Arrival of the Fittest: Solving Evolution's Greatest Puzzle (39 page)

BOOK: Arrival of the Fittest: Solving Evolution's Greatest Puzzle
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53
. A minor difference from my previous notions of phenotype and function is that any one circuit, any one wiring pattern, may be able to display more than one (computational) behavior, depending on the input to the Boolean logic function that it encodes. One can view a circuit that explores the circuit library to preserve an old, optimal computation while improving a newer, still suboptimal computation as walking along the circuit network in which both computations are unchanged, while exploring the neighborhood of this network for circuits that improve the new computation.

EPILOGUE: PLATO’S CAVE

 

1
. See Darwin (1969), 58.

2
. See proposition 168 in Wittgenstein (1983), 99.

3
. See Wigner (1960).

4
. See Tegmark (2008). A skeptic might argue that the correspondence between mathematics and reality is just an artifact of human history—that there is a huge space of all possible mathematics and we have “sliced” only those theorems from this space that actually describe the physical world. But that assertion raises the question of what the nature of this space is and why useful math exists at all in it.

BIBLIOGRAPHY
 

Abbott, E. A.
Flatland: A Romance of Many Dimensions
. New York: Perseus, 2002.

Akam, M. “Drosophila Development: Making Stripes Inelegantly.”
Nature
341 (1989): 282–83.

Alberch, P. “From Genes to Phenotype: Dynamical Systems and Evolvability.”
Genetica
84 (1991): 5–11.

Albert, R., and H. G. Othmer. “The Topology of the Regulatory Interactions Predicts the Expression Pattern of the Segment Polarity Genes in
Drosophila melanogaster
.”
Journal of Theoretical Biology
223 (2003): 1–18.

Alfred, R. “Oct. 21, 1879: Edison Gets the Bright Light Right.”
Wired,
October 21, 2009.

Amores, A., et al. “Zebrafish Hox Clusters and Vertebrate Genome Evolution.”
Science
282 (1998): 1711–14.

Arkin, R. C.
Behavior-Based Robotics
. Cambridge, MA: MIT Press, 1998.

Arthur, W. B.
The Nature of Technology: What It Is and How It Evolves
. New York: Free Press, 2009.

Ashery-Padan, R., et al. “Pax6 Activity in the Lens Primordium Is Required for Lens Formation and for Correct Placement of a Single Retina in the Eye.”
Genes and Development
14 (2000): 2701–11.

Avery, O. T., C. M. MacLeod, and M. McCarty. “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.”
Journal of Experimental Medicine
79 (1944): 137–58.

Babu, M. M., et al. “Structure and Evolution of Transcriptional Regulatory Networks.”
Current Opinion in Structural Biology
14 (2004): 283–91.

Bada, J. L., and A. Lazcano. “Origin of Life—Some Like It Hot, but Not the First Biomolecules.”
Science
296 (2002): 1982–83.

Balch, M.
Complete Digital Design
. New York: McGraw-Hill, 2003.

Banzhaf, W., and A. Leier, A. “Evolution on Neutral Networks in Genetic Programming.” In
Genetic Programming Theory and Practice III,
edited by T. Yu, R. Riolo, and B. Worzel, 207–21. New York: Springer, 2006.

Beatty, J. T., et al. “An Obligately Photosynthetic Bacterial Anaerobe from a Deep-Sea Hydrothermal Vent.”
Proceedings of the National Academy of Sciences of the United States of America
102 (2005): 9306–10.

Beerling, D. J., C. P. Osborne, and W. G. Chaloner. “Evolution of Leaf-Form in Land Plants Linked to Atmospheric CO
2
Decline in the Late Palaeozoic Era.”
Nature
410 (2001): 352–54.

Benfey, P., and A. Protopapas.
Genomics
. Upper Saddle River, NJ: Prentice Hall, 2005.

Bennick, A. “Interaction of Plant Polyphenols with Salivary Proteins.”
Critical Reviews in Oral Biology and Medicine
13 (2002): 184–96.

Bergthorsson, U., et al. “Widespread Horizontal Transfer of Mitochondrial Genes in Flowering Plants.”
Nature
424 (2003): 197–201.

