Arrival of the Fittest: Solving Evolution's Greatest Puzzle

Home > Science > Arrival of the Fittest: Solving Evolution's Greatest Puzzle > Page 29
Arrival of the Fittest: Solving Evolution's Greatest Puzzle Page 29

by Andreas Wagner

Draznin, B. “Molecular Mechanisms of Insulin Resistance: Serine Phosphorylation of Insulin Receptor Substrate-1 and Increased Expression of p85 Alpha—The Two Sides of a Coin.” Diabetes 55 (2006): 2392–97.

  Duarte, N. C., et al. “Global Reconstruction of the Human Metabolic Network Based on Genomic and Bibliomic Data.” Proceedings of the National Academy of Sciences of the United States of America 104 (2007): 1777–82.

  Dubnau, D. “DNA Uptake in Bacteria.” Annual Review of Microbiology 53 (1999): 217–44.

  Eco, U. Zeichen. Frankfurt: Suhrkamp, 1977.

  Ederer, M. M., et al. “PCP Degradation Is Mediated by Closely Related Strains of the Genus Sphingomonas.” Molecular Ecology 6 (1997): 39–49.

  Edwards, J. S., R. U. Ibarra, and B. O. Palsson. “In Silico Predictions of Escherichia coli Metabolic Capabilities Are Consistent with Experimental Data.” Nature Biotechnology 19 (2001): 125–30.

  Edwards, J. S., and B. O. Palsson. “The Escherichia coli MG1655 in Silico Metabolic Genotype: Its Definition, Characteristics, and Capabilities.” Proceedings of the National Academy of Sciences of the United States of America 97 (2000): 5528–33.

  Eigen, M. “Self-organization of Matter and Evolution of Biological Macromolecules.” Naturwissenschaften 58 (1971): 465.

  Eigen, M., and P. Schuster. The Hypercycle: A Principle of Natural Self-Organization. Berlin: Springer, 1979.

  Einstein, A. “On the Method of Theoretical Physics.” Philosophy of Science 1 (1934): 163–69.

  Ekland, E. H., J. W. Szostak, and D. P. Bartel. “Structurally Complex and Highly Active Ligases Derived from Random RNA Sequences.” Science 269 (1995): 364–70.

  Eldredge, G., and N. Eldredge. “Editorial.” Evolution: Education and Outreach (Special Issue: Evolution of the Eye) 1 (2008): 351.

  Eng, M. Y., S. E. Luczak, and T. I. Wall. “ALDH2, ADH1B, and ADH1C Genotypes in Asians: A Literature Review.” Alcohol Research and Health 30 (2007): 22–27.

  England, P. C., P. Molnar, and F. M. Richter. “Kelvin, Perry, and the Age of the Earth.” American Scientist 95 (2007): 342–49.

  Espinosa-Soto, C., P. Padilla-Longoria, and E. R. Alvarez-Buylla. “A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles.” Plant Cell 16 (2004): 2923–39.

  Feist, A. M., et al. “A Genome-Scale Metabolic Reconstruction for Escherichia coli K-12 MG1655 That Accounts for 1260 ORFs and Thermodynamic Information.” Molecular Systems Biology 3 (2007).

  Feist, A. M., et al. “Reconstruction of Biochemical Networks in Microorganisms.” Nature Reviews Microbiology 7 (2009): 129–43.

  Fell, D. Understanding the Control of Metabolism. Miami: Portland Press, 1997.

  Ferrada, E., and A. Wagner. “Evolutionary Innovation and the Organization of Protein Functions in Sequence Space.” PLoS ONE 5, no. 11 (2010): e14172.

  Ferris, J. P., et al. “Synthesis of Long Prebiotic Oligomers on Mineral Surfaces.” Nature 381 (1996): 59–61.

  Feuda, R., et al. “Metazoan Opsin Evolution Reveals a Simple Route to Animal Vision.” Proceedings of the National Academy of Sciences of the United States of America 109 (2012): 18868–72.

  Finkelstein, A. V. “Implications of the Random Characteristics of Protein Sequences for Their 3-Dimensional Structure.” Current Opinion in Structural Biology 4 (1994): 422–28.

  Fletcher, G. L., C. L. Hew, and P. L. Davies. “Antifreeze Proteins of Teleost Fishes.” Annual Review of Physiology 63 (2001): 359–90.

  Fong, S. S., et al. “Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes.” Journal of Biological Chemistry 281 (2006): 8024–33.

  Fong, S. S., and B. O. Palsson. “Metabolic Gene-Deletion Strains of Escherichia coli Evolve to Computationally Predicted Growth Phenotypes.” Nature Genetics 36 (2004): 1056–58.

