Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-cd9895bd7-hc48f Total loading time: 0 Render date: 2024-12-22T20:04:45.385Z Has data issue: false hasContentIssue false

Bibliography

Published online by Cambridge University Press:  05 April 2013

Paul Griffiths  and
Karola Stotz
Paul Griffiths
Affiliation:
University of Sydney
Karola Stotz
Affiliation:
University of Sydney
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Genetics and Philosophy
An Introduction
 , pp. 229 - 257
Publisher: Cambridge University Press
Print publication year: 2013

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alberch, Pere. 1982. Developmental constraints in evolutionary processes. In Evolution and Development, ed. Bonner, J. T.. New York: Springer Verlag, 313–32.CrossRefGoogle Scholar
Alberts, Jeffrey R. 1994. Learning as adaptation of the infant. Acta Paediatrica 83 (s397): 77–85.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Amundson, Ron. 2005. The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo. Cambridge University Press.CrossRefGoogle Scholar
Angers, Bernard, Castonguay, Emilie, and Massicotte, Rachel. 2010. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Molecular Ecology 19 (7): 1283–95.CrossRefGoogle ScholarPubMed
Anstey, Michael L., Rogers, Stephen M, Ott, Swidbert R, Burrows, Malcolm, and Simpson, Stephen J. 2009. Serotonin mediates behavioral gregarization underlying swarm formation in desert locusts. Science 323 (5914): 627–30.CrossRefGoogle ScholarPubMed
Athanasiadis, Alekos, Rich, Alexander, and Maas, Stefan. 2004. Widespread A-to-I RNA editing of alu-containing mRNAs in the human transcriptome. PLoS Biology 2 (12): e391.CrossRefGoogle ScholarPubMed
Badyaev, Alexander V. 2009. Evolutionary significance of phenotypic accommodation in novel environments: an empirical test of the Baldwin effect. Philosophical Transactions of the Royal Society, Biological Sciences 364: 1125–41.CrossRefGoogle ScholarPubMed
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 Royal Society, Biological Sciences 278: 1921–9.CrossRefGoogle ScholarPubMed
Badyaev, Alexander V., and Uller, Tobias. 2009. Parental effects in ecology and evolution: mechanisms, processes, and implications. Philosophical Transactions of the Royal Society, Biological Sciences 364: 1169–77.CrossRefGoogle ScholarPubMed
Baetu, Tudor. 2012. Genomic programs as mechanism schemas: a non-reductionist interpretation. British Journal for the Philosophy of Science, 63 (3): 649–71.CrossRefGoogle Scholar
Barak, Michal, Levanon, Erez Y., Eisenberg, Eli, Paz, Nurit, Rechavi, Gideon, Church, George M., and Mehr, Ramit. 2009. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Research 37 (20): 6905–15.CrossRefGoogle ScholarPubMed
Baranov, Pavel V., Gurvich, Olga L, Hammer, Andrew W, Gesteland, Raymond F, and Atkins, John F. 2003. Recode 2003. Nucleic Acids Research 31 (1): 87–9.CrossRefGoogle ScholarPubMed
Bass, Brenda. 2001. RNA Editing: Frontiers in Molecular Biology. Oxford University Press.Google Scholar
Bateson, P., Barker, D., Clutton-Brock, T., Deb, D., D’Udine, B., Foley, R. A., Gluckman, P. D., Godfrey, K., Kirkwood, T., Lahr, M. M., McNamara, J., Metcalfe, N. B., Monaghan, P., Spencer, H. G., and Sultan, S. E.. 2004. Developmental plasticity and human health. Nature 430: 419–21.CrossRefGoogle ScholarPubMed
Bateson, Patrick P. G., and Gluckman, Peter D. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press.CrossRefGoogle Scholar
Bateson, Patrick P. G., and Martin, Paul. 1999. Design for a Life: How Behavior and Personality Develop. London: Jonathan Cape.Google Scholar
Bateson, William. 1894. Materials for the Study of Variation. London: Macmillan.Google Scholar
Beatty, John. 1990. Evolutionary anti-reductionism: historical reflections. Biology and Philosophy 5 (2): 199–210.CrossRefGoogle Scholar
Bechtel, William. 2006. Discovering Cell Mechanisms: The Creation of Modern Cell Biology. Cambridge University Press.Google Scholar
Bechtel, William 2007. Reducing psychology while maintaining its autonomy via mechanistic explanation. In The Matter of the Mind: Philosophical Essays on Psychology, Neuroscience and Reduction, ed. Schouten, M. and de Jong, H. L.. Oxford: Blackwell, 172–98. Also at .Google Scholar
Bechtel, William 2008. Mental Mechanisms. New York: Routledge.Google Scholar
Bechtel, William, and Abrahamsen, Adele. 2005. Explanation: a mechanistic alternative. Studies in History and Philosophy of the Biological and Biomedical Sciences 36: 421–41.CrossRefGoogle Scholar
Bechtel, William, and Abrahamsen, Adele in press. Thinking dynamically about biological mechanisms: networks of coupled oscillators. Foundations of Science.
Bechtel, William, and Richardson, Richard C. 1993. Discovering Complexity: Decomposition and Localization as Strategies in Scientific Research. Princeton University Press.Google Scholar
Bentley, David. 2002. The mRNA assembly line: transcription and processing machines in the same factory. Current Opinion In Cell Biology 14 (3): 336–42.CrossRefGoogle ScholarPubMed
Bergstrom, Carl, and Rosvall, Martin. 2009. The transmission sense of information. Biology and Philosophy 26 (2): 159–76.CrossRefGoogle Scholar
Biliya, Shweta, and Bulla, Lee A. 2010. Genomic imprinting: the influence of differential methylation in the two sexes. Experimental Biology and Medicine 235 (2): 139–47.CrossRefGoogle ScholarPubMed
Bissell, Mina J. 1981. The differentiated state of normal and malignant cells or how to define a ‘normal’ cell in culture. International Review of Cytology 70: 27–100.CrossRefGoogle ScholarPubMed
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 and Evolutionary Biology, ed. Müller, G. B. and Newman, S. A.. Cambridge, MA: MIT Press, 103–17.Google Scholar
Blumenthal, Thomas, Evans, Donald, Link, Christopher D., Guffanti, Alessandro, Lawson, Daniel, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Chiu, Wei Lu, Duke, Kyle, Kiraly, Moni, and Kim, Stuart K.. 2002. A global analysis of Caenorhabditis elegans operons. Nature 417 (6891): 851–4.CrossRefGoogle ScholarPubMed
Bolker, Jessika. 1995. Model systems in developmental biology. Bioessays 17: 4515.CrossRefGoogle ScholarPubMed
Bonasio, Roberto, Shengjiang, Tu, and Reinberg, Danny. 2010. Molecular signals of epigenetic states. Science 330 (6004): 612–16.CrossRefGoogle ScholarPubMed
Bonduriansky, Russell. 2012. Rethinking heredity, again. TREE 27 (6): 330–6.Google Scholar
Bradbury, Jane. 2005. Alternative mRNA splicing: control by combination. PLoS Biology 3 (11): e369.Google Scholar
Braendle, Christian, and Flatt, Thomas. 2006. A role for genetic accommodation in evolution? Bioessays 28: 868–73.CrossRefGoogle Scholar
Brandon, Robert N., and McShea, Daniel W. 2010. Biology's First Law. University of Chicago Press.Google Scholar
Brentano, Franz. 1874. Psychologie vom empirischen Standpunkt. Leipzig: Duncker & Humbolt.Google Scholar
Brigandt, Ingo, and Love, Alan C. 2008. Reductionism in biology. In The Stanford Encyclopedia of Philosophy (Fall 2008 Edition), ed. E. N. Zalta. At .
Brigandt, Ingo, and Love, Alan C 2010. Evolutionary novelty and the evo-devo synthesis: field notes. Evolutionary Biology 37: 93–9.CrossRefGoogle Scholar
Buchler, Nicolas E., Gerland, Ulrich, and Hwa, Terence. 2003. On schemes of combinatorial transcription logic. Proceedings of the National Academy of Sciences of the United States of America 100: 5136–41.CrossRefGoogle ScholarPubMed
Burian, Richard M. 2004. Molecular epigenesis, molecular pleiotropy, and Molecular Gene Definitions. History and Philosophy of the Life Sciences 26 (1): 59–80.CrossRefGoogle ScholarPubMed
Carroll, Sean B. 2005. Evolution at two levels: on genes and form. PLoS Biology 3 (7): e245.CrossRefGoogle ScholarPubMed
Carroll, Sean B., Grenier, Jennifer K., and Weatherbee, Scott D.. 2001. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Malden, MA: Blackwell.Google Scholar
Carroll, Sean B 2005. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, 2nd edn. Malden, MA: Blackwell.Google Scholar
Caudevilla, C., Codony, C., Serra, D., Plasencia, G., Roman, R., Graessmann, A., Asins, G., Bach-Elias, M., and Hegardt, F. G.. 2001. Localization of an exonic spli-cing enhancer responsible for mammalian natural trans-splicing. Nucleic Acids Research 29 (14): 3108–15.CrossRefGoogle ScholarPubMed
Cawley, Simon, Bekiranov, Stefan, Ng, Huck H., Kapranov, Philipp, Sekinger, Edward A., Kampa, Dione, Piccolboni, Antonio, Sementchenko, Victor, Cheng, Jill, Williams, Alan J., Wheeler, Raymond, Wong, Brant, Drenkow, Jorg, Yamanaka, Mark, Patel, Sandeep, Brubaker, Shane, Tammana, Hari, and Gingeras, Thomas R.. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499–509.CrossRefGoogle ScholarPubMed
Celottoa, Alicia M., and Graveley, Brenton R.. 2001. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics 159: 599–608.Google Scholar
Chadarevian, S. de. 1998. Of worms and programs: Caenorhabitis Elegans and the study of development. Studies in History and Philosophy of the Biological and Biomedical Sciences 29 (1): 81–105.CrossRefGoogle Scholar
Champagne, Francis A., and Curley, James P.. 2009a. Epigenetic mechanisms mediating the long-term effects of maternal care on development. Neuroscience Bio-behaviour Review 33 (4): 593–600.CrossRefGoogle ScholarPubMed
