Arrival of the Fittest: Solving Evolution's Greatest Puzzle

Home > Science > Arrival of the Fittest: Solving Evolution's Greatest Puzzle > Page 30
Arrival of the Fittest: Solving Evolution's Greatest Puzzle Page 30

by Andreas Wagner


  Liang, Y. H., et al. “The Crystal Structure of Bar-Headed Goose Hemoglobin in Deoxy Form: The Allosteric Mechanism of a Hemoglobin Species with High Oxygen Affinity.” Journal of Molecular Biology 313 (2001): 123–37.

  Lihoreau, M., L. Chittka, and N. L. Raine. “Travel Optimization by Foraging Bumblebees through Readjustments of Traplines after Discovery of New Feeding Locations.” American Naturalist 176 (2010): 744–57.

  Lipman, D., and W. Wilbur. “Modeling Neutral and Selective Evolution of Protein Folding.” Proceedings of the Royal Society of London Series B: Biological Sciences 245 (1991): 7–11.

  Liu, X. Z., et al. 2001. “Avian Haemoglobins and Structural Basis of High Affinity for Oxygen: Structure of Bar-Headed Goose Aquomet Haemoglobin.” Acta Crystallographica Section D: Biological Crystallography 57 (1991): 775–83.

  Lohr, S. “John W. Backus, 82, Fortran Developer, Dies.” New York Times, March 20, 2007.

  Lopes, F. J. P., et al. “Spatial Bistability Generates Hunchback Expression Sharpness in the Drosophila Embryo.” PLoS Computational Biology 4 (2008).

  Loreto, E. L. S., C. M. A. Carareto, and P. Capy. “Revisiting Horizontal Transfer of Transposable Elements in Drosophila.” Heredity 100 (2008): 545–54.

  Lynch, M. The Origins of Genome Architecture. Sunderland, MA: Sinauer, 2007.

  Lynnerup, N., et al. “Radiocarbon Dating of the Human Eye Lens Crystallines Reveal Proteins without Carbon Turnover throughout Life.” PLoS ONE 3 (2008): e1529.

  Ma, H. W., and A. P. Zeng. “Phylogenetic Comparison of Metabolic Capacities of Organisms at Genome Level.” Molecular Phylogenetics and Evolution 31 (2004): 204–13.

  Martchenko, M., et al. “Transcriptional Rewiring of Fungal Galactose-Metabolism Circuitry. Current Biology 17 (2007): 1007–13.

  Martin, O. C., and A. Wagner. “Multifunctionality and Robustness Trade-Offs in Model Genetic Circuits.” Biophysical Journal 94 (2008): 2927–37.

  Martin, W., et al. “Hydrothermal Vents and the Origin of Life.” Nature Reviews Microbiology 6 (2008): 805–14.

  Maynard-Smith, J. “Natural Selection and the Concept of a Protein Space.” Nature 255 (1970): 563–64.

  Mayr, E. The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Cambridge, MA: Belknap Press of Harvard University Press, 1982.

  McCarthy, D. L., A. A. Claude, and S. D. Copley. “In Vivo Levels of Chlorinated Hydroquinones in a Pentachlorophenol-Degrading Bacterium.” Applied and Environmental Microbiology 63 (1997): 1883–88.

  McMahon, J. M., W. L. B. White, and R. T. Sayre. “Cyanogenesis in Cassava (Manihot esculenta Crantz).” Journal of Experimental Botany 46 (1995): 731–41.

  Mendel, G. “Versuche über Pflanzen-Hybriden.” Verhandlungen des Naturforschenden Vereins Brünn 4 (1866): 3–47.

  Merton, R. K. Social Theory and Social Structure. New York: Free Press, 1968.

  ———. “The Unanticipated Consequences of Purposive Social Action.” American Sociological Review 1 (1936): 894–904.

