They were as widely apart from the beginning as they are today. Hierarchical levels apparently include a biological reality, not only classificatory convention. In fact, the overwhelming taxonomic difficulty is to recognize relationships between phyla, not to distinguish between them” (464).

  32. Denton, Evolution, 313.

  33. Agassiz, “Evolution and the Permanence of Type,” 101.

  Chapter 19: The Rules of Science

  1. Cheste
rton, “The Invisible Man.”

  2. Murphy, “Phillip Johnson on Trial,” 33. Nancey Murphy is a philosopher and seminary professor who strongly affirms methodological naturalism. Here’s what she says in full: “Science qua science seeks naturalistic explanations for all natural processes. Christians and atheists alike must pursue scientific questions in our era without invoking a Creator… . Anyone who attributes the characteristics of living things to creative intelligence has by definition stepped into the arena of either metaphysics or theology.” See also Willey, “Darwin’s Place in the History of Thought,” 15 (“Science must be provisionally atheistic, or cease to be itself”); Grizzle, “Some Comments on the ‘Godless’ Nature of Darwinian Evolution,” 176.

  3. Meyer, “The Origin of Biological Information and the Higher Taxonomic Categories.”

  4. For detailed discussions of facts of the Sternberg case, see “Smithsonian Controversy,” www.richardsternberg.com/smithsonian.php; U.S. Office of Special Counsel Letter (2005) at www.discovery.org/f/1488; United States House of Representatives Committee on Government Reform, Subcommittee Staff Report, “Intolerance and the Politicization of Science at the Smithsonian” (December 2006), at www.discovery.org/f/1489; Appendix, United States House of Representatives Committee on Government Reform, Subcommittee Staff Report (December, 2006) at www.discovery.org/f/1490.

  5. See “Statement from the Council of the Biological Society of Washington,” originally at http://www.biolsocwash.org/id_statement.html; now at http://ncse.com/news/2004/10/bsw-strengthens-statement-repudiating-meyer-paper–00528 or http://web.archive.org/web/20070926214521/http://www.biolsocwash.org/id_statement.html.

  6. E-mail from Roy McDiarmid to Hans Sues, “Re: Request for information” (January 28, 2005, 2:25 p.m.), cited in United States House of Representatives Committee on Government Reform, “Intolerance and the Politicization of Science at the Smithsonian,” available at http://www.discovery.org/f/1489 (“I have seen the review file and comments from 3 reviewers on the Meyer paper. All three with some differences among the comments recommended or suggested publication. I was surprised but concluded that there was not inappropriate behavior vs a vis [sic] the review process”).

  7. Klinghoffer, “The Branding of a Heretic.”

  8. See “Statement from the Council of the Biological Society of Washington,” originally at http://www.biolsocwash.org/id_statement.html; now at http://ncse.com/news/2004/10/bsw-strengthens-statement-repudiating-meyer-paper–00528 or http://web.archive.org/web/20070926214521/http://www.biolsocwash.org/id_statement.html.

  9. “AAAS Board Resolution on Intelligent Design Theory,” AAAS News Archives, October 18, 2002, at http://www.aaas.org/news/releases/2002/1106id2.shtml.

