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14 - Could an intelligent alien predict earth's biochemistry?

Published online by Cambridge University Press:  18 December 2009

Stephen J. Freeland
Affiliation:
Associate Professor of Biological Sciences, University of Maryland, Baltimore County
John D. Barrow
Affiliation:
University of Cambridge
Simon Conway Morris
Affiliation:
University of Cambridge
Stephen J. Freeland
Affiliation:
University of Maryland, Baltimore
Charles L. Harper, Jr
Affiliation:
John Templeton Foundation
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Summary

This is a book about whether our universe is “biocentric.” The Oxford English Dictionary defines this term as “treating life as a central fact” [1]; thus a biocentric universe is one predisposed towards producing life (life's centrality is implicit if “the fitness of the environment [for life] far precedes the existence of the living organisms” [2]). To date, this unusual idea has been most thoroughly explored (and most widely publicized) under the umbrella term “Anthropic Principle” in physics [3]. In essence, this principle refers to a suite of fundamental physical parameters, dimensionless constants that interact to imbue our universe with such interrelated phenomena as a diverse periodic table of elements, a preponderance of carbon and water, stars that emit energy, and planets that orbit them [4]. It asserts that, without clear explanation at present, the constants responsible for this state of affairs appear finely tuned in our universe to values peculiarly sympathetic with life's emergence.

Even if we accept this view of physics at face value, we remain a long logical leap from establishing truly biocentric credentials for our universe. Understanding “what is” versus “what might have been” for physics must be met by an equivalent understanding in biology. Thus the interface of biochemistry, where physics becomes biology, deserves especially close scrutiny. In this context, the first and perhaps most important point of this chapter is to emphasize that in considering physics and biology, two fundamentally different sets of expectations collide.

Type
Chapter
Information
Fitness of the Cosmos for Life
Biochemistry and Fine-Tuning
, pp. 280 - 317
Publisher: Cambridge University Press
Print publication year: 2007

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References

Oxford English Dictionary, online edn. 2E: http://dictionary.oed.com/.
Henderson, L. J.. The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter (New York, NY: Macmillan (1913); repr. Boston, MA: Beacon Press (1958); Gloucester, MA: Peter Smith (1970), p. 278.Google Scholar
Barrow, J. D. and Tipler, F. J.. The Anthropic Cosmological Principle. Oxford: Oxford University Press (1986).Google Scholar
Rees, M. J.. Just Six: The Deep Forces That Shape the Universe. New York, NY: Basic Books (2000).Google Scholar
O. Gingerich. “God's goof,” and the universe that knew we were coming. In Science and Religion: Are They Compatible? ed. Kurtz, P.., Karr, B. and Sandhu, R.. Amherst, MA: Prometheus Books (2003), p. 53.Google Scholar
Tranter, G. E.. Parity-violating energy differences of chiral minerals and the origin of biomolecular homochirality. Nature, 318 (1985), 172.CrossRefGoogle Scholar
MacDermott, A. J.. Electroweak enantioselection and the origin of life. Origins of Life and Evolution of Biospheres, 25 (1995), 191–9.CrossRefGoogle ScholarPubMed
Schrödinger, E.. What Is Life? The Physical Aspect of the Living Cell.Cambridge, UK: Cambridge University Press (1944).Google Scholar
Smolin, L.. The Life of the Cosmos. Oxford: Oxford University Press (1997).Google Scholar
Dawkins, R.. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design. New York, NY: W. W. Norton (1986). (Quote here is to be found on pp. 1 and 2 of Norton's [1996] 2nd paperback edn.)Google Scholar
Reported in Nature, 294 (1981), 10: “ … Sir Fred Hoyle [offered] a statement for disbelieving conventional views about the evolution of the universe … the essence of his argument was that the information content of the higher forms of life is represented by the number 1040,000 … Evolutionary processes would, Hoyle said, require several Hubble times to yield such a result. The chance that higher life forms might have emerged in this way is comparable with the chance that ‘a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein’ … Of adherents of biological evolution, Hoyle said he was at a loss to understand ‘biologists’ widespread compulsion to deny what to me seems obvious.'”