  Miller, J. F., and P. Thomson. “Cartesian Genetic Programming.” In European Conference on Genetic Programming (EuroGP 2000), edited by R. Poli et al., 121–32. Edinburgh, Scotland, 2000.

  Miller, S. “A Production of Amino Acids under Possible Primitive Earth Conditions.” Science 117 (1953): 528–29.

  Miller, S. L. “The Endogenous Synthesis of Organic Compounds.” In The Molecular Origins of Life, edited by E. Brock, 59–85. Cambridge: Cambridge University Press, 1998.

  Mitchell, M. An Introduction to Genetic Algorithms. Cambridge, MA: MIT Press, 1998.

  Mjolsness, E., D. H. Sharp, and J. Reinitz. “A Connectionist Model of Development.” Journal of Theoretical Biology 152 (1991): 429–53.

  Moeckel, R., et al. “YaMoR and Bluemove—An Autonomous Modular Robot with Bluetooth Interface for Exploring Adaptive Locomotion.” In 8th International Conference on Climbing and Walking Robots (CLAWAR 2005), edited by M. O. Tokhi, G. S. Virk, and M. A. Hossain, 685–92. London, 2006.

  Mojzsis, S. J., et al. “Evidence for Life on Earth before 3,800 Million Years Ago.” Nature 384 (1996): 55–59.

  Mommsen, T. P., and P. J. Walsh. “Evolution of Urea Synthesis in Vertebrates: The Piscine Connection.” Science 243 (1989): 72–75.

  Monge, C., and F. Leonvelarde. “Physiological Adaptation to High Altitude—Oxygen Transport in Mammals and Birds.” Physiological Reviews 71 (1991): 1135–72.

  Moore, C., and S. Mertens. The Nature of Computation. Oxford: Oxford University Press, 2011.

  Moran, N. A., J. P. McCutcheon, and A. Nakabachi. “Genomics and Evolution of Heritable Bacterial Symbionts.” Annual Review of Genetics 42 (2008): 165–90.

  Moran, N. A., H. J. McLaughlin, and R. Sorek. “The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria.” Science 323 (2009): 379–82.

  Moran, N. A., and A. Mira. “The Process of Genome Shrinkage in the Obligate Symbiont Buchnera aphidicola.” Genome Biology 2 (2001): research0054–research0054.0012.

  Morano, I. “Tuning the Human Heart Molecular Motors by Myosin Light Chains.” Journal of Molecular Medicine 77 (1999): 544–55.

  Morgan, T. H. The Scientific Basis of Evolution. New York: Norton, 1932.

  Morowitz, H. J., et al. “The Origin of Intermediary Metabolism.” Proceedings of the National Academy of Sciences of the United States of America 97 (2000): 7704–8.

  Mrozikiewicz, P. M., et al. “The Significance of C3435T Point Mutation of the MDR1 Gene in Endometrial Cancer.” International Journal of Gynecological Cancer 17 (2007): 728–31.

  Murray, J. D. 1989. Mathematical Biology. New York: Springer, 2007.

  Nachmann, M. N., and S. L. Crowell. “Estimate of the Mutation Rate per Nucleotide in Humans.” Genetics (2000): 297–304.

  Neidhardt, F. C. Escherichia coli and Salmonella. Washington, DC: ASM Press, 1996.

  Nelson, K. E., M. Levy, and S. Miller. “Peptide Nucleic Acids Rather Than RNA May Have Been the First Genetic Molecule.” Proceedings of the National Academy of Sciences of the United States of America. 97 (2000): 3868–71.

  Nikaido, M., et al. “Genetically Distinct Coelacanth Population off the Northern Tanzanian Coast.” Proceedings of the National Academy of Sciences of the United States of America 108 (2011): 18009–13.

  Nohynek, L. J., et al. “Description of Four Pentachlorophenol-Degrading Bacterial Strains as Sphingomonas chlorophenolica sp nov.” Systematic and Applied Microbiology 18 (1996): 527–38.