  10. See Siegal, “Riled by Intelligent Design”; World Net Daily, “Intelligent Design Torpedoes Tenure”; Brumfiel, “Darwin Sceptic Says Views Cost Tenure”; Dillon, “Regents Deny Gonzalez’s Tenure Appeal”; Meyer, “A Scopes Trial for the ’90s”; West, Darwin Day in America, 234–38; “Background to the Guillermo Gonzalez Story,” at http://www.evolutionnews.org/gg-bckgrndr.final.pdf; “Intelligent Design Was the Issue After All (Updated),” at http://www.evolutionnews.org/ID_was_the_Issue_Gonzalez_Tenure.pdf; LeVake v. Independent School District, 625 N.W.2d 502, 506 (Minn. Ct. App. 2001), cert. denied, 534 U.S. 1081 (2002); Mims, “The Scientific American Affair”; Crocker, Free to Think; Vedantam, “Eden and Evolution”; Luskin, “Darwin’s Dilemma”; Anderson, “Cancellation of Darwin Film Creates Uproar”; Reardon, “California Science Center to Pay $110,000 Settlement Over Intelligent Design Film”; Boehm, “California Science Center Is Sued for Canceling a Film Promoting Intelligent Design”; Crowther, “Academic Freedom Expelled from Baylor University”; Briggs and Maaluf, “BU Had Role in Dembski Return”; Luskin, “Credibility Gap”; Black, “Intelligent Design Proponent Fired from NASA Lab”; Pitts, “Design Flaw?”; Associated Press, “Former NASA Specialist Claims He Was Fired over Intelligent Design”; Associated Press, “JPL Worker Sues over Intelligent Design Demotion”; Gallegos, “Intelligent Design Proponent Who Works at JPL Says He Experienced Religious Discrimination”; Luskin, “Intelligent Design Demoted.”

  11. Crick, What Mad Pursuit, 138.

  12. Lewontin, “Billions and Billions of Demons,” 28. The role of methodological materialism in artificially buttressing Darwin’s theory began with Darwin himself. According to historian of science Neal Gillespie: “The uneasy reservations about natural selection among Darwin’s contemporaries and the widespread rejection of it from the 1890s to the 1930s suggest that … it was more Darwin’s insistence on totally natural explanations than on natural selection that won their adherence… . The primary change had not been in speciation theory but in beliefs about the nature of science.” In short, Darwin’s new definition of science excluded “both direct and indirect design” in living things and thereby protected it from competition (Charles Darwin and the Problem of Creation, 123, 147, 152).

  13. Laudan, “The Demise of the Demarcation Problem”; Meyer, “The Demarcation of Science and Religion.”

  14. Newton, Newton’s Principia, 543–44; Alexander, The Leibniz-Clarke Correspondence, 92; Hutchison, “What Happened to Occult Qualities in the Scientific Revolution?”; Leibniz, New Essays on Human Understanding, 61, 65–67.

  15. As Newton wrote in his famous letter to Bishop Bentley: “The cause of gravity is what I do not pretend to know” (Cohen, Isaac Newton’s Papers and Letters on Natural Philosophy, 302).

  16. Laudan says, “There is no demarcation line between science and nonscience, or between science and pseudo-science, which would win assent from a majority of philosophers” (Beyond Positivism and Relativism, 210).

  17. Laudan, “The Demise of the Demarcation Problem.

  18. Newton, Newton’s Principia, 543–44; Alexander, The Leibniz-Clarke Correspondence, 92; Hutchison, “What Happened to Occult Qualities in the Scientific Revolution?”; Leibniz, New Essays on Human Understanding, 61, 65–67.

  19. Hutchison, “What Happened to Occult Qualities in the Scientific Revolution?” Leibniz, New Essays on Human Understanding, 61, 65–67.

  20. Laudan, “The Demise of the Demarcation Problem”; Eger, “A Tale of Two Controversies.”

  21. Gould, “Creationism”; Ruse, “Witness Testimony Sheet”; Ebert et al., Science and Creationism, 8–10.

  22. Kline, “Theories, Facts and Gods,” 42; Gould, “Evolution as Fact and Theory,” 120; Root-Bernstein, “On Defining a Scientific Theory,” 72.

  23. Root-Bernstein, “On Defining a Scientific Theory,” 73; Ruse, “A Philosopher’s Day in Court,” 28; Ebert et al., Science and Creationism, 8–10.

  24. Ruse, “Witness Testimony Sheet,” 301; “A Philosopher’s Day in Court,” 26; “Darwinism: Philosophical Preference, Scientific Inference, and a Good Research Strategy,” 1–6.

