Evolution 2.0

100
Cyber Top Cops. (2014). “Stock Market Spam—Hash Buster Text and Hash
Busting.” Retrieved from http://www.cybertopcops.com/stock-market-spamhash-
busting.php
101
Ashbrook, T. (2005, August 10). “On Point with Tom Ashbrook: Debate over
Intelligent Design.” National Public Radio. Retrieved from
http://onpoint.wbur.org/2005/08/10/debate-over-intelligent-design
102
Ayala, F. J. (1969). “Evolution of Fitness, v. Rate of Evolution of Irradiated
Populations of Drosophila.” Proceedings of the National Academy of Sciences
of the United States of America, 63, 790–793.
103
Bergman, J. (2006). “The ‘Nothing in Biology Makes Sense Except in the Light
of Evolution’ Myth: An Empirical Study and Evaluation.” Retrieved from
http://www.trueorigin.org/biologymyth.php
Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008). “Historical Contingency
and the Evolution of a Key Innovation in an Experimental Population of
104 Escherichia coli.” Proceedings of the National Academy of Sciences of the
United States of America, 105, 7899–7906.
105 Coyne, J. A. (2009). Why Evolution Is True. New York: Viking Adult.
106
Coyne, J. A. (2012, August 22). “James Shapiro Goes after Natural Selection
Again (Twice) on HuffPo.” The Huffington Post. Retrieved from
http://whyevolutionistrue.wordpress.com/2012/08/22/james-shapiro-goes-afternatural-
selection-again-twice-on-huffpo/
107
Crow, J. (1972). Proceedings of the 6th Berkeley Symposium on Mathematical
Statisitics and Probability. Volume 5: Darwinian, Neo-Darwinian, and Non-
Darwinian Evolution (Biostatistics of Genetical Processes in Human
Populations). Cambridge, UK: Cambridge University Press.
108
Darwin, C. (1859). On the Origin of Species by Means of Natural Selection,
or the Preservation of Favoured Races in the Struggle for Life. London: John
Murray.
109 Darwin, C. (1888). The Descent of Man, and Selection in Relation to Sex.
London: John Murray.
110 Dawkins, R. (1976). The Selfish Gene. Oxford, UK: Oxford University Press.
111 Dawkins, R. (1986). The Blind Watchmaker: Why the Evidence of Evolution
Reveals a Universe without Design. New York: W. W. Norton.
112 Dawkins, R. (1996). River out of Eden: A Darwinian View of Life. New York:
Basic Books.
113 Dawkins, R. (2000). Unweaving the Rainbow: Science, Delusion and the
Appetite for Wonder. New York: Mariner Books.
114 Dawkins, R. (2009). The Greatest Show on Earth: The Evidence for Evolution.
London: Transworld Digital.
115 Dawkins, R. (2010). The Rise of Atheism. Retrieved from
http://www.atheistconvention.org.au/richard-dawkins/
116 Dennett, D. C. (1996). Darwin’s Dangerous Idea: Evolution and the Meanings
of Life. New York: Penguin.
117 Dietrich, M. R. (2003). “Richard Goldschmidt: Hopeful Monsters and Other
‘Heresies.’” Nature Reviews, Genetics, 4, 68–74.
118 Dobzhansky, T. G. (1937). Genetics and the Origin of Species. New York:
Columbia University Press.
119 Dobzhansky, T. G. (1955). Evolution, Genetics, and Man. New York: Wiley.
120 Goldschmidt, R. B. (1982). The Material Basis of Evolution (Reissued). New
Haven, CT: Yale University Press.
121 Hall, B. K. (2001). Commentary. American Zoologist, 41, 1049–1051.
122 Hanson, F. B., & Heys, F. (1930). “A Possible Relation Between Natural (Earth)
Radiation and Gene Mutations.” Science, 71, 43–44.
123
Hanson, F. B., & Heys, F. (1932). “Radium and Lethal Mutations in Drosophila:
Further Evidence of the Proportionality Rule from a Study of the Effects of
Equivalent Doses Differently Applied.” American Naturalist, 66, 335–345.
124 Hoffer, Eric. (2006). The Passionate State of Mind and Other Aphorisms.
Titusville, NJ: Hopewell.
125 Hoyle, F. (1999). Mathematics of Evolution. Memphis, TN: Acorn Enterprises.
126
Kawaguchi, H., O’Huigin, C., & Klein, J. (1992). “Evolutionary Origin of
Mutations in the Primate Cytochrome P450c21 Gene.” American Journal of
Human Genetics, 50, 766–780.
127
Loony London—Men on Display in Zoo, “Just Another Primate.” (2005, August
29). LifeSiteNews.com. Retrieved from
https://www.lifesitenews.com/news/loony-london-men-on-display-in-zoo-justanother-
primate
128 Mayr, E., & Provine, W. B. (1998). The Evolutionary Synthesis: Perspectives
on the Unification of Biology. Cambridge, MA: Harvard University Press.
129
Merlin, F. (2010, September). “Evolutionary Chance Mutation: A Defense of the
Modern Synthesis’ Consensus View.” Philosophy & Theory in Biology, 2.
doi:10.3998/ptb.6959004.0002.003. Retrieved from
http://quod.lib.umich.edu/p/ptb/6959004.0002.003/--evolutionary-chancemutation-
a-defense-of-the-modern?rgn=main;view=fulltext
130 Meyer, S. C. (2013). Darwin’s Doubt: The Explosive Origin of Animal Life
and the Case for Intelligent Design. New York: HarperCollins.
131
Moorhead, P. S., Kaplan, M. M., & Brown, P. (1967). Mathematical
Challenges to the Neo-Darwinian Interpretation of Evolution: A Symposium
Held at the Wistar Institute of Anatomy and Biology, April 25 and 26, 1966.
Philadelphia: Wistar Institute Press.
132 Morgan, T. H. (1916). A Critique of the Theory of Evolution. Princeton, NJ:
Princeton University Press.
133
Newport, F. (2009, February 11). “On Darwin’s Birthday, Only 4 in 10 Believe
in Evolution.” Gallup. Retrieved from
http://www.gallup.com/poll/114544/darwin-birthday-believe-evolution.aspx
134
Sawyer, S. A., Zhang, Z., & Hartl, D. L. (2007). “Prevalence of Positive
Selection among Nearly Neutral Amino Acid Replacements in Drosophila.”
Proceedings of the National Academy of Sciences of the United States of
America, 104, 6504–6510.
135
Stein, R. (2012, August 9). “Gonorrhea Evades Antibiotics, Leaving Only One
Drug to Treat Disease.” NPR [Blog post]. Retrieved from
http://www.npr.org/blogs/health/2012/08/10/ 158464908/gonorrhea-evadesantibiotics-
leaving-only-one-drug-to-treat-disease
136
University of California at Berkeley. (n.d.). “Understanding Evolution for
Teachers: Mutations Are Random.” Retrieved from
http://evolution.berkeley.edu/evosite/evo101/IIIC1aRandom.shtml
137
Yates, D. (2012, March 12). “Study of Ribosome Evolution Challenges RNA
World Hypothesis” [Press release]. Retrieved from
http://news.illinois.edu/news/12/0312ribosome_GustavoCaetano-Anolles.html
200 Basic Biology & Science Definitions
200 BookRags. (2013). “Dissection—Research Article from World of Health.”
Retrieved from http://www.bookrags.com/research/dissection-woh
201
Ayala, F. J., & Rzhetskydagger, A. (1998, January 20). “Origin of the Metazoan
Phyla: Molecular Clocks Confirm Paleontological Estimates.” Proceedings of
the National Academy of Sciences of the United States of America, 95(2):
606–611. doi:10.1073/pnas.95.2.606
202 Behrens, S. J., & Parker, J. A. (2010). Language in the Real World: An
Introduction to Linguistics. New York: Taylor & Francis.
