Genetics and Philosophy: An introduction

Genetics and Philosophy: An Introduction

Volumn , Issue , 2011, Pages 1-270

  Griffiths, Paul ^a   Stotz, Karola ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84923206551     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511744082     Document Type: Book

References (469)

1. Alberch, Pere. 1982. Developmental constraints in evolutionary processes. in Evo-lution and Development, ed. J. T. Bonner. New York: Springer Verlag, 313-332.
2. Alberts, Jeffrey R. 1994. Learning as adaptation of the infant. Acta Paediatrica83 (s397): 77-85.
3. Alberts, Jeffrey R. 2008. The nature of nurturant niches in ontogeny. Philosophical Psychology 21 (3), special issue, Reconciling Nature and Nurture in the Study of Cognition and Behavior: 295-303.
4. Amundson, Ron. 2005. The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo. Cambridge University Press.
5. Angers, Bernard, Emilie Castonguay, and Rachel Massicotte. 2010. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Molecular Ecology19 (7): 1283-1295.
6. Anstey, Michael L., Stephen M. Rogers, Swidbert R. Ott, Malcolm Burrows, and Stephen J. Simpson. 2009. Serotoninmediates behavioral gregarization underlying swarm formation in desert locusts. Science 323 (5914): 627- 630.
7. Athanasiadis, Alekos, Alexander Rich, and Stefan Maas. 2004. Widespread A-to- I RNA editing of alu-containing mRNAs in the human transcriptome. PLoSBiology2 (12): e391.
8. Badyaev, Alexander V. 2009. Evolutionary significance of phenotypic accommodation in novel environments: anempirical test of the Baldwin effect. PhilosophicalTransactions of the Royal Society, Biological Sciences364: 1125-1141.
9. Badyaev, Alexander V. 2011. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology. Proceedings of the RoyalSociety, Biological Sciences278: 1921-1929.
10. Badyaev, Alexander V., and Tobias Uller. 2009. Parental effects in ecology and evolution: mechanisms, processes, and implications. Philosophical Transactionsof the Royal Society, Biological Sciences364: 1169-1177.
11. Baetu, Tudor. 2012. Genomic programs asmechanism schemas: a non-reductionist interpretation. British Journal for the Philosophy of Science, 63 (3): 649-671. 229
12. Barak, Michal, Erez Y. Levanon, Eli Eisenberg, Nurit Paz, Gideon Rechavi, George M. Church, and Ramit Mehr. 2009. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Research37 (20): 6905-6915.
13. Baranov, Pavel V., Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, and John F. Atkins. 2003. Recode 2003. Nucleic Acids Research31 (1): 87-89.
14. Bass, Brenda. 2001. RNA Editing: Frontiers in Molecular Biology. Oxford University Press.
15. Bateson, P., D. Barker, T. Clutton-Brock, D. Deb, B. D’Udine, R. A. Foley, P. D. Gluckman, K. Godfrey, T. Kirkwood, M. M. Lahr, J. McNamara, N. B. Metcalfe, P. Monaghan, H. G. Spencer, and S. E. Sultan. 2004. Developmental plasticity and human health. Nature430: 419-421.
16. Bateson, Patrick P. G., and Peter D. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press.
17. Bateson, Patrick P. G., and Paul Martin. 1999. Design for a Life: How Behavior and Personality Develop. London: Jonathan Cape.
18. Bateson, William. 1894. Materials for the Study of Variation. London: Macmillan.
19. Beatty, John. 1990. Evolutionary anti-reductionism: historical reflections. Biology and Philosophy5 (2): 199-210.
20. Bechtel, William. 2006. Discovering Cell Mechanisms: The Creation of Modern Cell Biology. Cambridge University Press.
21. Bechtel, William. 2007. Reducing psychology while maintaining its autonomy via mechanistic explanation. in The Matter of the Mind: Philosophical Essays on Psychology, Neuro-science and Reduction, ed. M. Schouten and H. L. De Jong. Oxford: Blackwell, 172-198. Also at http://mechanism.ucsd.edu.
22. Bechtel, William. 2008. Mental Mechanisms. New York: Routledge.
23. Bechtel, William. and Adele Abrahamsen. 2005. Explanation: a mechanistic alternative. Studies in History and Philosophy of the Biological and Biomedical Sciences36: 421-441.
24. Bechtel, William. and Adele Abrahamsen. in press. Thinking dynamically about biological mechanisms: networks of coupled oscillators. Foundations of Science.
25. Bechtel, William. and Richard C. Richardson. 1993. Discovering Complexity: Decom-position and Localization as Strategies in Scientific Research. Princeton UniversityPress.
26. Bentley, David. 2002. The mRNA assembly line: transcription and processing machines in the same factory. Current Opinion in Cell Biology14 (3): 336-342.
27. Bergstrom, Carl, and Martin Rosvall. 2009. The transmission sense of information. Biology and Philosophy26 (2): 159-176.
28. Biliya, Shweta, and Lee A. Bulla Jr. 2010. Genomic imprinting: the influence of differential methylation in the two sexes. Experimental Biology and Medicine235 (2): 139-147.
29. Bissell, Mina J. 1981. The differentiated state of normal and malignant cells or how to define a ‘normal’ cell in culture. International Review of Cytology70:27-100.
30. Bissell, Mina J. 2003. Tissue specificity: structural cues allow diverse phenotypes from a constant genotype. in Origination of Organismal Form: Beyond the Gene in Developmental andEvolutionary Biology, ed. G. B. M¨uller and S. A. Newman. Cambridge, MA: MIT Press, 103-117.
31. Blumenthal, Thomas, Donald Evans, Christopher D. Link, Alessandro Guffanti, Daniel Lawson, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Lu Chiu, Kyle Duke, Moni Kiraly, and Stuart K. Kim. 2002. A global analysis of Caenorhabditis elegans operons. Nature417 (6891): 851-854.
32. Bolker, Jessika. 1995. Model systems in developmental biology. Bioessays17: 4515.
33. Bonasio, Roberto, Shengjiang Tu, and Danny Reinberg. 2010. Molecular signals of epigenetic states. Science330 (6004): 612-616.
34. Bonduriansky, Russell. 2012. Rethinking heredity, again. TREE27 (6): 330-336.
35. Bradbury, Jane. 2005. Alternative mRNA splicing: control by combination. PLoS Biology3 (11): e369.
36. Braendle, Christian, and Thomas Flatt. 2006. A role for genetic accommodation in evolution? Bioessays28: 868-873.
37. Brandon, Robert N., and Daniel W. McShea. 2010. Biology’s First Law. University of Chicago Press.
38. Brentano, Franz. 1874. Psychologie vom empirischen Standpunkt. Leipzig: Duncker & Humbolt.
39. Brigandt, Ingo, and Alan C. Love. 2008. Reductionism in biology. in The Stanford Ency-clopedia of Philosophy (Fall 2008 Edition), ed. E. N. Zalta. at http://plato.stanford.edu/archives/fall2008/entries/reduction-biology/.
40. Brigandt, Ingo, and Alan C. Love. 2010. Evolutionary novelty and the evo-devo synthesis: field notes. Evolutionary Biology37: 93-99.
41. Buchler, Nicolas E., Ulrich Gerland, and Terence Hwa. 2003. On schemes of combinatorial transcription logic. Proceedings of the National Academy of Sciences of theUnited States of America100: 5136-5141.
42. Burian, Richard M. 2004. Molecular epigenesis, molecular pleiotropy, and Molecular Gene Definitions. History and Philosophy of the Life Sciences26 (1): 59-80.
43. Carroll, Sean B. 2005. Evolution at two levels: on genes and form. PLoS Biology3 (7): e245.
44. Carroll, Sean B., Jennifer K. Grenier, and Scott D. Weatherbee. 2001. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Malden, MA:Blackwell.
45. Carroll, Sean B., Jennifer K. Grenier, and Scott D. Weatherbee. 2005. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, 2nd edn. Malden, MA: Blackwell.
46. Caudevilla, C., C. Codony, D. Serra, G. Plasencia, R. Roman, A. Graessmann, G. Asins, M. Bach-Elias, and F. G. Hegardt. 2001. Localization of an exonic splicing enhancer responsible for mammalian natural trans-splicing. Nucleic AcidsResearch29 (14): 3108-3115.
47. Cawley, Simon, Stefan Bekiranov, Huck H. Ng, Philipp Kapranov, Edward A. Sekinger, Dione Kampa, Antonio Piccolboni, Victor Sementchenko, Jill Cheng, Alan J. Williams, Raymond Wheeler, Brant Wong, Jorg Drenkow, Mark Yamanaka, Sandeep Patel, Shane Brubaker, Hari Tammana, and Thomas R. Gingeras. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell116: 499-509.
48. Celottoa, Alicia M., and Brenton R. Graveley. 2001. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genet-ics159: 599-608.
49. Chadarevian, S. de. 1998. of worms and programs: Caenorhabitis Elegans and the study of development. Studies in History and Philosophy of the Biological and Biomed-ical Sciences29 (1): 81-105.
50. Champagne, Francis A., and James P. Curley. 2009a. Epigeneticmechanismsmediating the long-term effects of maternal care on development. Neuroscience Bio-behaviour Review33 (4): 593-600.
51. Champagne, Francis A., and James P. Curley. 2009b. The transgenerational influence of maternal care on offspring gene expression and behavior in rodents. in Maternal Effects in Mammals, ed. D. Maestripieri and J. M. Mateo. University of Chicago Press, 182-202.
52. Chapdelaine, Y., and L. Bonen. 1991. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-inpieces. Cell65 (3): 465-472.
53. Chen, Jianjun, Miao Sun, Sanggyu Lee, Guoline Zhou, Janet D. Rowley, and San Ming Wang. 2002. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proceedings of the National Academy of Sciencesof the United States of America99: 12257-12262.
54. Chen, Ling-Ling, and Gordon G. Carmichael. 2010. Decoding the function of nuclear long noncoding RNAs. Current Opinion in Cell Biology22 (3):357-364.