  Fontana, W., and L. W. Buss. “‘The Arrival of the Fittest’: Toward a Theory of Biological Organization.” Bulletin of Mathematical Biology 56 (1994): 1–64.

  Forster, J., et al. “Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network.” Genome Research 13 (2003): 244–53.

  Foster, P. L. “Adaptive Mutation: Implications for Evolution.” Bioessays 22 (2000): 1067–74.

  Futuyma, D. J. Evolutionary Biology. Sunderland, MA: Sinauer, 1998.

  Garcia-Fernandez, J., and P. W. H. Holland. “Archetypal Organization of the Amphioxus Hox Gene-Cluster.” Nature 370 (1994): 563–66.

  Gehring, W. J., and K. Ikeo. “Pax 6—Mastering Eye Morphogenesis and Eye Evolution.” Trends in Genetics 15 (1999): 371–77.

  Gerdes, S. Y., et al. “Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655.” Journal of Bacteriology 185 (2003): 5673–84.

  Gerhart, J., and M. Kirschner. Cells, Embryos, and Evolution. Boston: Blackwell, 1998.

  Giaever, G., et al. “Functional Profiling of the Saccharomyces cerevisiae Genome.” Nature 418 (2002): 387–91.

  Gierer, A., and H. Meinhard. “Theory of Biological Pattern Formation.” Kybernetik 12 (1972): 30–39.

  Gieryn, T. F. Science and Social Structure: A Festschrift for Robert K. Merton. New York: New York Academy of Sciences, 1980.

  Gilbert, S. F. Developmental Biology. 5th ed. Sunderland, MA: Sinauer, 1997.

  ———. Developmental Biology. 9th ed. Sunderland, MA: Sinauer, 2010.

  ———. “The Morphogenesis of Evolutionary Developmental Biology.” International Journal of Developmental Biology 47 (2003): 467–77.

  Gilbert, W. “Origin of Life—The RNA World.” Nature 319 (1986): 618.

  Goffeau, A., et al. “Life with 6000 Genes.” Science 274 (1996): 563–67.

  Golding, G. B., and A. M. Dean. “The Structural Basis of Molecular Adaptation.” Molecular Biology and Evolution 15 (1998): 355–69.

  Goldschmidt, R. The Material Basis of Evolution. New Haven, CT: Yale University Press, 1940.

  Goldsmith, T. H. “What Birds See.” Scientific American 295 (2006): 68–75.

  Gomez, C., and O. Pourquie. “Developmental Control of Segment Numbers in Vertebrates.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 312B (2009): 533–44.

  Goodman, F. R. “Limb Malformations and the Human HOX Genes.” American Journal of Human Genetics 112 (2002): 256–65.

  Goodman, M., et al. “An Evolutionary Tree for Invertebrate Globin Sequences.” Journal of Molecular Evolution 27 (1988): 236–49.

  Gottesman, M. M., et al. “Genetic Analysis of the Multidrug Transporter.” Annual Review of Genetics 29 (1995): 607–49.

  Gottschlich, D. E., and A. P. Smith. “Convective Heat-Transfer Characteristics of Toothed Leaves.” Oecologia 53 (1982): 418–20.

  Gould, S. J. “Betting on Chance—And No Fair Peeking.” In Eight Little Piggies: Reflections in Natural History, 396–408. New York: Norton, 1993.

  Gould, S. J., and R. C. Lewontin. “The Spandrels of San-Marco and the Panglossian Paradigm: A Critique of the Adaptationist Program.” Proceedings of the Royal Society of London Series B: Biological Sciences 205 (1979): 581–98.

  Gould, S. J., and E. Vrba. “Exaptation—A Missing Term in the Science of Form.” Paleobiology 8 (1982): 4–15.

  Graw, J. “Genetics of Crystallins: Cataract and Beyond.” Experimental Eye Research 88 (2009): 173–89.

  Greenwold, M. J., and R. H. Sawyer. “Linking the Molecular Evolution of Avian Beta (β) Keratins to the Evolution of Feathers.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 316B (2011): 609–16.

  Griffiths, A., et al. An Introduction to Genetic Analysis. New York: Freeman, 2004.

  Guerrier-Takada, C., et al. “The RNA Moiety of Ribonuclease-P Is the Catalytic Subunit of the Enzyme.” Cell 35 (1983): 849–57.

  Haldane, J. B. S. “A Mathematical Theory of Natural and Artificial Selection.” Transactions of the C
ambridge Philosophical Society 23 (1924): 19–40.

  ———. “The Origin of Life.” Rationalist Annual 148 (1929): 3–10.

  Hall, B. G. “Activation of the bgl Operon by Adaptive Mutation.” Molecular Biology and Evolution 15 (1998): 1–5.

  Hardison, R. C. “A Brief History of Hemoglobins: Plant, Animal, Protist, and Bacteria.” Proceedings of the National Academy of Sciences of the United States of America 93 (1996): 5675–79.