203 Beker, H., & Piper, F. (1982). Cipher Systems: The Protection of
Communications. London: Northwood Books.
204 Bernhardt, H. S. (2012). “The RNA World Hypothesis: The Worst Theory of the
Early Evolution of Life (Except for All the Others).” Biology Direct, 7, 23.
205
Bettelheim, F. A., Brown, W. H., Campbell, M. K., Farrell, S. O., & Torres, O.
J. (2010). Introduction to Organic and Biochemistry (8th ed.). Belmont, CA:
Brooks/Cole.
206 Bird, R. J. (2003). Chaos and Life: Complexity and Order in Evolution and
Thought. New York: Columbia University Press.
207 Cairns-Smith, A. G. (1982). Genetic Takeover and the Mineral Origins of Life.
Cambridge, UK: Cambridge University Press.
208 Chiras, D. D. (2011). Human Biology. Burlington, MA: Jones & Bartlett
Learning.
209
Conway Morris, S. (2000). “The Cambrian ‘Explosion’: Slow-Fuse or
Megatonnage?” Proceedings of the National Academy of Sciences of the
United States of America, 97, 4426–4429.
210
Cooper, G. M. (2000). “The Central Role of Enzymes as Biological Catalysts.”
In The Cell: A Molecular Approach, American Society for Microbiology (pp.
89–115). Sunderland, MA: Sinauer Associates. Retrieved from
http://www.ncbi.nlm.nih.gov/books/NBK9921
211 Curtis, H., & Barnes, N. S. (1994). Invitation to Biology. New York: W. H.
Freeman.
212
Emspak, J. (2011, October 14). “Scientists Build Self-Replicating Molecule.”
Discovery.com. Retrieved from
http://news.discovery.com/tech/biotechnology/scientists-buil-self-replicatingmolecule-
111014.htm
213 Frank, A. (1997, November 1). “Quantum Honeybees.” Discover Magazine.
Retrieved from http://discovermagazine.com/1997/nov/quantumhoneybees1263
214 Frizzell, R. A. (1993). “The Molecular Physiology of Cystic Fibrosis.”
Physiology, 8, 117–120.
215
Fruton, J. S. (1999). Proteins, Enzymes, Genes: The Interplay of Chemistry
and Biology. New Haven, CT: Yale University Press.
216 Gilbert, W. (1986). “Origin of Life: The RNA World.” Nature, 319(6055), 618.
doi:10.1038/319618a0
217 Gwynne, P., Begley, S., & Hager, M. (1979, August 20). “The Secrets of the
Human Cell,” Newsweek, 94, 48–54.
218 Hawking, S. (2007). God Created the Integers: The Mathematical
Breakthroughs That Changed History. Philadelphia: Running Press.
219 Hazen, R. M. (2005). Genesis: The Scientific Quest for Life’s Origin.
Washington, DC: Joseph Henry Press.
220
Heijmans, B. T., Tobi, E. W., Stein, A. D., Putter, H., Blauw, G. J., Susser, E. S.,
… Lumey, L. H. (2008). “Persistent Epigenetic Differences Associated with
Prenatal Exposure to Famine in Humans.” Proceedings of the National
Academy of Sciences of the United States of America, 105, 17046–17049.
221 Hirs, C. H., Timasheff, S. N., et al. (1964). Progress in Nucleic Acid Research
& Molecular Biology. New York: Academic Press.
222
Horgan, J. (2011, February 28). “Pssst! Don’t Tell the Creationists, but
Scientists Don’t Have a Clue How Life Began.” Cross-Check [Blog]. Retrieved
from http://blogs.scientificamerican.com/cross-check/2011/02/28/pssst-donttell-
the-creationists-but-scientists-dont-have-a-clue-how-life-began/
223 Kauffman, S. (1996). At Home in the Universe: The Search for the Laws of
Self-Organization and Complexity. New York: Oxford University Press.
224 Küppers, B. O. (1990). Information and the Origin of Life. Cambridge, MA:
MIT Press.
225 “Life.” (1974). In Encyclopedia Britannica: Macropaedia, pp. 893–894.
226 Dumont, M. L. (1873, April 3). “The Theory of Evolution in Germany.” In N.
Lockyer (Ed.), Nature, 7, 434.
227 Lowe, S. W., & Lin, A.W. (2000). “Apoptosis in Cancer.” Carcinogenesis, 21,
485–495.
228
Lupo, A., Coyne, S., & Berendonk, T. U. (2012). “Origin and Evolution of
Antibiotic Resistance: The Common Mechanisms of Emergence and Spread in
Water Bodies.” Frontiers in Microbiology, 3. Retrieved from
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266646
229 MacDonald, D. W. (2006). The Encyclopedia of Mammals: Facts on File. New
York: Natural Science Library.
230
Maher, B. (2012, September 9). “Brendan Maher Writes about ENCODE/Junk
DNA Publicity Fiasco.” Sandwalk [Blog]. Retrieved from
http://sandwalk.blogspot.com/2012/09/brendan-maher-writes-aboutencodejunk.
html
231 Margulis, L., & Chapman, M. J. (2009). Kingdoms and Domains: An
Illustrated Guide to the Phyla of Life on Earth. New York: Academic Press.
232
Mendel, J. G. (1901). “Versuche über Pflanzenhybriden Verhandlungen des
naturforschenden Vereines in Brünn, Bd. IV für das Jahr.” Journal of the Royal
Horticultural Society, 26, 1–32.
233 Meredith, S., Claybourne, A., Reiss, M. J., et al. (2006). The Usborne
Introduction to Genes & DNA: Internet Linked. London: Usborne.
234 Merlo, L. M. F., Pepper, J. W., Reid, J., & Maley, C. C. (2006). “Cancer as an
Evolutionary and Ecological Process.” Nature Reviews Cancer, 6, 924–935.
235 Miller, S. L. (1953). “A Production of Amino Acids under Possible Primitive
Earth Conditions.” Science, 117, 528–529.
236
Mitchell, A., & Pilpel, Y. (2011). “A Mathematical Model for Adaptive
Prediction of Environmental Changes by Microorganisms.” Proceedings of the
National Academy of Sciences of the United States of America, 108, 7271–
7276.
237 Moore, R. C., Vodopich, D. S., & Cotner, S. H. (2011). Arguing for Evolution:
An Encyclopedia for Understanding Science. Santa Barbara, CA: ABC-CLIO.
238
Nguyen, T., Brunson, D., Crespi, C. L., Penman, B. W., Wishnok, J. S., &
Tannenbaum, S. R. (1992). “DNA Damage and Mutation in Human Cells
Exposed to Nitric Oxide in Vitro.” Proceedings of the National Academy of
Sciences of the United States of America, 89(7), 3030–3034.