55. Cheng, J., P. Kapranov, J. Drenkow, S. Dike, S. Brubaker, S. Patel, J. Long, D. Stern, H. Tammana, G. Helt, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science308 (5725): 1149-1154.
56. Chomsky, Noam. 1988. Language and Problems of Knowledge: The Managua Lectures. Cambridge, MA: MIT Press.
57. Chong, Lisa, and L. Bryan Ray. 2002. Whole-istic biology. Science295 (5560): 1661.
58. Claverie, J. M. 2001. Gene number: what if there are only 30,000 human genes? Science291: 1255-1257.
59. Coelho, Paulo S. R., Anthony C. Bryan, Anuj Kumar, Gerald S. Shadel, and Michael Snyder. 2002. A novel mitochondrial protein, TAR1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes and Development16: 2755-2760.
60. Collins, Lesley J., Barbara Sch¨onfeld, and Xiaowei Sylvia Chen. 2011. The epigenetics of non-coding RNA. in Handbook of Epigenetics: The New Molecular and MedicalGenetics, ed. T. Tollefsbol. Amsterdam: Academic Press, 49-61.
61. Communi, Didier, Nathalie Suarez-Huerta, Danielle Dussossoy, Pierre Savi, and Jean-Marie Boeynaems. 2001. Cotranscription and intergenic splicing of human P2Y(11) SSF1 genes. Journal of Biological Chemistry276 (19): 16561-16566.
62. Conklin, Edwin G. 1908. The mechanism of heredity. Science27: 89-99.
63. Cope, Edwin Brinker. 1887. Origin of the Fittest: Essays in Evolution. New York: D. Appleton.
64. Craig, Lindsay R. 2010. The so-called extended synthesis and population genetics. Biological Theory5 (2): 117-123.
65. Craver, Carl F. 2007. Explaining the Brain: Mechanisms and the Mosaic Unity of Neuro-science. Oxford: Clarendon Press.
66. Craver, Carl F., and William Bechtel. 2007. Top-down causation without top-down causes. Biology and Philosophy22 (4), 547-563.
67. Crick, Francis H. C. 1958. On protein synthesis. Symposia of the Society for Experimental Biology12: 138-163.
68. Crick, Francis H. C. 1970. Central Dogma of molecular biology. Nature227: 561-563.
69. Cummins, Robert. 1975. Functional analysis. Journal of Philosophy72: 741-765.
70. Darden, Lindley, and Nandy Maull. 1977. Interfield theories. Philosophy of Science44(1): 43-64.
71. Darwin, Charles. 1964 [1859]. On the Origin of Species: A Facsimile of the First Edition. Cambridge, MA: Harvard University Press.
72. Davidson, Eric H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.
73. Davidson, Eric H., and Douglas H. Erwin. 2006. Gene regulatory networks and the evolution of animal body plans. Science311: 796-800.
74. Davidson, Eric H., and Michael Levine. 2005. Gene regulatory networks. PNAS102 (14): 4935.
75. Davidson, Nicholas O. 2002. The challenge of target sequence specificity in C→URNA editing. Journal of Clinical Investigation109 (3): 291-294.
76. Dawkins, Richard. 1976. The Selfish Gene. Oxford University Press.
77. Depew, David J., and Bruce H. Weber. 1995. Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection. Cambridge, MA: Bradford Books/MIT Press.
78. Devlin, Bernie, Michael Daniels, and Katherine Roeder. 1997. The heritability of IQ. Nature388 (6641): 468-471.
79. Dietrich, Michael R. 2000. From hopeful monsters to homeotic effects: Richard Goldschmidt’s integration of development, evolution and genetics. AmericanZoologist40: 738-747.
80. Dillon, Niall. 2003. Positions, please. Nature425 (6957): 457.
81. Djebali, S., C. A. Davis, A. Merkel, A. Dobin, T. Lassmann, A. Mortazavi, A. Tanzer, J. Lagarde, W. Lin, F. Schlesinger, et al. 2012. Landscape of transcription in human cells. Nature489 (7414): 101-108.
82. Djebali, Sarah, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cedric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, et al. 2012. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS ONE7 (1): e28213. doi:10.1371/journal.pone.0028213.
83. Dobzhansky, Theodosius. 1973. Nothing in biology makes sense except in the light of evolution. American Biology Teacher35: 125-129.
84. Donnellan, Keith S. 1966. Reference and definite descriptions. The Philosophical Review75 (3): 281-304.
85. Doolittle, W. Ford, and Carmen Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature284 (5757): 601-603.
86. Dorn, Rainer, Gunter Reuter, and Andrea Loewendorf. 2001. Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila. Proceedings of the National Academy of Sciences of the United States of America98 (17):9724-9729.
87. Downes, Stephen. 1992. The importance of models in theorizing: a deflationary semantic view. in Proceedings of the Philosophy of Science Association, Vol. 1, ed. D. Hull, M. Forbes and K. Okruhlik. East Lansing, MI: Philosophy of Science Association, 142-153.
88. Economist. 1999. Drowning in data. Economist, 26 June, 97-98.
89. Eddy, Sean R. 2001. Non-coding RNA genes and the modern RNA world. Nature Review Genetics2 (12): 919-929.
90. Eddy, Sean R. 2002. Computational genomics of noncoding RNA genes. Cell109 (2): 137-140.
91. Eisenberg, David, Edward M. Marcotte, Andrew D. McLachlan, and Matteo Pellegrini. 2006. Bioinformatic challenges for the next decade(s). PhilosophicalTransactions of the Royal Society, Biological Sciences361 (1467): 525.
92. ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature447: 799-816.
93. Falk, Raphael. 1984. The gene in search of an identity. Human Genetics68: 195-204.
94. Falk, Raphael. 1986. What is a gene? Studies in the History and Philosophy of Science17: 133-173.
95. Falk, Raphael. 2000. The gene: a concept in tension. in The Concept of the Gene in Development and Evolution, ed. P. Beurton, R. Falk and H.-J. Rheinberger. Cambridge UniversityPress, 317-348.
96. Falk, Raphael. 2004. Long live the genome! So should the gene. History and Philosophy of the Life Sciences26 (1): 105-121.
97. Falk, Raphael. 2007. Genetic analysis. in Philosophy of Biology, ed. M. Matthen and C. Stephens. Oxford: Elsevier, 249-308.
98. Falk, Raphael. 2009. Genetic Analysis: A History of Genetic Thinking. Cambridge University Press.
99. Finta, Csaba, and Peter G. Zaphiropoulos. 2000a. The human CYP2C locus: a prototype for intergenic and exon repetition splicing events. Genomics 63 (3):433-438.
100. Falk, Raphael. 2000b. The human cytochrome P450 3A locus: gene evolution by capture of downstream exons. Gene260 (1-2): 13-23.
101. Falk, Raphael. 2001. A statistical view of genome transcription. Journal of Molecular Evolution53:160-162.
102. Falk, Raphael. 2002. Intergenic mRNA molecules resulting from trans-splicing. Journal of Biolo-gical Chemistry277 (8): 5882-5890.
103. Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Transactions of the Royal Society of Edinburgh52: 399-433.
104. Fodor, Jerry A. 1974. Special sciences. Synthese28: 77-115.
105. Fogle, Thomas. 2000. The dissolution of protein coding genes in molecular biology. in The Concept of the Gene in Development and Evolution, ed. P. Beurton, R. Falk and H.-J. Rheinberger. Cambridge University Press, 3-25.
106. Fontana, Walter, and Leo W. Buss. 1994. ‘The arrival of the fittest’: toward a theory of biological organization. Bulletin of Mathematical Biology 56 (1): 164.
107. Ford, Donald H., and Richard M. Lerner. 1992. Developmental Systems Theory: An Integrative Approach. Newbury Park, CA: Sage.
108. Fox, Charles W., Monica S. Thakar, and Timothy A. Mousseau. 1997. Egg size plasticityin a seed beetle: an adaptive maternal effect. The American Naturalist149(1): 149-163.
109. Fox, Charles W., Kim J. Waddell, and Timothy A. Mousseau. 1995. Parental host plant affects offspring life histories in a seed beetle. Ecology76 (2): 402-411.
110. Frenkel-Morgenstern, M., V. Lacroix, I. Ezkurdia, Y. Levin, A. Gabashvili, J. Prilusky, A. Del Pozo, M. Tress, R. Johnson, R. Guigo, et al. 2012. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. GenomeResearch22: 1231-1242.
111. Frigg, Roman. 2010. Models and fiction. Synthese17 (2): 251-268.
112. Frigg, Roman, and Stephan Hartmann. 2009. Models in Science. at http://plato.stanford.edu/archives/sum2009/entries/models-science/.
113. Fuller, Trevon, Sahotra Sarkar, and D avid Crews. 2005. The use of norms of reaction to analyze genotypic and environmental influences on behavior in mice and rats. Neuroscience and Biobehavioral Reviews 29: 445-456.
114. Gagen, Michael J., and John S. Mattick. 2004. Inherent size constraints on prokaryote gene networks due to ‘accelerating’ growth. Theory in Biosciences123(4):381-411.
115. Garden, George. 1691. A discourse concerning the modern theory of generation. Philosophical Transactions of the Royal Society16 (1686-1692): 474-483.
116. Gehring, Walter J. 1985. The homeo box: a key to the understanding of development? Cell40: 3-5.
117. Gerstein, Mark B., Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, and Michael Snyder. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Research17 (6): 669-681.
118. GibbsW.Wayt. 2003. The unseen genome: gems among the junk. Scientific American289 (5): 46-53.
119. Giere, Ronald. 1988. Explaining Science: A Cognitive Approach. University of Chicago Press.
120. Gilbert, Scott F. 2000. Developmental Biology. Sunderland, MA: Sinauer Associates.
121. Gilbert, Scott F. 2001. Ecological developmental biology: developmental biology meets the real world. Developmental Biology233: 1-22.
122. Gilbert, Scott F. 2003. The reactive genome. in Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, ed. G. B. M¨uller and S. A. Newman.Cambridge, MA: MIT Press, 87-101.