Bersaglieri, T., et al. “Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene.”
American Journal of Human Genetics
74 (2004): 1111–20.

Bertalanffy, L. v.
General System Theory: Foundations, Development, Applications
. New York: George Braziller, 1968.

Bharathan, G., et al. “Homologies in Leaf Form Inferred from KNOXI Gene Expression during Development.”
Science
296 (2002): 1858–60.

Blattner, F. R., et al. “The Complete Genome Sequence of
Escherichia coli
K-12.”
Science
277 (1997): 1453–62.

Borges, J. L.
Fictions
. London: Calder, 1962.

Braakman, R., and E. Smith. “The Compositional and Evolutionary Logic of Metabolism.”
Physical Biology
10 (2013): 1–61.

Brakefield, P. M., et al. “Development, Plasticity and Evolution of Butterfly Eyespot Patterns.”
Nature
384 (1996): 236–42.

Brameier, M., and W. Banzhaf. “Neutral Variations Cause Bloat in Linear GP.” In
6th European Conference on Genetic Programming (EuroGP 2003),
edited by C. Ryan et al., 286–96. Colchester, England, 2003.

Branden, C., and J. Tooze.
Introduction to Protein Structure
. New York: Garland, 1999.

Brasier, M., et al. “A Fresh Look at the Fossil Evidence for Early Archaean Cellular Life.”
Philosophical Transactions of the Royal Society B: Biological Sciences
361 (2006): 887–902.

Bryson, B.
A Short History of Nearly Everything
. London: Random House, 2003.

Budin, I., R. J. Bruckner, and J. W. Szostak. “Formation of Protocell-Like Vesicles in a Thermal Diffusion Column.”
Journal of the American Chemical Society
131 (2009): 9628–29.

Budin, I., and J. W. Szostak. “Expanding Roles for Diverse Physical Phenomena during the Origin of Life.”
Annual Review of Biophysics
39
(
2010): 245–63.

Burchfield, J.
Lord Kelvin and the Age of the Earth
. Chicago: University of Chicago Press, 1990.

———. “Darwin and the Problem of Geological Time.
Isis
65 (1974): 300–21.

Burr, A. B., and G. E. Andrew.
The Unreasonable Effectiveness of Number Theory
. Washington, DC: American Mathematical Society, 1992.

Bushman, F.
Lateral DNA Transfer: Mechanisms and Consequences.
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2002.

Cairns, J., J. Overbaugh, and S. Miller. “The Origin of Mutants.”
Nature
335 (1988): 142–45.

Carroll, S. B., J. K. Grenier, and S. D. Weatherbee.
From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design.
Malden, MA: Blackwell, 2001.

Caspi, R., et al. “The MetaCyc Database of Metabolic Pathways and Enzymes and the BioCyc Collection of Pathway/Genome Databases.”
Nucleic Acids Research
40 (2012): D742–D753.

Cech, T. R. “Structural Biology—The Ribosome Is a Ribozyme.”
Science
289 (2000): 878–79.

Chang, A., et al. “BRENDA, AMENDA and FRENDA the Enzyme Information System: New Content and Tools in 2009.”
Nucleic Acids Research
37 (2009): D588–D592.

Cheng, C. C.-H. “Evolution of the Diverse Antifreeze Proteins.”
Current Opinion in Genetics and Development
8 (1998): 715–20.

Cheng, L. K. L., and P. J. Unrau. “Closing the Circle: Replicating RNA with RNA.”
Cold Spring Harbor Perspectives in Biology
2 (2010).

Ciliberti, S., O. C. Martin, and A. Wagner. “Circuit Topology and the Evolution of Robustness in Complex Regulatory Gene Networks.”
PLoS Computational Biology
3, no. 2 (2007a): e15.

———. “Innovation and Robustness in Complex Regulatory Gene Networks.”
Proceedings of the National Academy of Sciences of the United States of America
104 (2007b): 13591–96.

Cody, G. D., et al. “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate.”
Science
289 (2000): 1337–40.

Cohn, M. J., and C. Tickle. “Developmental Basis of Limblessness and Axial Patterning in Snakes.”
Nature
399 (1999): 474–79.