239 Nielsen, L. L., & Maneval, D. C. (1997). “P53 Tumor Suppressor Gene Therapy
for Cancer.” Cancer Gene Therapy 5(1), 52–63.
240
Pace, N. R. (2001). “The Universal Nature of Biochemistry.” Proceedings of
the National Academy of Sciences of the United States of America, 98, 805–
808.
241 Patton, J. T. (2008). Segmented Double-Stranded RNA Viruses: Structure and
Molecular Biology. Poole, UK: Horizon Scientific Press.
242 Reif, J. H. (2002). “Successes and Challenges.” Science, 296(5567), 478–479.
243 Robinson, T. R. (2005). Genetics for Dummies. Indianapolis, IN: Wiley.
244
Riordan, J. R., Rommens, J. M., Kerem, B., Alon, N., Rozmahel, R., Grzelczak,
Z., Zielinski, J., … Chou, J. L. (1989). “Identification of the Cystic Fibrosis
Gene: Cloning and Characterization of Complementary DNA.” Science,
245(4925), 1066–1073.
245 Rowland, M. (1992). Biology. Surrey, UK: Nelson.
246 Sanford, J. C. (2005). Genetic Entropy & the Mystery of the Genome.
Waterloo, NY: FMS Publications.
247 Shannon, C.E.. “An Algebra for Theoretical Genetics.” PhD dissertation,
Cambridge, MA: Massachusetts Institute of Technology, 1940.
248 Shimkets, R. A. (2004). Gene Expression Profiling: Methods and Protocols.
Totowa, NJ: Humana Press.
249
Smith, J., & Dixon, A. (2009, November 1). “Birds Do It. Bats Do It.” Greater
Good. Retrieved from
http://greatergood.berkeley.edu/article/item/birds_do_it_bats_do_it
250 Szent-Gyoergyi, A. (1966). “Drive in Living Matter to Perfect Itself.” Journal
of Individual Psychology, 22(2), 153–162.
251 Ullmann, A. (2007). “Pasteur-Koch: Distinctive Ways of Thinking about
Infectious Diseases.” Microbe, 2(, 383–387.
252
Von Neumann, J. (1951). “The General and Logical Theory of Automata.” In L.
A. Jeffress (Ed.), Cerebral Mechanisms in Behavior (pp. 1–41). Oxford, UK:
Wiley.
253 Wark, K. (1995). Advanced Thermodynamics for Engineers. New York:
McGraw-Hill.
254 Watson, J. D., & Berry, A. (2003). DNA: The Secret of Life. New York: Knopf.
255
Webber, M. A., & Piddock, L. J. V. (2003). “The Importance of Efflux Pumps in
Bacterial Antibiotic Resistance.” Journal of Antimicrobial Chemotherapy, 51,
9–11.
256
Wilkins, J. S. (2013). “The Salem Region: Two Mindsets about Science.” In M.
Pigliucci & M. Boudry (Eds.), Philosophy of Pseudoscience: Reconsidering
the Demarcation Problem (pp. 397–416). Chicago: University of Chicago
Press.
300 Genetic Code & Coding Theory
300
Bohlin, J., van Passel, M. W. J., Snipen, L., Kristoffersen, A. B., Ussery, D., &
Hardy, S. P. (2012). “Relative Entropy Differences in Bacterial Chromosomes,
Plasmids, Phages and Genomic Islands.” BMC Genomics, 13, 66.
doi:10.1186/1471-2164-13-66
301 Charrel, A. (1995). Tierra Network Version. ATR Technical Report TR-H-145.
302 Clayton, J., & Dennis, C. (Eds.). (2003). 50 Years of DNA. Hampshire, UK:
Palgrave Macmillan.
303
Crick, F. (1962, December 11). “Nobel Lecture: On the Genetic Code.”
Retrieved from
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1962/cricklecture.
html
304 Crick, F. (1968). “The Origin of the Genetic Code.” Journal of Molecular
Biology, 38, 367–379.
305
The ENCODE Project Consortium. (2011, April 19). “ENCODE: A User’s
Guide to the Encyclopedia of DNA Elements (ENCODE).” PLoS Biology.
Retrieved from http://dx.plos.org/10.1371/journal.pbio.1001046
306 Freeland, S. J., & Hurst, L. D. (1998). “The Genetic Code Is One in a Million.”
Journal of Molecular Evolution, 47, 238–248.
307 Friedberg, E. C. W., & Siede, W. (1995). “DNA Repair and Mutagenesis.”
Trends in Biochemical Sciences—Library Compendium, 20, 440.
308
Garcia, J. A., & Jose, M. V. (2005). “Mathematical Properties of DNA
Sequences from Coding and Noncoding Regions.” Revista Mexicana de Física,
51, 122–130.
Gitschier, J. (2012). “It Was Heaven: An Interview with Evelyn Witkin.” PLoS
309 Genetics 8, e1003009.
310 Gitt, W. (1997). In the Beginning Was Information. Bielefeld, Germany:
Christliche Literatur-Verbreitung.
311 Harold, F. M. (2001). The Way of the Cell: Molecules, Organisms, and the
Order of Life. New York: Oxford University Press.
312 Kunkel, T. A., & Eric, D. A. (2005). “DNA Mismatch Repair.” Annual Review
of Biochemistry, 74, 681–710.
313 Lee, T. F. (1991). The Human Genome Project: Cracking the Genetic Code of
Life. New York: Plenum.
314
Lipman, D. J., & Maizel, J. (1982). “Comparative Analysis of Nucleic Acid
Sequences by Their General Constraints.” Nucleic Acids Research, 10, 2723–
2739.
315 Ohno, S. (1972). “So Much ‘Junk’ DNA in Our Genome.” Brookhaven
Symposia in Biology, 23, 366–370.
316
Perez, J.-C. (2010). “Codon Populations in Single-Stranded Whole Human
Genome DNA Are Fractal and Fine-Tuned by the Golden Ratio 1.618.”
Interdisciplinary Sciences, 2(3), 228–240.
317 Pressing, J., & Reanney, D. C. (1984). “Divided Genomes and Intrinsic Noise.”
Journal of Molecular Evolution, 20, 135–146.
318 Ricard, J. (2006). Emergent Collective Properties, Networks, and Information
in Biology. New York: Elsevier.
319 Sadovsky, M. G. (2006). “Information Capacity of Nucleotide Sequences and Its
Applications.” Bulletin of Mathematical Biology, 68, 785–806.
320 Shannon, C. E. (1948). “A Mathematical Theory of Communication.” Bell
System Technical Journal, 27, 379–423.
321 Sklar, B. (2001). Digital Communications (2nd ed.). New York: Prentice Hall.
322
Walton, M. (2012, December 4). “Mice, Men Share 99 Percent of Genes.”
CNN.com. Retrieved from http://articles.cnn.com/2002-12-
04/tech/coolsc.coolsc.mousegenome_1_human-genome-new-human-genesgenes-
that-cause-disease?_s=PM:TECH
323
Wiener, N. (1961). Cybernetics: Or Control and Communication in the Animal
and the Machine, 25. Cambridge, MA: MIT Press.
