References

References

 [Apter & Wolpert, 1965]

Apter, M.J., & Wolpert, Lewis. 1965. Cybernetics and Development: I. Information Theory. Journal of Theoretical Biology, 8, 244-257. Is quite dismissive of attempts so far to apply information theory to organisms. However, proposes a new formulation, that the information content of DNA could be seen as subroutines to the `program' embodied in the (entire) egg.

 [Atlan & Koppel, 1990]

Atlan, Henri, & Koppel, Moshe. 1990. The cellular computer DNA: program or data. Bulletin of Mathematical Biology, 52(3), 335-348. Suggests that DNA is better viewed as data, but that the program is somewhere else entirely. Contains a proposal for an information-theory definition of "sophistication", which is interesting.

 [Black, 1998]

Black, Douglas L. 1998. Splicing in the inner ear: a familiar tune, but what are the instruments? Neuron, 20(February), 165-168. The hairs on chick cochlear cells are generated by recombination of the cSLO gene. The problem is that it isn't really clear who controls how the recombination is done, nor is it clear how it is decided which cell gets which recombination.

 [Boyd, 1993]

Boyd, Richard. 1993. Metaphor and theory change: What is "metaphor" a metaphor for? Pages 481-532 of: Ortony, Andrew (ed), Metaphor and Thought, 2d. edn. Cambridge University Press.

 [Buchner, 1996]

Buchner, J. 1996. Supervising the fold: functional principles of molecular chaperones. FASEB Journal, 10(1), 10-19.

 [Chaitin, 1995/1996]

Chaitin, G. J. 1995/1996. A New Version of Algorithmic Information Theory. Complexity, 1(4), 55-59.

 [Chargaff, 1968]

Chargaff, Erwin. 1968. What Really Is DNA? Remarks on the changing aspects of a scientific concept. Progress in Nucleic Acid Research and Molecular Biology, 8, 297-333. Very realistic statement of the state of affairs circa 1968. No hype. See esp. the "Modest Glimpse of the Future" section, and the Epilogue.

 [Coen, 1999]

Coen, Enrico. 1999. The Art of Genes: How Organisms Make Themselves. Oxford University Press. Good book, with a decent and clear explanation of homeotic genes, but the efforts to extend the analogy between painting and ontogeny were eventually tiring.

 [Crick, 1958]

Crick, Francis H.C. 1958. On Protein Synthesis. Pages 138-163 of: The Biological Replication of Macromolecules. Symposia of the Society for Experimental Biology. Academic Press. A concise and clear statement of the "Central Dogma" of biology: information flows from DNA to RNA to proteins, and not the other way round.

 [Crick, 1981]

Crick, Francis H.C. 1981. Life Itself. Simon & Schuster. Following the implications of the Central Dogma to their bitter end, Crick concludes that life must have begun elsewhere and been seeded here by aliens.

 [Crutchfield & Shalizi, 1998]

Crutchfield, J. P., & Shalizi, C. R. 1998. Thermodynamic Depth of Causal States: When Paddling around in Occam's Pool Shallowness is a Virtue. Santa Fe Institute Working Paper 98-06-047.

 [Delbruck, 1949]

Delbruck, Max. 1949. Génétique du bactériophage. Pages 91-103 of: Unités Biologiques Douées de Continuité Génétique. Colloques internationaux du Centre national de la recherche scientifique, vol. 8. CNRS.

 [Ephrussi et al., 1953]

Ephrussi, B.U., Leopold, U., Watson, James D., & Weigle, J.J. 1953. Terminology in Bacterial Genetics. Nature, 171(18 April), 701. A short note proposing to clear up some misunderstandings by adopting the word "information" when talking about bacteria genetics.

 [Etzkowitz et al., 2000]

Etzkowitz, Henry, Kemelgor, Carol, & Uzzi, Brian. 2000. Athena Unbound: The Advancement of Women in Science and Technology. Cambridge University Press. The source of the quotation about female scientists and the science career "pipeline.".

 [Gilbert, 2001]

Gilbert, Scott F. 2001. Ecological Developmental Biology: Developmental biology meets the real world. Developmental Biology, 210, 1-12. Good account of predator-induced polyphenism, and critique of lab systems (e.g. C. Elegans, Drosophila, etc.).

 [Gilbert & Faber, 1996]

Gilbert, Scott F., & Faber, Marion. 1996. Looking at embryos: The visual and conceptual aesthetics of emerging form. Pages 125-151 of: Tauber, A.I. (ed), The Elusive Synthesis: Aesthetics and Science. Kluwer. closing sentence: "In order to understand the embryonic process, one must see the embryo in a multiplicity of ways...as a living entity, a function of gene expression, and as a product of complex interactions... Otherwise one does not see the embryo.

 [Gilbert, 1992]

Gilbert, Walter. 1992. Visions of the Grail. Pages 83-97 of: Kevles, D.J., & Hood, L. (eds), The Code of Codes. Harvard University Press.

 [Hawley & Mori, 1999]

Hawley, R. Scott, & Mori, Catherine A. 1999. The Human Genome: A User's Guide. Academic Press. A triumphalist version of the current state of genetics. Meant to be either an introductory text or a deeper popular account.