For example, see Erwin, D. E.. The Goldilocks Hypothesis [review of S. Conway Morris's Life's Solution: Inevitable Humans in a Lonely Universe], Science, 302 (2003), 1682–3.CrossRefGoogle Scholar
See, for example, Weinberg, S.. A designer universe?New York Review of Books, 46 (1999), 46–8.Google Scholar
For example, see Coleman, S.. Black holes as red herrings: topological fluctuations and the loss of quantum coherence. Nuclear Physics, B307 (1988), 867.CrossRefGoogle Scholar
For example, see Smith, J. E., Eiben, A. E. and Smith, J. D. Introduction to Evolutionary Computing. New York: Springer-Verlag (2003).Google Scholar
Paley, W.. Natural Theology; or, Evidences of the Existence and Attributes of the Deity. London: Printed for J. Faulder (1809); 12th edn. Now available in the public domain: www.hti.umich. edu/cgi/p/pd-modeng/pd-modeng-idx?type=header&byte=53049351.Google Scholar
See http://exobiology.arc.nasa.gov/.
Dennett, D.. Possibility naturalized. In Darwin's Dangerous Idea. New York: Simon and Schuster (1995), pp. 118–23.Google Scholar
R. J. P. Willams, and J. J. R. Fraústo da Silva. Evolution revisited by inorganic chemists: Chapter 21, this volume.
M. J. Denton. Protein-based life as an emergent property of matter: the nature and biological fitness of the protein folds. Chapter 13, this volume.
The American portal to this information is provided by the National Center for Biotechnology Information at www3.ncbi.nlm.nih.gov/.
See Frisch, L., ed. The genetic code. Cold Spring Harbor Symposia on Quantitative Biology, 1 (1966), 747.Google Scholar
See Lazcano, A.et al. The evolutionary transition from RNA to DNA in early cells. Journal of Molecular Evolution, 27 (1988), 283–90.CrossRefGoogle ScholarPubMed
See Cech, T. R. The ribosome is a ribozyme. Science, 289 (2000), 878–9.CrossRefGoogle ScholarPubMed
Crick, F. H. C.. Protein synthesis directed by DNA phage messengers. Cold Spring Harbor Symposia on Quantitative Biology, 31 (1966), 157–71. See also comments regarding an RNA world in Crick, F. H. C.. The origin of the genetic code. Journal of Molecular Biology, 38 (1968), 367–79.Google Scholar
White, H. B.. Coenzymes as fossils of an earlier metabolic state. Journal of Molecular Evolution, 7 (1976), 101–4.CrossRefGoogle ScholarPubMed
Gesteland, R. F. and Atkins, J. F.. The RNA World. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press (1993). For updated progress, see also Gesteland, F. R., Cech, T. R. and Atkins, J. F.. The RNA World, 2nd edn., Monograph 37. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press (2000).Google Scholar
Freeland, S. J, Knight, R. D. and Landweber, L. F.. Do proteins predate DNA?Science, 286 (1999), 690–2.CrossRefGoogle ScholarPubMed
Cooper, G.et al. Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth. Nature, 414 (2001), 879–83.CrossRefGoogle ScholarPubMed
Star Trek: The Next Generation, Episode No. 246: “The Chase” (Stardate: 46731.5); aired April 26, 1993.
Pace, N. R.. The universal nature of biochemistry. Proceedings of the National Academy of Sciences, USA, 98 (2001), 805–8.CrossRefGoogle ScholarPubMed
Gould, S. J.. Darwin's dilemma: the odyssey of evolution. In Ever since Darwin (1977). Repr. London: Penguin (1991).Google Scholar
Spencer, H.. A System of Synthetic Philosophy, 2 vols. London: Williams and Norgate (1864, 1867), 2nd edn., pp. 1898–9.Google Scholar
See, for example, http://catholic.archives.nd.edu/cgi-bin/lookup. pl?stem=evolv&ending=ere.
Oxford English Dictionary, online edn. 2E: http://dictionary. oed.com/.
Bonnet, C.. Considérations sur les corps organisés. 2 vols. (Amsterdam, M. M. Rey: 1762): http://visualiseur. bnf.fr/Visualiseur?Destination=Gallica&O=NUMM-87656.Google Scholar
C. Bonnet. La Palingénésie philosophique. Geneva: Philibert et Chirol (1769): http://home.tiscalinet.ch/biografien/sources/bonnet_palingenesie.htm. The word “evolution” makes its debut in Partie 6: “Abuserois-je de la liberté de conjecturer, si je disois, que les plantes et les animaux qui éxistent aujourd'hui, sont provenus par une sorte d'évolution naturelle des êtres organisés qui peuploient ce premier monde sorti immédiatement des mains du créateur?” (“Would I abuse my liberty to conjecture if I said that the plants and animals that exist today were created by a sort of natural evolution from the organized beings who populated the initial world that came out immediately from the hands of the creator?”)
