An experience-based analysis of the causal powers of various explanatory hypotheses suggests purposive or intelligent design as a causally adequate– and perhaps the most causally adequate– explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent. For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biologists continue to wrestle with the problem of the origination of biological form and the higher taxa.
Adams, M. D. Et alia. 2000. The genome sequence of Drosophila melanogaster.– Science 287:2185-2195.
Aris-Brosou, S., & Z. Yang. 2003. Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa.– Molecular Biology and Evolution 20:1947-1954.
Arthur, W. 1997. The origin of animal body plans. Cambridge University Press, Cambridge, United Kingdom.
Axe, D. D. 2000. Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.– Journal of Molecular Biology 301(3):585-596.
______. 2004. Estimating the prevalence of protein sequences adopting functional enzyme folds.– Journal of Molecular Biology (in press).
Ayala, F. 1994. Darwin's revolution. Pp. 1-17 in J. Campbell and J. Schopf, eds., Creative evolution?! Jones and Bartlett Publishers, Boston, Massachusetts.
______. A. Rzhetsky, & F. J. Ayala. 1998. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates– Proceedings of the National Academy of Sciences USA. 95:606-611.
Becker, H., & W. Lonnig, 2001. Transposons: eukaryotic. Pp. 529-539 in Nature encyclopedia of life sciences, vol. 18. Nature Publishing Group, London, United Kingdom.
Behe, M. 1992. Experimental support for regarding functional classes of proteins to be highly isolated from each other. Pp. 60-71 in J. Buell and V. Hearn, eds., Darwinism: science or philosophy? Foundation for Thought and Ethics, Richardson, Texas.
______. 1996. Darwin's black box. The Free Press, New York.
______. 2004. Irreducible complexity: obstacle to Darwinian evolution. Pp. 352-370 in W. A. Dembski and M. Ruse, eds., Debating design: from Darwin to DNA. Cambridge University Press, Cambridge, United Kingdom.
Benton, M., & F. J. Ayala. 2003. Dating the tree of life– Science 300:1698-1700.
Berlinski, D. 2000. “On assessing genetic algorithms.” Public lecture. Conference: Science and evidence of design in the universe. Yale University, November 4, 2000.
Blanco, F., I. Angrand, & L. Serrano. 1999. Exploring the confirmational properties of the sequence space between two proteins with different folds: an experimental study.– Journal of Molecular Biology 285:741-753.
Bowie, J., & R. Sauer. 1989. Identifying determinants of folding and activity for a protein of unknown sequences: tolerance to amino acid substitution.– Proceedings of the National Academy of Sciences, U.S.A. 86:2152-2156.
Bowring, S. A., J. P. Grotzinger, C. E. Isachsen, A. H. Knoll, S. M. Pelechaty, & P. Kolosov. 1993. Calibrating rates of early Cambrian evolution.– Science 261:1293-1298.
______. 1998a. A new look at evolutionary rates in deep time: Uniting paleontology and high-precision geochronology.– GSA Today 8:1-8.
______. 1998b. Geochronology comes of age.– Geotimes 43:36-40.
Bradley, W. 2004. Information, entropy and the origin of life. Pp. 331-351 in W. A. Dembski and M. Ruse, eds., Debating design: from Darwin to DNA. Cambridge University Press, Cambridge, United Kingdom.
Brocks, J. J., G. A. Logan, R. Buick, & R. E. Summons. 1999. Archean molecular fossils and the early rise of eukaryotes.– Science 285:1033-1036.
Brush, S. G. 1989. Prediction and theory evaluation: the case of light bending.– Science 246:1124-1129.
Budd, G. E. & S. E. Jensen. 2000. A critical reappraisal of the fossil record of the bilaterial phyla.– Biological Reviews of the Cambridge Philosophical Society 75:253-295.
Carroll, R. L. 2000. Towards a new evolutionary synthesis.– Trends in Ecology and Evolution 15:27-32.
Cleland, C. 2001. Historical science, experimental science, and the scientific method.– Geology 29:987-990.
______. 2002. Methodological and epistemic differences between historical science and experimental science.– Philosophy of Science 69:474-496.