 [Jablonka & Lamb, 1995]

Jablonka, Eva, & Lamb, Marion J. 1995. Epigenetic Inheritance and Evolution: The Lamarckian Dimension. Oxford University Press. A review of what is currently known about epigenetic inheritance. Fairly technical. Authors are committed Darwinians, but want to make sure that this aspect is not ignored, since it appears to be real. Extensive bibliography.

 [Judson, 1979]

Judson, Horace Freeland. 1979. The Eighth Day Of Creation: The Makers Of The Revolution In Biology. Simon and Schuster. A detailed history of the discovery of the structure and function of DNA, as rendered through interviews with many of the principals a couple of decades after the fact. Most of the history is developed through the interviews, though there is a contribution from the scientific literature as well. Much of the tone is rather smug to those who turned out to be quite right in their misgivings, but this was written in the glory days before the Genome Project screwed it all up.

 [Kay, 2000]

Kay, Lily E. 2000. Who Wrote The Book Of Life? Stanford University Press. A history of the DNA-is-language metaphor, developed through parallel histories of molecular biology, information theory, and the militarization of scientific research, from 1945 to the present.

 [Keller, 2000]

Keller, Evelyn Fox. 2000. The Century of the Gene. Harvard University Press. A very sensible appraisal of what we know and what we don't know about genetics. The author is an active participant in some of the cooler currents in modern genetics.

 [Kohli et al., 1998]

Kohli, A., Leech, M., Laurie, D. A., & Christou, P. 1998. Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots. Proc Natl Acad Sci USA, 95(12), 7203-7208.

 [Lewontin, 2000]

Lewontin, Richard. 2000. The Triple Helix: Gene, Organism, And Environment. Harvard University Press.

 [McClintock, 1984]

McClintock, Barbara. 1984. The Significance of Responses of the Genome to Challenge. Science, 226(16 November), 792-801. Her Nobel address. Prefigures later findings about adaptive mutability.

 [Nanney, 1957]

Nanney, David L. 1957. The Role of The Cytoplasm In Heredity. Pages 134-166 of: McElroy, William D., & Glass, Bentley (eds), The Chemical Basis of Heredity, A Symposium. McCollum-Pratt Institute of Johns Hopkins University. Shows results from paramecia that challenge the view that heredity is exclusively a nuclear function. The paramecia are shown to have inherited traits in a non-mendelian fashion, but only when they exchanged cytoplasm.

 [Nanney, 1985]

Nanney, David L. 1985. Heredity without genes: ciliate explorations of clonal heredity. Trends in Genetics, 1(November), 295-298. A review of earlier work. Places some formerly inexplicable results within recent advances in the standard molecular genetic framework, but points out that some findings, with Paramecia, among others, remains unexplained by that same framework.

 [Radman, 1999]

Radman, Miroslav. 1999. Enzymes of evolutionary change. Nature, 401(28 October), 866-869.

 [Radman et al., 1999]

Radman, Miroslav, Matic, Ivan, & Taddei, François. 1999. Evolution of evolvability. Pages 146-155 of: Caporale, L.H. (ed), Molecular Strategies in Biological Evolution. Annals of the New York Academy of Sciences, vol. 870.

 [Sarkar, 1996]

Sarkar, Sahotra. 1996. Biological information: A skeptical look at some central dogmas of molecular biology. Pages 187-231 of: Sarkar, Sahotra (ed), The Philosophy and History of Molecular Biology: New Perspectives. Kluwer. Good skepticism.

 [Schön, 1977]

Schön, Donald A. 1977. Generative Metaphor: A perspective on problem-setting in social policy. Pages 138-163 of: Ortony, Andrew (ed), Metaphor and Thought, 2d. edn. Cambridge University Press. Source of the phrase "generative metaphor," although that was originally published in Schön, "Displacement of Concepts," Humanities Press, 1963. Contains a good discussion of how the solution to problems can be affected by the metaphor used to describe them. In this case it was housing policy.

 [Shapiro, 1999]

Shapiro, James A. 1999. Genome system architecture and natural genetic engineering in evolution. Pages 23-35 of: Caporale, L.H. (ed), Molecular Strategies in Biological Evolution. Annals of the New York Academy of Sciences, vol. 870. Contains a great figure about progress in understanding the lac operon.

 [Waddington, 1968]

Waddington, C.H. 1968. The Basic Ideas of Biology. Pages 1-32 of: Waddington, C.H. (ed), Towards a Theoretical Biology: Prolegomena. International Union of Biological Sciences Symposium. A brilliant summation of the problems faced by the "central dogma" version of biological analysis.

 [Watson & Crick, 1953]

Watson, James D., & Crick, Francis H.C. 1953. Genetical Implications of the Structure of Deoxyribonucleic Acid. Nature, 171(30 May), 964-967. The follow-up to the paper announcing the structure of DNA.

 [Wiener, 1963]

Wiener, Norbert. 1963. Cybernetics. 2d. edn. XXX.

 [Windels et al., 2001]

Windels, P., Taverniers, I., Depicker, A., Van Bockstaele, E., & De Loose, M. 2001. Characterisation of the Roundup Ready soybean insert. Eur Food Res Technol., 213, 107-112.

References