Stein, U., W. Walther, and V. Wunderlich. “Point Mutations in the MDR1 Promoter of Human Osteosarcomas Are Associated with In-Vitro Responsiveness to Multidrug-Resistance Relevant Drugs.” European Journal of Cancer 30A (1994): 1541–45.
Steppuhn, A., et al. “Nicotine’s Defensive Function in Nature.” PLoS Biology 2 (2004): 1074–80.
Stevens, M. “The Role of Eyespots as Anti-predator Mechanisms, Principally Demonstrated in the Lepidoptera.” Biological Reviews 80 (2005): 573–88.
Stevens, M., C. J. Hardman, and C. L. Stubbins. “Conspicuousness, Not Eye Mimicry, Makes ‘Eyespots’ Effective Antipredator Signals.” Behavioral Ecology 19 (2008): 525–31.
Stevens, M., C. L. Stubbins, and C. J. Hardman. “The Anti-predator Function of ‘Eyespots’ on Camouflaged and Conspicuous Prey.” Behavioral Ecology and Sociobiology 62 (2008): 1787–93.
Stewart, I. Flatterland. New York: Perseus, 2001.
———. In Pursuit of the Unknown: 17 Equations That Changed the World. New York: Basic Books, 2012.
Stone, J., and G. Wray. “Rapid Evolution of Cis-Regulatory Sequences via Local Point Mutations.” Molecular Biology and Evolution 18 (2001): 1764–70.
Strandh, S. “Christopher Polhem and His Mechanical Alphabet.” Techniques and Culture 10 (1987).
Stryer, L. Biochemistry. New York: Freeman, 1995.
Sumida, S. S., and C. A. Brochu. “Phylogenetic Context for the Origin of Feathers.” American Zoologist 40 (2000): 486–503.
Swallow, D. M. “Genetics of Lactase Persistence and Lactose Intolerance.” Annual Review of Genetics 37 (2003): 197–219.
Szegezdi, E., et al. “Mediators of Endoplasmic Reticulum Stress-Induced Apoptosis.” EMBO Reports 7 (2006): 880–85.
Szostak, J. W. “The Eightfold Path to Non-enzymatic RNA Replication.” Journal of Systems Chemistry 3 (2012): 2.
Takiguchi, M., et al. “Evolutionary Aspects of Urea Cycle Enzyme Genes.” Bioessays 10 (1989): 163–66.
Tamas, I., et al. “50 Million Years of Genomic Stasis in Endosymbiotic Bacteria.” Science 296 (2002): 2376–79.
Tanaka, F., R. Fuller, and C. F. Barbas. “Development of Small Designer Aldolase Enzymes: Catalytic Activity, Folding, and Substrate Specificity.” Biochemistry 44 (2005): 7583–92.
Tanay, A., A. Regev, and R. Shamir. “Conservation and Evolvability in Regulatory Networks: The Evolution of Ribosomal Regulation in Yeast.” Proceedings of the National Academy of Sciences of the United States of America 102 (2005): 7203–8.
Tanenbaum, A. S. Computer Networks. Englewood Cliffs, NJ: Prentice Hall, 1988.
Tanner, M. A., and T. R. Cech. “Activity and Thermostability of the Small Self-Splicing Group I Intron in the Pre-tRNA(IIe) of the Purple Bacterium Azoarcus.” RNA-a Publication of the RNA Society 2 (1996): 74–83.
Tautz, D. “Redundancies, Development and the Flow of Information.” Bioessays 14 (1992): 263–66.
Taylor, S. V., et al. “Searching Sequence Space for Protein Catalysts.” Proceedings of the National Academy of Sciences of the United States of America 98 (2001): 10596–601.
Tegmark, M. 2008. “The Mathematical Universe.” Foundations of Physics 38 (2001): 101–50.
Theissen, G. 2006. “The Proper Place of Hopeful Monsters in Evolutionary Biology.” Theory in Biosciences 124 (2001): 349–69.