Bowler, P. J.. Evolution, the History of an Idea. (1983). Repr. Berkeley and Los Angeles, CA: University of California Press (1989), pp. 59–63.Google Scholar
Id, pp. 82–9.
Darwin, C.. On the Origin of Species by Means of Natural Selection. London: John Murray (1859). An online version of this text is available in the public domain at www.literature.org /authors/darwin-charles/the-origin-of-species/.Google Scholar
For an excellent summary of the changes Darwin introduced over the course of six editions, see the introduction by Beer, G. in World's Classics Paperbacks Origin of Species. Amherst, MA: Prometheus (1996), pp. vii–xxix.Google Scholar
Miles, S. J.. Charles Darwin and Asa Gray discuss teleology and design. Perspectives on Science and Christian Faith, 53 (3) (2001), 196–201.Google Scholar
For example, see Darwin, C. (1860). The Correspondence of Charles Darwin, vol. 8. Cambridge, UK: Cambridge University Press (1993), p. 496; from a letter to Asa Gray, “But I grieve to say that I cannot honestly go as far as you do about Design … [Y]ou lead me to infer that you believe ‘that variation has been led along certain beneficial lines.’”Google Scholar
This statement appears in every edition of Origin (full reference found in [40] as the final sentence of the penultimate paragraph of the book).
Poulson, T. L.. Adaptations of cave fishes with some comparisons to deep sea fishes. Environmental Biology of Fishes, 62 (2001), 345–64.CrossRefGoogle Scholar
Brooks, D. R. and McLennan, D. A.. Parascript. Washington, DC: Smithsonian Institution Press (1993).Google Scholar
Dennett, D.. Darwin's Dangerous Idea. New York, NY: Simon and Schuster (1995). The term “skyhook” is defined on p. 74, but is integral to the whole thesis of the book and is discussed intermittently throughout.Google Scholar
For a context to this statement, see Cupitt, D.. Chapter 2, The mechanical universe. In The Sea of Faith. Cambridge, UK: Cambridge University Press (1988), pp. 36–55.Google Scholar
Lull, R. S.. Organic Evolution. New York, NY: Macmillan (1925).Google Scholar
Wilson, D. S. and Sober, E.. Reviving the superorganism. Journal of Theoretical Biology, 36 (1989), 337–56.CrossRefGoogle Scholar
See, for example, Queller, D. C. and Strassmann, J. E.. The many selves of social insects. Science, 296 (2002), 311–13.CrossRefGoogle ScholarPubMed
Camazine, S., Deneubourg, J.-L., Franks, N. R.et al. Unveiling Mechanisms of Collective Behavior. Princeton, NJ: Princeton University Press (2001).Google Scholar
Heisenberg, W.. Über den anschaulichen Inhalt der quantentheoretischen Kinematik und Mechanik. Zeitschrift für Physik, 43 (1927), 172–98.CrossRefGoogle Scholar
Lorenz, E.. Predictability: does the flap of a butterfly's wings in Brazil set off a tornado in Texas? Presented at the Meeting of the American Association for the Advancement of Science, Washington, DC (1972). (Full text in Appendix in E. Lorenz. The Essence of Chaos. Seattle, WA: University of Washington Press [1993].)Google Scholar
Welte, J. W.et al. Gambling participation in the U. S. – results from a national survey. Journal of Gambling Studies, 18 (2002), 313–37.CrossRefGoogle ScholarPubMed
Gould, S. J. and Lewontin, R. C.. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society, B205 (1979), 581–98.CrossRefGoogle Scholar
Maynard, J. Smithet al. Developmental constraints and evolution. Quarterly Review of Biology, 60 (1985), 265–87.Google Scholar
See Dennett, D.. The spandrel's thumb. In Darwin's Dangerous Idea. New York, NY: Simon and Schuster (1995), pp. 267–82.Google Scholar