Champagne, Francis A., and Curley, James P. 2009b. The transgenerational influence of maternal care on offspring gene expression and behavior in rodents. In Maternal Effects in Mammals, ed. Maestripieri, D. and Mateo, J. M.. University of Chicago Press, 182–202.CrossRefGoogle Scholar
Chapdelaine, Y., and Bonen, L.. 1991. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell 65 (3): 465–72.CrossRefGoogle ScholarPubMed
Chen, Jianjun, Sun, Miao, Lee, Sanggyu, Zhou, Guoline, Rowley, Janet D., and Wang, San Ming. 2002. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proceedings of the National Academy of Sciences of the United States of America 99: 12257–62.CrossRefGoogle ScholarPubMed
Chen, Ling-Ling, and Carmichael, Gordon G.. 2010. Decoding the function of nuclear long noncoding RNAs. Current Opinion in Cell Biology 22 (3): 357–64.CrossRefGoogle Scholar
Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 (5725): 1149–54.CrossRefGoogle ScholarPubMed
Chomsky, Noam. 1988. Language and Problems of Knowledge: The Managua Lectures. Cambridge, MA: MIT Press.Google Scholar
Chong, Lisa, and Ray, L. Bryan. 2002. Whole-istic biology. Science 295 (5560): 1661.CrossRefGoogle Scholar
Claverie, J. M. 2001. Gene number: what if there are only 30,000 human genes? Science 291: 1255–7.CrossRefGoogle ScholarPubMed
Coelho, Paulo S. R., Bryan, Anthony C., Kumar, Anuj, Shadel, Gerald S., and Snyder, Michael. 2002. A novel mitochondrial protein, TAR1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes and Development 16: 2755–60.CrossRefGoogle ScholarPubMed
Collins, Lesley J., Schönfeld, Barbara, and Sylvia Chen, Xiaowei. 2011. The epigenetics of non-coding RNA. In Handbook of Epigenetics: The New Molecular and Medical Genetics, ed. Tollefsbol, T.. Amsterdam: Academic Press,49–61.CrossRefGoogle Scholar
Communi, Didier, Suarez-Huerta, Nathalie, Dussossoy, Danielle, Savi, Pierre, and Boeynaems, Jean-Marie. 2001. Cotranscription and intergenic splicing of human P2Y(11) SSF1 genes. Journal of Biological Chemistry 276 (19): 16561–6.CrossRefGoogle ScholarPubMed
Conklin, Edwin G. 1908. The mechanism of heredity. Science 27: 89–99.CrossRefGoogle ScholarPubMed
Cope, Edwin Brinker. 1887. Origin of the Fittest: Essays in Evolution. New York: D. Appleton.CrossRefGoogle Scholar
Craig, Lindsay R. 2010. The so-called extended synthesis and population genetics. Biological Theory 5 (2): 117–23.CrossRefGoogle Scholar
Craver, Carl F. 2007. Explaining the Brain: Mechanisms and the Mosaic Unity of Neuroscience. Oxford: Clarendon Press.CrossRefGoogle Scholar
Craver, Carl F., and Bechtel, William. 2007. Top-down causation without top-down causes. Biology and Philosophy 22 (4), 547–63.CrossRefGoogle Scholar
Crick, Francis H. C. 1958. On protein synthesis. Symposia of the Society for Experimental Biology 12: 138–63.Google ScholarPubMed
Crick, Francis H. C. 1970. Central Dogma of molecular biology. Nature 227: 561–3.CrossRefGoogle ScholarPubMed
Cummins, Robert. 1975. Functional analysis. Journal of Philosophy 72: 741–65.CrossRefGoogle Scholar
Darden, Lindley, and Maull, Nandy. 1977. Interfield theories. Philosophy of Science 44 (1): 43–64.CrossRefGoogle Scholar
Darwin, Charles. 1964 [1859]. On the Origin of Species: A Facsimile of the First Edition. Cambridge, MA: Harvard University Press.Google Scholar
Davidson, Eric H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.Google Scholar
Davidson, Eric H., and Erwin, Douglas H.. 2006. Gene regulatory networks and the evolution of animal body plans. Science 311: 796–800.CrossRefGoogle ScholarPubMed
Davidson, Eric H., and Levine, Michael. 2005. Gene regulatory networks. PNAS 102 (14): 4935.CrossRefGoogle ScholarPubMed
Davidson, Nicholas O. 2002. The challenge of target sequence specificity in C→U RNA editing. Journal of Clinical Investigation 109 (3): 291–4.CrossRefGoogle ScholarPubMed
Dawkins, Richard. 1976. The Selfish Gene. Oxford University Press.Google Scholar
Depew, David J., and Weber, Bruce H.. 1995. Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection. Cambridge, MA: Bradford Books/MIT Press.Google Scholar
Devlin, Bernie, Daniels, Michael, and Roeder, Katherine. 1997. The heritability of IQ. Nature 388 (6641): 468–71.CrossRefGoogle ScholarPubMed
Dietrich, Michael R. 2000. From hopeful monsters to homeotic effects: Richard Goldschmidt's integration of development, evolution and genetics. American Zoologist 40: 738–47.Google Scholar
Dillon, Niall. 2003. Positions, please … Nature 425 (6957): 457.CrossRefGoogle ScholarPubMed
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. 2012. Landscape of transcription in human cells. Nature 489 (7414): 101–8.CrossRefGoogle ScholarPubMed
Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M., Howald, Cedric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, et al. 2012. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS ONE 7 (1): e28213. .CrossRefGoogle ScholarPubMed
Dobzhansky, Theodosius. 1973. Nothing in biology makes sense except in the light of evolution. American Biology Teacher 35: 125–9.CrossRefGoogle Scholar
Donnellan, Keith S. 1966. Reference and definite descriptions. The Philosophical Review 75 (3): 281–304.CrossRefGoogle Scholar
Doolittle, W. Ford, and Sapienza, Carmen. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284 (5757): 601–3.CrossRefGoogle ScholarPubMed
Dorn, Rainer, Reuter, Gunter, and Loewendorf, Andrea. 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 America 98 (17): 9724–9.CrossRefGoogle ScholarPubMed
Downes, Stephen. 1992. The importance of models in theorizing: a deflationary semantic view. In Proceedings of the Philosophy of Science Association, Vol. 1, ed. Hull, D., Forbes, M. and Okruhlik, K.. East Lansing, MI: Philosophy of Science Association, 142–53.Google Scholar
Economist. 1999. Drowning in data. Economist, 26 June, 97–8.
Eddy, Sean R. 2001. Non-coding RNA genes and the modern RNA world. Nature Review Genetics 2 (12): 919–29.CrossRefGoogle ScholarPubMed
Eddy, Sean R. 2002. Computational genomics of noncoding RNA genes. Cell 109 (2): 137–40.CrossRefGoogle ScholarPubMed
Eisenberg, David, Marcotte, Edward M., McLachlan, Andrew D., and Pellegrini, Matteo. 2006. Bioinformatic challenges for the next decade(s). Philosophical Transactions of the Royal Society, Biological Sciences 361 (1467): 525.CrossRefGoogle Scholar
ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816.CrossRefGoogle Scholar
Falk, Raphael. 1984. The gene in search of an identity. Human Genetics 68: 195–204.CrossRefGoogle ScholarPubMed
Falk, Raphael 1986. What is a gene? Studies in the History and Philosophy of Science 17: 133–73.CrossRefGoogle ScholarPubMed
Falk, Raphael 2000. The gene: a concept in tension. In The Concept of the Gene in Development and Evolution, ed. Beurton, P., Falk, R. and Rheinberger, H.-J.. Cambridge University Press, 317–48.CrossRefGoogle Scholar
Falk, Raphael 2004. Long live the genome! So should the gene. History and Philosophy of the Life Sciences 26 (1): 105–21.CrossRefGoogle ScholarPubMed
Falk, Raphael 2007. Genetic analysis. In Philosophy of Biology, ed. Matthen, M. and Stephens, C.. Oxford: Elsevier, 249–308.CrossRefGoogle Scholar
Falk, Raphael 2009. Genetic Analysis: A History of Genetic Thinking. Cambridge University Press.CrossRefGoogle Scholar
Finta, Csaba, and Zaphiropoulos, Peter G.. 2000a. The human CYP2C locus: a prototype for intergenic and exon repetition splicing events. Genomics 63 (3): 433–8.CrossRefGoogle ScholarPubMed
Finta, Csaba, and Zaphiropoulos, Peter G. 2000b. The human cytochrome P450 3A locus: gene evolution by capture of downstream exons. Gene 260 (1–2): 13–23.CrossRefGoogle ScholarPubMed
Finta, Csaba, and Zaphiropoulos, Peter G. 2001. A statistical view of genome transcription. Journal of Molecular Evolution 53: 160–2.CrossRefGoogle ScholarPubMed
Finta, Csaba, and Zaphiropoulos, Peter G. 2002. Intergenic mRNA molecules resulting from trans-splicing. Journal of Biolo-gical Chemistry 277 (8): 5882–90.CrossRefGoogle ScholarPubMed
Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Transactions of the Royal Society of Edinburgh 52: 399–433.Google Scholar
Fodor, Jerry A. 1974. Special sciences. Synthese 28: 77–115.Google Scholar
Fogle, Thomas. 2000. The dissolution of protein coding genes in molecular biology. In The Concept of the Gene in Development and Evolution, ed. Beurton, P., Falk, R. and Rheinberger, H.-J.. Cambridge University Press, 3–25.CrossRefGoogle Scholar
Fontana, Walter, and Buss, Leo W.. 1994. ‘The arrival of the fittest’: toward a theory of biological organization. Bulletin of Mathematical Biology 56 (1): 164.Google Scholar
Ford, Donald H., and Lerner, Richard M.. 1992. Developmental Systems Theory: An Integrative Approach. Newbury Park, CA: Sage.Google Scholar
Fox, Charles W., Thakar, Monica S., and Mousseau, Timothy A.. 1997. Egg size plasticity in a seed beetle: an adaptive maternal effect. The American Naturalist 149 (1): 149–63.CrossRefGoogle Scholar
Fox, Charles W., Waddell, Kim J., and Mousseau, Timothy A.. 1995. Parental host plant affects offspring life histories in a seed beetle. Ecology 76 (2): 402–11.CrossRefGoogle Scholar
Frenkel-Morgenstern, M., Lacroix, V., Ezkurdia, I., Levin, Y., Gabashvili, A., Prilusky, J., Del Pozo, A., Tress, M., Johnson, R., Guigo, R., et al. 2012. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Research 22: 1231–42.CrossRefGoogle ScholarPubMed
Frigg, Roman. 2010. Models and fiction. Synthese 17 (2): 251–68.CrossRefGoogle Scholar
Frigg, Roman, and Hartmann, Stephan. 2009. Models in Science. At .