Cole, S., and T. J. Phelan. “The Scientific Productivity of Nations.”
Minerva
37 (1999): 1–23.

Cook, L. M., et al. “Selective Bird Predation on the Peppered Moth: The Last Experiment of Michael Majerus.”
Biology Letters
8 (2012): 609–12.

Copley, S. D. “Evolution of a Metabolic Pathway for Degradation of a Toxic Xenobiotic: The Patchwork Approach.”
Trends in Biochemical Sciences
25 (2000): 261–65.

Copley, S. D., et al. “The Whole Genome Sequence of
Sphingobium chlorophenolicum
L-1:
Insights into the Evolution of the Pentachlorophenol Degradation Pathway.”
Genome Biology and Evolution
4 (2012): 184–98.

Copley, S. D., E. Smith, and H. J. Morowitz. “The Origin of the RNA World: Co-evolution of Genes and Metabolism.”
Bioorganic Chemistry
35 (2007): 430–43.

Corcos, A., and F. Monaghan. “Role of de Vries in the Recovery of Mendel’s Work. 1. Was de Vries Really an Independent Discoverer of Mendel?”
Journal of Heredity
76 (1985): 187–90.

Corliss, J. B., et al. “Submarine Thermal Springs on the Galápagos Rift.”
Science
203 (1979): 1073–83.

Cotterell, J., and J. Sharpe. “An Atlas of Gene Regulatory Networks Reveals Multiple Three-Gene Mechanisms for Interpreting Morphogen Gradients.”
Molecular Systems Biology
6 (2010): 425.

Cropper, W. H.
Great Physicists
. New York: Oxford University Press, 2001.

Dantas, G., et al. “Bacteria Subsisting on Antibiotics.”
Science
320 (2008): 100–103.

Darwin, C.
On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life.
1st ed. London: John Murray, 1859.

———.
The Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life
. 6th ed. London: John Murray, 1872. Reprint, New York: A. L. Burt.

———.
The Autobiography of Charles Darwin, 1809–1882
. New York: Norton, 1969.

Davidson, A. R., and R. T. Sauer. “Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences.”
Proceedings of the National Academy of Sciences of the United States of America
91 (1994): 2146–50.

Davis, M. C., R. D. Dahn, and N. H. Shubin. “An Autopodial-Like Pattern of Hox Expression in the Fins of a Basal Actinopterygian Fish.”
Nature
447 (2007): 473–76.

Dawkins, R.
Climbing Mount Improbable
. New York: Norton, 1997.

———.
Unweaving the Rainbow: Science, Delusion, and the Appetite for Wonder
. Boston: Houghton Miffin, 1998.

de Vries, H.
Species and Varieties, Their Origin by Mutation.
Chicago: Open Court Publishing Company, 1905.

Deamer, D. W. “Membrane Compartments in Prebiotic Evolution.” In
The Molecular Origins of Life,
edited by E. Brock, 189–205. Cambridge: Cambridge University Press, 1998.

Dekel, E., and U. Alon. “Optimality and Evolutionary Tuning of the Expression Level of a Protein.”
Nature
436 (2005): 588–92.

Delsemme, A. H. “Cosmic Origin of the Biosphere.” In
The Molecular Origins of Life,
edited by E. Brock, 100–118. Cambridge: Cambridge University Press, 1998.

Desmond, A., and J. Moore.
Darwin: The Life of a Tormented Evolutionist.
New York: Norton, 1994.

Dong, J., and J. Vagners. “Parallel Evolutionary Algorithms for UAV Planning.” In
AIAA First Intelligent Systems Technical Conference.
Chicago, 2004.

Dong, P. D. S., J. S. Dicks, and G. Panganiban. “Distal-less and Homothorax Regulate Multiple Targets to Pattern the Drosophila Antenna.”
Development
129 (2002): 1967–74.

Drake, J. W., et al. “Rates of Spontaneous Mutation.”
Genetics
148 (1998): 1667–86.

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.

BOOK: Arrival of the Fittest: Solving Evolution's Greatest Puzzle
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