Thomas, G. H., et al. “A Fragile Metabolic Network Adapted for Cooperation in the Symbiotic Bacterium Buchnera aphidicola.” BMC Systems Biology 3 (2009): 24.
Tirosh, I., et al. “A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation.” Science 324 (2009): 659–62.
Tishkoff, S. A., et al. “Convergent Adaptation of Human Lactase Persistence in Africa and Europe.” Nature Genetics 39 (2007): 31–40.
Tomarev, S., and J. Piatigorsky. “Lens Crystallins of Invertebrates—Diversity and Recruitment from Detoxification Enzymes and Novel Proteins.” European Journal of Biochemistry 235 (1996): 449–65.
Tomasz, A. “Antibiotic Resistance in Streptococcus pneumoniae.” Clinical Infectious Diseases 24 (1997): S85–S88.
True, J. R., and S. B. Carroll. “Gene Co-option in Physiological and Morphological Evolution.” Annual Review of Cell and Developmental Biology 18 (2002): 53–80.
Tucker, V. A. “The Deep Fovea, Sideways Vision and Spiral Flight Paths in Raptors.” Journal of Experimental Biology 203 (2000): 3745–54.
Tzoulaki, I., I. M. S. White, and I. M. Hanson. “PAX6 Mutations: Genotype-Phenotype Correlations.” BMC Genetics 6 (2005).
van der Meer, J. R. “Evolution of Novel Metabolic Pathways for the Degradation of Chloroaromatic Compounds.” In Beijerinck Centennial Symposium on Microbial Physiology and Gene Regulation—Emerging Principles and Applications, 159–78. The Hague, Netherlands, 1995.
van der Meer, J. R., et al. “Evolution of a Pathway for Chlorobenzene Metabolism Leads to Natural Attenuation in Contaminated Groundwater.” Applied and Environmental Microbiology 64 (1998): 4185–93.
van Ham, R., et al. “Reductive Genome Evolution in Buchnera aphidicola.” Proceedings of the National Academy of Sciences of the United States of America 100 (2003): 581–86.
Venter, J. C. “A Part of the Human Genome Sequence.” Science 299 (2003): 1183–84.
Vermeij, G. J. “Historical Contingency and the Purported Uniqueness of Evolutionary Innovations.” Proceedings of the National Academy of Sciences of the United States of America 103 (2006): 1804–9.
von Dassow, G., et al. “The Segment Polarity Network Is a Robust Development Module.” Nature 406 (2000): 188–92.
Wachtershauser, G. “Evolution of the First Metabolic Cycles.” Proceedings of the National Academy of Sciences of the United States of America 87 (1990): 200–204.
———. “Groundworks for an Evolutionary Biochemistry—The Iron Sulfur World.” Progress in Biophysics and Molecular Biology 58 (1992): 85–201.
Waddington, C. H. “Canalization of Development and the Inheritance of Acquired Characters. Nature 150 (1942): 563–65.
———. “The Genetic Assimilation of an Acquired Character.” Evolution 7 (1953): 118–26.
———. The Strategy of the Genes. New York: Macmillan, 1959.
Wagner, A. “Redundant Gene Functions and Natural Selection.” Journal of Evolutionary Biology 12 (1999): 1–16.
———. “Distributed Robustness versus Redundancy as Causes of Mutational Robustness.” Bioessays 27 (2005a): 176–88.
———. Robustness and Evolvability in Living Systems. Princeton, NJ: Princeton University Press, 2005b.
———. “Robustness and Evolvability: A Paradox Resolved.” Proceedings of the Royal Society B: Biological Sciences 275 (2008): 91–100.
———. “Evolutionary Constraints Permeate Metabolic Networks.” BMC Evolutionary Biology 9 (2009a): 231.
———. Paradoxical Life. New Haven, CT: Yale University Press, 2009b.
———. The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems. Oxford: Oxford University Press, 2011.