Chothia, C., I. Gelfland, & A. Kister. 1998. Structural determinants in the sequences of immunoglobulin variable domain.– Journal of Molecular Biology 278:457-479.
Conway Morris, S. 1998a. The question of metazoan monophyly and the fossil record.– Progress in Molecular and Subcellular Biology 21:1-9.
______. 1998b. Early Metazoan evolution: Reconciling paleontology and molecular biology.– American Zoologist 38 (1998):867-877.
______. 2000. Evolution: bringing molecules into the fold.– Cell 100:1-11.
______. 2003a. The Cambrian “explosion” of metazoans. Pp. 13-32 in G. B. Muller and S. A. Newman, eds., Origination of organismal form: beyond the gene in developmental and evolutionary biology. The M.I.T. Press, Cambridge, Massachusetts.
______. 2003b. Cambrian “explosion” of metazoans and molecular biology: would Darwin be satisfied?– International Journal of Developmental Biology 47(7-8):505-515.
______. 2003c. Life's solution: inevitable humans in a lonely universe. Cambridge University Press, Cambridge, United Kingdom.
Crick, F. 1958. On protein synthesis.– Symposium for the Society of Experimental Biology. 12(1958):138-163.
Darwin, C. 1859. On the origin of species. John Murray, London, United Kingdom.
______. 1896. Letter to Asa Gray. P. 437 in F. Darwin, ed., Life and letters of Charles Darwin, vol. 1., D. Appleton, London, United Kingdom.
Davidson, E. 2001. Genomic regulatory systems: development and evolution. Academic Press, New York, New York.
Dawkins, R. 1986. The blind watchmaker. Penguin Books, London, United Kingdom.
______. 1995. River out of Eden. Basic Books, New York.
______. 1996. Climbing Mount Improbable. W. W. Norton & Company, New York.
Dembski, W. A. 1998. The design inference. Cambridge University Press, Cambridge, United Kingdom.
______. 2002. No free lunch: why specified complexity cannot be purchased without intelligence. Rowman & Littlefield, Lanham, Maryland.
______. 2004. The logical underpinnings of intelligent design. Pp. 311-330 in W. A. Dembski and M. Ruse, eds., Debating design: from Darwin to DNA. Cambridge University Press, Cambridge, United Kingdom.
Denton, M. 1986. Evolution: a theory in crisis. Adler & Adler, London, United Kingdom.
______. 1998. Nature's density. The Free Press, New York.
Eden, M. 1967. The inadequacies of neo-Darwinian evolution as a scientific theory. Pp. 5-12 in P. S. Morehead and M. M. Kaplan, eds., Mathematical challenges to the Darwinian interpretation of evolution. Wistar Institute Symposium Monograph, Allen R. Liss, New York.
Eldredge, N., & S. J. Gould. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Pp. 82-115 in T. Schopf, ed., Models in paleobiology. W. H. Freeman, San Francisco.
Erwin, D. H. 1994. Early introduction of major morphological innovations.– Acta Palaeontologica Polonica 38:281-294.
______. 2000. Macroevolution is more than repeated rounds of microevolution.– Evolution & Development 2:78-84.
______. 2004. One very long argument.– Biology and Philosophy 19:17-28.
______, J. Valentine, & D. Jablonski. 1997. The origin of animal body plans.– American Scientist 85:126-137.
______, ______, & J. J. Sepkoski. 1987. A comparative study of diversification events: the early Paleozoic versus the Mesozoic.– Evolution 41:1177-1186.
Foote, M. 1997. Sampling, taxonomic description, and our evolving knowledge of morphological diversity.– Paleobiology 23:181-206.
______, J. P. Hunter, C. M. Janis, & J. J. Sepkoski. 1999. Evolutionary and preservational constraints on origins of biologic groups: Divergence times of eutherian mammals.– Science 283:1310-1314.
Frankel, J. 1980. Propagation of cortical differences in tetrahymena.– Genetics 94:607-623.
Gates, B. 1996. The road ahead. Blue Penguin, Boulder, Colorado.
Gerhart, J., & M. Kirschner. 1997. Cells, embryos, and evolution. Blackwell Science, London, United Kingdom.
Gibbs, W. W. 2003. The unseen genome: gems among the junk.– Scientific American. 289:46-53.