  Harris, G. A. “A New Theory of the Origin of Species.” The Open Court 18 (1904): 193–202.

  Hartl, D., and A. Clark. Principles of Population Genetics. Sunderland, MA: Sinauer, 2007.

  Hay, A., and M. Tsiantis. “The Genetic Basis for Differences in Leaf Form between Arabidopsis thaliana and Its Wild Relative Cardamine hirsuta.” Nature Genetics 38 (2006): 942–47.

  Hayden, E., E. Ferrada, and A. Wagner. “Cryptic Genetic Variation Promotes Rapid Evolutionary Adaptation in an RNA Enzyme.” Nature 474 (2011): 92–95.

  Hedges, S. B., and S. Kumar. “Genomic Clocks and Evolutionary Timescales.” Trends in Genetics 19 (2003): 200–206.

  ———. “Precision of Molecular Time Estimates.” Trends in Genetics 20 (2004): 242–47.

  Hersey, G. L., and R. Freedman. Possible Palladian Villas (Plus a Few Instructively Impossible Ones). Cambridge, MA: MIT Press, 1992.

  Hingorani, M., I. Hanson, and V. van Heyningen. “Aniridia.” European Journal of Human Genetics 20 (2012): 1011–17.

  Hofacker, I., et al. “Fast Folding and Comparison of RNA Secondary Structures.” Monatshefte für Chemie 125 (1994): 167–88.

  Holm, N. G. “Why Are Hydrothermal Systems Proposed as Plausible Environments for the Origin of Life?” Origins of Life and Evolution of the Biosphere 22 (1992): 5–14.

  Holm, N. G., and E. M. Andersson. “Hydrothermal Systems.” In The Molecular Origins of Life, edited by E. Brock, 86–99. Cambridge: Cambridge University Press, 1998.

  Horowitz, N. H. “The Origin of Life.” Engineering and Science 20 (1956): 21–25.

  Houssaye, A., et al. “Three-Dimensional Pelvis and Limb Anatomy of the Cenomanian Hind-Limbed Snake Eupodophis descouensi (Squamata, Ophidia) Revealed by Synchrotron-Radiation Computed Laminography.” Journal of Vertebrate Paleontology 31 (2011): 2–7.

  Hsu-Kim, H., et al. “Formation of Zn- and Fe-Sulfides near Hydrothermal Vents at the Eastern Lau Spreading Center: Implications for Sulfide Bioavailability to Chemoautotrophs.” Geochemical Transactions 9, no. 6 (2008).

  Huang, W. H., and J. P. Ferris. “One-Step, Regioselective Synthesis of Up to 50-mers of RNA Oligomers by Montmorillonite Catalysis.” Journal of the American Chemical Society 128 (2006): 8914–19.

  Hugler, M., et al. “Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle in Different Lineages within the Phylum Aquificae: Evidence for Two Ways of Citrate Cleavage.” Environmental Microbiology 9 (2007): 81–92.

  Huxley, J. Evolution: The Modern Synthesis. London: George Allen & Unwin, 1942.

  Isalan, M., et al. “Evolvability and Hierarchy in Rewired Bacterial Gene Networks.” Nature 452 (2008): 840–45.

  Jäger, J., et al. “Dynamic Control of Positional Information in the Early Drosophila Embryo.” Nature 430 (2004): 368–71.

  Johannsen, W. L. Elemente der exakten Erblichkeitslehre. Jena: Gustav Fischer, 1913.

  Johnson, S. Where Good Ideas Come From: The Natural History of Innovation. New York: Riverhead, 2010.

  Johnston, W. K., et al. “RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension.” Science 292 (2001): 1319–25.

  Jörg, T., O. Martin, and A. Wagner. “Neutral Network Sizes of Biological RNA Molecules Can Be Computed and Are Not Atypically Small.” BMC Bioinformatics 9 (2008): 464.

  Jornvall, H., et al. “Zeta-Crystallin versus Other Members of the Alcohol-Dehydrogenase Superfamily—Variability as a Functional Characteristic.” FEBS Letters 322 (1993): 240–44.

  Kacser, H., and R. Beeby. “Evolution of Catalytic Proteins or On the Origin of Enzyme Species by Means of Natural Selection.” Journal of Molecular Evolution 20 (1984): 38–51.

  Kamath, R., et al. “Systematic Functional Analysis of the Caenorhabditis elegans Genome Using RNAi.” Nature 421 (2003): 231–37.

  Kapp, O. H., et al. “Alignment of 700 Globin Sequences—Extent of Amino-Acid Substitution and Its Correlation with Variation in Volume.” Protein Science 4 (1995): 2179–90.