  Nüsslein-Volhard, C., and E. Wieschaus. “Mutations Affecting Segment Number and Polarity in Drosophila.” Nature 287 (1980): 795–801.

  O’Brien, P. J., and D. Herschlag. “Catalytic Promiscuity and the Evolution of New Enzymatic Activities.” Chemistry and Biology 6 (1999): R91–R105.

  Ochman, H., and L. B. Jones. “Evolutionary Dynamics of Full Genome Content in Escherichia coli.” EMBO Journal 19 (2000): 6637–43.

  Ochman, H., E. Lerat, and V. Daubin. “Examining Bacterial Species under the Specter of Gene Transfer and Exchange.” Proceedings of the National Academy of Sciences of the United States of America 102 (2005): 6595–99.

  Ochoa-Espinosa, A., et al. “Anterior-Posterior Positional Information in the Absence of a Strong Bicoid Gradient.” Proceedings of the National Academy of Sciences of the United States of America 106 (2009): 3823–28.

  Ogata, H., et al. “KEGG: Kyoto Encyclopedia of Genes and Genomes.” Nucleic Acids Research 27 (1999): 29–34.

  Ogburn, W. F., and D. Thomas. “Are Inventions Inevitable? A Note on Social Evolution.” Political Science Quarterly 37 (1922): 83–98.

  Ohtaka, C., and H. Ishikawa. “Effects of Heat Treatment on the Symbiotic System of an Aphid Mycetocyte.” Symbiosis 11 (1991): 19–30.

  Oparin, A. I. The Origin of Life. New York: Dover, 1952.

  Oqueta, M., et al. “The Influence of Adh Function on Ethanol Preference and Tolerance in Adult Drosophila melanogaster.” Chemical Senses 35 (2010): 813–22.

  Pal, C., B. Papp, an
d M. J. Lercher. “Horizontal Gene Transfer Depends on Gene Content of the Host.” In Joint Meeting of the 4th European Conference on Computational Biology/6th Meeting of the Spanish-Bioinformatics-Network, 222–23. Madrid, 2005.

  Panganiban, G., and J. L. R. Rubenstein. “Developmental Functions of the Distal-less/Dlx Homeobox Genes.” Development 129 (2002): 4371–86.

  Pasteur, L. “Des générations spontanées. Soirées scientifiques de la Sorbonne.” Revue des cours scientifiques I 21 (1864): 258–65.

  Piatigorsky, J. “Gene Sharing in Lens and Cornea: Facts and Implications.” Progress in Retinal and Eye Research 17 (1998): 145–74.

  Piatigorsky, J., and G. J. Wistow. “Enzyme Crystallins: Gene Sharing as an Evolutionary Strategy.” Cell 57 (1989): 197–99.

  Poole, A. R., et al. “Composition and Structure of Articular Cartilage—A Template for Tissue Repair.” Clinical Orthopaedics and Related Research 391 (2001): S26–S33.

  Postgate, J. R. The Outer Reaches of Life. Cambridge: Cambridge University Press, 1994.

  Povolotskaya, I. S., and F. A. Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature 465 (2010): 922–26.

  Price, N. D., J. L. Reed, and B. O. Palsson. “Genome-Scale Models of Microbial Cells: Evaluating the Consequences of Constraints.” Nature Reviews Microbiology 2 (2004): 886–97.

  Ptashne, M. A Genetic Switch: Phage Lambda and Other Organisms. Cambridge, MA: Cell Press, 1992.

  Putman, M., W. H. van Veen, and W. N. Konings. “Molecular Properties of Bacterial Multidrug Transporters.” Microbiology and Molecular Biology Reviews 64 (2000): 672–93.

  Putnam, H. “The Meaning of ‘Meaning.’” In Mind, Language and Reality: Philosophical Papers, vol. 2: 215–71. Cambridge: Cambridge University Press, 1975.

  Radetsky, P. “Life’s Crucible.” Earth 7 (1998): 34–41.