Gilbert, S. F., J. M. Opitz, & R. A. Raff. 1996. Resynthesizing evolutionary and developmental biology.– Developmental Biology 173:357-372.
Gillespie, N. C. 1979. Charles Darwin and the problem of creation. University of Chicago Press, Chicago.
Goodwin, B. C. 1985. What are the causes of morphogenesis?– BioEssays 3:32-36.
______. 1995. How the leopard changed its spots: the evolution of complexity. Scribner's, New York, New York.
Gould, S. J. 1965. Is uniformitarianism necessary?– American Journal of Science 263:223-228.
Gould, S. J. 2002. The structure of evolutionary theory. Harvard University Press, Cambridge, Massachusetts.
Grant, P. R. 1999. Ecology and evolution of Darwin's finches. Princeton University Press, Princeton, New Jersey.
Grimes, G. W., & K. J. Aufderheide. 1991. Cellular aspects of pattern formation: the problem of assembly. Monographs in Developmental Biology, vol. 22. Karger, Baseline, Switzerland.
Grotzinger, J. P., S. A. Bowring, B. Z. Saylor, & A. J. Kaufman. 1995. Biostratigraphic and geochronologic constraints on early animal evolution.– Science 270:598-604.
Harold, F. M. 1995. From morphogenes to morphogenesis.– Microbiology 141:2765-2778.
______. 2001. The way of the cell: molecules, organisms, and the order of life. Oxford University Press, New York.
Hodge, M. J. S. 1977. The structure and strategy of Darwin's long argument.– British Journal for the History of Science 10:237-245.
Hooykaas, R. 1975. Catastrophism in geology, its scientific character in relation to actualism and uniformitarianism. Pp. 270-316 in C. Albritton, ed., Philosophy of geohistory (1785-1970). Dowden, Hutchinson & Ross, Stroudsburg, Pennsylvania.
John, B., & G. Miklos. 1988. The eukaryote genome in development and evolution. Allen & Unwinding, London, United Kingdom.
Kauffman, S. 1995. At home in the universe. Oxford University Press, Oxford, United Kingdom.
Kenyon, D., & G. Mills. 1996. The RNA world: a critique.– Origins & Design 17(1):9-16.
Kerr, R. A. 1993. Evolution's Big Bang gets even more explosive.– Science 261:1274-1275.
Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, United Kingdom.
Koonin, E. 2000. How many genes can make a cell?: the minimal genome concept.– Annual Review of Genomics and Human Genetics 1:99-116.
Kuppers, B. O. 1987. On the prior probability of the existence of life. Pp. 355-369 in L. Kruger et al., eds., The probabilistic revolution. M.I.T. Press, Cambridge, Massachusetts.
Lange, B. M. H., A. J. Faragher, P. March, & K. Gull. 2000. Centriole duplication and maturation in animal cells. Pp. 235-249 in R. E. Palazzo and G. P. Schatten, eds., The centrosome in cell replication and early development. Current Topics in Developmental Biology, vol. 49. Academic Press, San Diego.
Lawrence, P. A., & G. Struhl. 1996. Morphogens, compartments and pattern: lessons from Drosophila?– Cell 85:951-961.
Lenior, T. 1982. The strategy of life. University of Chicago Press, Chicago.
Levinton, J. 1988. Genetics, paleontology, and macroevolution. Cambridge University Press, Cambridge, United Kingdom.
______. 1992. The big bang of animal evolution.– Scientific American 267:84-91.
Lewin, R. 1988. A lopsided look at evolution.– Science 241:292.
Lewontin, R. 1978. Adaptation. Pp. 113-125 in Evolution: a Scientific American book. W. H. Freeman & Company, San Francisco.
Lipton, P. 1991. Inference to the best explanation. Routledge, New York.
Lonnig, W. E. 2001. Natural selection. Pp. 1008-1016 in W. E. Craighead and C. B. Nemeroff, eds., The Corsini encyclopedia of psychology and behavioral sciences, 3rd edition, vol. 3. John Wiley & Sons, New York.