G. C. Williams. A defense of reductionism in evolutionary biology. Oxford Surveys in Evolutionary Biology, vol. 2, ed. Dawkins, R. and Ridley, M.. Oxford: Oxford University Press (1985).Google Scholar
Queller, D. C.. The spaniels of St. Marx and the Panglossian paradox: a critique of a rhetorical programme. Quarterly Review of Biology, 70 (1995), 485–9.CrossRefGoogle Scholar
See, for example, Kerr, R. A.. Mass extinction. Extinction by a whoosh, not a bang?Science, 302 (2003), 1315, and references therein.CrossRefGoogle Scholar
For example, contrast Gould, S. J.'s Wonderful Life. New York, NY: Norton (1989), ch. 5, section on mass extinction, with S. Conway Morris's Life's Solution: Inevitable Humans in a Lonely Universe. Cambridge, UK: Cambridge University Press (2003), pp. 94–5.Google Scholar
See, for example, Byerly, G. R.et al. An archean impact layer from the Pilbara and Kaapvaal cratons. Science, 297 (2002), 1325–7, and references therein.CrossRefGoogle ScholarPubMed
For example, see A. Weismann (1883). In Poulton, E. B., Sholand, S and Shipley, A. E., eds. Essays upon Heredity and Kindred Biological Problems. Oxford: Oxford University Press (1993), pp. 1–66.Google Scholar
Lynch, M. and Conery, J. S.. The origins of genome complexity. Science, 302 (2003), 1401–4.CrossRefGoogle ScholarPubMed
Partridge, L. and Hurst, L. D.. Sex and conflict. Science, 281 (1998), 2003–8.CrossRefGoogle ScholarPubMed
Wright, S. E.. Roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the sixth Annual Congress of Genetics, 1 (1932), 356–66. The construct has been criticized in W. B. Provine. Sewall Wright and Evolutionary Biology. Chicago, IL: University of Chicago Press (1986). It has been defended in M. Ruse. Are pictures really necessary? The case of Sewall Wright's “adaptive landscapes.” PSA: Proceedings of the Biennial Meeting of The Philosophy of Science Association, Vol. 2: Symposia and Invited Papers (1990), pp. 63–77. Suffice it to say that the simple rendition described here is the adaptive landscape at its simplest and most defensible.Google Scholar
Mayr, E.. Systematics and the Origin of Species. New York, NY: Columbia University Press (1942).Google Scholar
Gould, S. J. (1989). Wonderful Life. New York, NY: Norton (1989). The specific quote may be found in ch. 1, p. 48 of the Penguin edn. (repr.) London: Penguin (1991).Google Scholar
Usually attributed to the Comte de Buffon. For example, see A. O. Lovejoy. Buffon and the problem of species. In Forerunners of Darwin, ed. Glass, B.et al. Baltimore, MD: Johns Hopkins University Press (1968), pp. 84–113 (esp. p. 111).Google Scholar
For example, see the recent review by Omland, K. and Funk, D.. Species level paraphyly and polyphyly. Annual Reviews in Ecology, Evolution and Systematics, 34 (2003), 397–423.Google Scholar
For example, see the Answers in Genesis web resource: www. answersingenesis.org.
For example, see Rundle, H. D.et al. Natural selection and parallel speciation in sticklebacks. Science, 287 (2000), 306–8. Also see Glor, R. E.et al. Phylogenetic analysis of ecological and morphological diversification in Hispaniolan trunk-ground anoles (Anolis cybotes group). International Journal of Organic Evolution, 57 (2003), 2383–97.CrossRefGoogle ScholarPubMed
See, for example, the lucid description given in ch. 2 of J. Felsenstein. Inferring Phylogenies. Sunderland, MA: Sinauer Associates (2004). It is purely coincidental that the programming algorithms being described are inferring biological evolutionary relationships; the point is that the quasi-natural-selection approach used by the computer software to find the best possible tree of relationships is one that benefits from stochastic noise.