Fuller, Trevon, Sarkar, Sahotra, and Crews, David. 2005. The use of norms of reaction to analyze genotypic and environmental influences on behavior in mice and rats. Neuroscience and Biobehavioral Reviews 29: 445–56.CrossRefGoogle ScholarPubMed
Gagen, Michael J., and Mattick, John S.. 2004. Inherent size constraints on prokaryote gene networks due to ‘accelerating’ growth. Theory in Biosciences 123(4): 381–411.CrossRefGoogle Scholar
Garden, George. 1691. A discourse concerning the modern theory of generation. Philosophical Transactions of the Royal Society 16 (1686–1692): 474–83.CrossRefGoogle Scholar
Gehring, Walter J. 1985. The homeo box: a key to the understanding of development? Cell 40: 3–5.CrossRefGoogle ScholarPubMed
Gerstein, Mark B., Bruce, Can, Rozowsky, Joel S., Zheng, Deyou, Du, Jiang, Korbel, Jan O., Emanuelsson, Olof, Zhang, Zhengdong D., Weissman, Sherman, and Snyder, Michael. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Research 17 (6): 669–81.CrossRefGoogle ScholarPubMed
Gibbs, W. Wayt. 2003. The unseen genome: gems among the junk. Scientific American 289 (5): 46–53.CrossRefGoogle ScholarPubMed
Giere, Ronald. 1988. Explaining Science: A Cognitive Approach. University of Chicago Press.CrossRefGoogle Scholar
Gilbert, Scott F. 2000. Developmental Biology. Sunderland, MA: Sinauer Associates.Google Scholar
Gilbert, Scott F. 2001. Ecological developmental biology: developmental biology meets the real world. Developmental Biology 233: 1–22.CrossRefGoogle ScholarPubMed
Gilbert, Scott F. 2003. The reactive genome. In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, ed. Müller, G. B. and Newman, S. A.. Cambridge, MA: MIT Press, 87–101.Google Scholar
Gilbert, Scott F., and Epel, David. 2009. Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sunderland, MA: Sinauer Associates.Google Scholar
Gilbert, Scott F., and Sarkar, Sahotra. 2000. Embracing complexity: organicism for the twenty-first century. Developmental Dynamics 219: 1–9.3.0.CO;2-A>CrossRefGoogle Scholar
Gissis, Snait B., and Jablonka, Eva (eds.). 2011. Transformations of Lamarckism: From Subtle Fluids to Molecular Biology. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Gluckman, Peter D., and Hanson, Mark A.. 2005a. The Fetal Matrix: Evolution, Development and Disease. Cambridge University Press.Google Scholar
Gluckman, Peter D., and Hanson, Mark A. (eds.). 2005b. Developmental Origin of Health and Disease. Cambridge University Press.Google Scholar
Gluckman, Peter D., and Hanson, Mark A. 2006. Mismatch: Why Our World No Longer Fits Our Bodies. Oxford University Press.Google Scholar
Gluckman, Peter D., Hanson, Mark A., Bateson, Patrick, Beedle, Alan S., Law, Catherine M., Bhutta, Zulfiqar A., Anokhin, Konstantin V., Bougnères, Pierre, Chandak, Giriraj Ratan, Dasgupta, Partha, Smith, George Davey, Ellison, Peter T., Forrester, Terrence E., Gilbert, Scott F., Jablonka, Eva, Kaplan, Hillard, Prentice, Andrew M., Simpson, Stephen J., Uauy, Ricardo, and West-Eberhard, Mary Jane. 2009. Towards a new developmental synthesis: adaptive developmental plasticity and human disease. Lancet 373 (9675): 1654–7.CrossRefGoogle ScholarPubMed
Gluckman, Peter D., Hanson, Mark A., and Beedle, Alan S.. 2007. Early life events and their consequences for later disease: a life history and evolutionary perspective. American Journal of Human Biology 19: 1–19.CrossRefGoogle ScholarPubMed
Gluckman, Peter D., Hanson, Mark A., and Spencer, Hamish G.. 2005. Predictive adaptive responses and human evolution. Trends in Ecology and Evolution 20 (10): 527–33.CrossRefGoogle ScholarPubMed
Godfrey, K. M., Sheppard, A., Gluckman, P. D., Lillycrop, K. A., Burdge, G. C., McLean, C., Rodford, J., Slater-Jefferies, J. L., Garratt, E., Crozier, S. R., Emerald, B. S., Gale, C. R., Inskip, H. M., Cooper, C., and Hanson, M. A.. 2011. Epigenetic gene promoter methylation at birth is associated with child's later adiposity. Diabetes 30 (5): 1528–34.CrossRefGoogle Scholar
Godfrey-Smith, Peter. 1989. Misinformation. Canadian Journal of Philosophy 19 (5): 533–50.CrossRefGoogle Scholar
Godfrey-Smith, Peter 1999. Genes and codes: lessons from the philosophy of mind? In Biology Meets Psychology: Constraints, Conjectures, Connections, ed. Hardcastle, V. G.. Cambridge, MA: MIT Press, 305–31.Google Scholar
Godfrey-Smith, Peter 2000a. On the theoretical role of ‘genetic coding’. Philosophy of Science 67 (1): 26–44.CrossRefGoogle Scholar
Godfrey-Smith, Peter 2000b. ‘Explanatory symmetries, preformation, and developmental systems theory.’ Philosophy of Science 67 (Supplementary Proceedings of the 1998 Biennial Meetings of the Philosophy of Science Association. Part II: Symposia Papers): S322–S331.CrossRefGoogle Scholar
Godfrey-Smith, Peter 2001. On the status and explanatory structure of developmental systems theory. In Cycles of Contingency: Developmental Systems and Evolution, ed. Oyama, S., Griffiths, P. E. and Gray, R. D.. Cambridge, MA: MIT Press, 283–97.Google Scholar
Godfrey-Smith, Peter 2006. The strategy of model-based science. Biology and Philosophy 21: 725–40.CrossRefGoogle Scholar
Godfrey-Smith, Peter 2011. Senders, receivers, and genetic information: comments on Bergstrom and Rosvall. Biology and Philosophy 26 (2): 177–81.CrossRefGoogle Scholar
Goodwin, Brian C. 1994. How the Leopard Changed Its Spots: The Evolution of Complexity. New York: Charles Scribner & Sons.Google Scholar
Gott, Jonathan M., and Emeson, Ronald B.. 2000. Functions and mechanisms of RNA editing. Annual Review of Genetics 34: 499–531.CrossRefGoogle ScholarPubMed
Gottlieb, Gilbert. 1992. Individual Development and Evolution. Oxford University Press.Google Scholar
Gottlieb, Gilbert 1995. Some conceptual deficiencies in ‘developmental’ behavior genetics. Human Development 38: 131–41.CrossRefGoogle Scholar
Gottlieb, Gilbert 1997. Synthesizing Nature–Nurture: Prenatal Roots of Instinctive Behavior. Hillsdale, NJ: Lawrence Erlbaum Associates.Google Scholar
Gottlieb, Gilbert 2001. A developmental psychobiological systems view: early formulation and current status. In Cycles of Contingency: Developmental Systems and Evolution, ed. Oyama, S., Griffiths, P. E. and Gray, R. D.. Cambridge, MA: MIT Press, 41–54.Google Scholar
Gottlieb, Gilbert 2003. On making behavioral genetics truly developmental. Human Development 46 (6): 337–55.CrossRefGoogle Scholar
Gould, Stephen Jay. 1977. Ontogeny and Phylogeny. Cambridge, MA: Harvard University Press.Google Scholar
Graveley, Brenton R. 2005. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123: 65–73.CrossRefGoogle ScholarPubMed
Gray, M. W. 2003. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55 (4–5): 227–33.CrossRefGoogle ScholarPubMed
Gray, Russell D. 1992. Death of the gene: developmental systems strike back. In Trees of Life: Essays in the Philosophy of Biology, ed. Griffiths, Paul E.. Dordrecht: Kluwer, 165–210.CrossRefGoogle Scholar
Greenspan, Ralph J. 2001. The flexible genome. Nature Reviews Genetics 2: 383–7.CrossRefGoogle ScholarPubMed
Grice, H. P. 1957. Meaning. Philosophical Review 66: 377–88.CrossRefGoogle Scholar
Griffiths, Paul E. 2001. Genetic information: a metaphor in search of a theory. Philosophy of Science 68 (3): 394–412.CrossRefGoogle Scholar
Griffiths, Paul E 2003. Beyond the Baldwin effect: James Mark Baldwin's ‘social heredity’, epigenetic inheritance and niche-construction. In Evolution and Learning: The Baldwin Effect Reconsidered, ed. Weber, B. H. and Depew, D. J.. Cambridge, MA: MIT Press, 193–215.Google Scholar
Griffiths, Paul E 2004. Instinct in the ’50s: The British reception of Konrad Lorenz's theory of instinctive behaviour. Biology and Philosophy 19 (4): 609–31.CrossRefGoogle Scholar
Griffiths, Paul E 2009. In what sense does ‘nothing in biology make sense except in the light of evolution’? Acta Biotheoretica 57 (1–2): 11–32.CrossRefGoogle ScholarPubMed
Griffiths, Paul E., and Gray, Russell D.. 1994. Developmental systems and evolutionary explanation. Journal of Philosophy 91 (6): 277–304.CrossRefGoogle Scholar
Griffiths, Paul E 1997. Replicator II: judgment day. Biology and Philosophy 12 (4): 471–92.CrossRefGoogle Scholar
Griffiths, Paul E 2005. Three ways to misunderstand developmental systems theory. Biology and Philosophy 20 (2): 417–25.CrossRefGoogle Scholar
Griffiths, Paul E., and Knight, Rob D.. 1998. What is the developmentalist challenge? Philosophy of Science 65 (2): 253–8.CrossRefGoogle Scholar
Griffiths, Paul E., and Stotz, Karola. 2006. Genes in the postgenomic era. Theoretical Medicine and Bioethics 27 (6): 499–521.CrossRefGoogle ScholarPubMed
Griffiths, Paul E 2007. Gene. In Cambridge Companion to the Philosophy of Biology, ed. Hull, D. and Ruse, M.. Cambridge University Press, 85–102.CrossRefGoogle Scholar
Griffiths, Paul E., and Tabery, James G.. 2008. Behavioral genetics and development. New Ideas in Psychology 26 (3): 332–52.CrossRefGoogle Scholar
Haack, Susan. 1987. Surprising noises: Rorty and Hesse on metaphor. Proceedings of the Aristotelian Society 88: 293–301.CrossRefGoogle Scholar
Hacking, Ian. 1983. Representing and Intervening: Introductory Topics in the Philosophy of Natural Science. Cambridge University Press.CrossRefGoogle Scholar
Haig, David. 2000. The kinship theory of genomic imprinting. Annual Review of Ecology and Systematics 31: 9–32.CrossRefGoogle Scholar
Haig, David 2004. The (dual) origin of epigenetics. Cold Spring Harbor Symposia on Quantitative Biology 69: 67–70.CrossRefGoogle ScholarPubMed