123. Gilbert, Scott F., and David Epel. 2009. Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sunderland, MA: Sinauer Associates.
124. Gilbert, Scott F., and Sahotra Sarkar. 2000. Embracing complexity: Organicism for the twenty-first century. Developmental Dynamics219: 1-9.
125. Gissis, Snait B., and Eva Jablonka (eds.). 2011. Transformations of Lamarckism: From Subtle Fluids to Molecular Biology. Cambridge, MA: MIT Press.
126. Gluckman, Peter D., and Mark A. Hanson. 2005a. The Fetal Matrix: Evolution, Develop- ment and Disease. Cambridge University Press.
127. Gluckman, Peter D., and Mark A. Hanson.(eds.). 2005b. Developmental Origin of Health and Disease. Cambridge University Press.
128. Gluckman, Peter D., and Mark A. Hanson. 2006. Mismatch: Why Our World No Longer Fits Our Bodies. Oxford University Press.
129. Gluckman, Peter D., Mark A. Hanson, Patrick Bateson, Alan S. Beedle, Catherine M. Law, Zulfiqar A. Bhutta, Konstantin V. Anokhin, Pierre Bougn`eres, Giriraj Ratan Chandak, Partha Dasgupta, George Davey Smith, Peter T. Ellison, Terrence E. Forrester, Scott F. Gilbert, Eva Jablonka, Hillard Kaplan, Andrew M. Prentice, Stephen J. Simpson, Ricardo Uauy, and Mary Jane West-Eberhard. 2009. Towards a new developmental synthesis: adaptive developmental plasticity and human disease. Lancet 373 (9675): 1654-1657.
130. Gluckman, Peter D., Mark A. Hanson, and Alan S. Beedle. 2007. Early life events and their consequences for later disease: a life history and evolutionary perspective. American Journal of Human Biology19: 1-19.
131. Gluckman, Peter D., Mark A. Hanson, and Hamish G. Spencer. 2005. Predictive adaptive responses and human evolution. Trends in Ecology and Evolution20 (10): 527-533.
132. Godfrey, K. M., A. Sheppard, P. D. Gluckman, K. A. Lillycrop, G. C. Burdge, C. McLean, J. Rodford, J. L. Slater Jefferies, E. Garratt, S. R. Crozier, B. S. Emerald, C. R. Gale, H. M. Inskip, C. Cooper, and M. A. Hanson. 2011. Epigenetic gene promoter methylation at birth is associated with child’s later adiposity. Diabetes30 (5):1528-1534.
133. Godfrey-Smith, Peter. 1989. Misinformation. Canadian Journal of Philosophy19 (5):533-550.
134. Godfrey-Smith, Peter. 1999. Genes and codes: lessons from the philosophy of mind? in Biology Meets Psychology: Constraints, Conjectures, Connections, ed. V. G. Hardcastle. Cambridge, MA: MIT Press, 305-331.
135. Godfrey-Smith, Peter. 2000a. On the theoretical role of ‘genetic coding’. Philosophy of Science67 (1):26-44.
136. Godfrey-Smith, Peter. 2000b. ‘Explanatory symmetries, preformation, and developmental systems theory.’ Philosophy of Science 67 (Supplementary Proceedings of the 1998 Biennial Meetingsof the Philosophy of Science Association. Part II: Symposia Papers): S322-S331.
137. Godfrey-Smith, Peter. 2001. On the status and explanatory structure of developmental systems theory. in Cycles of Contingency: Developmental Systems and Evolution, ed. S. Oyama, P. E. Griffiths and R. D. Gray. Cambridge, MA: MIT Press, 283-297.
138. Godfrey-Smith, Peter. 2006. The strategy of model-based science. Biology and Philosophy21: 725-740.
139. Godfrey-Smith, Peter. 2011. Senders, receivers, and genetic information: comments on Bergstrom and Rosvall. Biology and Philosophy26 (2): 177-181.
140. Goodwin, Brian C. 1994. How the Leopard Changed Its Spots: The Evolution of Complexity. New York: Charles Scribner & Sons.
141. Gott, Jonathan M., and Ronald B. Emeson. 2000. Functions and mechanisms of RNA editing. Annual Review of Genetics34: 499-531.
142. Gottlieb, Gilbert. 1992. Individual Development and Evolution. Oxford University Press.
143. Gottlieb, Gilbert.1995. Some conceptual deficiencies in ‘developmental’ behavior genetics. HumanDevelopment38: 131-141.
144. Gottlieb, Gilbert. 1997. Synthesizing Nature-Nurture: Prenatal Roots of Instinctive Behavior. Hillsdale, NJ: Lawrence Erlbaum Associates.
145. Gottlieb, Gilbert. 2001. A developmental psychobiological systems view: early formulation and current status. in Cycles of Contingency: Developmental Systems and Evolution, ed.S. Oyama, P. E. Griffiths and R. D. Gray. Cambridge, MA: MIT Press, 41-54.
146. Gottlieb, Gilbert. 2003. On making behavioral genetics truly developmental. Human Development46 (6): 337-355.
147. Gould, Stephen Jay. 1977. Ontogeny and Phylogeny. Cambridge, MA: Harvard University Press.
148. Graveley, Brenton R. 2005. Mutually exclusive splicing of the insect Dscam premRNA directed by competing intronic RNA secondary structures. Cell123:65-73.
149. Gray, M. W. 2003. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life55 (4-5): 227-233.
150. Gray, Russell D. 1992. Death of the gene: developmental systems strike back. in Trees of Life: Essays in the Philosophy of Biology, ed. Paul E. Griffiths. Dordrecht: Kluwer, 165-210.
151. Greenspan, Ralph J. 2001. The flexible genome. Nature Reviews Genetics2: 383-387.
152. Grice, H. P. 1957. Meaning. Philosophical Review66: 377-388.
153. Griffiths, Paul E. 2001. Genetic information: a metaphor in search of a theory. Philosophy of Science68 (3): 394-412.
154. Griffiths, Paul E. 2003. Beyond the Baldwin effect: James Mark Baldwin’s ‘social heredity’, epigenetic inheritance and niche-construction. in Evolution and Learning: The BaldwinEffect Reconsidered, ed. B. H. Weber and D. J. Depew. Cambridge, MA: MIT Press, 193-215.
155. Griffiths, Paul E. 2004. Instinct in the’50s: The British reception of Konrad Lorenz’s theory of instinctive behaviour. Biology and Philosophy19 (4): 609-631.
156. Griffiths, Paul E. 2009. in what sense does ‘nothing in biology make sense except in the light of evolution’? Acta Biotheoretica57 (1-2): 11-32.
157. Griffiths, Paul E., and Russell D. Gray. 1994. Developmental systems and evolutionary explanation. Journal of Philosophy91 (6): 277-304.
158. Griffiths, Paul E., and Russell D. Gray. 1997. Replicator II: judgment day. Biology and Philosophy12 (4): 471-492.
159. Griffiths, Paul E., and Russell D. Gray. 2005. Three ways to misunderstand developmental systems theory. Biology and Philosophy20 (2): 417-425.
160. Griffiths, Paul E., and Rob D. Knight. 1998. What is the developmentalist challenge? Philosophy of Science65 (2): 253-258.
161. Griffiths, Paul E., and Karola Stotz. 2006. Genes in the postgenomic era. Theoretical Medicine and Bioethics27 (6): 499-521.
162. Griffiths, Paul E., and Karola Stotz. 2007. Gene. in Cambridge Companion to the Philosophy of Biology, ed. D. Hull and M. Ruse. Cambridge University Press, 85-102.
163. Griffiths, Paul E., and James G. Tabery. 2008. Behavioral genetics and development. New Ideas in Psychology26 (3): 332-352.
164. Haack, Susan. 1987. Surprising noises: Rorty and Hesse on metaphor. Proceedings of the Aristotelian Society88: 293-301.
165. Hacking, Ian. 1983. Representing and Intervening: Introductory Topics in the Philosophy of Natural Science. Cambridge University Press.
166. Haig, David. 2000. The kinship theory of genomic imprinting. Annual Review of Ecology and Systematics31: 9-32.
167. Haig, David. 2004. The (dual) origin of epigenetics. Cold Spring Harbor Symposia on Quantitative Biology69: 67-70.
168. Haldane, J. B. S., and Helen Spurway. 1954. A statistical analysis of communication in ‘Apis mellifera’ and a comparison with communication in other animals. Insectes Sociaux1 (3): 247-283.
169. Hall, Brian K. 1992. Evolutionary Developmental Biology. New York: Chapman & Hall.
170. Hall, Brian K. 1998. Evolutionary Developmental Biology. 2nd edn. New York: Chapman & Hall.
171. Hall, Brian K. 2011. A brief history of the term and concept of epigenetics. in Epigenetics: Linking Genotype and Phenotype in Development and Evolution, ed. B. Hallgrimsson andB. K. Hall. Berkeley: University of California Press, 9-13.
172. Hallgrimsson, Benedict, and Brian K. Hall. 2011. Introduction. in Epigenetics: Linking Genotype and Phenotype in Develoment and Evolution, ed. B. Hallgrimsson and B. K.Hall. Berkeley: University of California Press, 1-5.
173. Hamer, Dean. 2002. Rethinking behavior genetics. Science298: 71-72.
174. Hardison, Ross C. 2000. Conserved non-coding sequences are reliable guides to regulatory elements. Trends in Genetics16 (9): 369-372.
175. Harrison, Paul M., Anuj Kumar, Ning Lang, Michael Snyder, and Mark Gerstein. 2002.A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Research30 (5): 1083-1090.
176. H¨asler, J., T. Samuelsson, and K. Strub. 2007. Useful ‘junk’: Alu RNAs in the human transcriptome. Cellular and Molecular Life Sciences 64 (14): 1793-1800.
177. Hauber, M. E., P. W. Sherman, and D. Paprika. 2000. Self-referent phenotypematching in a brood parasite: the armpit effect in brown-headed cowbirds (Molothrusater). Animal Cognition3 (2): 113-117.