  Kappe, G., et al. “Explosive Expansion of Beta Gamma-Crystallin Genes in the Ancestral Vertebrate.” Journal of Molecular Evolution 71 (2010): 219–30.

  Kashefi, K., and D. R. Lovley. “Extending the Upper Temperature Limit for Life.” Science 301 (2003): 934.

  Kauffman, S. A. “Autocatalytic Sets of Proteins.” Journal of Theoretical Biology 1 (1986): 1–24.

  Keats, J. The Complete Poems of John Keats. New York: Modern Library, 1994.

  Keefe, A. D., and J. W. Szostak. “Functional Proteins from a Random-Sequence Library.” Nature 410 (2001): 715–18.

  Kelley, D. S., et al. “A Serpentinite-Hosted Ecosystem: The Lost City Hydrothermal Field.” Science 307 (2005): 1428–34.

  Kelley, T., and J. Littman. The Art of Innovation: Lessons in Creativity from IDEO, America’s Leading Design Firm. New York: Crown, 2001.

  Kelman, Z., and M. O’Donnell. “DNA Polymerase III Holoenzyme: Structure and Function of a Chromosomal Replicating Machine.” Annual Review of Biochemistry 64 (1995).

  Kenrick, P. “Turning Over a New Leaf.” Nature 410 (2001): 309–10.

  Kern, A. D., and F. A. Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial tRNAs.” Nature Genetics 36 (2004): 1207–12.

  Kettlewell, H. B. D. The Evolution of Melanism: The Study of a Recurring Necessity. Oxford: Blackwell, 1973.

  Keys, D. N., et al. “Recruitment of a Hedgehog Regulatory Circuit in Butterfly Eyespot Evolution.” Science 283 (1999): 532–34.

  Knight, R. D., S. J. Freeland, and L. F. Landweber. “Rewiring the Keyboard: Evolvability of the Genetic Code.” Nature Reviews Genetics 2 (2001): 49–58.

  Kottler, M. J. “Hugo de Vries and the Rediscovery of Mendel’s Laws.” Annals of Science 36 (1979): 517–38.

  Koza, J. R. Genetic Programming: On the Programming of Computers by Means of Natural Selection. Cambridge, MA: MIT Press, 1992.

  Kreitman, M. “Nucleotide Polymorphism at the Alcohol Dehydrogenase Gene Region of Drosophila melanogaster.” Nature 304 (1983): 412–17.

  Kruger, K., et al. “Self-Splicing RNA: Auto-Excision and Auto-Cyclization of the Ribosomal-RNA Intervening Sequence of Tetrahymena.” Cell 31 (1982): 147–57.

  Kuhn, T. S. The Structure of Scientific Revolutions. Chicago: University of Chicago Press, 1962.

  Kun, A., M. Santos, and E. Szathmary. “Real Ribozymes Suggest a Relaxed Error Threshold.” Nature Genetics 37 (2005): 1008–11.

  Land, M. F., and R. D. Fernald. “The Evolution of Eyes.” Annual Review of Neuroscience 15 (1992): 1–29.

  Land, M. F., and D.-E. Nilsson. Animal Eyes. Oxford: Oxford University Press, 2002.

  Lander, E. S., et al. “Initial Sequencing and Analysis of the Human Genome.” Nature 409 (2001): 860–921.

  Lau, K. F., and K. A. Dill. “A Lattice Statistical Mechanics Model of the Conformational and Sequence Spaces of Proteins.” Macromolecules 22 (1989): 3986–97.

  Lawrence, J. G., and H. Ochman. “Molecular Archaeology of the Escherichia coli Genome.” Proceedings of the National Academy of Sciences of the United States of America 95 (1998): 9413–17.

  Lawrence, P. A. The Making of a Fly. Oxford: Blackwell, 1992.

  LeHello, S., et al. “Highly Drug-Resistant Salmonella enterica Serotype Kentucky ST198-X1: A Microbiological Study.” The Lancet Infectious Diseases 13 (2013): 672–79.

  Lepland, A., et al. “Questioning the Evidence for Earth’s Earliest Life—Akilia Revisited.” Geology 33 (2005): 77–79.

  Levitt, M. “Nature of the Prote
in Universe.” Proceedings of the National Academy of Sciences of the United States of America 106 (2009): 11079–84.

  Lewin, B. Genes VI. New York: Oxford University Press, 1997.

  Lewis, E. B. “Gene Complex Controlling Segmentation in Drosophila.” Nature 276 (1978): 565–70.

  Lewontin, R. C., and J. L. Hubby. “A Molecular Approach to the Study of Genic Heterozygosity in Natural Populations, II. Amount of Variation and Degree of Heterozygosity in Natural Populations of Drosophila pseudoobscura.” Genetics 54 (1966): 595–609.

 

‹ Prev