  Raman, K., and Wagner, A. “The Evolvability of Programmable Hardware.” Journal of the Royal Society Interface 8 (2011): 269–81.

  Razin, S., D. Yogev, and Y. Naot. “Molecular Biology and Pathogenicity of Mycoplasmas.” Microbiology and Molecular Biology Reviews 62 (1998): 1094–56.

  Rechenberg, I. Evolutionsstrategie. Stuttgart: Frommann-Holzboog, 1973.

  Redfield, R. J. “Genes for Breakfast—The Have-Your-Cake-and-Eat-It-Too of Bacterial Transformation.” Journal of Heredity 84 (1993): 400–404.

  Rehmann, L., and A. J. Daugulis. “Enhancement of PCB Degradation by Burkholderia xenovorans LB400 in Biphasic Systems by Manipulating Culture Conditions.” Biotechnology and Bioengineering 99 (2008): 521–28.

  Reidhaar-Olson, J. F., and R. T. Sauer. “Functionally Acceptable Substitutions in Two Alpha-Helical Regions of Lambda Repressor.” Proteins 7 (1990): 306–16.

  Reidys, C. M. “Random Induced Subgraphs of Generalized n-Cubes.” Advances in Applied Mathematics 19 (1997): 360–77.

  Reidys, C. M., P. Stadler, and P. Schuster. “Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures.” Bulletin of Mathematical Biology 59 (1997): 339–97.

  Reinhold-Hurek, B., and D. A. Shub. “Self-Splicing Introns in Transfer-RNA Genes of Widely Divergent Bacteria.” Nature 357 (1992): 173–76.

  Reinitz, J., E. Mjolsness, and D. H. Sharp. “Model for Cooperative Control of Positional Information in Drosophila by Bicoid and Maternal Hunchback.” Journal of Experimental Zoology 271 (1995): 47–56.

  Riddle, R. D., et al. “Sonic-Hedgehog Mediates the Polarizing Activity of the ZPA.” Cell 75 (1993): 1401–16.

  Rizzi, M., et al. “Structure of the Sulfide-Reactive Hemoglobin from the Clam Lucina pectinata—Crystallographic Analysis at 1.5 Å Resolution.” Journal of Molecular Biology 244 (1994): 86–99.

  Rodrigues, J. F., and A. Wagner. “Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks.” PLoS Computational Biology 5 (2009): e1000613.

  ———. “Genotype Networks, Innovation, and Robustness in Sulfur Metabolism.” BMC Systems Biology 5 (2011): 39.

  Rosen, W. The Most Powerful Idea in the World. Chicago: University of Chicago Press, 2010.

  Rothschild, L. J. “The Evolution of Photosynthesis . . . Again?” Philosophical Transactions of the Royal Society B: Biological Sciences 363 (2008): 2787–2801.

  Russell, P. J. iGenetics. San Francisco: Benjamin Cummings, 2002.

  Samal, A., et al. “Genotype Networks in Metabolic Reaction Spaces.” BMC Systems Biology 4 (2010): 30.

  Sanchez, R., and J. T. Mahoney. “Modularity, Flexibility, and Knowledge Management in Product and Organization Design.” Strategic Management Journal 17 (1996): 63–76.

  Sanghera, D. K., and P. S. Blackett. “Type 2 Diabetes Genetics: Beyond GWAS.” Journal of Diabetes and Metabolism 3 (2012): 6948.

  Schmitt-Kopplin, P., et al. “High Molecular Diversity of Extraterrestrial Organic Matter in Murchison Meteorite Revealed 40 Years after Its Fall.” Proceedings of the National Academy of Sciences of the United States of America 107 (2010): 2763–68.

  Schopf, J. W., et al. “Laser-Raman Imagery of Earth’s Earliest Fossils.” Nature 416 (2002): 73–76.