Haldane, J. B. S., and Spurway, Helen. 1954. A statistical analysis of communication in ‘Apis mellifera’ and a comparison with communication in other animals. Insectes Sociaux 1 (3): 247–83.CrossRefGoogle Scholar
Hall, Brian K. 1992. Evolutionary Developmental Biology. New York: Chapman & Hall.CrossRefGoogle Scholar
Hall, Brian K 1998. Evolutionary Developmental Biology. 2nd edn. New York: Chapman & Hall.Google Scholar
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. Hallgrimsson, B. and Hall, B. K.. Berkeley: University of California Press, 9–13.Google Scholar
Hallgrimsson, Benedict, and Hall, Brian K.. 2011. Introduction. In Epigenetics: Linking Genotype and Phenotype in Develoment and Evolution, ed. Hallgrimsson, B. and Hall, B. K.. Berkeley: University of California Press, 1–5.Google Scholar
Hamer, Dean. 2002. Rethinking behavior genetics. Science 298: 71–2.CrossRefGoogle ScholarPubMed
Hardison, Ross C. 2000. Conserved non-coding sequences are reliable guides to regulatory elements. Trends in Genetics 16 (9): 369–72.CrossRefGoogle Scholar
Harrison, Paul M., Kumar, Anuj, Lang, Ning, Snyder, Michael, and Gerstein, Mark. 2002. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Research 30 (5): 1083–90.CrossRefGoogle Scholar
Häsler, J., Samuelsson, T., and Strub, K.. 2007. Useful ‘junk’: Alu RNAs in the human transcriptome. Cellular and Molecular Life Sciences 64 (14): 1793–800.CrossRefGoogle ScholarPubMed
Hauber, M. E., Sherman, P. W., and Paprika, D.. 2000. Self-referent phenotype matching in a brood parasite: the armpit effect in brown-headed cowbirds (Molothrus ater). Animal Cognition 3 (2): 113–17.CrossRefGoogle Scholar
Helden, Jacques, Naim, Avi, Mancuso, Renato, Eldridge, Matthew, Wernisch, Lorenz, Gilbert, David, and Wodak, Shoshana J. 2000. Representing and analysing molecular and cellular function using the computer. Journal of Biological Chemistry 381: 921–35.Google ScholarPubMed
Herring, Susan W. 1993. Formation of the vertebrate face: epigenetic and functional influences. American Zoologist 33 (4): 472–83.CrossRefGoogle Scholar
Hesse, Mary B. 1966. Models and Analogies in Science. University of Notre Dame Press.Google Scholar
Hesse, Mary B 1988. The cognitive claims of metaphor. Journal of Speculative Philosophy 2 (1): 1–16.Google Scholar
Hirotsune, Shinji, Yoshida, Noriyuki, Chen, Amy, Garrett, Lisa, Sugiyama, Fumihiro, Takahashi, Satoru, Yagami, Ken-ichi, Wynshaw-Boris, Anthony, and Yoshiki, Atsushi. 2003. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423 (6935): 91–6.CrossRefGoogle ScholarPubMed
Holliday, Robin. 1987. The inheritance of epigenetic defects. Science 238 (4824): 163–70.CrossRefGoogle ScholarPubMed
Holliday, Robin 1994. Introduction: epigenetics, an overview. Developmental Genetics 15: 453–7.CrossRefGoogle Scholar
Holliday, Robin 2006. Epigenetics: a historical overview. Epigenetics 1 (2): 76–80.CrossRefGoogle ScholarPubMed
Hood, Kathryn E., Tucker Halpern, Carolyn, Greenberg, Gary, and Lerner, Richard M. (eds.). 2010. Handbook of Developmental Science, Behavior and Genetics. Oxford: Wiley-Blackwell.CrossRefGoogle Scholar
Hull, David. 1972. Reduction in genetics – biology or philosophy? Philosophy of Science 39 (4): 491–9.CrossRefGoogle Scholar
Hull, David 1974. Philosophy of Biological Science. Englewood Cliffs, NJ: Prentice-Hall.Google Scholar
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. Cohen, R. S. and Michalos, A.. Dordrecht: Reidel, 653–70.Google Scholar
Hundley, Heather A., and Bass, Brenda L.. 2010. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends in Biochemical Sciences 35 (7): 377–83.CrossRefGoogle ScholarPubMed
Hüttenhofer, A., Kiefmann, M., Meier-Ewert, S., O’Brien, J., Lehrach, H., Bachellerie, J. P., and Brosius, J.. 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO Journal 20 (11): 2943–53.CrossRefGoogle Scholar
Huxley, Julian. 1972 [1932]. Problems of Relative Growth. New York: Dover.Google Scholar
Istrail, Sorin, and Davidson, Eric H.. 2005. Logic functions of the genomic cis-regulatory code. Proceedings of the National Academy of Sciences 102 (14): 4954–9.CrossRefGoogle ScholarPubMed
Jablonka, Eva. 2001. The systems of inheritance. In Cycles of Contingency: Developmental Systems and Evolution, ed. Oyama, S., Griffiths, P. E. and Gray, R. D.. Cambridge, MA: MIT Press, 99–116.Google Scholar
Jablonka, Eva 2002. Information interpretation, inheritance, and sharing. Philosophy of Science 69 (4): 578–605.CrossRefGoogle Scholar
Jablonka, Eva, and Avital, Eytan. 2001. Animal Traditions : Behavioural Inheritance in Evolution. Cambridge University Press.Google Scholar
Jablonka, Eva, and Lamb, Marion J.. 1995. Epigenetic Inheritance and Evolution: The Lamarckian Dimension. Oxford University Press.Google Scholar
Jablonka, Eva, and Lamb, Marion J. 2005. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge, MA: MIT Press.Google Scholar
Jablonka, Eva, and Raz, Gal. 2009. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Quarterly Review of Biology 84 (2): 131–76.CrossRefGoogle Scholar
Jacob, François, and Monod, Jacques. 1961. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318–56.CrossRefGoogle ScholarPubMed
Jenuwein, Thomas, and Allis, C. David. 2001. Translating the histone code. Science 293: 1074–80.CrossRefGoogle ScholarPubMed
Johannsen, William. 1911. The genotype conception of heredity. American Naturalist 45 (531): 129–59.CrossRefGoogle Scholar
Johnson, J. M., Edwards, S., Shoemaker, D. D., and Schadt, E. E.. 2005. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends in Genetics 21: 93–102.CrossRefGoogle ScholarPubMed
Johnston, Timothy D. 1987. The persistence of dichotomies in the study of behavioural development. Developmental Review 7: 149–82.CrossRefGoogle Scholar
Juarrero, Alicia. 1998. Causality as constraints. In Evolving Systems, ed. Van de Vijver, G., Salthe, S., and Delpos, M.. Dordrecht: Kluwer.Google Scholar
Kampa, Dione, Cheng, Jill, Kapranov, Philipp, Yamanaka, Mark, Brubaker, Shane, Cawley, Simon, Drenkow, Jorg, Piccolboni, Antonio, Bekiranov, Stefan, Helt, Gregg, Tammana, Hari, and Gingeras, Thomas R.. 2004. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research 14: 331–42.CrossRefGoogle ScholarPubMed
Kaplan, Jonathan Michael. 2000. The Limits and Lies of Human Genetic Research. Oxford: Routledge.Google Scholar
Kapranov, Phillip, Drenkow, Jorg, Cheng, Jill, Long, Jeffrey, Helt, Gregg, Dike, Sujit, and Gingeras, Thomas R. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research 15: 987–97.CrossRefGoogle ScholarPubMed
Kauffman, Stuart A. 1993. The Origins of Order: Self-Organisation and Selection in Evolution. New York: Oxford University Press.Google Scholar
Kay, Lily E. 2000. Who Wrote the Book of Life: A History of the Genetic Code. Palo Alto, CA: Stanford University Press.Google Scholar
Kendler, Kenneth S. 2005. ‘A gene for …’: the nature of gene action in psychiatric disorders. American Journal of Psychiatry 162 (7): 1243–52.CrossRefGoogle Scholar
Kim, Jaegwon. 1993. Supervenience and Mind: Selected Philosophical Essays. Cambridge University Press.CrossRefGoogle Scholar
Kirschner, Marc W. and Gerhart, John C.. 1998. Evolvability. Proceedings of the National Academy of Sciences of the United States of America 95, 8420–7.CrossRefGoogle ScholarPubMed
Kirschner, Marc W. and Gerhart, John C. 2005. The Plausibility of Life: Resolving Darwin's Dilemma. London: Yale University Press.Google Scholar
Kirschner, Marc W. and Gerhart, John C. 2010. Facilitated variation. In Evolution: The Extended Synthesis, ed. Mueller, G. B. and Pigliucci, M.. Cambridge, MA: MIT Press.Google Scholar
Kirschner, Marc W., Gerhart, John C., and Mitchison, Tim. 2000. Molecular ‘vitalism’. Cell 100: 79–88.CrossRefGoogle Scholar
Kitcher, Philip. 1982. Genes. British Journal of Philosophy of Science 33: 337–59.CrossRefGoogle Scholar
Kitcher, Philip 1984. 1953 and all that: a tale of two sciences. Philosophical Review 93: 335–73.CrossRefGoogle Scholar
Kitcher, Philip 2001. Battling the undead: how (and how not) to resist genetic determinism. In Thinking about Evolution: Historical, Philosophical and Political Perspectives (Festschrift for Richard Lewontin), ed. Singh, R., Krimbas, K., Paul, D. and Beatty, J.. Cambridge University Press, 369–414.Google Scholar
Kohler, Robert E. 1994. Lords of the Fly. Drosophila Genetics and the Experimental Life. University of Chicago Press.Google Scholar
Kroh, Evan M., Parkin, Rachael K., Mitchell, Patrick S., and Tewari, Muneesh. 2010. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50 (4): 298–301.CrossRefGoogle Scholar
Kuhn, Thomas. 1962. The Structure of Scientific Revolutions. University of Chicago Press.Google Scholar
Lacey, Elizabeth R. 1998. What is an adaptive environmentally induced parental effect? In Maternal Effects as Adaptations, ed. Mousseau, R. A. and Fox, C. W.. New York: Oxford University Press, 54–66.Google Scholar
Ladd, Andrea N., and Cooper, Thomas A.. 2002. Finding signals that regulate alternative splicing in the post-genomic era. Genome Biology 3 (11): 1–6.CrossRefGoogle ScholarPubMed
Laland, Kevin N., Odling-Smee, F. John, and Gilbert, Scott F.. 2008. EvoDevo and niche construction: building bridges. Journal of Experimental Zoology, Part B: Molecular and Developmental Evolution 310: 549–66.CrossRefGoogle ScholarPubMed
Laland, Kevin N., Sterelny, Kim, Odling-Smee, John, Hoppitt, W., and Uller, Tobias. 2011. Cause and effect in biology revisited: is Mayr's proximate-ultimate dichotomy still useful? Science 334 (6062): 1512–16.CrossRefGoogle ScholarPubMed