324 Wiener, N. (1965). Cybernetics: Or Control and Communication in the Animal
and the Machine, 25. Cambridge, MA: MIT Press.
325 Yockey, H. P. (2000). “Origin of Life on Earth and Shannon’s Theory of
Communication.” Computers & Chemistry, 24, 105–123.
326 Yockey, H. P. (2005). Information Theory, Evolution, and the Origin of Life.
Cambridge, UK: Cambridge University Press.
400 Linguistic Models of DNA
400 Bassler, B. L. (2002). “Small Talk: Cell-to-Cell Communication in Bacteria.”
Cell, 109, 421–424.
401
Ben Jacob, E., Becker, I., Shapira, Y., & Levine, H. (2004). “Bacterial
Linguistic Communication and Social Intelligence.” Trends in Microbiology,
12(, 366–372.
402 Jerne, N. K. (1985). “The Generative Grammar of the Immune System.”
Bioscience Reports, 5, 439–451.
403 Ji, S. (1999). “The Linguistics of DNA: Words, Sentences, Grammar, Phonetics,
and Semantics.” Annals of the New York Academy of Sciences, 870, 411–417.
404 Katz, G. (2008). “The Hypothesis of a Genetic Protolanguage: An
Epistemological Investigation.” Biosemiotics, 1, 57–73.
405 Searls, D. B. (2002). “The Language of Genes.” Nature, 420, 211–217.
406 Smith, A. D. (1997). Oxford Dictionary of Biochemistry and Molecular
Biology. New York: Oxford University Press.
407
Witzany, G. (2008). “Bio-Communication of Bacteria and Their Evolutionary
Roots in Natural Genome Editing Competences of Viruses.” Open Evolution
Journal, 2, 44–54.

400 Linguistic Models of DNA
400 Bassler, B. L. (2002). “Small Talk: Cell-to-Cell Communication in Bacteria.”
Cell, 109, 421–424.
401
Ben Jacob, E., Becker, I., Shapira, Y., & Levine, H. (2004). “Bacterial
Linguistic Communication and Social Intelligence.” Trends in Microbiology,
12(, 366–372.
402 Jerne, N. K. (1985). “The Generative Grammar of the Immune System.”
Bioscience Reports, 5, 439–451.
403 Ji, S. (1999). “The Linguistics of DNA: Words, Sentences, Grammar, Phonetics,
and Semantics.” Annals of the New York Academy of Sciences, 870, 411–417.
404 Katz, G. (2008). “The Hypothesis of a Genetic Protolanguage: An
Epistemological Investigation.” Biosemiotics, 1, 57–73.
405 Searls, D. B. (2002). “The Language of Genes.” Nature, 420, 211–217.
406 Smith, A. D. (1997). Oxford Dictionary of Biochemistry and Molecular
Biology. New York: Oxford University Press.
407
Witzany, G. (2008). “Bio-Communication of Bacteria and Their Evolutionary
Roots in Natural Genome Editing Competences of Viruses.” Open Evolution
Journal, 2, 44–54.
500 Cellular Cognition
500
Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006, May 16).
“Synthetic Biology: New Engineering Rules for an Emerging Discipline.”
Molecular Systems Biology, 2:2006.0028.
501
Baluška, F., Mancuso, S., Volkmann, D., & Barlow, P. W. (2009). “The ‘Root-
Brain’ Hypothesis of Charles and Francis Darwin: Revival after More Than 125
Years.” Plant Signaling & Behavior, 4, 1121–1127.
502
Chowdhury, D., Nishinari, K., & Schadschneider, A. (2004). “Self-Organized
Patterns and Traffic Flow in Colonies of Organisms: From Bacteria and Social
Insects to Vertebrates.” Phase Transitions, 77, 601–624.
503 Duke, R. C., Ojcius, D. M., & Young, J. D. E. (1996). “Cell Suicide in Health
and Disease.” Scientific American, 275, 80–87.
504 Dworkin, M. (1983). “Tactic Behavior of Myxococcus xanthus.” Journal of
Bacteriology, 154, 452–459.
505
Engelberg-Kulka, H., Amitai, S., Kolodkin, I., & Hazan, R. (2006). “Bacterial
Programmed Cell Death and Multicellular Behavior in Bacteria.” PLoS
Genetics, 2, e135.
506
Fraser, C. M., Gocayne, J. D., White, O., Adams., M. D., Clayton, R. A.,
Fleischmann, R. D., Bult, C. J., … Venter, J. C. (1995). “The Minimal Gene
Complement of Mycoplasma genitalium.” Science, 270(5235), 397–403.
507
Golden, J. W., Robinson, S. J., & Haselkorn, R. (1985). “Rearrangement of
Nitrogen Fixation Genes during Heterocyst Differentiation in the
Cyanobacterium Anabaena.” Nature, 314, 419–423.
508 Hoffmeyer, J. (2000). “The Biology of Signification.” Perspectives in Biology
and Medicine, 43, 252–268.
509
Lindqvist, A., Rodriguez, V., & Medema, R. H. (2009). “The Decision to Enter
Mitosis: Feedback and Redundancy in the Mitotic Entry Network.” The Journal
of Cell Biology, 185, 193–202.
510 Liu, R., & Ochman, H. (2007). “Origins of Flagellar Gene Operons and
Secondary Flagellar Systems.” Journal of Bacteriology, 189, 7098–7104.
511
Li, Z., Rosenbaum, M. A., Venkataraman, A., Tam, T. K., Katz, E., & Angenent,
L. T. (2011). “Bacteria-Based AND Logic Gate: A Decision-Making and Self-
Powered Biosensor.” Chemical Communications, 47, 3060–3062.
512
Loewenstein, W. R. (1999). The Touchstone of Life: Molecular Information,
Cell Communication, and the Foundations of Life. New York: Oxford
University Press.
513
Lyon, P. (2007). “From Quorum to Cooperation: Lessons from Bacterial
Sociality for Evolutionary Theory.” Studies in History and Philosophy of
Biological and Biomedical Sciences, 38, 820–833.
514
Martincorena, I., Seshasayee, A. S. N., & Luscombe, N. M. (2012). “Evidence
of Non-Random Mutation Rates Suggests an Evolutionary Risk Management
Strategy.” Nature, 485, 95–98.
515 McMenamin, G. R. (2002). Forensic Linguistics: Advances in Forensic
Stylistics. Boca Raton, FL: CRC.
516 Miller, M. B., & Bassler, B. L. (2001). “Quorum Sensing in Bacteria.” Annual
Reviews in Microbiology, 55, 165–199.
517
Morita, Y., Kataoka, A., Shiota, S., Mizushima, T., & Tsuchiya, T. (2000).
“NorM of Vibrio parahaemolyticus Is an Na+-Driven Multidrug Efflux Pump.”
Journal of Bacteriology, 182, 6694–6697.
518 Nakagaki, T. (2001). “Smart Behavior of True Slime Mold in a Labyrinth.”
Research in Microbiology, 152, 767–770.
519
Nakagaki, T., Kobayashi, R., Nishiura, Y., & Ueda, T. (2004). “Obtaining
Multiple Separate Food Sources: Behavioural Intelligence in the Physarum
Plasmodium.” Proceedings of the Royal Society of London. Series B:
Biological Sciences, 271, 2305–2310.