______, & H. Saedler. 2002. Chromosome rearrangements and transposable elements.– Annual Review of Genetics 36:389-410.
Lovtrup, S. 1979. Semantics, logic and vulgate neo-darwinism.– Evolutionary Theory 4:157-172.
Marshall, W. F. & J. L. Rosenbaum. 2000. Are there nucleic acids in the centrosome? Pp. 187-205 in R. E. Palazzo and G. P. Schatten, eds., The centrosome in cell replication and early development. Current Topics in Developmental Biology, vol. 49. San Diego, Academic Press.
Maynard Smith, J. 1986. Structuralism versus selection– is Darwinism enough? Pp. 39-46 in S. Rose and L. Appignanesi, eds., Science and Beyond. Basil Blackwell, London, United Kingdom.
Mayr, E. 1982. Foreword. Pp. xi-xii in M. Ruse, Darwinism defended. Pearson Addison Wesley, Boston, Massachusetts.
McDonald, J. F. 1983. The molecular basis of adaptation: a critical review of relevant ideas and observations.– Annual Review of Ecology and Systematics 14:77-102.
McNiven, M. A. & K. R. Porter. 1992. The centrosome: contributions to cell form. Pp. 313-329 in V. I. Kalnins, ed., The centrosome. Academic Press, San Diego.
Meyer, S. C. 1991. Of clues and causes: a methodological interpretation of origin of life studies. Unpublished doctoral dissertation, University of Cambridge, Cambridge, United Kingdom.
______. 1998. DNA by design: an inference to the best explanation for the origin of biological information.– Rhetoric & Public Affairs, 1(4):519-555.
______. The scientific status of intelligent design: The methodological equivalence of naturalistic and non-naturalistic origins theories. Pp. 151-211 in Science and evidence for design in the universe. Proceedings of the Wethersfield Institute. Ignatius Press, San Francisco.
______. 2003. DNA and the origin of life: information, specification and explanation. Pp. 223-285 in J. A. Campbell and S. C. Meyer, eds., Darwinism, design and public education. Michigan State University Press, Lansing, Michigan.
______. 2004. The Cambrian information explosion: evidence for intelligent design. Pp. 371-391 in W. A. Dembski and M. Ruse, eds., Debating design: from Darwin to DNA. Cambridge University Press, Cambridge, United Kingdom.
______, M. Ross, P. Nelson, & P. Chien. 2003. The Cambrian explosion: biology's big bang. Pp. 323-402 in J. A. Campbell & S. C. Meyer, eds., Darwinism, design and public education. Michigan State University Press, Lansing. See also Appendix C: Stratigraphic first appearance of phyla body plans, pp. 593-598.
Miklos, G. L. G. 1993. Emergence of organizational complexities during metazoan evolution: perspectives from molecular biology, palaeontology and neo-Darwinism.– Mem. Ass. Australas. Palaeontols, 15:7-41.
Monastersky, R. 1993. Siberian rocks clock biological big bang.– Science News 144:148.
Moss, L. 2004. What genes can't do. The M.I.T. Press, Cambridge, Massachusetts.
Muller, G. B. & S. A. Newman. 2003. Origination of organismal form: the forgotten cause in evolutionary theory. Pp. 3-12 in G. B. Muller and S. A. Newman, eds., Origination of organismal form: beyond the gene in developmental and evolutionary biology. The M.I.T. Press, Cambridge, Massachusetts.
Nanney, D. L. 1983. The ciliates and the cytoplasm.– Journal of Heredity, 74:163-170.
Nelson, P., & J. Wells. 2003. Homology in biology: problem for naturalistic science and prospect for intelligent design. Pp. 303-322 in J. A. Campbell and S. C. Meyer, eds., Darwinism, design and public education. Michigan State University Press, Lansing.
Nijhout, H. F. 1990. Metaphors and the role of genes in development.– BioEssays 12:441-446.
Nusslein-Volhard, C., & E. Wieschaus. 1980. Mutations affecting segment number and polarity in Drosophila.– Nature 287:795-801.
Ohno, S. 1996. The notion of the Cambrian pananimalia genome.– Proceedings of the National Academy of Sciences, U.S.A. 93:8475-8478.
Orgel, L. E., & F. H. Crick. 1980. Selfish DNA: the ultimate parasite.– Nature 284:604-607.