Lamm, Ehud, and Jablonka, Eva. 2008. The nurture of nature: hereditary plasticity in evolution. Philosophical Psychology 21 (3): 305–19.CrossRefGoogle Scholar
Lande, R., and Price, T.. 1989. Genetic correlations and maternal effect coefficients obtained from offspring-parent regression. Genetics 122 (4): 915–22.Google ScholarPubMed
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860–921.CrossRefGoogle ScholarPubMed
Lander, Eric S., and Weinberg, Robert A. 2000. Journey to the centre of biology. Science 287 (5459): 1777–82.CrossRefGoogle Scholar
Lederberg, Joshua. 1956a. Comments on gene–enzyme relationship. In Enzymes: Units of Biological Structure and Function, ed. Gaebler, E. H.. New York: Academic Press, 161–9.Google Scholar
Lederberg, Joshua 1956b. Genetic transduction. American Scientist 44 (3): 264–80.Google Scholar
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: New Perspectives, ed. Sarkar, S.. Dordrecht: Kluwer, 15–26.CrossRefGoogle Scholar
Lehrman, Daniel S. 1970. Semantic and conceptual issues in the nature–nurture problem. In Development and Evolution of Behaviour, ed. Lehrman, D. S.. San Francisco: W. H. Freeman, 17–52.Google Scholar
Leipzig, Jeremy, Pevzner, Pavel, and Heber, Steffen. 2004. The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research 32 (13): 3977–83.CrossRefGoogle ScholarPubMed
Lettice, Laura A., Horikoshi, Taizo, Heaney, Simon J. H., van Baren, Marijke J., van der Linde, Herma C., Breedveld, Guido J., Joosse, Marijke, Akarsu, Nurten, Oostra, Ben A., Endo, Naoto, Shibata, Minoru, Suzuki, Mikio, Takahashi, Eiichi, Shinka, Toshikatsu, Nakahori, Yutaka, Ayusawa, Dai, Nakabayashi, Kazuhiko, Scherer, Stephen W., Heutink, Peter, Hill, Robert E., and Noji, Sumihare. 2002. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proceedings of the National Academy of Sciences 99 (11): 7548–53.CrossRefGoogle ScholarPubMed
Levit, Georgy S., Hossfeld, Uwe, and Olsson, Lennart. 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 Evolution 306: 89–106.CrossRefGoogle Scholar
Levy, Arnon. 2011. Information in biology: a fictionalist account. Nous 45 (4): 640–57.CrossRefGoogle Scholar
Lewis, David K. 1966. An argument for the identity theory. Journal of Philosophy 63 (1): 17–25.CrossRefGoogle Scholar
Lewontin, Richard C. 1982. Organism and environment. In Learning, Development, Culture, ed. Plotkin, H.. New York: John Wiley, 151–70.Google Scholar
Lewontin, Richard C 1983a. Gene, organism and environment. In Evolution: From Molecules to Man, ed. Bendall, D. S.. Cambridge University Press, 273–85.Google Scholar
Lewontin, Richard C 1983b. The organism as the subject and object of evolution. Scientia 118: 65–82.Google Scholar
Lewontin, Richard C 1996. Evolution as engineering. In Integrative Approaches to Molecular Biology, ed. Collado-Vides, J., Magasanik, B. and Smith, T. F.. Cambridge, MA: MIT Press, 1–10.Google Scholar
Lipovich, L., Johnson, R., and Lin, C. Y.. 2010. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochimica et Biophysica Acta 1799 (9): 597–615.CrossRefGoogle Scholar
Liu, Yilei, and Elliott, David J.. 2010. Coupling genetics and post-genomic approaches to decipher the cellular splicing code at a systems-wide level. Biochemistry Society Transactions 38: 237–41.CrossRefGoogle Scholar
Lloyd, Elizabeth A. 1988. The Structure and Confirmation of Evolutionary Theory. Westport, CT: Greenwood Press.Google Scholar
Lorenz, Konrad Z. 1965. Evolution and the Modification of Behaviour. University of Chicago Press.Google Scholar
Love, Alan C. 2001. Evolutionary morphology, innovation, and the synthesis of evolution and development. Biology and Philosophy 18 (2): 309–45.CrossRefGoogle Scholar
Love, Alan C 2008. Explaining evolutionary innovation and novelty: criteria of adequacy and multidisciplinary prerequisites. Philosophy of Science 75: 874–86.CrossRefGoogle Scholar
McEachern, Lori A., and Loyd, Vett. 2011. The epigenetics of genomic imprinting. In Epigenetics: Linking Genotype and Phenotype in Develoment and Evolution, ed. Hallgrimsson, B. and Hall, B. K.. Berkeley: University of California Press, 43–69.Google Scholar
Maestripieri, Dario. 2009. Maternal influences in offspring growth, reproduction, and behavior in primates. In Maternal Effects in Mammals, ed. Maestripieri, D. and Mateo, J. M.. University of Chicago Press, 256–91.CrossRefGoogle Scholar
Maestripieri, Dario, and Mateo, Jill M. (eds.). 2009. Maternal Effects in Mammals. University of Chicago Press.CrossRefGoogle Scholar
Maher, Brendan. 2012. The human encyclopedia: making a genome manual. Nature 489 (7414): 46–8.CrossRefGoogle Scholar
Maienschein, Jane. 2005. Epigenesis and preformationism. In The Stanford Encyclopedia of Philosophy, ed. E. N. Zalta. At .
Malek, Olaf, and Knoop, Volker. 1998. Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort. RNA 4 (12): 1599–609.CrossRefGoogle Scholar
Manolio, Teri A., Collins, Francis S., Cox, Nancy J., Goldstein, David B., Hindorff, Lucia A., Hunter, David J., McCarthy, Mark I., Ramos, Erin M., Cardon, Lon R., Chakravarti, Aravinda, Cho, Judy H., Guttmacher, Alan E., Kong, Augustine, Kruglyak, Leonid, Mardis, Elaine, Rotimi, Charles N., Slatkin, Montgomery, Valle, David, Whittemore, Alice S., Boehnke, Michael, Clark, Andrew G., Eichler, Evan E., Gibson, Greg, Haines, Jonathan L., Mackay, Trudy F. C., McCarroll, Steven A., and Visscher, Peter M.. 2009. Finding the missing heritability of complex diseases. Nature 461 (7265): 747–53.CrossRefGoogle ScholarPubMed
Matthen, Mohan, and Ariew, André. 2002. Two ways of thinking about fitness and natural selection. Journal of Philosophy 992: 55–83.CrossRefGoogle Scholar
Mattick, John S. 2001. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Reports 2 (11): 986–91.CrossRefGoogle ScholarPubMed
Mattick, John S 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25 (10): 930–9.CrossRefGoogle ScholarPubMed
Mattick, John S 2004. RNA regulation: a new genetics? Nature Reviews Genetics 5 (4): 316–23.CrossRefGoogle ScholarPubMed
Maynard Smith, John. 2000. The concept of information in biology. Philosophy of Science 67 (2): 177–94.CrossRefGoogle Scholar
Maynard Smith, J., Burian, R., Kauffman, S., Alberch, P., Campbell, J., Goodwin, B., Lande, R., Raup, D., and Wolpert, L.. 1985. Developmental constraints and evolution. Quarterly Review of Biology 60 (3): 265–87.CrossRefGoogle Scholar
Smith, Maynard, John, , and Szathmáry, Eörs. 1995. The Major Transitions in Evolution. New York: W. H. Freeman.Google Scholar
Mayr, Ernst. 1961. Cause and effect in biology. Science 134 (3489): 1501–6.CrossRefGoogle ScholarPubMed
Mayr, Ernst 1964. The evolution of living systems. Proceedings of the National Academy of Sciences of the United States of America 51 (5): 934–41.CrossRefGoogle ScholarPubMed
Mayr, Ernst 1976 [1959]. Typological versus populational thinking. In Evolution and the Diversity of Life, ed. Mayr, E.. Cambridge, MA: Harvard University Press, 26–9.Google Scholar
Mayr, Ernst, and Provine, William B.. 1980. The Evolutionary Synthesis: Perspectives on the Unification of Biology. Cambridge, MA: Harvard University Press, 43–69.CrossRefGoogle Scholar
Meaney, Michael J. 2001a. Nature, nurture, and the disunity of knowledge. Annals of the New York Academy of Sciences 935 (1): 50–61.CrossRefGoogle Scholar
Meaney, Michael J 2001b. Maternal care, gene expression, and the transmission of individual differences in stress reactivity across generations. Annual Review of Neuroscience 24: 1161–92.CrossRefGoogle Scholar
Meaney, Michael J 2004. The nature of nurture: maternal effect and chromatin modelling. In Essays in Social Neuroscience, ed. Cacioppo, J. T. and Berntson, G. G.. Cambridge, MA: MIT Press.Google Scholar
Meaney, Michael J., and Szyf, Moshe. 2005. Environmental programming of stress responses through DNA methylation: life at the interface between a dynamic environment and a fixed genome. Dialogues in Clinical Neuroscience 7 (2): 103–23.Google Scholar
Mendel, Gregor. 1866. Versuche über Pflanzenhybriden [Experiments in plant hybridization]. Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr 1865, Abhandlungen: 3–47.Google Scholar
Michel, George F., and Moore, Celia L.. 1995. Developmental Psychobiology: An Interdisciplinary Science. Cambridge, MA: MIT Press.Google Scholar
Millikan, Ruth Garrett. 1984. Language, Thought and Other Biological Categories. Cambridge, MA: MIT Press.Google Scholar
Mitchell, Sandra D. 2009. Unsimple Truths: Science, Complexity, and Policy. University of Chicago Press.CrossRefGoogle Scholar
Moore, Celia L. 1984. Maternal contributions to the development of masculine sexual behavior in laboratory rats. Developmental Psychobiology 17: 346–56.CrossRefGoogle ScholarPubMed
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 Sciences 662: 160–77.CrossRefGoogle ScholarPubMed
Moore, David S. 2001. The Dependent Gene: The Fallacy of ‘Nature vs. Nurture’. New York: Henry Holt/Times Books.Google Scholar
Morange, Michel. 2000 [1998]. A History of Molecular Biology, trans. Matthew Cobb. Cambridge, MA: Harvard University Press.Google Scholar
Morange, Michel 2002. The relations between genetics and epigenetics: a historical point of view. Annals of the New York Academy of Sciences 981: 50–60.CrossRefGoogle ScholarPubMed
Morange, Michel 2008. Life Explained. New Haven, CT: Yale University Press.Google Scholar
Morgan, Thomas Hunt. 1926. The Theory of the Gene. New Haven, CT: Yale University Press.Google Scholar
Morgan, Thomas Hunt 1934. The relation of genetics to physiology and medicine. Nobel lecture, 4 June. At .