Conway, S. Morris. Life's Solution: Inevitable Humans in a Lonely Universe. Cambridge, UK: Cambridge University Press (2003).CrossRefGoogle Scholar
Harvey, P. and Pagel, M.. The Comparative Method of Evolutionary Biology. Oxford: Oxford University Press (1991).Google Scholar
Including, of course, many of contemporary concern, such as HIV and SARS. A good overview is given in Moya, A., Holmes, E. C. and Gonzalez-Candelas, F.. The population genetics and evolutionary epidemiology of RNA viruses. National Review of Microbiology, 2 (2004), 279–88.CrossRefGoogle ScholarPubMed
Knight, R. D., Freeland, S. J. and Landweber, L. F.. Rewiring the keyboard: evolvability of the genetic code. Nature Reviews Genetics, 2 (2001), 49–58.CrossRefGoogle ScholarPubMed
See Atkins, J. and Gesteland, R.. The 22nd amino acid. Science, 296 (2002), 1409–10 and references therein.CrossRefGoogle ScholarPubMed
First predicted by Fisher, R. A in The Genetical Theory of Natural Selection. Oxford: Oxford University Press (1930). For recent empirical corroboration, see, for example, C. Burch and L. Chao. Evolution by small steps and rugged landscapes in the RNA virus phi6. Genetics, 151 (1999), 921–7.CrossRefGoogle Scholar
Jacob, F.. Evolution and tinkering. Science, 196 (1997), 1161–6.CrossRefGoogle Scholar
Crick, F. H. C.. The origin of the genetic code. Journal of Molecular Biology, 38 (1968), 367–79 (see esp. pp. 369–70).CrossRefGoogle ScholarPubMed
T. M. Sonneborn. Degeneracy in the genetic code: extent, nature and genetic implications. In Evolving Genes and Proteins, ed. Bryson, V. and Vogel, H. J.. New York, NY, and London: Academic Press (1965).Google ScholarPubMed
E. Zuckerkandland and L. Pauling. Evolutionary divergence and convergence in proteins. In Evolving Genes and Proteins, ed. Bryson, V. and Vogel, H. J.. New York, NY, and London: Academic Press (1965).Google ScholarPubMed
Woese, C. R.. On the evolution of the genetic code. Proceedings of the National Academy of Sciences, USA, 54 (1965), 1546–52.CrossRefGoogle ScholarPubMed
Crick, F. H. C.. Codon–anticodon pairing: the wobble hypothesis. Journal of Molecular Biology, 19 (1966), 548–55.CrossRefGoogle ScholarPubMed
For an excellent history of these strange theories and the experimental evidence that turned them on their head, see Hayes, B.. The invention of the genetic code. American Scientist, 86 (1998), 8–14.CrossRefGoogle Scholar
Barrell, B. G., Bankier, A. T. and Drouin, J.. A different genetic code in human mitochondria. Nature, 282 (1979), 189–94.CrossRefGoogle ScholarPubMed
For example, see Osawa, S. and Jukes, T. H.. Codon reassignment (codon capture) in evolution. Journal of Molecular Evolution, 21 (1989), 271–78. For an alternative view, see Santos, M. A.et al. Driving change: the evolution of alternative genetic codes. Trends in Genetics, 20 (2004), 95–102.CrossRefGoogle Scholar
Maynard, J. Smith. Optimization theory in evolution. Annual Review of Ecology and Systematics, 9 (1978), 31–56.Google Scholar
For example, see Charnov, E. L.. Optimal foraging: attack strategy of a mantid. American Naturalist, 110 (1976), 141–51, for a simple, elegant, and pioneering contribution in this field.CrossRefGoogle Scholar
For example., Xia, X.. Body temperature, rate of biosynthesis, and evolution of genome size. Molecular Biology and Evolution, 12 (1995), 834–42.Google ScholarPubMed
For example, Haig, D. and Hurst, L. D.. A quantitative measure of error minimisation within the genetic code. Journal of Molecular Evolution, 33 (1991), 412–17.CrossRefGoogle Scholar
Freeland, S. J. and Hurst, L. D.. The genetic code is one in a million. Journal of Molecular Evolution, 47 (1998), 238–48.CrossRefGoogle ScholarPubMed
A comprehensive review is given in Freeland, S. J., Wu, T. and Keulmann, N.. The case for an error minimizing standard genetic code. Origins of Life and Evolution of Biospheres, 33 (2003), 457–77.CrossRefGoogle ScholarPubMed
Knight, R. D. and Landweber, L. F.. The early evolution of the genetic code. Cell, 101 (2000), 569–72.CrossRefGoogle ScholarPubMed
Wong, J. T.. Evolution of the genetic code. Microbiological Science, 5 (1988), 174–81.Google ScholarPubMed
Freeland, S. J., Knight, R. D., Landweber, L. F.et al. Early fixation of an optimal genetic code. Molecular Biology and Evolution, 17 (2000), 511–18.CrossRefGoogle ScholarPubMed
R. D. Knight, S. J. Freeland and L. F Landweber. Adaptive evolution of the genetic code. In The Genetic Code and the Origin of Life, ed. Pouplana, L. R.. Georgetown/New York, NY: Landes Bioscience and Kluwer Academic/Plenum (2004), pp. 204–23.Google Scholar
Chapters 3 and 4 of S. Conway Morris's Life's Solution: Inevitable Humans in a Lonely Universe. Cambridge, UK: Cambridge University Press (2003), pp. 32–63, give a somewhat more skeptical overview of these topics; in particular, the author's views are pessimistic regarding the ready availability of amino acids in a prebiotic world.