178. Helden, Jacques van, Avi Naim, Renato Mancuso, Matthew Eldridge, Lorenz Wernisch, David Gilbert, and Shoshana J. Wodak. 2000. Representing and analysing molecular and cellular function using the computer. Journal of Bio-logical Chemistry381: 921-935.
179. Herring, Susan W. 1993. Formation of the vertebrate face: epigenetic and functional influences. American Zoologist33 (4): 472-483.
180. Hesse, Mary B. 1966. Models and Analogies in Science. University of Notre Dame Press.
181. Hesse, Mary B. 1988. The cognitive claims ofmetaphor. Journal of Speculative Philosophy2 (1): 1-16.
182. Hirotsune, Shinji, Noriyuki Yoshida, Amy Chen, Lisa Garrett, Fumihiro Sugiyama, Satoru Takahashi, Ken-ichi Yagami, Anthony Wynshaw-Boris, and Atsushi Yoshiki. 2003. An expressed pseudogene regulates the messenger RNA stability of its homologous coding gene. Nature423 (6935): 91-96.
183. Holliday, Robin. 1987. The inheritance of epigenetic defects. Science238 (4824): 163-170.
184. Holliday, Robin. 1994. Introduction: epigenetics, an overview. Developmental Genetics15: 453-457.
185. Holliday, Robin. 2006. Epigenetics: a historical overview. Epigenetics1 (2): 76-80.
186. Hood, Kathryn E., Carolyn Tucker Halpern, Gary Greenberg, and Richard M. Lerner (eds.). 2010. Handbook of Developmental Science, Behavior and Genetics. Oxford: Wiley-Blackwell.
187. Hull, David. 1972. Reduction in genetics - biology or philosophy? Philosophy of Science39 (4): 491-499.
188. Hull, David. 1974. Philosophy of Biological Science. Englewood Cliffs, NJ: Prentice-Hall.
189. Hull, David. 1975. Informal aspects of theory reduction. in Boston Studies in the Philosophy of Science; Proceedings of the Biennial Meeting of the Philosophy of Science Association, 1974, ed. R. S. Cohen and A. Michalos. Dordrecht: Reidel, 653-670.
190. Hundley, Heather A., and Brenda L. Bass. 2010. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends in Biochemical Sciences35 (7):377-383.
191. H¨uttenhofer, A., M. Kiefmann, S. Meier-Ewert, J. O’Brien, H. Lehrach, J. P. Bachellerie, and J. Brosius. 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO Journal 20 (11): 2943-2953.
192. Huxley, Julian. 1972 [1932]. Problems of Relative Growth. New York: Dover.
193. Istrail, Sorin, and Eric H. Davidson. 2005. Logic functions of the genomic cisregulatory code. Proceedings of the National Academy of Sciences102 (14): 4954-4959.
194. Jablonka, Eva. 2001. The systems of inheritance. in Cycles of Contingency: Developmental Systems and Evolution, ed. S. Oyama, P. E. Griffiths and R. D. Gray. Cambridge, MA: MIT Press, 99-116.
195. Jablonka, Eva. 2002. Information interpretation, inheritance, and sharing. Philosophy of Science69 (4): 578-605.
196. Jablonka, Eva, and Eytan Avital. 2001. Animal Traditions: Behavioural Inheritance in Evolution. Cambridge University Press.
197. Jablonka, Eva, and Marion J. Lamb. 1995. Epigenetic Inheritance and Evolution: The Lamarckian Dimension. Oxford University Press.
198. Jablonka, Eva, and Marion J. Lamb. 2005. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Varia-tion in the History of Life. Cambridge, MA: MIT Press.
199. Jablonka, Eva, and Gal Raz. 2009. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Quarterly Review of Biology84 (2): 131-176.
200. Jacob, Franc¸ois, and Jacques Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology3: 318-356.
201. Jenuwein, Thomas, and C. David Allis. 2001. Translating the histone code. Science293: 1074-1080.
202. Johannsen, William. 1911. The genotype conception of heredity. American Naturalist45 (531): 129-159.
203. Johnson, J. M., S. Edwards, D. D. Shoemaker, and E. E. Schadt. 2005. Dark matterin the genome: evidence of widespread transcription detected by microarraytiling experiments. Trends in Genetics21: 93-102.
204. Johnston, Timothy D. 1987. The persistence of dichotomies in the study of behavioural development. Developmental Review7: 149-182.
205. Juarrero, Alicia. 1998. Causality as constraints. in Evolving Systems, ed. G. Van de Vijver, S. Salthe, and M. Delpos. Dordrecht: Kluwer.
206. Kampa, Dione, Jill Cheng, Philipp Kapranov, Mark Yamanaka, Shane Brubaker, Simon Cawley, Jorg Drenkow, Antonio Piccolboni, Stefan Bekiranov, Gregg Helt, Hari Tammana, and Thomas R. Gingeras. 2004. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research 14: 331-342.
207. Kaplan, Jonathan Michael. 2000. The Limits and Lies of Human Genetic Research. Oxford: Routledge.
208. Kapranov, Phillip, Jorg Drenkow, Jill Cheng, Jeffrey Long, Gregg Helt, Sujit Dike, and Thomas R. Gingeras. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. GenomeResearch15: 987-997.
209. Kauffman, StuartA. 1993. The Origins of Order: Self-Organisation and Selection in Evolution. New York: Oxford University Press.
210. Kay, Lily E. 2000. Who Wrote the Book of Life: A History of the Genetic Code. Palo Alto, CA: Stanford University Press.
211. Kendler, Kenneth S. 2005. ‘A gene for the nature of gene action in psychiatric disorders. American Journal of Psychiatry 162 (7): 1243-1252.
212. Kim, Jaegwon. 1993. Supervenience and Mind: Selected Philosophical Essays. Cambridge University Press.
213. Kirschner, Marc W. and John C.Gerhart. 1998. Evolvability. Proceedings of the National Academy of Sciences of the United States of America95, 8420-8427.
214. Kirschner, Marc W. and John C.Gerhart. 2005. The Plausibility of Life: Resolving Darwin’s Dilemma. London: Yale University Press.
215. Kirschner, Marc W. and John C.Gerhart. 2010. Facilitated variation. in Evolution: The Extended Synthesis, ed. G. B. Mueller and M. Pigliucci. Cambridge, MA: MIT Press.
216. Kirschner, Marc W., John C.Gerhart, and Tim Mitchison. 2000. Molecular ‘vitalism’. Cell100: 79-88.
217. Kitcher, Philip. 1982. Genes. British Journal of Philosophy of Science33: 337-359.
218. Kitcher, Philip. 1984. 1953 and all that: a tale of two sciences. Philosophical Review 93:335-373.
219. Kitcher, Philip. 2001. Battling the undead: how (and how not) to resist genetic determinism. in Thinking about Evolution: Historical, Philosophical and Political Perspectives (Festschriftfor Richard Lewontin), ed. R. Singh, K. Krimbas, D. Paul and J. Beatty. Cambridge University Press, 369-414.
220. Kohler, Robert E. 1994. Lords of the Fly. Drosophila Genetics and the Experimental Life. University of Chicago Press.
221. Kroh, Evan M., Rachael K. Parkin, Patrick S. Mitchell, and Muneesh Tewari. 2010. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50 (4): 298-301.
222. Kuhn, Thomas. 1962. The Structure of Scientific Revolutions. University of Chicago Press.
223. Lacey, Elizabeth R. 1998. What is an adaptive environmentally induced parental effect? in Maternal Effects as Adaptations, ed. R. A. Mousseau and C. W. Fox. New York: Oxford University Press, 54-66.
224. Ladd, Andrea N., and Thomas A. Cooper. 2002. Finding signals that regulate alternative splicing in the post-genomic era. Genome Biology3 (11): 1-6.
225. Laland, KevinN., F. John Odling-Smee and Scott F. Gilbert. 2008. EvoDevo and niche construction: building bridges. Journal of Experimental Zoology, Part B: Molecularand Developmental Evolution310: 549-566.
226. Laland, Kevin N., Kim Sterelny, John Odling-Smee W. Hoppitt, and Tobias Uller. 2011. Cause and effect in biology revisited: Is Mayr’s proximate-ultimate dichotomy still useful? Science334 (6062): 1512-1516.
227. Lamm, Ehud, and Eva Jablonka. 2008. The nurture of nature: hereditary plasticity in evolution. Philosophical Psychology21 (3): 305-319.
228. Lande, R., and T. Price. 1989. Genetic correlations and maternal effect coefficients obtained from offspring-parent regression. Genetics122 (4): 915-922.
229. Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, et al. 2001. Initial sequencing and analysis of the human genome. Nature409: 860-921.
230. Lander, Eric S., and Robert A. Weinberg. 2000. Journey to the centre of biology. Science287 (5459): 1777-1782.
231. Lederberg, Joshua. 1956a. Comments on gene-enzyme relationship. in Enzymes: Units of Biological Structure and Function, ed. E. H. Gaebler. New York: AcademicPress, 161-169.
232. Lederberg, Joshua. 1956b. Genetic transduction. American Scientist44 (3): 264-280.
233. Lederberg, Joshua. 1996. What the double helix (1953) has meant for basic biomedical science: a personal commentary. in The Philosophy and History of Molecular Biology: NewPerspectives, ed. S. Sarkar. Dordrecht: Kluwer, 15-26.
234. Lehrman, Daniel S. 1970. Semantic and conceptual issues in the nature-nurture problem. in Development and Evolution of Behaviour, ed. D. S. Lehrman. San Francisco: W. H. Freeman, 17-52.
235. Leipzig, Jeremy, Pavel Pevzner, and Steffen Heber. 2004. The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. NucleicAcids Research32 (13): 3977-3983.