Watson, J. D., and F. H. Crick. “A Structure for Deoxyribose Nucleic Acids.” Nature 171 (1953): 737–38.
Whitehead, A. N. Process and Reality. Corrected ed. New York: Free Press, 1978.
Wierenga, R. K. “The TIM-Barrel Fold: A Versatile Framework for Efficient Enzymes.” FEBS Letters 492 (2001): 193–98.
Wigner, E. P. “The Unreasonable Effectiveness of Mathematics in the Natural Sciences.” Communications on Pure and Applied Mathematics 13 (1960): 1–14.
Williams, L. B., et al. “Birth of Biomolecules from the Warm Wet Sheets of Clays near Spreading Centers.” In Earliest Life on Earth: Habitats, Environments, and Methods of Detection, edited by S. D. Golding and M. Glikson, 79–112. Dordrecht: Springer, 2011.
Winzeler, E. A., et al. “Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis.” Science 285 (1999): 901–6.
Wittgenstein, L. Remarks on the Foundation of
Mathematics. Revised ed. Cambridge, MA: MIT Press, 1983.
Wittkopp, P. J., B. K. Haerum, and A. G. Clark. “Evolutionary Changes in Cis and Trans Gene Regulation.” Nature 430 (2004): 85–88.
———. “Regulatory Changes Underlying Expression Differences within and between Drosophila Species.” Nature Genetics 40 (2008): 346–50.
Wolfenden, R., and Y. Yuan. “Rates of Spontaneous Cleavage of Glucose, Fructose, Sucrose, and Trehalose in Water, and the Catalytic Proficiencies of Invertase and Trehalase.” Journal of the American Chemical Society 130 (2008): 7548–49.
Wright, P. A., A. Felskie, and P. M. Anderson. “Induction of Ornithine-Urea Cycle Enzymes and Nitrogen Metabolism and Excretion in Rainbow Trout (Oncorhynchus mykiss) during Early Life Stages.” Journal of Experimental Biology 198 (1995): 127–35.
Ycas, M. “A Note on the Origin of Life.” Proceedings of the National Academy of Sciences of the United States of America 41 (1955): 714–16.
Yu, T., and J. F. Miller. “Through the Interaction of Neutral and Adaptive Mutations, Evolutionary Search Finds a Way.” Artificial Life 12 (2006): 525–51.
Yus, E., et al. “Impact of Genome Reduction on Bacterial Metabolism and Its Regulation.” Science 326 (2009): 1263–68.
Zaher, H. S., and P. J. Unrau. “Selection of an Improved RNA Polymerase Ribozyme with Superior Extension and Fidelity.” RNA 13 (2007): 1017–26.
Zakany, J., and D. Duboule. “The Role of Hox Genes during Vertebrate Limb Development.” Current Opinion in Genetics and Development 17 (2007): 359–66.
Zhang, X. V., and S. T. Martin. “Driving Parts of Krebs Cycle in Reverse through Mineral Photochemistry.” Journal of the American Chemical Society 128 (2006): 16032–33.
Zhao, C., et al. “Charcot-Marie-Tooth Disease Type 2A Caused by Mutation in a Microtubule Motor KIF1B Beta.” Cell 105 (2001): 587–97.
Zimmer, C. Evolution: The Triumph of an Idea. New York: HarperCollins, 2001.
INDEX
The page numbers in this index refer to the printed version of this book. To find the corresponding locations in the text of this digital version, please use the “search” function on your e-reader. Note that not all terms may be searchable.