Miller, S. L. and Urey, H. C.. Production of amino acids under possible primitive earth conditions. Science, 117 (1953), 528–9; Miller, S. L. and Urey, H. C.. Production of some organic compounds under possible primitive earth conditions. Journal of the American Chemical Society, 77 (1955), 2351–61.CrossRefGoogle ScholarPubMed
Miller, S. L., Urey, H. C. and Oro, J.. Origin of organic compounds on the primitive earth and in meteorites. Journal of Molecular Evolution, 9 (1976), 59–72.CrossRefGoogle ScholarPubMed
Kvenvolden, K., Lawless, J., Pering, K.et al. Evidence for extraterrestrial amino-acids and hydrocarbons in the Murchison meteorite. Nature, 5 (1970), 923–6.CrossRefGoogle Scholar
See, for example, Bernstein, M. P., Dworking, J. P., Sandford, S. A.et al. Racemic amino acids from the ultraviolet photolysis of interstellar ice analogues. Nature, 416 (2002), 401–3.CrossRefGoogle ScholarPubMed
See comparison tables offered in Wong, J. T.-F. and Bronskill, P. M.. Inadequacy of pre-biotic synthesis as the origin of proteinaceous amino acids. Journal of Molecular Evolution, 13 (1979), 115–25.CrossRefGoogle Scholar
Wong, J. T.-F.. A co-evolution theory of the genetic code. Proceedings of the National Academy of Sciences, USA, 72 (1975), 1909–12.CrossRefGoogle ScholarPubMed
Amirnovin, R.. An analysis of the metabolic theory of the origin of the genetic code. Journal of Molecular Evolution, 44 (1997), 473–6.CrossRefGoogle ScholarPubMed
Ronneberg, T. A., Landweber, L. F. and Freeland, S. J.. Testing a biosynthetic theory of the genetic code: fact or artifact?Proceedings of the National Academy of Sciences, USA, 97 (2000), 13690–5.CrossRefGoogle ScholarPubMed
Trifonov, E. N.. Consensus temporal order of amino acids and evolution of the triplet code, Gene, 261 (2000), 139–51.CrossRefGoogle ScholarPubMed
Di, M. Giulio. Genetic code origin: are the pathways of type Glu-tRNA(Gln) ‎ Gln-tRNA(Gln) molecular fossils or not?Journal of Molecular Evolution, 55 (2002), 616–22.Google Scholar
Weber, A. L. and Miller, S. L.. Reasons for the occurrence of the twenty coded protein amino acids. Journal of Molecular Evolution, 17 (1981), 273–84.CrossRefGoogle ScholarPubMed
For example, Mathur, P., Ramakumar, S. and Chauhan, V. S.. Peptide design using alpha, beta-dehydro amino acids: from beta-turns to helical hairpins. Biopolymers, 76 (2004), 150–61.CrossRefGoogle ScholarPubMed
Although mainstream protein structural prediction methods are turning ever more to “learning” patterns from proteins that have evolved in nature, first principles prediction methods are steadily improving; for example, see Rohl, C. A.et al. Modeling structurally variable regions in homologous proteins with rosetta. Proteins, 55 (3) (2004), 656–77.CrossRefGoogle ScholarPubMed
Wong, J. T.-F.. The evolution of a universal genetic code. Proceedings of the National Academy of Sciences, USA, 73 (1976), 2336–40.CrossRefGoogle ScholarPubMed
Suggested by Szathmáry, E.. Four letters in the genetic alphabet: a frozen evolutionary optimum?Proceedings of the Royal Society, B245 (1991), 91–9.CrossRefGoogle ScholarPubMed
For example, see Wei, Y. and Hecht, M. H.. Enzyme-like proteins from an unselected library of designed amino acid sequences. Protein Engineering Design and Selection, 17 (2004), 67–75.CrossRefGoogle ScholarPubMed
For example, see Baker, E. N., Arcus, V. L. and Lott, J. S.. Protein structure prediction and analysis as a tool for functional genomics. Applied Bioinformatics, 2 (suppl. 3) (2003), S3–10.Google ScholarPubMed