  25. Ruse, Darwinism Defended, 59; “Witness Testimony Sheet,” 305; Gould, “Evolution as Fact and Theory,” 121; Root-Bernstein, “On Defining a Scientific Theory,” 74.

  26. Kehoe, “Modern Anti-Evolutionism”; Ruse, “Witness Testimony Sheet,” 305; “A Philosopher’s Day in Court,” 28; Ebert et al., Science and Creationism, 8.

  27. Kitcher, Abusing Science, 126–27, 176–77.

  28. Skoog, “A View from the Past”; Root-Bernstein, “On Defining a Scientific Theory,” 74; Scott, “Keep Science Free from Creationism,” 30.

  29. Lyell, Principles of Geology.

  30. Meyer, Signature in the Cell, 481–97.

  31. See Meyer, Signature in the Cell, 416–38; see also Meyer, “The Scientific Status of Intelligent Design: The Methodological Equivalence of Naturalistic and Non-Naturalistic Origins Theories,” 151–212; Meyer, “The Nature of Historical Science and the Demarcation of Design and Descent” 91–130; Meyer, “Laws, Causes and Facts: A Response to Professor Ruse,” 29–40; Meyer, “Sauce for the Goose: Intelligent Design, Scientific Methodology, and the Demarcation Problem,” 95–131; Meyer, “The Methodological Equivale
nce of Design and Descent,” 67–112.

  32. See Meyer, Signature in the Cell, 441–42.

  33. Meyer, Signature in the Cell, 373–95.

  34. Asher, Evolution and Belief, 32.

  35. Asher, Evolution and Belief, 32.

  36. Asher, Evolution and Belief, 32.

  37. Asher, Evolution and Belief, 32.

  38. Oddly, also Asher observes that overall “Meyer professes a low regard for naturalism, but high regard for uniformitarianism” (Evolution and Belief, 32). If by naturalism, he means treating the principle of methodological naturalism as normative for all scientific inquiry, his characterization of my position is, in this respect, accurate.