520 Neuman, Y. (2008). Reviving the Living: Meaning Making in Living Systems.
New York: Elsevier.
521 Perkins, T. J., & Swain, P. S. (2009). “Strategies for Cellular Decision-
Making.” Molecular Systems Biology, 5(1), 326.
522 Shapiro, J. A. (1988). “Bacteria as Multicellular Organisms.” Scientific
American, 258, 82–89.
523 Shapiro, J. A., & Dworkin, M. (1997). Bacteria as Multicellular Organisms.
New York: Oxford University Press.
524 Sudo, S. Z., & Dworkin, M. (1973). “Comparative Biology of Prokaryotic
Resting Cells.” Advances in Microbial Physiology, 9, 153–224.
525
Zohar, A., & Ginossar, S. (1998). “Lifting the Taboo Regarding Teleology and
Anthropomorphism in Biology Education—Heretical Suggestions.” Science
Education, 82, 679–697.
600 Post-Darwinian Models of Evolution
600
Adhya, S. L., & Shapiro, J. A. (1969). “The Galactose Operon of E. COLI K-
12. I. Structural and Pleiotropic Mutations of the Operon.” Genetics, 62, 231–
247.
601 Ahmadjian, V. (1962). “Investigations on Lichen Synthesis.” American Journal
of Botany, 49(3), 277–283.
602
Alkan, C., Ventura, M., Archdiacono, N., Rocchi, M., Sahinalp, S. C., & Eichler,
E. E. (2007). “Organization and Evolution of Primate Centromeric DNA from
Whole-Genome Shotgun Sequence Data.” PLoS Computational Biology, 3,
1807–1818.
603 Barbash, D. A. (2010). “Ninety Years of Drosophila melanogaster Hybrids.”
Genetics, 186, 1–8.
604
Bassler, B. L. (2009, February). “How Bacteria ‘Talk.’” TED2009. Retrieved
from
http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html
605
Randal Bollinger, R., Barbas, A. S., Bush, E. L., Lin, S. S., & Parker, W. (2007).
“Biofilms in the Large Bowel Suggest an Apparent Function of the Human
Vermiform Appendix.” Journal of Theoretical Biology, 249, 826–831.
606
Bradt, S. (2009, October . “A Look Inside: Scientists Have Deciphered 3-D
Structure of the Human Genome.” Harvard Gazette. Retrieved from
http://news.harvard.edu/gazette/story/2009/10/3-d-human-genome/
607
Brandon, R. A. (1977). “Interspecific Hybridization among Mexican and United
States Salamanders of the Genus Ambystoma Under Laboratory Conditions.”
Herpetologica, 33(2), 133–152.
608 Bray, D. (2009). Wetware: A Computer in Every Living Cell. New Haven, CT:
Yale University Press.
609 Cavalier-Smith, T. (2003). “Microbial Muddles.” BioScience, 53, 1008–1013.
610 Chamovitz, D. (2012). What a Plant Knows: A Field Guide to the Senses. New
York: Macmillan.
611
Conova, S. (2014, February 5). “Drawing Back DNA ‘Curtains’ on New Gene-
Editing Method.” Columbia University Medical Center Newsroom. Retrieved
from http://newsroom.cumc.columbia.edu/blog/2014/02/05/Dna-curtains-drawback-
secrets-new-gene-editing-method/
612 Diekmann, Y., & Pereira-Leal, J. B. “Evolution of Intracellular
Compartmentalization,” Biochemical Journal, 449(2), 319–331.
613
Duharcourt, S., Lepère, G., & Meyer, E. (2009). “Developmental Genome
Rearrangements in Ciliates: A Natural Genomic Subtraction Mediated by Non-
Coding Transcripts.” Trends in Genetics, 25(, 344–350. Retrieved from
http://www.ncbi.nlm.nih.gov/pubmed/19596481
614
Eldredge, N., & Gould, S. J. (1972). “Punctuated Equilibria: An Alternative to
Phyletic Gradualism.” In T. J. M. Schopf (Ed.), Models in Paleobiology (pp.
82–115). San Francisco: Freeman, Cooper.
615
Fall, S., Mercier, A., Bertolla, F., Calteau, A., Gueguen, L., Perrière, G., …
Simonet, P. (2007). “Horizontal Gene Transfer Regulation in Bacteria as a
‘Spandrel’ of DNA Repair Mechanisms.” PLoS One 2: e1055. Retrieved from
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001055
616 Gould, S. J. (1977). “Evolution’s Erratic Pace.” Natural History, 86, 12–16.
617 Gould, S. J. (1980). “Is a New and General Theory of Evolution Emerging?”
Paleobiology, 6(1), 119–130.
618 Gould, S. J. (2002). Rocks of Ages. New York: Vintage/Ebury.
619 Grant, T., & Woods, A. (2002). Reason in Revolt: Dialectical Philosophy and
Modern Science. New York: Algora.
620
Gray, T. A. (2013). “Distributive Conjugal Transfer in Mycobacteria Generates
Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a
Mating Identity Locus,” PLoS Biology, 11: e1001602.
621 Ho, M. W. (n.d.). “Horizontal Gene Transfer.” Institute of Science in Society.
Retrieved from http://online.sfsu.edu/rone/GEessays/horizgenetransfer.html
622 Holt, S., & Aguirre, L. (2007, July 24). “Epigenetics” [Video and Transcript].
Nova. Retrieved from http://www.pbs.org/wgbh/nova/body/epigenetics.html
623 Horgan, J. (1997). The End of Science: Facing the Limits of Knowledge in the
Twilight of the Scientific Age. Reading, MA: Addison-Wesley.
624 Jeon, K. W. (1987). “Change of Cellular ‘Pathogen’ into Required Cell
Components.” Annals of the New York Academy of Sciences, 503, 359–371.
625 Jeon, T. J., & Jeon, K. W. (2004). “Gene Switching in Amoeba Proteus Caused
by Endosymbiotic Bacteria.” Journal of Cell Science, 117(4), 535–543.
626 Kasahara, M. (2007). “The 2R Hypothesis: An Update.” Current Opinion in
Immunology, 19, 547–552.
627 Keller, E. F. (1984). A Feeling for the Organism, 10th Aniversary Edition: The
Life and Work of Barbara McClintock. New York: Times Books.
628
Kelly, M. “Far from Random, Evolution Follows a Predictable Genetic Pattern,
Princeton Researchers Find.” Princeton University News Archive. Retrieved
from http://www.princeton.edu/main/news/archive/S35/06/74S40/
629
Kolata, G. “Bits of Mystery Data, Far from ‘Junk,’ Play Crucial Role.” The New
York Times. Retrieved from http://www.nytimes.com/2012/09/06/science/farfrom-
junk-dna-dark-matter-proves-crucial-to-health.html
630
Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S.,
Kheradpour, P., … Kellis, M. (2011). “A High-Resolution Map of Human
Evolutionary Constraint Using 29 Mammals.” Nature, 478, 476–482.
631
Liu, R., & Ochman, H. (2007). “Stepwise Formation of the Bacterial Flagellar
System.” Proceedings of the National Academy of Sciences of the United
States of America, 104, 7116–7121.