236. Lettice, Laura A., Taizo Horikoshi, Simon J. H. Heaney, Marijke J. van Baren, Herma C. van der Linde, Guido J. Breedveld, Marijke Joosse, Nurten Akarsu, Ben A. Oostra, Naoto Endo, Minoru Shibata, Mikio Suzuki, Eiichi Takahashi, Toshikatsu Shinka, Yutaka Nakahori, Dai Ayusawa, Kazuhiko Nakabayashi, Stephen W. Scherer, Peter Heutink, Robert E. Hill, and Sumihare Noji. 2002. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proceedings of the National Academy of Sciences99 (11): 7548-7553.
237. Levit, Georgy S., Uwe Hossfeld, and Lennart Olsson. 2006. From the ‘Modern Synthesis’ to cybernetics: Ivan Ivanovich Schmalhausen (1884-1963) and his research program for a synthesis of evolutionary and developmental biology. Journal of Experimental Zoology, Part B: Molecular and Developmental Evolution306:89-106.
238. Levy, Arnon. 2011. Information in biology: a fictionalist account. Nous45 (4): 640-657.
239. Lewis, David K. 1966. An argument for the identity theory. Journal of Philosophy63 (1): 17-25.
240. Lewontin, Richard C. 1982. Organism and environment. in Learning, Development, Culture, ed. H. Plotkin. New York: John Wiley, 151-170.
241. Lewontin, Richard C. 1983a. Gene, organism and environment. in Evolution: From Molecules to Man, ed. D. S. Bendall. Cambridge University Press, 273-285.
242. Lewontin, Richard C. 1983b. The organism as the subject and object of evolution. Scientia118: 65-82.
243. Lewontin, Richard C. 1996. Evolution as engineering. in Integrative Approaches to Molecular Biology, ed. J. Collado Vides, B. Magasanik and T. F. Smith. Cambridge, MA: MIT Press, 1-10.
244. Lipovich, L., R. Johnson, and C. Y. Lin. 2010. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochimica et Biophysica Acta1799 (9): 597-615.
245. Liu, Yilei, and David J. Elliott. 2010. Coupling genetics and post-genomic approaches to decipher the cellular splicing code at a systems-wide level. Biochemistry Society Transactions38: 237-241.
246. Lloyd, Elizabeth A. 1988. The Structure and Confirmation of Evolutionary Theory. Westport, CT: Greenwood Press.
247. Lorenz, Konrad Z. 1965. Evolution and the Modification of Behaviour. University of Chicago Press.
248. Love, Alan C. 2001. Evolutionary morphology, innovation, and the synthesis of evolution and development. Biology and Philosophy18 (2): 309-345.
249. Love, Alan C. 2008. Explaining evolutionary innovation and novelty: criteria of adequacy and multidisciplinary prerequisites. Philosophy of Science75: 874-886.
250. McEachern, Lori A., and Vett Loyd. 2011. The epigenetics of genomic imprinting. in Epigenetics: Linking Genotype and Phenotype in Develoment and Evolution, ed. B. Hallgrimsson and B. K. Hall. Berkeley: University of California Press, 43-69.
251. Maestripieri, Dario. 2009. Maternal influences in offspring growth, reproduction, and behavior in primates. in Maternal Effects in Mammals, ed. D. Maestripieri and J. M. Mateo. University of Chicago Press, 256-291.
252. Maestripieri, Dario, and Jill M. Mateo (eds.). 2009. Maternal Effects in Mammals. University of Chicago Press.
253. Maher, Brendan. 2012. The human encyclopedia:making a genome manual. Nature489 (7414): 46-48.
254. Maienschein, Jane. 2005. Epigenesis and preformationism. in The Stanford Encyclo- pedia of Philosophy, ed. E. N. Zalta. at http://plato.stanford.edu/entries/_?PMU?_epigenesis/.
255. Malek, Olaf, and Volker Knoop. 1998. Trans-splicing group II introns in plant mitochondria: the complete set of cis arranged homologs in ferns, fern allies, and a hornwort. RNA4 (12): 1599-1609.
256. Manolio, Teri A., Francis S. Collins, Nancy J. Cox, David B. Goldstein, Lucia A. Hindorff, David J. Hunter, Mark I. McCarthy, Erin M. Ramos, Lon R. Cardon, Aravinda Chakravarti, Judy H. Cho, Alan E. Guttmacher, Augustine Kong, Leonid Kruglyak, Elaine Mardis, Charles N. Rotimi, Montgomery Slatkin, David Valle, Alice S.Whittemore, Michael Boehnke, Andrew G. Clark, Evan E. Eichler, Greg Gibson, Jonathan L. Haines, Trudy F. C. Mackay, Steven A. Mc Carroll, and Peter M. Visscher. 2009. Finding the missing heritability of complex diseases.Nature 461 (7265): 747-753.
257. Matthen, Mohan, and Andr´e Ariew. 2002. Two ways of thinking about fitness and natural selection. Journal of Philosophy992: 55-83.
258. Mattick, John S. 2001. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Reports2 (11): 986-991.
259. Mattick, John S. 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays25 (10): 930-939.
260. Mattick, John S. 2004. RNA regulation: a new genetics? Nature Reviews Genetics5 (4): 316-23.
261. Maynard Smith, John. 2000. The concept of information in biology. Philosophy of Science67 (2): 177-194.
262. Maynard Smith, J., R. Burian, S. Kauffman, P. Alberch, J. Campbell, B. Goodwin, R. Lande, D. Raup, and L. Wolpert. 1985. Developmental constraints and evolution. Quarterly Review of Biology60 (3): 265-287.
263. Maynard Smith, John, and E¨ors Szathm´ary. 1995. The Major Transitions in Evolution.New York: W. H. Freeman.
264. Mayr, Ernst. 1961. Cause and effect in biology. Science134 (3489): 1501-1506.
265. Mayr, Ernst. 1964. The evolution of living systems. Proceedings of the National Academy of Sciences of the United States of America51 (5): 934-941.
266. Mayr, Ernst. 1976 [1959]. Typological versus populational thinking. in Evolution and the Diver-sity of Life, ed. E. Mayr. Cambridge, MA: Harvard University Press, 26-29.
267. Mayr, Ernst, and William B. Provine. 1980. The Evolutionary Synthesis: Perspec- tives on the Unification of Biology. Cambridge, MA: Harvard University Press,43-69.
268. Meaney, Michael J. 2001a. Nature, nurture, and the disunity of knowledge. Annals of the New York Academy of Sciences935 (1): 50-61.
269. Meaney, Michael J. 2001b. Maternal care, gene expression, and the transmission of individual differences in stress reactivity across generations. Annual Review of Neuroscience24:1161-1192.
270. Meaney, Michael J. 2004. The nature of nurture:maternal effect and chromatin modelling. in Essays in Social Neuroscience, ed. J. T. Cacioppo and G. G. Berntson. Cambridge, MA:MITPress.
271. Meaney, Michael J., and Moshe Szyf. 2005. Environmental programming of stress responses through DNA methylation: life at the interface between a dynamic environment and a fixed genome. Dialogues in Clinical Neuroscience7 (2): 103-213.
272. Mendel, Gregor. 1866. Versuche ¨uber Pflanzenhybriden [Experiments in plant hybridization]. Verhandlungen des naturforschenden Vereines in Br¨unn, Bd. IV f¨urdas Jahr 1865, Abhandlungen: 3-47.
273. Michel, George F., and Celia L. Moore. 1995. Developmental Psychobiology: An Interdis- ciplinary Science. Cambridge, MA: MIT Press.
274. Millikan, Ruth Garrett. 1984. Language, Thought and Other Biological Categories. Cambridge, MA: MIT Press.
275. Mitchell, Sandra D. 2009. Unsimple Truths: Science, Complexity, and Policy. University of Chicago Press.
276. Moore, Celia L. 1984. Maternal contributions to the development of masculine sexual behavior in laboratory rats. Developmental Psychobiology17: 346-356.
277. Moore, Celia L. 1992. The role of maternal stimulation in the development of sexual behavior and its neural basis. Annals of the New York Academy of Sciences662: 160-177.
278. Moore, David S. 2001. The Dependent Gene: The Fallacy of ‘Nature vs. Nurture’. New York: Henry Holt/Times Books.
279. Morange, Michel. 2000 [1998]. A History of Molecular Biology, trans. Matthew Cobb. Cambridge, MA: Harvard University Press.
280. Morange, Michel. 2002. The relations between genetics and epigenetics: a historical point of view. Annals of the New York Academy of Sciences981: 50-60.
281. Morange, Michel. 2008. Life Explained. New Haven, CT: Yale University Press.
282. Morgan, Thomas Hunt. 1926. The Theory of the Gene. New Haven, CT: Yale University Press.
283. Morgan, Thomas Hunt. 1934. The relation of genetics to physiology and medicine. Nobel lecture, 4 June. at www.nobelprize.org/nobel prizes/medicine/laureates/1933/morgan-lecture.pdf.
284. Morgan, Thomas Hunt, Alfred H. Sturtevant, H. J. Mullen and Calvin B. Bridges. 1915. The Mechanism of Mendelian Heredity. New York: Holt.
285. Morowitz, Harold J. 2003. The Emergence of Everything: How the World Became Complex. Oxford University Press.
286. Morris, Kevin V. 2008. RNA mediated transcriptional gene silencing. in RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity, ed. K. V. Morris.Norfolk, UK: Caister Academic Press, 19-28.
287. Morris, Kevin V. (ed.). 2012. Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection. Norfolk, UK: Caister Academic Press.
288. Moss, Lenny. 2003. What Genes Can’t Do. Cambridge, MA: MIT Press.
289. Mousseau, Timothy A., and Charles W. Fox (eds.). 1998. Maternal Effects as Adaptations. Oxford University Press.
290. Mueller, Michael, Lennart Martens, and Rolf Apweiler. 2007. Annotating the human proteome: beyond establishing a parts list. Biochimica et Biophysica Acta(BBA) - Proteins and Proteomics1774 (2): 175-191.
291. M¨uller, Gerd B. 1990. Developmental mechanisms as the origin of morphological novelty: a side-effect hypothesis. in Evolutionary Innovations, ed. M. H. Nitecki. University of Chicago Press, 99-130.