Perutz, M. F., & H. Lehmann. 1968. Molecular pathology of human hemoglobin.– Nature 219:902-909.
Polanyi, M. 1967. Life transcending physics and chemistry.– Chemical and Engineering News, 45(35):54-66.
______. 1968. Life's irreducible structure.– Science 160:1308-1312, especially p. 1309.
Pourquie, O. 2003. Vertebrate somitogenesis: a novel paradigm for animal segmentation?– International Journal of Developmental Biology 47(7-8):597-603.
Quastler, H. 1964. The emergence of biological organization. Yale University Press, New Haven, Connecticut.
Raff, R. 1999. Larval homologies and radical evolutionary changes in early development, Pp. 110-121 in Homology. Novartis Symposium, vol. 222. John Wiley & Sons, Chichester, United Kingdom.
Reidhaar-Olson, J., & R. Sauer. 1990. Functionally acceptable solutions in two alpha-helical regions of lambda repressor.– Proteins, Structure, Function, and Genetics, 7:306-316.
Rutten, M. G. 1971. The origin of life by natural causes. Elsevier, Amsterdam.
Sapp, J. 1987. Beyond the gene. Oxford University Press, New York.
Sarkar, S. 1996. Biological information: a skeptical look at some central dogmas of molecular biology. Pp. 187-233 in S. Sarkar, ed., The philosophy and history of molecular biology: new perspectives. Kluwer Academic Publishers, Dordrecht.
Schutzenberger, M. 1967. Algorithms and the neo-Darwinian theory of evolution. Pp. 73-75 in P. S. Morehead and M. M. Kaplan, eds., Mathematical challenges to the Darwinian interpretation of evolution. Wistar Institute Symposium Monograph. Allen R. Liss, New York.
Shannon, C. 1948. A mathematical theory of communication.– Bell System Technical Journal 27:379-423, 623-656.
Shu, D. G., H. L. Loud, S. Conway Morris, X. L. Zhang, S. X. Hu, L. Chen, J. Han, M. Zhu, Y. Li, & L. Z. Chen. 1999. Lower Cambrian vertebrates from south China.– Nature 402:42-46.
Shubin, N. H., & C. R. Marshall. 2000. Fossils, genes, and the origin of novelty. Pp. 324-340 in Deep time. The Paleontological Society.
Simpson, G. 1970. Uniformitarianism: an inquiry into principle, theory, and method in geohistory and biohistory. Pp. 43-96 in M. K. Hecht and W. C. Steered, eds., Essays in evolution and genetics in honor of Theodosius Dobzhansky. Appleton-Century-Crofts, New York.
Sober, E. 2000. The philosophy of biology, 2nd edition. Westview Press, San Francisco.
Sonneborn, T. M. 1970. Determination, development, and inheritance of the structure of the cell cortex. In Symposia of the International Society for Cell Biology 9:1-13.
Sole, R. V., P. Fernandez, & S. A. Kauffman. 2003. Adaptive walks in a gene network model of morphogenesis: insight into the Cambrian explosion.– International Journal of Developmental Biology 47(7-8):685-693.
Stadler, B. M. R., P. F. Stadler, G. P. Wagner, & W. Fontana. 2001. The topology of the possible: formal spaces underlying patterns of evolutionary change.– Journal of Theoretical Biology 213:241-274.
Steiner, M., & R. Reitner. 2001. Evidence of organic structures in Ediacara-type fossils and associated microbial mats.– Geology 29(12):1119-1122.
Taylor, S. V., K. U. Walter, P. Kast, & D. Hilvert. 2001. Searching sequence space for protein catalysts.– Proceedings of the National Academy of Sciences, U.S.A. 98:10596-10601.
Thaxton, C. B., W. L. Bradley, & R. L. Olsen. 1992. The mystery of life's origin: reassessing current theories. Lewis and Stanley, Dallas, Texas.
Thompson, D. W. 1942. On growth and form, 2nd edition. Cambridge University Press, Cambridge, United Kingdom.
Thomson, K. S. 1992. Macroevolution: The morphological problem.– American Zoologist 32:106-112.