adenosine triphosphate (ATP), 64–65, 118
alcoholdehydrogenase gene, 27–28
algorithms, evolutionary, 202–4
alleles, 18
Alon, Uri, 140
Altman, Sidney, 43–44
amino acids. See proteins and amino acids
amphiphilic lipid molecules, 55–56
Anaximander, 8
antibiotic resistance, 113, 192
antifreeze proteins, 107, 111, 178–79
aphids, 189–91
Arctic cod, 107, 111, 178–79
Arthur, W. Brian, 201
ATP (adenosine triphosphate), 64–65, 118
autocatalysis, 54–55, 56, 66
Avery, Oswald, 23–24
Backus, John, 196
bacteria. See microbes
bar-headed goose, 112, 120, 197
Bartel, David, 130–31
beta-galactosidase (beta-gal) protein, 138–41
bicoid protein, 147–48
biochemistry, 22–23
BioCyc database, 70
biomass building blocks, 59, 64–65, 69, 83–84, 101
birds
bar-headed goose, 112, 120, 197
evolutionary exaptation of feathers, 200
peregrine falcon, 2–3
Boolean logic functions and logic gates, 207–15
Boreogadus saida (Arctic cod), 107, 111, 178–79
Buchner, Eduard, 22–23
Buchnera aphidicola, 190–93
building blocks of life, 59, 64–65, 69, 83–84, 101
Burkholderia xenovorans, 73
Cambrian explosion, 196
canalization. See robustness
carbon fixation, 199
Carroll, Lewis, 187–88
catalysts, 22–23, 48, 62–63
Cech, Thomas, 43–44
Celera Genomics, 29
cell division, 57–58
chemosynthesis, 50
Christian theology, 9
circuits. See gene regulation and regulation circuits
citric acid cycle, 53–54, 56, 60
combinatorial innovation, 66, 72–73, 75, 83, 102, 200–201
complexity
phenotypes, 22, 31, 33–34, 37–38, 71, 84–88
regulation circuits, 142, 145–46, 150–51, 188
robustness and, 186–87, 191–93
technological innovation, 215
computers and computation. See also technological innovation
Boolean logic functions and logic gates, 207–15
evolutionary algorithms, 202–4
Game of Life self-replication model, 217–18
machine learning, 211–12
in modern biological research, 31–32, 95
mutation, 202–3, 213
conservation of innovations, 3, 5, 14–15, 176–79
Conway, John, 217
co-option of earlier innovations for new purposes, 153, 154, 178, 200
Crick, Francis, 24, 43
crystallins, 3–4, 143–44, 177–78
Cuvier, Georges, 9–10
Darwin, Charles
on adaptation of organs to new purposes, 200
on common ancestry of all life, 10
ignorance of causes of new variations, 14, 21
ignorance of heritability, 11
on limitations inherent in natural selection theory, 177
on mathematics, 218
publication of The Origin of Species, 7, 8, 12, 22, 23
warm-pond hypothesis of origin of life, 39, 48–49
databases of metabolic information, 69–70, 117, 220–21
deep-ocean volcanoes, 49–51
Dekel, Erez, 140
developmental biology, 142
de Vries, Hugo, 13, 15
digital electronics, 207–12
disorder, genotypic, 169–70, 175, 179, 186
distalless protein, 154–55
DNA. See also specific molecular processes
biomass building blocks, 59
components existing in interstellar space, 40
copying errors, 117, 120
duplicate genes, 172–73, 189
energy required for replication, 46–47
horizontal gene transfer and gene deletion, 78–80
Human Genome Project, 29–30
as information repository, 43, 59
in molecular evolutionary biology, 27
molecular structure of, 23–24
in organism’s genome, 29
polymerase transcription enzyme, 138–40
recombination standards, 205
replication process, 42–43
sequencing technology, 29–30
silent mutations, 27–28
Dobzhansky, Theodosius, 11
Drosophila melanogaster (fruit flies)
alcoholdehydrogenase gene, 27–28
computer simulator, 151
Pax6 gene, 146
regulation circuits, 147–50
duplicate genes, 172–73, 189
earth, age of, 1–2
E. coli. See Escherichia coli
Edison, Thomas, 196
Eigen, Manfred/Eigen’s paradox, 45–46
Einstein, Albert, 20
embryology, 21–22
embryonic development
fruit flies, 147–51
Hox code expression, 153
humans, 149–50
endosymbiotic mutualism, 190–91
energy storage molecules, 64–65