292. M¨uller, Gerd B. 2003. Homology: the evolution of morphological organization. in Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, ed. G.B. M¨uller and S. A. Newman. Cambridge, MA: MIT Press, 51-69.
293. M¨uller, Gerd B. 2010. Epigenetic innovation. in Evolution - The Extended Synthesis, ed. M. Pigliucci and G. B. M¨uller. Cambridge, MA: MIT Press, 307-332.
294. M¨uller, Gerd B., and Stuart A. Newman. 2003. Origination of organismal form: the forgotten cause in evolutionary theory. in Origination of Organismal Form, ed.G.B. M¨uller and S. A. Newman. Cambridge, MA: MIT Press, 3-10.
295. M¨uller, Gerd B., and G¨unter P. Wagner. 1991. Novelty in evolution: restructuring the concept. Annual Review of Ecology and Systematics 22: 229-256.
296. Muller, Hermann J. 1947. Pilgrim Trust Lecture: the gene. Proceedings of the Royal Society of London Series B: Biological Sciences134 (874): 1-37.
297. M¨uller-Wille, Staffan, and Hans-J¨org Rheinberger. 2012. A Cultural History of Heredity. University of Chicago Press.
298. Nagel, Ernest. 1961. The Structure of Science: Problems in the Logic of Scientific Explanation. London: Routledge & Kegan Paul.
299. Nanney, D. L. 1958. Epigenetic control systems. Proceedings of the National Academy of Sciences of the United States of America44: 712.
300. Nathanielsz, PeterW., and Kent L. Thornburg. 2003. Fetal programming: from gene to functional systems - an overview. Journal of Physiology547: 3-4.
301. Nature Genetics. 2010. On beyond GWAS. (Editorial). Nature Genetics42 (7):551.
302. Newman, Stuart A. 2003. From physics to development: the evolution of morphogenetic mechanisms. in Origination of Organismal Form: Beyond the Gene inDevelopmental and Evolutionary Biology, ed. G. B. M¨uller and S. A. Newman. Cambridge, MA: MIT Press, 221-239.
303. Newman, Stuart A. 2010. Dynamic patterning modules. in Evolution - The Extended Synthesis, ed. M. Pigliucci and G. B. M¨uller. Cambridge, MA: MIT Press, 281-306.
304. Newman, Stuart A., and Gerd B. M¨uller. 2000. The epigenetic basis of character origination. Journal of Experimental Zoology (Molecular and Developmental Evolution) 288: 304-17.
305. Nijhout, H. F. 1990. Metaphors and the role of genes in development. BioEssays12(9): 441-446.
306. Noble, Denis. 2002. Modeling the heart: from genes to cells to the whole organ. Science295: 1678-1682.
307. Noble, Denis. 2006. The Music of Life: Biology beyond Genes. Oxford University Press.
308. O’Malley, Maureen A., and John Dupre. 2005. Fundamental issues in systems biology. BioEssays27 (12): 1270-1276.
309. O’Malley, Maureen A., and Karola Stotz. 2011. Intervention, integration and translation in obesity research: genetic, developmental and metaorganismal approaches. Philosophy, Ethics, and Humanities in Medicine6 (2): doi:10.1186/1747-5341-6-2.
310. Odling-Smee F. John. 1988. Niche-constructing phenotypes. in The Role of Behavior in Evolution, ed. H. C. Plotkin. Cambridge, MA: MIT Press, 73-132.
311. Odling-Smee F. John, Kevin N. Laland, and Marcus W. Feldman. 2003. Niche Con- struction: The Neglected Process in Evolution. Princeton University Press.
312. Olby, Robert C. 1974. The Path to the Double Helix. Seattle: University of Washington Press.
313. Olby, Robert C. 1985. The Origins of Mendelism, 2nd edn. University of Chicago Press.
314. Olby, Robert C. 2009. Francis Crick: Hunter of Life’s Secret. Cold Spring Harbor Laboratory Press.
315. Oliver, Brian, and Benoit Leblanc. 2003. How many genes in a genome? Genome Biology 5 (1): 204.1-3.
316. Oliver, Stephen G. 2006. From genomes to systems: the path with yeast. Philosophical Transactions of the Royal Society, Biological Sciences361: 477-482.
317. Orgel, Leslie E., and Francis H. Crick. 1980. Selfish DNA: the ultimate parasite. Nature284: 604-607.
318. Oyama, Susan. 1985. The Ontogeny of Information: Developmental Systems and Evolution. Cambridge University Press.
319. Oyama, Susan. 2000a. Causal democracy and causal contributions in developmental systems theory. Philosophy of Science67 (s1): S332.
320. Oyama, Susan. 2000b. Evolution’s Eye: A Systems View of the Biology-Culture Divide.Durham, NC:Duke University Press.
321. Oyama, Susan. Paul E. Griffiths, and Russell D. Gray (eds.). 2001. Cycles of Contingency: Developmental Systems and Evolution. Cambridge, MA: MIT Press.
322. Pang, Ken C., Stuart Stephen, P¨ar G. Engstr¨om, Khairina Tajul-Arifin, Weisan Chen, ClaesWahlestedt, Boris Lenhard, Yoshihide Hayashizaki, and John S. Mattick. 2005. RNAdb - a comprehensive mammalian noncoding RNA database. NucleicAcids Research33 (Database issue): D125-D130.
323. Papineau, David. 1987. Reality and Representation. Oxford: Blackwell.
324. Park, E., B. Williams, B. J.Wold, and A. Mortazavi. 2012. RNA editing in the human ENCODE RNA-seq data. Genome Research 22 (9): 1626-1633.
325. Paz-Yaacov, N., E. Y. Levanon, E. Nevo, Y. Kinar, A. Harmelin, J. Jacob-Hirsch, N. Amariglio, E. Eisenberg, and G. Rechavi. 2010. Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the NationalAcademy of Sciences of the United States of America107 (27): 12174-12179.
326. Pearson, Karl. 1900 [1892]. The Grammar of Science, 2nd edn. London: Black.
327. Pearson, Karl, G. U. Yule, Norman Blanchard, and Alice Lee. 1903. The law of ancestral heredity. Biometrika2 (2): 211-236.
328. Pennisi, Elizabeth. 2008. Deciphering the genetics of evolution: powerful personalities lock horns over how the genome changes to set the stage for evolution. Science321: 670-673.
329. Pennisi, Elizabeth. 2010. Shining a light on genome’s ‘dark matter’. Science330: 1614.
330. Pigliucci, Massimo. 2001. Phenotypic Plasticity: Beyond Nature and Nurture, Syntheses in Ecology and Evolution. Baltimore, MD: Johns Hopkins University Press.
331. Pigliucci, Massimo. 2007. Do we need an extended evolutionary synthesis? Evolution61 (12): 2743-2749.
332. Pigliucci, Massimo. 2009. An extended synthesis for evolutionay biology. Annals of the New York Academy of Sciences1168: 218-228.
333. Pigliucci, Massimo, and Jonathan Kaplan. 2006. Making Sense of Evolution: The Con- ceptual Foundations of Evolutionary Biology. University of Chicago Press.
334. Pigliucci, Massimo, and Gert B. M¨uller. 2010a. Evolution - The Extended Synthesis. Cambridge, MA: MIT Press.
335. Pigliucci, Massimo, and Gert B. M¨uller. 2010b. Elements of an extended evolutionary synthesis. in Evolution: The Extended Synthesis, ed. M. Pigliucci and G. B. M¨uller. Cambridge, MA: MIT Press, 3-17.
336. Plomin, Robert, and Denise Daniels. 1987. Why are children from the same family so different from one another? Behavioral and Brain Sciences10: 1-60.
337. Plomin, R., J. C. DeFries, and J. Loehlin. 1977. Genotype-environment interaction and correlation in the analysis of human behavior. Psychological Bulletin84:309-322.
338. Ponicsan, Steven L., Jennifer F. Kugel, and James A. Goodrich. 2010. Genomic gems: SINE RNAs regulate mRNA production. Current Opinion in Genetics andDevelopment20 (2): 149-155.
339. Portin, Petter. 1993. The concept of the gene: short history and present status. The Quarterly Review of Biology68 (2): 173-223.
340. Ptashne, Mark. 2007. On the use of the word ‘epigenetic’. Current Biology17: R233-R236.
341. Ptashne, Mark, and Alexander Gann. 2002. Genes and Signals. Cold Spring Harbor Laboratory Press.
342. Putnam, Hilary. 1975. Themeaning of ‘meaning’. in Philosophical Papers. Vol. 2: Mind, Language and Reality. Cambridge University Press.
343. Rassoulzadegan, Minoo, Val´erie Grandjean, Pierre Gounon, St´ephane Vincent, Isabelle Gillot, and Franc¸ois Cuzin. 2006. RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature441: 469-474.
344. Rechavi, Oded, Gregory Minevich, and Oliver Hober. 2011. Transgenerational inheritance of an acquired small RNA based antiviral response in C. elegans. Cell147 (6): 1248-1256.
345. Reik, Wolf, and J¨orn Walter. 2001a. Evolution of imprinting mechanisms: the battle of the sexes begins in the zygote. Nature Genetics27: 255-256.
346. Reik, Wolf, and J¨orn Walter. 2001b. Genomic imprinting: parental influence on the genome. Nature Reviews Genetics2: 21-32.
347. Rivier, Christian, Michel Goldschmidt-Clermont, and Jean-David Rochaix. 2001. Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO Journal20 (7): 1765-1773.
348. Robert, Jason S. 2000. Schizophrenia epigenesis? Theoretical Medicine and Bioethics21 (2): 191-215.
349. Robert, Jason S. 2001. Interpreting the homeobox: metaphors of gene action and activation in development and evolution. Evolution and Development3 (4): 287-295.
350. Robert, Jason S. 2004. Embryology, Epigenesis and Evolution: Taking Development Seriously. Cambridge University Press.
351. Robert, Jason S., Brian K.Hall, andWendy M. Olson. 2001. Bridging the gap between developmental systems theory and evolutionary developmental biology. Bioes-says 23 (10): 954-962.