Morgan, Thomas Hunt, Sturtevant, Alfred H., Mullen, H. J. and Bridges, Calvin B.. 1915. The Mechanism of Mendelian Heredity. New York: Holt.CrossRefGoogle Scholar
Morowitz, Harold J. 2003. The Emergence of Everything: How the World Became Complex. Oxford University Press.Google Scholar
Morris, Kevin V. 2008. RNA mediated transcriptional gene silencing. In RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity, ed. Morris, K. V.. Norfolk, UK: Caister Academic Press, 19–28.Google Scholar
Morris, Kevin V (ed.). 2012. Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection. Norfolk, UK: Caister Academic Press.Google Scholar
Moss, Lenny. 2003. What Genes Can't Do. Cambridge, MA: MIT Press.Google Scholar
Mousseau, Timothy A., and Fox, Charles W. (eds.). 1998. Maternal Effects as Adaptations. Oxford University Press.Google Scholar
Mueller, Michael, Martens, Lennart, and Apweiler, Rolf. 2007. Annotating the human proteome: beyond establishing a parts list. Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 1774 (2): 175–91.CrossRefGoogle Scholar
Müller, Gerd B. 1990. Developmental mechanisms as the origin of morphological novelty: a side-effect hypothesis. In Evolutionary Innovations, ed. Nitecki, M. H.. University of Chicago Press, 99–130.Google Scholar
Müller, Gerd B 2003. Homology: the evolution of morphological organization. In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, ed. Müller, G. B. and Newman, S. A.. Cambridge, MA: MIT Press, 51–69.Google Scholar
Müller, Gerd B 2010. Epigenetic innovation. In Evolution – The Extended Synthesis, ed. Pigliucci, M. and Müller, G. B.. Cambridge, MA: MIT Press, 307–32.CrossRefGoogle Scholar
Müller, Gerd B., and Newman, Stuart A.. 2003. Origination of organismal form: the forgotten cause in evolutionary theory. In Origination of Organismal Form, ed. Müller, G. B. and Newman, S. A.. Cambridge, MA: MIT Press, 3–10.Google Scholar
Müller, Gerd B., and Wagner, Günter P.. 1991. Novelty in evolution: restructuring the concept. Annual Review of Ecology and Systematics 22: 229–56.CrossRefGoogle Scholar
Muller, Hermann J. 1947. Pilgrim Trust Lecture: the gene. Proceedings of the Royal Society of London Series B: Biological Sciences 134 (874): 1–37.CrossRefGoogle Scholar
Müller-Wille, Staffan, and Rheinberger, Hans-Jörg. 2012. A Cultural History of Heredity. University of Chicago Press.CrossRefGoogle Scholar
Nagel, Ernest. 1961. The Structure of Science: Problems in the Logic of Scientific Explanation. London: Routledge & Kegan Paul.Google Scholar
Nanney, D. L. 1958. Epigenetic control systems. Proceedings of the National Academy of Sciences of the United States of America 44: 712.CrossRefGoogle ScholarPubMed
Nathanielsz, Peter W., and Thornburg, Kent L.. 2003. Fetal programming: from gene to functional systems – an overview. Journal of Physiology 547: 3–4.CrossRefGoogle Scholar
Nature Genetics. 2010. On beyond GWAS. (Editorial). Nature Genetics 42 (7): 551.CrossRefGoogle Scholar
Newman, Stuart A. 2003. From physics to development: the evolution of morphogenetic mechanisms. In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, ed. Müller, G. B. and Newman, S. A.. Cambridge, MA: MIT Press, 221–39.Google Scholar
Newman, Stuart A 2010. Dynamic patterning modules. In Evolution – The Extended Synthesis, ed. Pigliucci, M. and Müller, G. B.. Cambridge, MA: MIT Press, 281–306.CrossRefGoogle Scholar
Newman, Stuart A., and Müller, Gerd B.. 2000. The epigenetic basis of character origination. Journal of Experimental Zoology (Molecular and Developmental Evolution) 288: 304–17.3.0.CO;2-G>CrossRefGoogle Scholar
Nijhout, H. F. 1990. Metaphors and the role of genes in development. BioEssays 12 (9): 441–6.CrossRefGoogle ScholarPubMed
Noble, Denis. 2002. Modeling the heart: from genes to cells to the whole organ. Science 295: 1678–82.CrossRefGoogle ScholarPubMed
Noble, Denis 2006. The Music of Life: Biology beyond Genes. Oxford University Press.Google Scholar
O’Malley, Maureen A., and Dupre, John. 2005. Fundamental issues in systems biology. BioEssays 27 (12): 1270–6.CrossRefGoogle ScholarPubMed
O’Malley, Maureen A., and Stotz, Karola. 2011. Intervention, integration and translation in obesity research: genetic, developmental and metaorganismal approaches. Philosophy, Ethics, and Humanities in Medicine 6 (2): .Google ScholarPubMed
Odling-Smee, F. John. 1988. Niche-constructing phenotypes. In The Role of Behavior in Evolution, ed. Plotkin, H. C.. Cambridge, MA: MIT Press, 73–132.Google Scholar
Odling-Smee, F. John, KevinLaland, N., and Feldman, Marcus W.. 2003. Niche Construction: The Neglected Process in Evolution. Princeton University Press.Google Scholar
Olby, Robert C. 1974. The Path to the Double Helix. Seattle: University of Washington Press.Google Scholar
Olby, Robert C 1985. The Origins of Mendelism, 2nd edn. University of Chicago Press.Google Scholar
Olby, Robert C 2009. Francis Crick: Hunter of Life's Secret. Cold Spring Harbor Laboratory Press.Google Scholar
Oliver, Brian, and Leblanc, Benoit. 2003. How many genes in a genome? Genome Biology 5 (1): 204.1–3.CrossRefGoogle ScholarPubMed
Oliver, Stephen G. 2006. From genomes to systems: the path with yeast. Philosophical Transactions of the Royal Society, Biological Sciences 361: 477–82.CrossRefGoogle ScholarPubMed
Orgel, Leslie E., and Crick, Francis H.. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604–7.CrossRefGoogle ScholarPubMed
Oyama, Susan. 1985. The Ontogeny of Information: Developmental Systems and Evolution. Cambridge University Press.Google Scholar
Oyama, Susan 2000a. Causal democracy and causal contributions in developmental systems theory. Philosophy of Science 67 (s1): S332.CrossRefGoogle Scholar
Oyama, Susan 2000b. Evolution's Eye: A Systems View of the Biology–Culture Divide. Durham, NC: Duke University Press.CrossRefGoogle Scholar
Oyama, Susan, Griffiths, Paul E., and Gray, Russell D. (eds.). 2001. Cycles of Contingency: Developmental Systems and Evolution. Cambridge, MA: MIT Press.Google Scholar
Pang, Ken C., Stephen, Stuart, Engström, Pär G., Tajul-Arifin, Khairina, Chen, Weisan, Wahlestedt, Claes, Lenhard, Boris, Hayashizaki, Yoshihide, and Mattick, John S.. 2005. RNAdb – a comprehensive mammalian noncoding RNA database. Nucleic Acids Research 33 (Database issue): D125–30.CrossRefGoogle ScholarPubMed
Papineau, David. 1987. Reality and Representation. Oxford: Blackwell.Google Scholar
Park, E., Williams, B., Wold, B. J., and Mortazavi, A.. 2012. RNA editing in the human ENCODE RNA-seq data. Genome Research 22 (9): 1626–33.CrossRefGoogle ScholarPubMed
Paz-Yaacov, N., Levanon, E. Y., Nevo, E., Kinar, Y., Harmelin, A., Jacob-Hirsch, J., Amariglio, N., Eisenberg, E., and Rechavi, G.. 2010. Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the National Academy of Sciences of the United States of America 107 (27): 12174–9.CrossRefGoogle ScholarPubMed
Pearson, Karl. 1900 [1892]. The Grammar of Science, 2nd edn. London: Black.Google Scholar
Pearson, Karl, Yule, G. U., Blanchard, Norman, and Lee, Alice. 1903. The law of ancestral heredity. Biometrika 2 (2): 211–36.CrossRefGoogle Scholar
Pennisi, Elizabeth. 2008. Deciphering the genetics of evolution: powerful personalities lock horns over how the genome changes to set the stage for evolution. Science 321: 670–3.Google Scholar
Pennisi, Elizabeth 2010. Shining a light on genome's ‘dark matter’. Science 330: 1614.CrossRefGoogle ScholarPubMed
Pigliucci, Massimo. 2001. Phenotypic Plasticity: Beyond Nature and Nurture, Syntheses in Ecology and Evolution. Baltimore, MD: Johns Hopkins University Press.Google Scholar
Pigliucci, Massimo 2007. Do we need an extended evolutionary synthesis? Evolution 61 (12): 2743–9.CrossRefGoogle ScholarPubMed
Pigliucci, Massimo 2009. An extended synthesis for evolutionay biology. Annals of the New York Academy of Sciences 1168: 218–28.CrossRefGoogle Scholar
Pigliucci, Massimo, and Kaplan, Jonathan. 2006. Making Sense of Evolution: The Conceptual Foundations of Evolutionary Biology. University of Chicago Press.CrossRefGoogle Scholar
Pigliucci, Massimo, and Müller, Gert B.. 2010a. Evolution – The Extended Synthesis. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Pigliucci, Massimo, and Kaplan, Jonathan 2010b. Elements of an extended evolutionary synthesis. In Evolution: The Extended Synthesis, ed. Pigliucci, M. and Müller, G. B.. Cambridge, MA: MIT Press, 3–17.CrossRefGoogle Scholar
Plomin, Robert, and Daniels, Denise. 1987. Why are children from the same family so different from one another? Behavioral and Brain Sciences 10: 1–60.CrossRefGoogle Scholar
Plomin, R., DeFries, J. C., and Loehlin, J.. 1977. Genotype-environment interaction and correlation in the analysis of human behavior. Psychological Bulletin 84: 309–22.CrossRefGoogle ScholarPubMed
Ponicsan, Steven L., Kugel, Jennifer F., and Goodrich, James A.. 2010. Genomic gems: SINE RNAs regulate mRNA production. Current Opinion in Genetics and Development 20 (2): 149–55.CrossRefGoogle ScholarPubMed
Portin, Petter. 1993. The concept of the gene: short history and present status. The Quarterly Review of Biology 68 (2): 173–223.CrossRefGoogle ScholarPubMed
Ptashne, Mark. 2007. On the use of the word ‘epigenetic’. Current Biology 17: R233–6.CrossRefGoogle Scholar
Ptashne, Mark, and Gann, Alexander. 2002. Genes and Signals. Cold Spring Harbor Laboratory Press.Google Scholar
Putnam, Hilary. 1975. The meaning of ‘meaning’. In Philosophical Papers. Vol. 2: Mind, Language and Reality. Cambridge University Press.CrossRefGoogle Scholar
Rassoulzadegan, Minoo, Grandjean, Valérie, Gounon, Pierre, Vincent, Stéphane, Gillot, Isabelle, and Cuzin, François. 2006. RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441: 469–74.CrossRefGoogle ScholarPubMed
Rechavi, Oded, Minevich, Gregory, and Hober, Oliver. 2011. Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans. Cell 147 (6): 1248–56.CrossRefGoogle ScholarPubMed
Reik, Wolf, and Walter, Jörn. 2001a. Evolution of imprinting mechanisms: the battle of the sexes begins in the zygote. Nature Genetics 27: 255–6.CrossRefGoogle ScholarPubMed
Reik, Wolf, and Walter, Jörn 2001b. Genomic imprinting: parental influence on the genome. Nature Reviews Genetics 2: 21–32.CrossRefGoogle ScholarPubMed
Rivier, Christian, Goldschmidt-Clermont, Michel, and Rochaix, Jean-David. 2001. Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO Journal 20 (7): 1765–73.CrossRefGoogle ScholarPubMed
Robert, Jason S. 2000. Schizophrenia epigenesis? Theoretical Medicine and Bioethics 21 (2): 191–215.CrossRefGoogle ScholarPubMed
Robert, Jason S 2001. Interpreting the homeobox: metaphors of gene action and activation in development and evolution. Evolution and Development 3 (4): 287–95.CrossRefGoogle ScholarPubMed
Robert, Jason S 2004. Embryology, Epigenesis and Evolution: Taking Development Seriously. Cambridge University Press.CrossRefGoogle Scholar
Robert, Jason S., Hall, Brian K., and Olson, Wendy M.. 2001. Bridging the gap between developmental systems theory and evolutionary developmental biology. Bioessays 23 (10): 954–62.CrossRefGoogle ScholarPubMed
Robinson, Victoria L. 2009. Rethinking the Central Dogma: noncoding RNAs are biologically relevant. Urologic Oncology 27 (3): 304–6.CrossRefGoogle ScholarPubMed
Rosenberg, Alex. 1978. The supervenience of biological concepts. Philosophy of Science 45: 368–86.CrossRefGoogle Scholar
Rosenberg, Alex 1985. The Structure of Biological Science. Cambridge University Press.CrossRefGoogle Scholar
Rosenberg, Alex 2006. Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology. University of Chicago Press.CrossRefGoogle Scholar
Rowen, Lee, Young, Janet, Birditt, Brian, Kaur, Amardeep, Madan, Anup, Philipps, Dana L., Qin, Shizhen, Minx, Patrick, Wilson, Richard K., Hood, Leroy, and Graveley, Brenton R.. 2002. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 79 (4): 587–98.CrossRefGoogle ScholarPubMed
Ruddle, Frank H., Amemiya, Chris T., Carr, Janet L., Kim, Chang-Bae, Ledje, Christina, Shashikant, Cooduvalli S, and Wagner, Guenter P.. 1999. Evolution of chordate Hox gene clusters. In Molecular Strategies in Biological Evolution, ed. Caporale, L. H.. New YorkAcademy of Sciences, 238–50.Google Scholar
Ruse, Michael E. 1971. Reduction, replacement, and molecular biology. Dialectica 25 (1): 39–72.CrossRefGoogle Scholar
Sapp, Jan. 1987. Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. Oxford University Press.Google Scholar
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. Sarkar, S.. Dordrecht: Kluwer, 187–231.CrossRefGoogle Scholar
Sarkar, Sahotra 1998. Genetics and Reductionism. Cambridge University Press.CrossRefGoogle Scholar
Sarkar, Sahotra 1999. From the Reaktionsnorm to the adaptive norm: the norm of reaction 1909–1960. Biology and Philosophy 14: 235–52.CrossRefGoogle Scholar
Sarkar, Sahotra 2005. Molecular Models of Life: Philosophical Papers on Molecular Biology. Cambridge, MA: MIT Press.Google Scholar
Schaffner, Kenneth F. 1967. Antireductionism and molecular biology. In Man and Nature: Philosophical Issues in Biology, ed. Munson, R.. New York: Dell, 44–54.Google Scholar
Schaffner, Kenneth F 1969. The Watson-Crick model and reductionism. British Journal for the Philosophy of Science 20: 325–48.CrossRefGoogle Scholar
Schaffner, Kenneth F 1993. Discovery and Explanation in Biology and Medicine. University of Chicago Press.Google Scholar
Schaffner, Kenneth F 1996. Theory structure and knowledge representation in molecular biology. In The Philosophy and History of Molecular Biology: New Perspectives, ed. Sarkar, S.. Dordrecht: Kluwer, 27–46.CrossRefGoogle Scholar
Schaffner, Kenneth F 1998. Genes, behavior and developmental emergentism: one process, indivisible?Philosophy of Science 65 (2): 209–52.CrossRefGoogle Scholar
Schaffner, Kenneth F 2006a. Behaving: its nature and nurture, part 1. In Wrestling with Behavioral Genetics: Implications for Understanding Selves and Society, ed. Parens, E., Chapman, A. and Press, N.. Baltimore, MD: Johns Hopkins University Press, 3–39.Google Scholar
Schaffner, Kenneth F 2006b. Behaving: its nature and nurture, part 2. In Wrestling with Behavioral Genetics: Implications for Understanding Selves and Society, ed. Parens, E., Chapman, A. and Press, N.. Baltimore, MD: Johns Hopkins University Press, 40–73.Google Scholar
Schaffner, Kenneth F Forthcoming. Behaving: What's Genetic, What's Not, and Why Should We Care?New York: Oxford University Press.