For example, see Elkin, P. L.. Primer on medical genomics part V: bioinformatics. Mayo Clinic Proceedings, 78 (2003), 57–64.CrossRefGoogle ScholarPubMed
Bourne, P. E.. CASP and CAFASP experiments and their findings. Methods of Biochemical Analysis, 44 (2003), 501–7.Google ScholarPubMed
Keefe, A. D.et al. One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag. Protein Expression and Purification, 23 (2001), 440–6.CrossRefGoogle ScholarPubMed
For example, see Piccirilli, J., Krauch, T., Moroney, S.et al. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature, 343 (1990), 33–7; Bergstrom, D. E., Zhang, P. and Johnson, W. T.. Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5′-d(CGCXAATTYGCG)-3′. Nucleic Acids Research, 25 (1997), 1935–42, and references therein; Delaney, J. C.et al. High-fidelity in vivo replication of DNA base shape mimics without Watson–Crick hydrogen bonds. Proceedings of the National Academy of Sciences, USA, 100 (8) (2003), 4469–73.CrossRefGoogle ScholarPubMed
Grosjean, H. and Benne, R.. Modification and Editing of RNA. Washington, DC: American Society for Microbiology Press (1998).CrossRefGoogle Scholar
Szathmáry, E.. Why are there four letters in the genetic alphabet?Nature Reviews Genetics, 4 (2003), 995–1001. See also Gardner, P. P., Holland, B. R., Moulton, V., Hendy, D. and Penny, D.. Optimal alphabets for an RNA world. Proceedings of the Royal Society, B270 (2003), 1177–82.CrossRefGoogle ScholarPubMed
Eschenmoser, A.. Chemical etiology of nucleic acid structure. Science, 28 (1999), 2118–24.CrossRefGoogle Scholar
Szathmáry, E. and Maynard, J. Smith. The Major Transitions in Evolution (Oxford: Oxford University Press, 1995); see chapters 3–5 for discussions of the inherent advantages of template-based genetics.Google Scholar
Pace, N. R.. The universal nature of biochemistry. Proceedings of the National Academy of Sciences, USA, 98 (2001), 805–8.CrossRefGoogle ScholarPubMed
Bartel, D. and Unrau, P.. Constructing an RNA world. Trends in the Biochemical Sciences, 24 (Millennium Issue) (1999), M9–M13.CrossRefGoogle Scholar
For example, Shapiro, R.. The prebiotic role of adenine: a critical analysis. Origins of Life and Evolution of Biospheres, 25 (1995), 83–98.CrossRefGoogle ScholarPubMed
Shapiro, R.. Prebiotic ribose synthesis, a critical analysis. Origins of Life and Evolution of Biospheres, 18 (1988), 71–85.CrossRefGoogle ScholarPubMed
A graphic account is given in Decker, P., Schweer, H. and Pohlmann, R.. Identification of formose sugars, presumable prebiotic metabolites, using capillary gas chromatography/gas chromatography–mass spectrometry of n-butoximine trifluoroacetates on OV-225. Journal of Chromatography, 244 (1982), 281–91.CrossRefGoogle Scholar
Larralde, R., Robertson, M. P. and Miller, S. L.. Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proceedings of the National Academy of Sciences, USA, 84 (1995), 4398–402.Google Scholar
Keefe, A. and Miller, S. L.. Potentially pre-biotic syntheses of condensed phosphates. Origins of Life and Evolution of Biospheres, 26 (1996), 15–25; but see also Glindemann, D., Graaf, R. M. and Schwartz, A. W.. Chemical reduction of phosphate on the primitive earth. Origins of Life and Evolution of Biospheres, 29 (1999), 555–61.CrossRefGoogle Scholar
An excellent, if ultra-skeptical, overview is given in Shapiro, R.. Origins: A Skeptic's Guide to the Creation of Life on Earth. New York, NY: Bantam (1987), pp. 182–4.Google Scholar