  39. Asher, Evolution and Belief, 32.

  40. Ecker et al., “Genomics.”

  41. Ecker et al., “Genomics,” 52.

  42. Orgel and Crick, “Selfish DNA.”

  43. Dembski, “Science and Design,” 26.

  44. The ENCODE Project Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome,” 57.

  45. Shapiro and Von Sternberg, “Why Repetitive DNA is Essential to Genome Function”; Von Sternberg and Shapiro, “How Repeated Retroelements Format Genome Function”; Han, Szak, and Boeke, “Transcriptional Disruption by the L1 Retrotransposon”; Janowski et al., “Inhibiting Gene Expression at Transcription Start Sites in Chromosomal DNA with Antigene RNAs”; Goodrich and Kugel, “Noncoding-RNA Regulators of RNA Polymerase II Transcription”; Li et al., “Small dsRNAs Induce Transcriptional Activation in Human Cells”; Pagano et al., “New Small Nuclear RNA Gene-like Transcriptional Units”; Van de Lagemaat et al., “Transposable Elements in Mammals”; Donnelly, Hawkins, and Moss, “A Conserved Nuclear Element”; Dunn, Medstrand, and Mager, “An Endogenous Retroviral Long Terminal Repeat”; Burgess-Beusse et al., “The Insulation of Genes from External Enhancers and Silencing Chromatin”; Medstrand, Landry, and Mager, “Long Terminal Repeats Are Used as Alternative Promoters”; Mariño-Ramírez et al., “Transposable Elements Donate Lineage-Specific Regulatory Sequences to Host Genomes”; Green, “The Role of Translocation and Selection”; Figueiredo et al., “A Central Role for Plasmodium Falciparum Subtelomeric Regions”; Henikoff, Ahmad, and Malik, “The Centromere Paradox”; Bell, West, and Felsenfeld, “Insulators and Boundaries”; Pardue and Debaryshe, “Drosophila Telomeres”; Henikoff, “Heterochromatin Function in Complex Genomes”; Schueler et al., “Genomic and Genetic Definition of a Functional Human Centromere”; Jordan et al., “Origin of a Substantial Fraction of Human Regulatory Sequences from Transposable Elements”; Chen, DeCerbo, and Carmichael, “Alu Element-Mediated Gene Silencing”; Jurka, “Evolutionary Impact of Human Alu Repetitive Elements”; Lev-Maor et al., “The Birth of an Alternatively Spliced Exon”; Kondo-Iida et al., “Novel Mutations and Genotype–Phenotype Relationships in 107 Families”; Mattick and Makunin, “Noncoding RNA”; McKenzie and Brennan, “The Two Small Introns of the Drosophila affinidisjuncta Adh Gene”; Arnaud et al., “SINE Retroposons Can Be Used In Vivo”; Rubin, Kimura, and Schmid, “Selective Stimulation of Translational Expression by Alu RNA”; Bartel, “MicroRNAs”; Mattick and Makunin, “Small Regulatory RNAs in Mammals”; Dunlap et al., “Endogenous Retroviruses Regulate Periimplantation Placental Growth and Differentiation”; Hyslop et al., “Downregulation of NANOG Induces Differentiation”; Peaston et al., “Retrotransposons Regulate Host Genes in Mouse Oocytes and Preimplantation Embryos”; Morrish et al., “DNA Repair Mediated by Endonuclease-Independent LINE–1 Retrotransposition”; Tremblay, Jasin, and Chartrand, “A Double-Strand Break in a Chromosomal LINE Element Can Be Repaired”; Grawunder et al., “Activity of DNA Ligase IV Stimulated by Complex Formation with XRCC4 Protein in Mammalian Cells”; Wilson, Grawunder, and Liebe, “Yeast DNA Ligase IV Mediates NonHomologous DNA End Joining”; Mura et al., “Late Viral Interference Induced by Transdominant Gag of an Endogenous Retrovirus”; Goh et al., “A Newly Discovered Human Alpha-Globin Gene”; Kandouz et al., “Connexin43 Pseudogene Is Expressed”; Tam et al., “Pseudogene-Derived Small Interfering RNAs Regulate Gene Expression in Mouse Oocytes”; Watanabe et al., “Endogenous siRNAs from Naturally Formed dsRNAs Regulate Transcripts in Mouse Oocytes”; Piehler et al., “The Human ABC Transporter Pseudogene Family”; Mattick and Gagen, “The Evolution of Controlled Multitasked Gene Networks”; Pandey and Mukerji, “From ‘JUNK’ to Just Unexplored Noncoding Knowledge”; Balakirev and Ayala, “Pseudogenes”; Pink et al., “Pseudogenes”; Wen et al., “Pseudogenes Are Not Pseudo Any More”; Franco-Zorrilla et al., “Target Mimicry Provides a New Mechanism for Regulation of MicroRNA Activity”; Colas et al., “Whole-Genome MicroRNA Screening Identifies let-7 and miR-18 as Regulators”; Carrier et al., “Long NonCoding Antisense RNA Controls Uchl1 Translation”; Kelley and Rinn, “Transposable Elements Reveal a Stem Cell Specific Class of Long Noncoding RNAs”; Wang et al., “Alternative Isoform Regulation in Human Tissue Transcriptomes”; Louro et al., “Conserved Tissue Expression Signatures of Intronic Noncoding RNAs”; Hoeppner et al., “Evolutionarily Stable Association of Intronic SnoRNAs and MicroRNAs with Their Host Genes”; Monteys et al., “Structure and Activity of Putative Intronic miRNA Promoters”; Mondal et al., “Characterization of the RNA Content of Chromatin”; Rodriguez-Campos and Azorin, “RNA Is an Integral Component of Chromatin That Contributes to Its Structural Organization”; George et al., “Evolution of Diverse Mechanisms for Protecting Chromosome Ends”; Von Sternberg, “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System.”