Arrival of the Fittest: Solving Evolution's Greatest Puzzle (40 page)

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 Cambridge 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 CO
₂
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.