632
Lokki, J., Suomalainen, E., Saura, A., & Lankinen, P. (1975). “Genetic
Polymorphism and Evolution in Parthenogenetic Animals. II. Diploid and
Polyploid SOLENOBIA TRIQUETRELLA (Lepidoptera: Psychidae).” Genetics,
79, 513–525.
633
Lutz, B., Lu, H. C., Eichele, G., Miller, D., & Kaufman, T. C. (1996). “Rescue of
Drosophila Labial Null Mutant by the Chicken Ortholog Hoxb-1 Demonstrates
That the Function of Hox Genes Is Phylogenetically Conserved.” Genes &
Development, 10(2), 176–184. doi:10.1101/gad.10.2.176.
634 Lyne, J., & Howe, H. F. (1986). “‘Punctuated Equilibria’: Rhetorical Dynamics
of a Scientific Controversy.” Quarterly Journal of Speech, 72, 132–147.
635 Mann, C. (1991). “Lynn Margulis: Science’s Unruly Earth Mother.” Science,
252, 378–381.
636 Margulis, L., & Fester, R. (1991). Symbiosis as a Source of Evolutionary
Innovation: Speciation and Morphogenesis. Cambridge, MA: MIT Press.
637 Margulis, L., & Sagan, D. (2003). Acquiring Genomes: A Theory of the Origin
of Species. New York: Basic Books.
638
Lynn Margulis is quoted in chapter 5 of Horgan, J. (1997). The End of Science:
Facing the Limits of Knowledge in the Twilight of the Scientific Age (pp. 140–
141). Reading, MA: Addison-Wesley.
639
McClintock, B. (1950). “The Origin and Behavior of Mutable Loci in Maize.”
Proceedings of the National Academy of Sciences of the United States of
America, 36, 344–355.
640
McClintock, B. (1983, December . “Nobel Lecture: The Significance of
Responses of the Genome to Challenge.” Retrieved from
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintocklecture.
html
641 Meyer, A., & dePeer, Y. (2005). “From 2R to 3R: Evidence for a Fish-Specific
Genome Duplication (FSGD).” BioEssays, 27, 937–945.
642 Comfort, N. C. (2003). The Tangled Field: Barbara McClintock’s Search for
the Patterns of Genetic Control. Cambridge, MA: Harvard University Press.
643 Noble, D. (2015). “Evolution Beyond Neo-Darwinism: A New Conceptual
Framework.” The Journal of Experimental Biology, 218(1), 7–13.
644 Noble, D. (2008). The Music of Life: Biology beyond Genes. New York:
Oxford University Press.
645 Noble, D. (2013). “Physiology Is Rocking the Foundations of Evolutionary
Biology.” Experimental Physiology, 98(, 1235–1243.
646
Noble, D. “Physiology and the Revolution in Evolutionary Biology.” Keynote
speech at the International Conference of Physiological Sciences in 2012,
Suzhou, China. VOX: Voices from Oxford [Video]. Retrieved from
http://www.voicesfromoxford.org/video/physiology-and-the-revolution-inevolutionary-
biology/184
647 Novick, R. P. (1980). “Plasmids.” Scientific American, 243, 102.
648 Ohno, S., et al. (1970). Evolution by Gene Duplication. London: George Allen
& Unwin.
649 Pennisi, E. (2012, September 7). “ENCODE Project Writes Eulogy for Junk
DNA.” Science, 337, 1159–1161.
650 Prescott, D. M. (2000). “Genome Gymnastics: Unique Modes of DNA Evolution
and Processing in Ciliates.” Nature Reviews Genetics, 1, 191–198.
651 Rapp, R. A., & Wendel, J. F. (2005). “Epigenetics and Plant Evolution.” New
Phytologist, 168, 81–91.
652 Ryan, F. (2011). Virolution. New York: HarperCollins.
653 Ryan, F. (2002). Darwin’s Blind Spot: Evolution beyond Natural Selection.
New York: Houghton Mifflin Harcourt.
654
Sapp, J., Carrapico, F., & Zolotonosov, M. (2002). “Symbiogenesis: The
Hidden Face of Constantin Merezhkowsky.” History and Philosophy of the Life
Sciences, 24, 413–440.
655
Schmidt, M. (2009). Beyond Antibiotics: Strategies for Living in a World of
Emerging Infections and Antibiotic-Resistant Bacteria. Berkeley, CA: North
Atlantic Books.
656 Schrödinger, Erwin. (1944). What Is Life—The Physical Aspect of the Living
Cell. Cambridge, UK: Cambridge University Press.
657 Shapiro, J. A. (2005). “Barbara McClintock, 1902–1992.” BioEssays, 14, 791–
792.
658 Shapiro, J. A. (2009). “Letting Escherichia Coli Teach Me about Genome
Engineering.” Genetics, 183, 1205–1214.
659 Shapiro, J. A. (2011). Evolution: A View from the 21st Century. Upper Saddle
River, NJ: FT Press.
660
Shapiro, J. A. (2012, March 25). “DNA as Poetry: Multiple Messages in a
Single Sequence.” The Huffington Post. Retrieved from
http://www.huffingtonpost.com/james-a-shapiro/dna-as-poetry-multipleme_
b_1229190.html
661
Shapiro, J. A. (2012, April 7). “Purposeful, Targeted Genetic Engineering in
Immune System Evolution.” The Huffington Post. Retrieved in 2012 from
http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering-immunesystem-
evolution_b_1255771.html
662
Shapiro, J. A. (2012, May 19). “Cell Cognition and Cell Decision Making.” The
Huffington Post. Retrieved from http://www.huffingtonpost.com/james-ashapiro/
cell-cognition_b_1354889.html
663
Shapiro, J. A. (1999). “Genome System Architecture and Natural Genetic
Engineering in Evolution.” Annals of the New York Academy of Sciences,
870(1), 23–35.
664 Shapiro, J. A. (2013). “How Life Changes Itself: The Read–Write (RW)
Genome.” Physics of Life Reviews, 10(3), 287–323.
665
Shapiro, J. A. (2009). “Revisiting the Central Dogma in the 21st Century.”
Annals of the New York Academy of Sciences, 1178, 6–28. doi:10.1111/j.1749-
6632.2009.04990.x
666
Shapiro, J. A. (2013, January 30). “Why the ‘Gene’ Concept Holds Back
Evolutionary Thinking.” The Huffington Post. Retrieved from
http://www.huffingtonpost.com/james-a-shapiro/why-the-gene-concepthold_
b_2207245.html
667
Singer, E. (2009, February 4). “A Comeback for Lamarckian Evolution?”
Technology Review. Retrieved from
http://www.technologyreview.com/news/411880/a-comeback-for-lamarckianevolution
668 Smith, D. C., & Douglas, A. E. (1987). The Biology of Symbiosis. London:
Edward Arnold.
669
Somit, A., & Peterson, S. A. (1992). The Dynamics of Evolution: The
Punctuated Equilibrium Debate in the Natural and Social Sciences. Ithaca,
NY: Cornell University Press.
670
“Spider DNA Spurs Search into Arachnid Secrets.” (2014, May 6). PhysOrg.
Retrieved from http://phys.org/news/2014-05-spider-dna-spurs-arachnidsecrets.
html
671 Stadler, D., & Moyer, R. (1981). “Induced Repair of Genetic Damage in
Neurospora.” Genetics, 98, 763–774.