352. Robinson, Victoria L. 2009. Rethinking the Central Dogma: noncoding RNAs are biologically relevant. Urologic Oncology27 (3): 304-306.
353. Rosenberg, Alex. 1978. The supervenience of biological concepts. Philosophy of Science45: 368-386.
354. Rosenberg, Alex. 1985. The Structure of Biological Science. Cambridge University Press.
355. Rosenberg, Alex. 2006. Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology. University of Chicago Press.
356. Rowen, Lee, Janet Young, Brian Birditt, Amardeep Kaur, Anup Madan, Dana L. Philipps, Shizhen Qin, Patrick Minx, Richard K. Wilson, Leroy Hood, and Brenton R. Graveley. 2002. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics79 (4): 587-598.
357. Ruddle, Frank H., Chris T. Amemiya, Janet L. Carr, Chang-Bae Kim, Christina Ledje, Cooduvalli S. Shashikant, and Guenter P.Wagner. 1999. Evolution of chordate Hox gene clusters. in Molecular Strategies in Biological Evolution, ed. L. H. Caporale. New York Academy of Sciences, 238-250.
358. Ruse, Michael E. 1971. Reduction, replacement, and molecular biology. Dialectica25 (1): 39-72.
359. Sapp, Jan. 1987. Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. Oxford University Press.
360. Sarkar, Sahotra. 1996. Biological information: a skeptical look at some central dogmas of molecular biology. in The Philosophy and History of Molecular Biology:New Perspectives, ed. S. Sarkar. Dordrecht: Kluwer, 187-231.
361. Sarkar, Sahotra. 1998. Genetics and Reductionism. Cambridge University Press.
362. Sarkar, Sahotra. 1999. From the Reaktionsnorm to the adaptive norm: the norm of reaction 1909-1960. Biology and Philosophy14: 235-252.
363. Sarkar, Sahotra. 2005. Molecular Models of Life: Philosophical Papers on Molecular Biology. Cambridge, MA: MIT Press.
364. Schaffner, Kenneth F. 1967. Antireductionism and molecular biology. in Man and Nature: Philosophical Issues in Biology, ed. R. Munson. New York: Dell, 44-54.
365. Schaffner, Kenneth F. 1969. The Watson-Crick model and reductionism. British Journal for the Philosophy of Science20: 325-348.
366. Schaffner, Kenneth F. 1993. Discovery and Explanation in Biology and Medicine. University of Chicago Press.
367. Schaffner, Kenneth F. 1996. Theory structure and knowledge representation in molecular biology. in The Philosophy and History of Molecular Biology: New Perspectives, ed. S. Sarkar. Dordrecht: Kluwer, 27-46.
368. Schaffner, Kenneth F. 1998. Genes, behavior and developmental emergentism: one process, indivisible? Philosophy of Science65 (2): 209-252.
369. Schaffner, Kenneth F. 2006a. Behaving: Its nature and nurture, part 1. in Wrestling with Behavioral Genet- ics: Implications for Understanding Selves and Society, ed. E. Parens, A. Chapmanand N. Press. Baltimore, MD: Johns Hopkins University Press, 3-39.
370. Schaffner, Kenneth F. 2006b. Behaving: Its nature and nurture, part 2. in Wrestling with Behavioral Genet-ics: Implications for Understanding Selves and Society, ed. E. Parens, A. Chapmanand N. Press. Baltimore, MD: Johns Hopkins University Press, 40-73.
371. Schlichting, Carl D., and Massimo Pigliucci. 1998. Phenotypic Evolution: A Reaction Norm Perspective. Sunderland, MA: Sinauer.
372. Schlitt, Thomas, and Alvis Brazma. 2006. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philosophical Transactions of the Royal Society B:Biological Sciences361: 483-494.
373. Schmalhausen, I. I. 1949. Factors of Evolution: The Theory of Stabilising Selection, trans. I. Dordick. Philadelphia and Toronto: Blakeston.
374. Schr¨odinger, Erwin. 1944. What if Life? Cambridge University Press.
375. Sesardic, Neven. 2005. Making Sense of Heritability. Cambridge University Press.
376. Shabalina, Svetlana A., Aleksey Yu Ogurtsov, Vasily A. Kondrashov, and Aleksey S. Kondrashov. 2001. Selective constraint in intergenic regions of human and mouse genomes. Trends in Genetics17: 373-376.
377. Shannon, Claude E., and WarrenWeaver. 1949. The Mathematical Theory of Communication. University of Illinois Press.
378. Shea, Nicholas. 2007a. Consumers need information: supplementing teleosemantics with an input condition. Philosophy and Phenomenological Research75 (2):404-435.
379. Shea, Nicholas. 2007b. Representation in the genome and in other inheritance systems. Biology and Philosophy22: 313-331.
380. Shea, Nicholas. 2011a. Developmental systems theory formulated as a claim about inherited information. Philosophy of Science78: 60-82.
381. Shea, Nicholas. 2011b. What’s transmitted? Inherited information. Biology and Philosophy26 (2):183-189.
382. Shea, Nicholas. in press. Inherited representations are read in development. British Journal for the Philosophy of Science. First published online 29 February 2012. at http://bjps.oxfordjournals.org/content/early/2012/02/29/bjps.axr050.full.pdf+html.
383. Shin, Chanseok, and James L. Manley. 2004. Cell signalling and the control of pre-mRNA splicing. Nature Reviews Molecular Cell Biology5: 727-738.
384. Simpson, George G. 1953. The Baldwin effect. Evolution7: 110-117.
385. Sloan, Phillip R., and Brandon Fogel (eds.). 2012. Creating a Physical Biology: The Three-Man Paper and Early Molecular Biology. University of Chicago Press.
386. Smith, Christopher W. J., and Juan Valc´arcel. 2000. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends in Biochemical Sciences25: 381-388.
387. Snyder, Michael, and Mark Gerstein. 2003. Defining genes in the genomics era. Science300 (5617): 258-260.
388. Sober, Elliott. 1984. The Nature of Selection: Evolutionary Theory in Philosophical Focus. Cambridge, MA: MIT Press.
389. Sober, Elliott. 1999. The multiple realizability argument against reductionism. Philosophy of Science66 (4): 542-564.
390. Stamm, Stefan 2002. Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Human Molecular Genetics 11 (20): 2409-2416.
391. Stanford, P. Kyle, and Philip Kitcher. 2000. Refining the causal theory of reference for natural kind terms. Philosophical Studies97: 99-129.
392. Star, Susan Leigh, and James R. Griesemer. 1998. Institutional ecology, ‘translation,’ and boundary objects: amateurs and professionals in Berkeley’sMuseum of Vertebrate Zoology, 1907-39 (abridged). in The Science Studies Reader, ed. M. Biagioli. New York: Routledge, 505-524.
393. Stein, Lincoln D. 2001. Genome annotation: from sequence to biology. Nature Reviews Genetics2: 493-503.
394. Sterelny, Kim, Michael Dickison, and Kelly Smith. 1996. The extended replicator. Biology and Philosophy11 (3): 377-403.
395. Sterelny, Kim, and Paul E. Griffiths. 1999. Sex and Death: An Introduction to the Philosophy of Biology. University of Chicago Press.
396. Stern, David, and Virginie Orgogozo. 2008. The loci of evolution: how predictable is genetic evolution? Evolution62(9): 2155-2177.
397. Stotz, Karola. 2006a. With genes like that, who needs an environment? Postgenomics’ argument for the ontogeny of information. Philosophy of Science73 (5):905-917.
398. Stotz, Karola. 2006b. Molecular epigenesis: distributed specificity as a break in the Central Dogma. History and Philosophy of the Life Sciences28 (4): 527-544.
399. Stotz, Karola. 2008. The ingredients for a postgenomic synthesis of nature and nurture. Philosophical Psychology21 (3): 359-381.
400. Stotz, Karola. 2010. Human nature and cognitive-developmental niche construction. Phe- nomenology and the Cognitive Sciences9 (4): 483-501.
401. Stotz, Karola, and Colin Allen (eds.). 2008. Philosophical Psychology 21 (3: special issue, Reconciling Nature and Nurture in the Study of Behavior).
402. Stotz, Karola, Adam Bostanci, and Paul E. Griffiths. 2006. Tracking the shift to ‘post-genomics’. Community Genetics9 (3): 190-196.
403. Sturm, Nancy R., and David A. Campbell. 1999. The role of intron structures in trans-splicing and Cap 4 formation for the Leishmania spliced leader RNA. Journal of Biological Chemistry274 (27): 19361-19367.
404. Sultan, Sonia E. 2007. Development in context: the timely emergence of eco-devo. Trends in Ecology and Evolution22 (11): 575-582.
405. Suomi, Stephen J. 2004. How gene-environment interactions can influence emotional development in rhesus monkeys. in Nature and Nurture: The ComplexInterplay of Genetic and Environmental Influences on Human Behavior and Development, ed. C. Garcia-Coll, E. L. Bearer, and R. M. Lerner. Mahwah, NJ: Lawrence Erlbaum Associates, 35-51.
406. Suppes, Patrick. 1960. A comparison of the meaning and uses of models in mathematics and the empirical sciences. Synthese12: 287-301.
407. Suzuki, Y., and H. F. Nijhout. 2006. Evolution of a polyphenism by genetic accommodation. Science311 (5761): 650-652.
408. Tabery, James G. 2007. Biometric and developmental gene-environment interactions: looking back, moving forward. Development and Psychopathology19: 971-976.
409. Tabery, James G. 2008. R. A. Fisher, Lancelot Hogben, and the origin(s) of genotype-environment interaction. Journal of the History of Biology41 (4): 717-761.
410. Tabery, James G. 2009. Difference mechanisms: explaining variation with mechanisms. Biology and Philosophy21 (5): 645-664.
411. Tabery, James G., and Paul E. Griffiths. 2010. Historical and philosophical perspectives on behavioral genetics and developmental science. in Handbook ofDevelopmental Science, Behavior and Genetics, ed. K. E. Hood, C. T. Halpern, G. Greenberg and R. M. Lerner. Oxford: Wiley-Blackwell, 41-60.