  Schuck, C., B. Haetzer, and J. Becker. “An Interface for a Decentralized 2D Reconfiguration on Xilinx Virtex-FPGAs for Organic Computing.” International Journal of Reconfigurable Computing 2009 (2009): Article ID 273791, doi: dx.doi.org/10.1155/2009/273791.

  Schultes, E., and D. Bartel. “One Sequence, Two Ribozymes: Implications for the Emergence of New Ribozyme Folds.” Science 289 (2000): 448–52.

  Schuster, P. “Prediction of RNA Secondary Structures: From Theory to Models and Real Molecules.” Reports on Progress in Physics 69 (2006): 1419–77.

  Schuster, P., et al. “From Sequences to Shapes and Back—A Case-Study in RNA Secondary Structures. Proceedings of the Royal Society of London Series B: Biological Sciences 255 (1994): 279–84.

  Schwab, I. R. Evolution’s Witness: How Eyes Evolved. New York: Oxford University Press, 2012.

  Schwartz, J. H. Sudden Origins: Fossils, Genes, and the Emergence of Species. New York: Wiley, 1999.

  Searcoid, M. O. Metric Spaces. London: Springer, 2007.

  Sedaghat, A. R., A. Sherman, and M. J. Quon. “A Mathematical Model of Metabolic Insulin Signaling Pathways.” American Journal of Physiology: Endocrinology and Metabolism 283 (2002): E1084–E1101.

  Segre, D., D. Vitkup, and G. Church. “Analysis of Optimality in Natural and Perturbed Metabolic Networks. Proceedings of the National Academy of Sciences of the United States of America 99 (2002): 15112–17.

  Senecal, P. K., D. T. Montgomery, and R. D. Reitz. “A Methodology for Engine Design Using Multi-dimensional Modelling and Genetic Algorithms with Validation through Experiments.” International Journal of Engine Research 1 (2000): 229–48.

  Sephton, M. A. “Meteoritics—Life’s Sweet Beginnings?” Nature 414 (2001): 857–58.

  Shimeld, S. M., et al. “Urochordate βγ-Crystallin and the Evolutionary Origin of the Vertebrate Eye Lens.” Current Biology 15 (2005): 1684–89.

  Shrestha, B., et al. “Evolution of a Major Drug Metabolizing Enzyme Defect in the Domestic Cat and Other Felidae: Phylogenetic Timing and the Role of Hypercarnivory.” PLoS ONE (2011): 6.

  Sibley, D. A. The Sibley Guide to Bird Life and Behavior. New York: Knopf, 2001.

  Sim, L., et al. “Structural Basis for Substrate Selectivity in Human Maltase-Glucoamylase and Sucrase-Isomaltase N-Terminal Domains.” Journal of Biological Chemistry 285 (2010): 17763–70.

  Sleep, N. H. “The Hadean-Archaean Environment.” Cold Spring Harbor Perspectives in Biology 2 (2010): a002527.

  Smil, V. Enriching the Earth: Fritz Haber, Carl Bosch, and the Transformation of World Food Production. Cambridge, MA: MIT Press, 2000.

  Smillie, C. S., et al. “Ecology Drives a Global Network of Gene Exchange Connecting the Human Microbiome.” Nature 480 (2011): 241–44.

  Smith, E., and H. J. Morowitz. “Universality in Intermediary Metabolism.” Proceedings of the National A
cademy of Sciences of the United States of America 101 (2004): 13168–73.

  Sordino, P., F. Vanderhoeven, and D. Duboule. “Hox Gene-Expression in Teleost Fins and the Origin of Vertebrate Digits.” Nature 375 (1995): 678–81.

  Sproewitz, A., et al. “Learning to Move in Modular Robots Using Central Pattern Generators and Online Optimization.” International Journal of Robotics Research 27 (2008): 423–43.

  Stankiewicz, R. “The Concept of Design Space.” In Technological Innovation as an Evolutionary Process, edited by J. Ziman, 234–47. Cambridge: Cambridge University Press, 2000.

 

‹ Prev