672
Starrett, J., Garb, J. E., Kuelbs, A., Azubuike, U. O., & Hayashi, C. Y. (2012)
“Early Events in the Evolution of Spider Silk Genes,” PLoS One 7(6), e38084.
Retrieved from http://journals.plos.org/plosone/article?
id=10.1371/journal.pone.0038084
673 Stebbins, G. L. (1951). “Cataclysmic Evolution.” Scientific American, 184, 54–
59.
674 Syvanen, M., & Kado, C. I. (2002). Horizontal Gene Transfer. New York:
Academic Press.
675 Talbott, S. L. (2012, July 3). “Biology Worthy of Life: Getting Over the Code
Delusion.” Retrieved from http://natureinstitute.org/txt/st/mqual/genome_4.htm
676 Taylor, G. R. (1983). The Great Evolution Mystery. HarperCollins.
677 Thomas, E. A. (1939). Uber die Biologie von Flechtenbildnern (9th ed.).
Beiträge zur Kryptogamenflora der Schweiz.
678 Trafton, A. (2009, October 9) “A New Dimension for Genome Studies.” MIT
News. Retrieved from http://web.mit.edu/newsoffice/2009/3d-genome.html
679
ScienceDaily. (2012, July 3). “Two Species Fused to Give Rise to Plant Pest a
Few Hundred Years Ago.” Retrieved from
http://www.sciencedaily.com/releases/2012/07/120703133725.htm
680 Woese, C. R. (2004). “A New Biology for a New Century.” Microbiology and
Molecular Biology Reviews, 68, 173–186.
681
Woese, C. R., & Fox, G. E. (1977). “Phylogenetic Structure of the Prokaryotic
Domain: The Primary Kingdoms.” Proceedings of the National Academy of
Sciences of the United States of America, 74, 5088–5090.
682
Yandell, K. (2013, July 9). “Bacterial Gene Transfer Gets Sexier.” The
Scientist. Retrieved from http://www.the-scientist.com/?
articles.view/articleNo/36410/title/Bacterial-Gene-Transfer-Gets-Sexier/
683
Zhang, T. Y., & Meaney, M. J. (2010). “Epigenetics and the Environmental
Regulation of the Genome and Its Function.” Annual Review of Psychology, 61,
439–466.
700 Technology
Adami, C., & Brown, C. T. (1994). “Evolutionary Learning in the 2D Artificial
700 Life System ‘Avida.’” In R. A. Brooks & P. Maes (Eds.), Artificial Life IV:
Proceedings of the Fourth International Workshop on the Synthesis and
Simulation of Living Systems (pp. 377–381). Cambridge, MA: MIT Press.
701 Altshuller, G. S., Shulyak, L., & Rodman, S. (1997). 40 Principles: TRIZ Keys
to Innovation. Worcester, MA: Technical Innovation Center.
702 Banzal, S. (2007). Data and Computer Network Communication. Bangalore:
Firewall Media/Laxmi Publications.
703
FoxBlitzz. (2006, August 11). “Corrupting Super Mario Bros” [Video].
Retrieved from https://www.youtube.com/watch?
v=gN0sY0rX8rI&feature=youtube
704
Holland, J. H. (1975). Adaptation in Natural and Artificial Systems: An
Introductory Analysis with Applications to Biology, Control, and Artificial
Intelligence. Ann Arbor, MI: University of Michigan Press.
705 Jaki, S. L. (1969). Brain, Mind, and Computers. New York: Herder & Herder.
706
Koza, J. R., Bennett, F. H., Andre, D., & Keane, M. A. (2003). “Genetic
Programming: Biologically Inspired Computation That Creatively Solves Non-
Trivial Problems.”
In L. F. Landweber & E. Winfree (Eds.), Evolution as Computation: DIMACS
Workshop (pp. 95–124). Berlin: Springer-Verlag.
707 Kurzweil, R. (2005). The Singularity Is Near: When Humans Transcend
Biology. New York: Viking Adult.
708
Marshall, P. S., & Rinaldi, J. S. (2005). Industrial Ethernet: How to Plan,
Install, and Maintain TCP/IP Ethernet Networks: The Basic Reference Guide
for Automation and Process Control Engineers. Research Triangle Park, NC:
ISA.
709 Ray, T. S. (1991). Scientific Excellence in Supercomputing: The IBM 1990
Contest Prize Papers. Athens, GA: Baldwin Press.
710 Ray, T. S. (1992). Evolution, Ecology and Optimization of Digital Organisms
(Report No. 92-08-942). Santa Fe, NM: Santa Fe Institute.
711 Runyon, J. (2012, August 2). “An Unexpected Ass Kicking” [Blog post].
Retrieved from http://joelrunyon.com/two3/an-unexpected-ass-kicking
712 Stranneby, D., & Walker, W. (2004). Digital Signal Processing and
Applications. Oxford, UK: Newness.
713 Turing, A. M. (1950). “Computing Machinery and Intelligence.” Mind, 59, 433–
460.
714 Watson, R. A., & Pollack, J. B. (2002). “A Computational Model of Symbiotic
Composition in Evolutionary Transitions.” Biosystems, 69, 187–209.
800 Mathematics
800
Chaitin, G. J. (1990). Information Randomness & Incompleteness: Papers on
Algorithmic Information Theory. Teaneck, NJ: World Scientific Publishing
Company Incorporated. Reprinted from Chaitin, G. J. (1975). “Randomness and
Mathematical Proof.” Scientific American, 232(5), 47–52.
801 Gabbay, D. M., Thagard, P., Woods, J., Bandyopadhyay, P. S., & Forster, M. R.
(2011). Philosophy of Statistics, 7. New York: Elsevier.
802
Pellionisz, A. J., Graham, R., Pellionisz, P. A., & Perez, J. (2013). “Recursive
Genome Function of the Cerebellum: Geometric Unification of Neuroscience
and Genomics.” In Handbook of the Cerebellum and Cerebellar Disorders,
1381–1423. Springer Netherlands.
900 History, Philosophy, & Theology
900 “Science and Religion” [Special issue]. (1999, July–August). The Skeptical
Inquirer, 23(4).
901 Holy Bible: New International Translation. (1984). Grand Rapids, MI:
Zondervan.
902
Boyle, R. (1989). “Of the Excellency and Grounds of the Corpuscular or
Mechanical Philosophy.” In M. R. Matthews, The Scientific Background to
Modern Philosophy: Selected Readings (pp. 109–123). Indianapolis: Hackett.
(Original work published 1674.)
903
Brown, N. M. (2011, January 3). “Everything You Think You Know about the
Dark Ages Is Wrong” [Blog post]. Retrieved from
http://religiondispatches.org/everything-you-think-you-know-about-the-darkages-
is-wrong/
904 Butler, S. (1879). Evolution, Old and New. London: Harwick & Bogue.
905 Clark, R. W. (1984). Einstein: The Life and Times. New York: Avon.
906 Collins, F. S. (2006). The Language of God: A Scientist Presents Evidence for
Belief. New York: Simon & Schuster.