Levy, M. and Miller, S. L.. The stability of the RNA bases: implications for the origin of life. Proceedings of the National Academy of Sciences, USA, 95 (1998), 7933–8.CrossRefGoogle ScholarPubMed
Shapiro, R.. A replicator was not involved in the origin of life. International Union of Biochemistry and Molecular Biology Life, 49 (2000), 173–6.CrossRefGoogle Scholar
Joyce, G. F., Schwartz, A. W., Miller, S. L.et al. The case for an ancestral genetic system involving simple analogs of the nucleotides. Proceedings of the National Academy of Sciences, USA, 84 (1987), 107–19.CrossRefGoogle Scholar
Nelson, K. E., Levy, M. and Miller, S. L.. Peptide nucleic acids rather than RNA may have been the first genetic molecule. Proceedings of the National Academy of Sciences, USA, 97 (2000), 3868–71.CrossRefGoogle ScholarPubMed
Schöning, K.-U., Scholz, P., Guntha, S.et al. Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3′‎ 2′) oligonucleotide system. Science, 290 (2000), 1347–51.CrossRefGoogle ScholarPubMed
Weber, A. L.. Thermal synthesis and hydrolysis of polyglyceric acid. Origins of Life and Evolution of Biospheres, 19 (1989), 7–19.CrossRefGoogle ScholarPubMed
Cairns-Smith, A. G.. Genetic Takeover and the Mineral Origins of Life. Cambridge, UK: Cambridge University Press (1982).Google Scholar
Freeland, S. J., Knight, R. D. and Landweber, L. F.. Do proteins pre-date DNA?Science, 286 (1999), 690–2.CrossRefGoogle Scholar
Picirilli, J. A., Krauch, T., Moroney, S. E.et al. Enzymatic incorporation of a new base into DNA and RNA extends the genetic alphabet. Nature, 343 (1990), 33–7.CrossRefGoogle Scholar
Wu, Y.et al. Efforts toward expansion of the genetic alphabet: optimization of interbase hydrophobic interactions. Journal of the American Chemical Society, 122 (2000), 7621–32.CrossRefGoogle Scholar
Benner, S. A., Battersby, T. R., Eschgfaller, B.et al. Redesigning nucleic acids. Pure and Applied Chemistry, 70 (2) (1998), 263–6.CrossRefGoogle ScholarPubMed
Berger, M., Wu, Y., Ogawa, A. K.et al. Universal bases for hybridization, replication and chain termination. Nucleic Acids Research, 28 (15) (2000), 2911–14.CrossRefGoogle ScholarPubMed
Levy, M. and Miller, S. L.. The prebiotic synthesis of modified purines and their potential role in the RNA world. Journal of Molecular Evolution, 48 (1999), 631–7.CrossRefGoogle ScholarPubMed
Zhu, W. and Freeland, S. J.. The standard genetic code enhances adaptive evolution of proteins. Journal of Theoretical Biology, 239 (2006), 63–70.CrossRefGoogle ScholarPubMed
Siemens, D. F. Jr.On Moreland: spurious freedom, mangled science, muddled philosophy. Perspectives on Science and Christian Faith, 49 (1997), 196–9.Google Scholar
Midgley, M.. Evolution as religion, a comparison of prophecies. Zygon, 22 (1987), 179–94.CrossRefGoogle Scholar
I. Kant. Sammtliche Werke. In chronologischer Reihenfolge herausgegeben von Hartenstein, G.. Leipzig: Leopold Voss (1867) [–68]; vol. i, pp. 207–345.Google Scholar
For example, the non-overlapping magisteria argument presented by Gould. Rocks of Ages: Science and Religion in the Fullness of Life. New York, NY: Ballantine Books (1999).
For example, the lucid discussion from J. F. Haught, Is fine-tuning remarkable? Chapter 3, this volume.
For example, see discussion in Glavin, D. P. and Bada, J. L.. Survival of amino acids in micrometeorites during atmospheric entry. Astrobiology, 1 (2001), 259–69.CrossRefGoogle ScholarPubMed
Voltaire. Candide (1759), ed. Stanley, Appelbaum. Mineola, NY: Dover Publications (1991).Google Scholar

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