Schlichting, Carl D., and Pigliucci, Massimo. 1998. Phenotypic Evolution: A Reaction Norm Perspective. Sunderland, MA: Sinauer.Google Scholar
Schlitt, Thomas, and Brazma, Alvis. 2006. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philosophical Transactions of the Royal Society B:Biological Sciences 361: 483–94.CrossRefGoogle ScholarPubMed
Schmalhausen, I. I. 1949. Factors of Evolution: The Theory of Stabilising Selection, trans. I. Dordick. Philadelphia and Toronto: Blakeston.Google Scholar
Schrödinger, Erwin. 1944. What if Life?Cambridge University Press.Google Scholar
Sesardic, Neven. 2005. Making Sense of Heritability. Cambridge University Press.CrossRefGoogle Scholar
Shabalina, Svetlana A., Ogurtsov, Aleksey Yu, Kondrashov, Vasily A., and Kondrashov, Aleksey S.. 2001. Selective constraint in intergenic regions of human and mouse genomes. Trends in Genetics 17: 373–6.CrossRefGoogle ScholarPubMed
Shannon, Claude E., and Weaver, Warren. 1949. The Mathematical Theory of Communication. University of Illinois Press.Google Scholar
Shea, Nicholas. 2007a. Consumers need information: supplementing teleosemantics with an input condition. Philosophy and Phenomenological Research 75 (2): 404–35.CrossRefGoogle Scholar
Shea, Nicholas 2007b. Representation in the genome and in other inheritance systems. Biology and Philosophy 22: 313–31.CrossRefGoogle Scholar
Shea, Nicholas 2011a. Developmental systems theory formulated as a claim about inherited information. Philosophy of Science 78: 60–82.CrossRefGoogle Scholar
Shea, Nicholas 2011b. What's transmitted? Inherited information. Biology and Philosophy 26 (2): 183–9.CrossRefGoogle Scholar
Shea, Nicholas in press. Inherited representations are read in development. British Journal for the Philosophy of Science. First published online 29 February 2012. At .
Shin, Chanseok, and Manley, James L.. 2004. Cell signalling and the control of pre-mRNA splicing. Nature Reviews Molecular Cell Biology 5: 727–38.CrossRefGoogle ScholarPubMed
Simpson, George G. 1953. The Baldwin effect. Evolution 7: 110–17.CrossRefGoogle Scholar
Sloan, Phillip R., and Fogel, Brandon (eds.). 2012. Creating a Physical Biology: The Three-Man Paper and Early Molecular Biology. University of Chicago Press.Google Scholar
Smith, Christopher W. J., and Valcárcel, Juan. 2000. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends in Biochemical Sciences 25: 381–8.CrossRefGoogle ScholarPubMed
Snyder, Michael, and Gerstein, Mark. 2003. Defining genes in the genomics era. Science 300 (5617): 258–60.CrossRefGoogle ScholarPubMed
Sober, Elliott. 1984. The Nature of Selection: Evolutionary Theory in Philosophical Focus. Cambridge, MA: MIT Press.Google Scholar
Sober, Elliott 1999. The multiple realizability argument against reductionism. Philosophy of Science 66 (4): 542–64.CrossRefGoogle Scholar
Stamm, Stefan 2002. Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Human Molecular Genetics 11 (20): 2409–16.CrossRefGoogle ScholarPubMed
Stanford, P. Kyle, and Kitcher, Philip. 2000. Refining the causal theory of reference for natural kind terms. Philosophical Studies 97: 99–129.CrossRefGoogle Scholar
Star, Susan Leigh, and Griesemer, James R.. 1998. Institutional ecology, ‘translation,’ and boundary objects: amateurs and professionals in Berkeley's Museum of Vertebrate Zoology, 1907–39 (abridged). In The Science Studies Reader, ed. Biagioli, M.. New York: Routledge, 505–24.Google Scholar
Stein, Lincoln D. 2001. Genome annotation: from sequence to biology. Nature Reviews Genetics 2: 493–503.CrossRefGoogle ScholarPubMed
Sterelny, Kim, Dickison, Michael, and Smith, Kelly. 1996. The extended replicator. Biology and Philosophy 11 (3): 377–403.CrossRefGoogle Scholar
Sterelny, Kim, and Griffiths, Paul E.. 1999. Sex and Death: An Introduction to the Philosophy of Biology. University of Chicago Press.Google Scholar
Stern, David, and Orgogozo, Virginie. 2008. The loci of evolution: how predictable is genetic evolution? Evolution 62 (9): 2155–77.CrossRefGoogle ScholarPubMed
Stotz, Karola. 2006a. With genes like that, who needs an environment? Postgenomics’ argument for the ontogeny of information. Philosophy of Science 73 (5): 905–17.CrossRefGoogle Scholar
Stotz, Karola 2006b. Molecular epigenesis: distributed specificity as a break in the Central Dogma. History and Philosophy of the Life Sciences 28 (4): 527–44.Google ScholarPubMed
Stotz, Karola 2008. The ingredients for a postgenomic synthesis of nature and nurture. Philosophical Psychology 21 (3): 359–81.CrossRefGoogle Scholar
Stotz, Karola 2010. Human nature and cognitive-developmental niche construction. Phenomenology and the Cognitive Sciences 9 (4): 483–501.CrossRefGoogle Scholar
Stotz, Karola, and Allen, Colin (eds.). 2008. Philosophical Psychology 21 (3: special issue, Reconciling Nature and Nurture in the Study of Behavior).Google Scholar
Stotz, Karola, Bostanci, Adam, and Griffiths, Paul E.. 2006. Tracking the shift to ‘post-genomics’. Community Genetics 9 (3): 190–6.Google Scholar
Sturm, Nancy R., and Campbell, David A.. 1999. The role of intron structures in trans-splicing and Cap 4 formation for the Leishmania spliced leader RNA. Journal of Biological Chemistry 274 (27): 19361–7.CrossRefGoogle ScholarPubMed
Sultan, Sonia E. 2007. Development in context: the timely emergence of eco-devo. Trends in Ecology and Evolution 22 (11): 575–82.CrossRefGoogle ScholarPubMed
Suomi, Stephen J. 2004. How gene–environment interactions can influence emotional development in rhesus monkeys. In Nature and Nurture: The Complex Interplay of Genetic and Environmental Influences on Human Behavior and Development, ed. Garcia-Coll, C., Bearer, E. L., and Lerner, R. M.. Mahwah, NJ: Lawrence Erlbaum Associates, 35–51.Google Scholar
Suppes, Patrick. 1960. A comparison of the meaning and uses of models in mathematics and the empirical sciences. Synthese 12: 287–301.CrossRefGoogle Scholar
Suzuki, Y., and Nijhout, H. F.. 2006. Evolution of a polyphenism by genetic accommodation. Science 311 (5761): 650–2.CrossRefGoogle ScholarPubMed
Tabery, James G. 2007. Biometric and developmental gene–environment interactions: looking back, moving forward. Development and Psychopathology 19: 971–6.CrossRefGoogle ScholarPubMed
Tabery, James G 2008. R. A. Fisher, Lancelot Hogben, and the origin(s) of genotype–environment interaction. Journal of the History of Biology 41 (4): 717–61.CrossRefGoogle Scholar
Tabery, James G 2009. Difference mechanisms: explaining variation with mechanisms. Biology and Philosophy 21 (5): 645–64.CrossRefGoogle Scholar
Tabery, James G., and Griffiths, Paul E.. 2010. Historical and philosophical perspectives on behavioral genetics and developmental science. In Handbook of Developmental Science, Behavior and Genetics, ed. Hood, K. E., Halpern, C. T., Greenberg, G. and Lerner, R. M.. Oxford: Wiley-Blackwell, 41–60.Google Scholar
Tasic, Bosiljka, Nabholz, Christoph E, Baldwin, Kristin K., Kim, Youngwook, Rueckert, Erroll H., Ribick, Scott A., Cramer, Paula, Wu, Qiang, Axel, Richard, and Maniatis, Tom. 2002. Promoter choice determines splice site selection in protocadherin alpha and -gamma pre-mRNA splicing. Molecular Cell 10 (1): 21–33.CrossRefGoogle ScholarPubMed
Thompson, Paul. 1989. The Structure of Biological Theories. Albany: State University of New York Press.Google Scholar
Thornburg, B. G., Gotea, V., and Makałowski, W.. 2006. Transposable elements as a significant source of transcription regulating signals. Gene 365: 104–10.CrossRefGoogle ScholarPubMed
Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., and Guigó, R.. 2012. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Research 22 (9): 1616–25.CrossRefGoogle ScholarPubMed
Tinbergen, Nikolaas. 1963. On the aims and methods of ethology. Zeitschrift für Tierpsychologie 20: 410–33.CrossRefGoogle Scholar
Turkheimer, Eric. 2000. Three laws of behavior genetics and what they mean. Current Directions in Psychological Science 9 (5): 160–4.CrossRefGoogle Scholar
Turney, Jon. 2005. The sociable gene. EMBO Reports 6 (9): 809–10.CrossRefGoogle ScholarPubMed
Uller, Tobias. 2008. Developmental plasticity and the evolution of parental effects. Trends in Ecology and Evolution 23 (8): 432–8.CrossRefGoogle ScholarPubMed
van Fraassen, Bas. 1980. The Scientific Image. Oxford University Press.CrossRefGoogle Scholar
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. 2001. The sequence of the human genome. Science 291: 1304–51.CrossRefGoogle ScholarPubMed
Visscher, Peter M. 2008. Sizing up human height variation. Nature Genetics 40 (5): 489–90.CrossRefGoogle ScholarPubMed
Waddington, Conrad H. 1940. Organisers and Genes. Cambridge University Press.Google Scholar
Waddington, Conrad H 1952. The evolution of developmental systems. In Twenty-eighth Meeting of the Australian and New Zealand Association for the Advancement of Science, ed. Herbert, D. A.. Brisbane, Australia: A. H. Tucker, Government Printer Brisbane.Google Scholar