412. Tasic, Bosiljka, Christoph E. Nabholz, Kristin K. Baldwin, Youngwook Kim, Erroll H. Rueckert, Scott A. Ribick, Paula Cramer, Qiang Wu, Richard Axel, and Tom Maniatis. 2002. Promoter choice determines splice site selection in protocadherin alpha and -gamma pre-mRNA splicing. Molecular Cell10 (1): 21-33.
413. Thompson, Paul. 1989. The Structure of Biological Theories. Albany: State University of New York Press.
414. Thornburg, B. G., V. Gotea, and W. Maka lowski. 2006. Transposable elements as a significant source of transcription regulating signals. Gene365: 104-110.
415. Tilgner, H., D. G. Knowles, R. Johnson, C. A. Davis, S. Chakrabortty, S. Djebali, J. Curado, M. Snyder, T. R. Gingeras, and R. Guig´o. 2012. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Research22 (9): 1616-1625.
416. Tinbergen, Nikolaas. 1963. On the aims and methods of ethology. Zeitschrift f¨ur Tierpsychologie20: 410-433.
417. Turkheimer, Eric. 2000. Three laws of behavior genetics and what they mean. Current Directions in Psychological Science9 (5): 160-164.
418. Turney, Jon. 2005. The sociable gene. EMBO Reports6 (9): 809-810.
419. Uller, Tobias. 2008. Developmental plasticity and the evolution of parental effects. Trends in Ecology and Evolution23 (8): 432-438.
420. Van Fraassen, Bas. 1980. The Scientific Image. Oxford University Press.
421. Venter, J. C., M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, H. O. Smith, M. Yandell, C. A. Evans, R. A. Holt, et al. 2001. The sequence of the human genome. Science291: 1304-1351.
422. Visscher, Peter M. 2008. Sizing up human height variation. Nature Genetics40 (5): 489-490.
423. Waddington, Conrad H. 1940. Organisers and Genes. Cambridge University Press.
424. Waddington, Conrad H. 1952. The evolution of developmental systems. in Twenty-eighth Meeting of theAustralian and New Zealand Association for the Advancement of Science, ed. D. A.Herbert. Brisbane, Australia: A. H. Tucker, Government Printer Brisbane.
425. Waddington, Conrad H. 1953a. Genetic assimilation of an acquired character. Evolution7: 118-126.
426. Waddington, Conrad H. 1953b. The ‘Baldwin effect’, ‘genetic assimilation’ and ‘homeostasis’. Evolution7(4): 386-387.
427. Waddington, Conrad H. 1957. The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. London: Ruskin House/George Allen & Unwin.
428. Wade, Michael J. 1998. The evolutionary genetics of maternal effects. in Maternal Effects as Adaptations, ed. T. A. Mousseau and C.W. Fox. Oxford University Press,5-21.
429. Wagner, G¨unter P. 1994. Homology and the mechanisms of development. in Homology: The Hierarchical Basis of Comparative Biology, ed. B. K. Hall. New York: AcademicPress,273-299.
430. Wagner, G¨unter P. 1995. The biological role of homologues: a building block hypothesis. Neues Jahrbuch f¨ur Geologie und Pal¨aontologie, Abhandlungen195: 279-288.
431. Wagner, G¨unter P. 1996. Homologues, natural kinds and the evolution of modularity. American Zoologist36: 36-43.
432. Wahlsten, Douglas. 1990. Insensitivity of the analysis of variance to heredity environment interaction. Behavioral and Brain Sciences13: 109-161.
433. Wahlsten, Douglas, and Gilbert Gottlieb. 1997. The invalid separation of effects of nature and nurture: lessons from animal experimentation. in Intelligence, Heredity and Environment, ed. R. J. Sternberg and E. Grigorenko. Cambridge University Press, 163-192.
434. Walters, Ryan D., Jennifer F. Kugel, and James A. Goodrich. 2009. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. UBMB Life61 (8): 831-837.
435. Waters, C. Kenneth. 1990. Why the antireductionist consensus won’t survive the case of classical Mendelian genetics. in Proceedings of the Biennial Meeting of thePhilosophy of Science Association. Vol. 1: Contributed Papers, ed. A. Fine, M. Forbes, and L. Wessells. Philosophy of Science Association, 125-139.
436. Waters, C. Kenneth. 1994. Genes made molecular. Philosophy of Science61: 163-185.
437. Waters, C. Kenneth. 2000. Moleculesmade biological. Revue Internationale de Philosophie4 (214): 539-564.
438. Waters, C. Kenneth. 2004. What was classical genetics? Studies in History and Philosophy of Science35 (4): 783-809.
439. Waters, C. Kenneth. 2006. A pluralist interpretation of gene-centered biology. in Scientific Pluralism, Vol. 19, ed. S. Kellert, H. E. Longino and C. K. Waters. Minneapolis: Universityof Minnesota Press, 190-214.
440. Waters, C. Kenneth. 2007. Causes that make a difference. Journal of Philosophy104 (11): 551-579.
441. Watson, James D., and Francis H. C. Crick. 1953a. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature171: 737.
442. Watson, James D., and Francis H. C. Crick. 1953b. Genetical implications of the structure of deoxyribose nucleic acid. Nature171: 964-967.
443. Weaver, Ian C. G., Nadia Cervoni, Frances A. Champagne, Ana C. D’Alessio, Shakti Sharma, Jonathan R. Seckl, Sergiy Dymov, Moshe Szyf, and Michael J. Meaney. 2004. Epigenetic programming by maternal behavior. Nature Neuroscience7 (8): 847-854.
444. Weber, Bruce H., and David J. Depew. 1996. Natural selection and self-organisation. Biology and Philosophy11: 33-65.
445. Weber, Bruce H., and David J. Depew. (eds.). 2003. Learning, Meaning and Emergence: Possible Baldwinian Mechanisms in the Co-evolution of Language and Mind. Cambridge, MA: MIT Press.
446. Weber, Marcel. 2005. Philosophy of Experimental Biology. Cambridge University Press.
447. Weber, Marcel. 2006. The Central Dogma as a thesis of causal specificity. History and Philosophy of the Life Sciences28 (4): 595-609.
448. Weiss, Kenneth M., and Anne V. Buchanan. 2009. The cooperative genome: Organisms as social contracts. International Journal of Developmental Biology53: 753-763.
449. West, Meredith J., and Andrew P. King. 1987. Settling nature and nurture into an ontogenetic niche. Developmental Psychobiology20 (5): 549-562.
450. West, Meredith J., and Andrew P. King. 1988. Female visual displays affect the development of male song in the cowbird. Nature334: 244-246.
451. West, Meredith J., and Andrew P. King. 2008. Deconstructing innate illusions: reflections on nature-nurture-niche from an unlikely source. Philosophical Psychology21 (3): 383-395.
452. West, Meredith J., Andrew P. King, and Anne A. Arberg. 1988. The inheritance of niches: the role of ecological legacies in ontogeny. in Handbook of BehavioralNeurobiology. Vol. 9: Developmental Psychobiology and Behavioral Ecology, ed. E. M. Blass. New York: Plenum Press, 41-62.
453. West, Meredith J., Andrew P. King, and David J. White. 2003. The case for developmental ecology. Animal Behaviour66: 617-622.
454. West, Meredith J., Andrew P. King, David J.White, Julie Gros-Louis, and Grace Freed-Brown. 2006. The development of local song preferences in female cowbirds (Molothrus ater): flock living stimulates learning. Ethology112: 1095-1107.
455. West-Eberhard, Mary Jane. 1998. Evolution in the light of developmental and cell biology, and vice versa. PNAS95: 8417-8419.
456. West-Eberhard, Mary Jane. 2003. Developmental Plasticity and Evolution. Oxford University Press.
457. West-Eberhard, Mary Jane. 2005a. Developmental plasticity and the origin of species differences. PNAS102 (Suppl. 1): 6543-6549.
458. West-Eberhard, Mary Jane. 2005b. Phenotypic accommodation: adaptive innovation due to developmental plasticity. Journal of Experimental Zoology, Part B: Molecular and DevelopmentalEvolution304: 610-618.
459. Wilkins, Adam. 2011. Epigenetic inheritance: where does the field stand today? What do we still need to know? in Transformations of Lamarckism: From SubtleFluids to Molecular Biology, ed. S. B. Gissis and E. Jablonka. Cambridge, MA: MIT Press, 389-393.
460. Williams, George C. 1966. Adaptation and Natural Selection. Princeton University Press.
461. Williams, George C. 1992. Natural Selection: Domains, Levels and Challenges. New York: Oxford University Press.
462. Wimsatt, William C. 1986a. Forms of aggregativity. in Human Nature and Natural Knowledge, ed. M. G. Grene, A. Donaghan, A. N. Perovich, and M. V. Wedin.Dordrecht: Reidel, 259-291.
463. Wimsatt, William C. 1986b. Developmental constraints, generative entrenchment and the innateaquired distinction. in Integrating Scientific Disciplines, ed. W. Bechtel. Dordrecht: Martinus Nijhoff.
464. Winther, Rasmus G. 2006. Parts and theories in compositional biology. Biology and Philosophy21 (4): 471-499.
465. Wissinger, B., W. Schuster, and A. Brennicke. 1991. Trans splicing in Oenothera Mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell65 (3): 473-482.
466. Wolkenhauer, Olaf. 2001. Systems biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics2 (3): 258-270.
467. Woodward, James. 2003. Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.
468. Woodward, James. 2010. Causation in biology: stability, specificity, and the choice of levels of explanation. Biology and Philosophy25 (3): 287-318.
469. Yang, Jian, Beben Benyamin, Brian P. McEvoy, Scott Gordon, Anjali K. Henders, Dale R. Nyholt, Pamela A. Madden, Andrew C. Heath, Nicholas G. Martin, Grant W. Montgomery, Michael E. Goddard, and Peter M. Visscher. 2010. Common SNPs explain a large proportion of the heritability for human height. Nature Genetics42 (7): 565-569.