Valentine, J. W. 1995. Late Precambrian bilaterians: grades and clades. Pp. 87-107 in W. M. Fitch and F. J. Ayala, eds., Temporal and mode in evolution: genetics and paleontology 50 years after Simpson. National Academy Press, Washington, D.C.
______. 2004. On the origin of phyla. University of Chicago Press, Chicago, Illinois.
______, & D. H. Erwin, 1987. Interpreting great developmental experiments: the fossil record. Pp. 71-107 in R. A. Raff and E. C. Raff, eds., Development as an evolutionary process. Alan R. Liss, New York.
______, & D. Jablonski. 2003. Morphological and developmental macroevolution: a paleontological perspective.– International Journal of Developmental Biology 47:517-522.
Wagner, G. P. 2001. What is the promise of developmental evolution? Part II: A causal explanation of evolutionary innovations may be impossible.– Journal of Experimental Zoology (Mol. Dev. Evol.) 291:305-309.
______, & P. F. Stadler. 2003. Quasi-independence, homology and the Unity-C of type: a topological theory of characters.– Journal of Theoretical Biology 220:505-527.
Webster, G., & B. Goodwin. 1984. A structuralist approach to morphology.– Rivista di Biologia 77:503-10.
______, & ______. 1996. Form and transformation: generative and relational principles in biology. Cambridge University Press, Cambridge, United Kingdom.
Weiner, J. 1994. The beak of the finch. Vintage Books, New York.
Willmer, P. 1990. Invertebrate relationships: patterns in animal evolution. Cambridge University Press, Cambridge, United Kingdom.
______. 2003. Convergence and homoplasy in the evolution of organismal form. Pp. 33-50 in G. B. Muller and S. A. Newman, eds., Origination of organismal form: beyond the gene in developmental and evolutionary biology. The M.I.T. Press, Cambridge, Massachusetts.
Woese, C. 1998. The universal ancestor.– Proceedings of the National Academy of Sciences, U.S.A. 95:6854-6859.
Wray, G. A., J. S. Levinton, & L. H. Shapiro. 1996. Molecular evidence for deep Precambrian divergences among metazoan phyla.– Science 274:568-573.
Yockey, H. P. 1978. A calculation of the probability of spontaneous biogenesis by information theory.– Journal of Theoretical Biology 67:377-398.
______, 1992. Information theory and molecular biology, Cambridge University Press, Cambridge, United Kingdom.
1 Specifically, Gilbert et al. (1996) argued that changes in morphogenetic fields might produce large-scale changes in the developmental programs and, ultimately, body plans of organisms. Yet they offered no evidence that such fields– if indeed they exist– can be altered to produce advantageous variations in body plan, though this is a necessary condition of any successful causal theory of macroevolution.
2 If one takes the fossil record at face value and assumes that the Cambrian explosion took place within a relatively narrow 5-10 million year window, explaining the origin of the information necessary to produce new proteins, for example, becomes more acute in part because mutation rates would not have been sufficient to generate the number of changes in the genome necessary to build the new proteins for more complex Cambrian animals (Ohno 1996:8475-8478). This review will argue that, even if one allows several hundred million years for the origin of the metazoan, significant probabilistic and other difficulties remain with the neo-Darwinian explanation of the origin of form and information.
3 As Crick put it, “information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein” (Crick 1958:144, 153).
4 To solve this problem Ohno himself proposes the existence of a hypothetical ancestral form that possessed virtually all the genetic information necessary to produce the new body plans of the Cambrian animals. He asserts that this ancestor and its “pananimalian genome” might have arisen several hundred million years before the Cambrian explosion. On this view, each of the different Cambrian animals would have possessed virtually identical genomes, albeit with considerable latent and unexpressed capacity in the case of each individual form (Ohno 1996:8475-8478). While this proposal might help explain the origin of the Cambrian animal forms by reference to preexisting genetic information, it does not solve, but instead merely displaces, the problem of the origin of the genetic information necessary to produce these new forms.
5 Some have suggested that mutations in “master regulator” Hox genes might provide the raw material for body plan morphogenesis. Yet there are two problems with this proposal. First, Hox gene expression begins only after the foundation of the body plan has been established in early embryogenesis. (Davidson 2001:66). Second, Hox genes are highly conserved across many disparate phyla and so cannot account for the morphological differences that exist between the phyla (Valentine 2004:88).