907
Coperincus, N. (1543). “Dedication (Excerpts).” In On the Revolutions of the
Heavenly Bodies. Retrieved from
http://www.historyguide.org/earlymod/dedication.html
908 Darling, D. (2004). The Universal Book of Mathematics: From Abracadabra
to Zeno’s Paradoxes. Hoboken, NJ: Wiley.
909 Darlington, C. D. (1977). “Obituary: TD Lysenko.” Nature, 266, 287–288.
910 Davies, P. (1993). Mind of God: The Scientific Basis for a Rational World.
New York: Simon & Schuster.
911
Davies, P. “Stephen Hawking’s Big Bang Gaps.” (2010, September 4). The
Guardian UK. Retrieved from
http://www.guardian.co.uk/commentisfree/belief/2010/sep/04/stephen-hawkingbig-
bang-gap
912 Dilley, S. (2012). “Charles Darwin’s Use of Theology in the Origin of Species.”
British Journal for the History of Science, 45, 29–56.
913 Einstein, A. (1934). Mein Weltbild. Amsterdam: Querido Verlag.
914 Oxford Dictionaries. (2015). “The OEC: Facts about the Language.” Retrieved
from http://oxforddictionaries.com/words/the-oec-facts-about-the-language
915 Ferngren, G. B. (2002). Science and Religion: A Historical Introduction.
Baltimore, MD: Johns Hopkins University Press.
916
Gaither, C., & Cavazos-Gaither, A. E. (2012). Gaither’s Dictionary of
Scientific Quotations: A Collection of Approximately 27,000 Quotations
Pertaining to Archaeology, Architecture, Astronomy, Biology, Botany,
Chemistry, Cosmology, Darwinism, Engineering, Geology, Mathematics,
Medicine, Nature, Nursing, Paleontology, Philosophy, Physics, Probability,
Science, Statistics, Technology, Theory, Universe, and Zoology. New York:
Springer.
917
Galileo, G. (1957). “Letter to Madame Christina of Lorraine, Grand Duchess of
Tuscany, Concerning the Use of Biblical Quotations in Matters of Science.” In S.
Drake (Ed. and Trans.), Discoveries and Opinions of Galileo (pp. 175–216).
New York: Doubleday.
918 Greer, R., Trans. (1979). Origen: An Exhortation to Martyrdom, Prayer and
Selected Works. Classics of Western Spirituality. Mahwah, NJ: Paulist Press.
919 Gies, J. (1995). Cathedral, Forge and Waterwheel. New York: Harper
Perennial.
920 Gigot, F. (1912). “Book of Wisdom.” In The Catholic Encyclopedia. New York:
Robert Appleton. Retrieved from http://www.newadvent.org/cathen/15666a.htm
921 Godart, O., & Heller, M. (1985). “Cosmology of Lemaître.” Tucson, AZ:
Pachart.
922 Grcic, J., & Grcic, P. D. J. (2009). Facing Reality: An Introduction to
Philosophy, Revised Edition. Bloomington, IN: AuthorHouse.
923 Ham, K., & Hodge, B. (2011). How Do We Know the Bible Is True? Green
Forest, AR: Master Books.
924 Hawking, S., & Mlodinow, L. (2010). The Grand Design. London: Transworld
Digital.
925 Hitchens, Peter. The Rage Against God. Bloomsbury, 2010.
926
Hume, D. (1890). A Treatise of Human Nature: Being an Attempt to Introduce
the Experimental Method of Reasoning into Moral Subjects; And, Dialogues
Concerning Natural Religion. London: Longmans, Green.
927 Jaki, S. L. (1978). The Road of Science and the Ways to God. Chicago:
University of Chicago Press.
928 Jammer, M. (2002). Einstein and Religion: Physics and Theology. Princeton,
NJ: Princeton University Press.
929 Johnson, P. (2012). History of Christianity. New York: Simon & Schuster.
930 Kaplan, A., & Elman, Y. (1993). Immortality, Resurrection, and the Age of the
Universe: A Kabbalistic View. Jersey City, NJ: Ktav.
931 Kepler, J. (1596). Mysterium Cosmographicum.
932 Kramer, M. (Ed.). (1999). The Black Book of Communism: Crimes, Terror,
Repression. Cambridge, MA: Harvard University Press.
933 Moreland, J. P., & Craig, W. L. (2003). Philosophical Foundations for a
Christian Worldview. Downer’s Grove, IL: IVP Academic.
934
Nagel, T. (2012). Mind and Cosmos: Why the Materialist Neo-Darwinian
Conception of Nature Is Almost Certainly False. New York: Oxford University
Press.
935
Newton, I. (1714). Philosophiæ Naturalis Principia Mathematica. Sumptibus
Societatis. Newton, I. Extract from Untitled Treatise on Revelation (section
1.1). Yahuda Ms edition. National Library of Israel, Jerusalem, Israel, f. 14r.9.
936 Philipse, H. (2012). God in the Age of Science? A Critique of Religious
Reason. New York: Oxford University Press.
938 Pigliucci, M. (2012). “Who Knows What: The War between Science and the
Humanities.” Aeon. Retrieved from http://philpapers.org/rec/PIGWKW
939 Planck, M. (1955). Religion und naturwissenschaft, vortrag gehalten im mai
1937. Leipzig, Germany: JA Barth.
940
Piatt, C. (2014, July 11). “Frank Schaeffer: The God-Believing Atheist.” The
Huffington Post. Retrieved from http://www.huffingtonpost.com/christianpiatt/
frank-schaeffer-the-god-b_b_5306149.html
941 Potts, D. (1996). Mesopotamian Civilization: The Material Foundations.
Ithaca, NY: Cornell University Press.
942 Russell, B. (1919). Mysticism and Logic: And Other Essays. New York,
London: Longmans, Green.
943 Stark, R. (2005). The Victory of Reason: How Christianity Led to Freedom,
Capitalism, and Western Success. New York: Random House.
944 Stark, R. (2011). The Triumph of Christianity: How the Jesus Movement
Became the World’s Largest Religion. New York: HarperOne.
945 Ussher, J., Pierce, L., & Pierce, M. (Eds.) (2003). Annals of the World (Vol. 1).
Green Forest, AR: New Leaf.
946 Walton, J. H. (2010). The Lost World of Genesis One: Ancient Cosmology and
the Origins Debate. Downer’s Grove, IL: IVP Academic.
947 Wells, P. S. (2009). Barbarians to Angels: The Dark Ages Reconsidered. New
York: W. W. Norton.
948
O’Brian, N. F. (2006). “What’s a 13th-Century Pope Got to Do with Stem Cells?
Nothing at All.” Catholic News Service. Retrieved from
http://www.catholicnews.com/data/stories/cns/0604116.htm
949
Whitefield, R. (2006, June 12). “The Hebrew Word ‘Yom’ Used with a Number
in Genesis 1. What Does ‘Yom’ Mean in Genesis 1?” Retrieved from
http://www.godandscience.org/youngearth/yom_with_number.pdf
950
Winsley, J. (2005). Why Do They That Know Him Not See His Days? Studies
in God’s Millennial Week. Hokitika, New Zealand: Touching the King
Publications.
951 Dimitrov, T. (2010, March). “Part I. 50 Nobel Laureates Who Believe in GOD:
Nobel Scientists (1).” Scientific GOD Journal, 1(3), 151, 263.