Waddington, Conrad H 1953a. Genetic assimilation of an acquired character. Evolution 7: 118–26.CrossRefGoogle Scholar
Waddington, Conrad H 1953b. The ‘Baldwin effect’, ‘genetic assimilation’ and ‘homeostasis’. Evolution 7 (4): 386–7.Google Scholar
Waddington, Conrad H 1957. The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. London: Ruskin House/George Allen & Unwin.Google Scholar
Wade, Michael J. 1998. The evolutionary genetics of maternal effects. In Maternal Effects as Adaptations, ed. Mousseau, T. A. and Fox, C. W.. Oxford University Press, 5–21.Google Scholar
Wagner, Günter P. 1994. Homology and the mechanisms of development. In Homology: The Hierarchical Basis of Comparative Biology, ed. Hall, B. K.. New York: Academic Press, 273–99.CrossRefGoogle Scholar
Wagner, Günter P 1995. The biological role of homologues: a building block hypothesis. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 195: 279–88.CrossRefGoogle Scholar
Wagner, Günter P 1996. Homologues, natural kinds and the evolution of modularity. American Zoologist 36: 36–43.CrossRefGoogle Scholar
Wahlsten, Douglas. 1990. Insensitivity of the analysis of variance to heredity–environment interaction. Behavioral and Brain Sciences 13: 109–61.CrossRefGoogle Scholar
Wahlsten, Douglas, and Gottlieb, Gilbert. 1997. The invalid separation of effects of nature and nurture: lessons from animal experimentation. In Intelligence, Heredity and Environment, ed. Sternberg, R. J. and Grigorenko, E.. Cambridge University Press, 163–92.Google Scholar
Walters, Ryan D., Kugel, Jennifer F., and Goodrich, James A.. 2009. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. UBMB Life 61 (8): 831–7.CrossRefGoogle ScholarPubMed
Waters, C. Kenneth. 1990. Why the antireductionist consensus won't survive the case of classical Mendelian genetics. In Proceedings of the Biennial Meeting of the Philosophy of Science Association. Vol. 1: Contributed Papers, ed. Fine, A., Forbes, M., and Wessells, L.. Philosophy of Science Association, 125–39.Google Scholar
Waters, C. Kenneth 1994. Genes made molecular. Philosophy of Science 61: 163–85.CrossRefGoogle Scholar
Waters, C. Kenneth 2000. Molecules made biological. Revue Internationale de Philosophie 4 (214): 539–64.Google Scholar
Waters, C. Kenneth 2004. What was classical genetics? Studies in History and Philosophy of Science 35 (4): 783–809.CrossRefGoogle ScholarPubMed
Waters, C. Kenneth 2006. A pluralist interpretation of gene-centered biology. In Scientific Pluralism, Vol. 19, ed. Kellert, S., Longino, H. E. and Waters, C. K.. Minneapolis: University of Minnesota Press, 190–214.Google Scholar
Waters, C. Kenneth 2007. Causes that make a difference. Journal of Philosophy 104 (11): 551–79.CrossRefGoogle Scholar
Watson, James D., and Crick, Francis H. C.. 1953a. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171: 737.CrossRefGoogle ScholarPubMed
Watson, James D., and Crick, Francis H. C. 1953b. Genetical implications of the structure of deoxyribose nucleic acid. Nature 171: 964–7.CrossRefGoogle Scholar
Weaver, Ian C. G., Cervoni, Nadia, Champagne, Frances A., D’Alessio, Ana C., Sharma, Shakti, Seckl, Jonathan R., Dymov, Sergiy, Szyf, Moshe, and Meaney, Michael J.. 2004. Epigenetic programming by maternal behavior. Nature Neuroscience 7 (8): 847–54.CrossRefGoogle ScholarPubMed
Weber, Bruce H., and Depew, David J.. 1996. Natural selection and self-organisation. Biology and Philosophy 11: 33–65.CrossRefGoogle Scholar
Weber, Bruce H (eds.). 2003. Learning, Meaning and Emergence: Possible Baldwinian Mechanisms in the Co-evolution of Language and Mind. Cambridge, MA: MIT Press.Google Scholar
Weber, Marcel. 2005. Philosophy of Experimental Biology. Cambridge University Press.Google Scholar
Weber, Marcel 2006. The Central Dogma as a thesis of causal specificity. History and Philosophy of the Life Sciences 28 (4): 595–609.Google ScholarPubMed
Weiss, Kenneth M., and Buchanan, Anne V.. 2009. The cooperative genome: organisms as social contracts. International Journal of Developmental Biology 53: 753–63.CrossRefGoogle ScholarPubMed
West, Meredith J., and King, Andrew P.. 1987. Settling nature and nurture into an ontogenetic niche. Developmental Psychobiology 20 (5): 549–62.CrossRefGoogle ScholarPubMed
West, Meredith J., and King, Andrew P. 1988. Female visual displays affect the development of male song in the cowbird. Nature 334: 244–6.CrossRefGoogle Scholar
West, Meredith J., and King, Andrew P. 2008. Deconstructing innate illusions: reflections on nature–nurture–niche from an unlikely source. Philosophical Psychology 21 (3): 383–95.CrossRefGoogle Scholar
West, Meredith J., King, Andrew P., and Arberg, Anne A.. 1988. The inheritance of niches: the role of ecological legacies in ontogeny. In Handbook of Behavioral Neurobiology. Vol. 9: Developmental Psychobiology and Behavioral Ecology, ed. Blass, E. M.. New York: Plenum Press, 41–62.Google Scholar
West, Meredith J., King, Andrew P., and White, David J.. 2003. The case for developmental ecology. Animal Behaviour 66: 617–22.CrossRefGoogle Scholar
West, Meredith J., King, Andrew P., White, David J., Gros-Louis, Julie, and Freed-Brown, Grace. 2006. The development of local song preferences in female cowbirds (Molothrus ater): flock living stimulates learning. Ethology 112: 1095–107.CrossRefGoogle Scholar
West-Eberhard, Mary Jane. 1998. Evolution in the light of developmental and cell biology, and vice versa. PNAS 95: 8417–19.CrossRefGoogle ScholarPubMed
West-Eberhard, Mary Jane 2003. Developmental Plasticity and Evolution. Oxford University Press.Google Scholar
West-Eberhard, Mary Jane 2005a. Developmental plasticity and the origin of species differences. PNAS 102 (Suppl. 1): 6543–9.CrossRefGoogle ScholarPubMed
West-Eberhard, Mary Jane 2005b. Phenotypic accommodation: adaptive innovation due to developmental plasticity. Journal of Experimental Zoology, Part B: Molecular and Developmental Evolution 304: 610–18.CrossRefGoogle ScholarPubMed
Wilkins, Adam. 2011. Epigenetic inheritance: where does the field stand today? What do we still need to know? In Transformations of Lamarckism: From Subtle Fluids to Molecular Biology, ed. Gissis, S. B. and Jablonka, E.. Cambridge, MA: MIT Press, 389–93.CrossRefGoogle Scholar
Williams, George C. 1966. Adaptation and Natural Selection. Princeton University Press.Google Scholar
Williams, George C 1992. Natural Selection: Domains, Levels and Challenges. New York: Oxford University Press.Google Scholar
Wimsatt, William C. 1986a. Forms of aggregativity. In Human Nature and Natural Knowledge, ed. Grene, M. G., Donaghan, A., Perovich, A. N., and Wedin, M. V.. Dordrecht: Reidel, 259–91.CrossRefGoogle Scholar
Wimsatt, William C 1986b. Developmental constraints, generative entrenchment and the innate-aquired distinction. In Integrating Scientific Disciplines, ed. Bechtel, W.. Dordrecht: Martinus Nijhoff.Google Scholar
Winther, Rasmus G. 2006. Parts and theories in compositional biology. Biology and Philosophy 21 (4): 471–99.CrossRefGoogle Scholar
Wissinger, B., Schuster, W., and Brennicke, A.. 1991. Trans splicing in Oenothera Mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65 (3): 473–82.CrossRefGoogle ScholarPubMed
Wolkenhauer, Olaf. 2001. Systems biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics 2 (3): 258–70.CrossRefGoogle ScholarPubMed
Woodward, James. 2003. Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.Google Scholar
Woodward, James 2010. Causation in biology: stability, specificity, and the choice of levels of explanation. Biology and Philosophy 25 (3): 287–318.CrossRefGoogle Scholar
Yang, Jian, Benyamin, Beben, McEvoy, Brian P, Gordon, Scott, Henders, Anjali K, Nyholt, Dale R, Madden, Pamela A, Heath, Andrew C, Martin, Nicholas G, Montgomery, Grant W, Goddard, Michael E, and Visscher, Peter M. 2010. Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 42 (7): 565–9.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

  • Bibliography
  • Paul Griffiths, University of Sydney, Karola Stotz, University of Sydney
  • Book: Genetics and Philosophy
  • Online publication: 05 April 2013
  • Chapter DOI: https://doi.org/10.1017/CBO9780511744082.010
Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

  • Bibliography
  • Paul Griffiths, University of Sydney, Karola Stotz, University of Sydney
  • Book: Genetics and Philosophy
  • Online publication: 05 April 2013
  • Chapter DOI: https://doi.org/10.1017/CBO9780511744082.010
Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

  • Bibliography
  • Paul Griffiths, University of Sydney, Karola Stotz, University of Sydney
  • Book: Genetics and Philosophy
  • Online publication: 05 April 2013
  • Chapter DOI: https://doi.org/10.1017/CBO9780511744082.010
Available formats
×