6 Notable differences in the developmental pathways of similar organisms have been observed. For example, congeneric species of sea urchins (from genus Heliocidaris) exhibit striking differences in their developmental pathways (Raff 1999:110-121). Thus, it might be argued that such differences show that early developmental programs can in fact be mutated to produce new forms. Nevertheless, there are two problems with this claim. First, there is no direct evidence that existing differences in sea urchin development arose by mutation. Second, the observed differences in the developmental programs of different species of sea urchins do not result in new body plans, but instead in highly conserved structures. Despite differences in developmental patterns, the endpoints are the same. Thus, even if it can be assumed that mutations produced the differences in developmental pathways, it must be acknowledged that such changes did not result in novel form.
7 Of course, many post-translation processes of modification also play a role in producing a functional protein. Such processes make it impossible to predict a protein's final sequencing from its corresponding gene sequence alone (Sarkar 1996:199-202).
8 Erwin (2004:21), although friendly to the possibility of species selection, argues that Gould provides little evidence for its existence. “The difficulty” writes Erwin of species selection, “…is that we must rely on Gould's arguments for theoretical plausibility and sufficient relative frequency. Rarely is a mass of data presented to justify and support Gould's conclusion.” Indeed, Gould (2002) himself admitted that species selection remains largely a hypothetical construct: “I freely admit that well-documented cases of species selection do not permeate the literature” (p. 710).
9”I do not deny either the wonder, or the powerful importance, of organized adaptive complexity. I recognize that we know no mechanism for the origin of such organismal features other than conventional natural selection at the organismic level– for the sheer intricacy and elaboration of good biomechanical design surely precludes either random production, or incidental origin as a side consequence of active processes at other levels” (Gould 2002:710). “Thus, we do not challenge the efficacy or the cardinal importance of organismal selection. As previously discussed, I fully agree with Dawkins (1986) and others that one cannot invoke a higher-level force like species selection to explain 'things that organisms do'– in particular, the stunning panoply of organismic adaptations that has always motivated our sense of wonder about the natural world, and that Darwin (1859) described, in one of his most famous lines (3), as 'that perfection of structure and coadaptation which most justly excites our admiration'“ (Gould 2002:886).
10 Theories in the historical sciences typically make claims about what happened in the past, or what happened in the past to cause particular events to occur (Meyer 1991:57-72). For this reason, historical scientific theories are rarely tested by making predictions about what will occur under controlled laboratory conditions (Cleland 2001:987, 2002:474-496). Instead, such theories are usually tested by comparing their explanatory power against that of their competitors with respect to already known facts. Even in the case in which historical theories make claims about past causes they usually do so on the basis of preexisting knowledge of cause and effect relationships. Nevertheless, prediction may play a limited role in testing historical scientific theories since such theories may have implications as to what kind of evidence is likely to emerge in the future. For example, neo-Darwinism affirms that new functional sections of the genome arise by trial and error process of mutation and subsequent selection. For this reason, historically many neo-Darwinists expected or predicted that the large non-coding regions of the genome– so-called “junk DNA”– would lack function altogether (Orgel & Crick 1980). On this line of thinking, the nonfunctional sections of the genome represent nature's failed experiments that remain in the genome as a kind of artifact of the past activity of the mutation and selection process. Advocates of the design hypotheses on the other hand, would have predicted that non-coding regions of the genome might well reveal hidden functions, not only because design theorists do not think that new genetic information arises by a trial and error process of mutation and selection, but also because designed systems are often functionally polyvalent. Even so, as new studies reveal more about the functions performed by the non-coding regions of the genome (Gibbs 2003), the design hypothesis can no longer be said to make this claim in the form of a specifically future-oriented prediction. Instead, the design hypothesis might be said to gain confirmation or support from its ability to explain this now known evidence, albeit after the fact. Of course, neo Darwinists might also amend their original prediction using various auxiliary hypotheses to explain away the presence of newly discovered functions in the non-coding regions of DNA. In both cases, considerations of ex post facto explanatory power reemerge as central to assessing and testing competing historical theories.