Genes in the Postgenomic Era

Article

Abstract

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype.

Keywords

Gene definition gene concepts postgenomics history of genetics conceptual change 

References

  1. Alberts B., Bray D., Lewis J., Raff M., Roberts K. and Watson J.D. (1994) The Molecular Biology of the Cell. 3 ed. Garland, New York and London.Google Scholar
  2. Alberts B., Bray D., Lewis J., Raff M., Roberts K. and Watson J.D. (2002) Molecular Biology of the Cell, 4 ed. Garland, New York.Google Scholar
  3. Baranov Pavel. V., Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland and John F. Atkins (2003) Recode 2003. Nucleic Acids Research 31(1):87–89.CrossRefGoogle Scholar
  4. Blumenthal T., Evans D., Link C. D., Guffanti A., Lawson D., Thierry-Mieg, D., Thierry-Mieg W. L., Chiu K. Duke, Duke, M., Kiraly M. and S. Kim (2002) A global analysis of Caenorhabditis elegans operons. Nature 417(6891):851–854.CrossRefGoogle Scholar
  5. Burian Richard M. (2004) Molecular Epigenesis, Molecular Pleiotropy and Molecular Gene Definitions. History and Philosophy of the Life Sciences 26(1):59–80.CrossRefGoogle Scholar
  6. Chapdelaine Y., 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 Scholar
  7. Coelho P.S.R., Bryan A.C., et al. (2002) A Novel Mitochondrial Protein,Tar1p, Is Encoded on the Antisense Strand of the Nuclear 25S rDNA. Genes andDevelopment 16:2755–2760.CrossRefGoogle Scholar
  8. Communi D., Suarez-Huerta N., et al. (2001) Cotranscription and intergenic splicing of human P2Y(11) SSF1 genes. Journal of Biological Chemistry 276(19):16561–16566.CrossRefGoogle Scholar
  9. Dawkins Richard (1976) The Selfish Gene. Oxford University Press ,Oxford.Google Scholar
  10. Dawkins Richard (1982) The Extended Phenotype: The Long Reach of the Gene. Freeman, San Francisco.Google Scholar
  11. Dietrich Michael R. (2000) From Hopeful Monsters to Homeotic Effects: Richard Goldschmidt’s Integration of Development, Evolution and Genetics. American Zoologist 40:738–47.CrossRefGoogle Scholar
  12. Dietrich Michael R. (2000) The Problem of the Gene. Comptes Rendus de l’Académie des Sciences - Series III - Sciences de la Vie 323(12):1139–46.CrossRefGoogle Scholar
  13. Dillon Niall. (2003) Positions, Please... Nature 425:457.CrossRefGoogle Scholar
  14. Falk, Raphael. “Genetic Analysis,” In International Handbook of the Philosophy of Biology. Edited by Mohan Matthen and Chris Stephens. Elsevier, In Press.Google Scholar
  15. Falk Raphael (2000) The Gene: A Concept in Tension. In: Peter B., Falk R., Rheinberger H.-J. (eds) The Concept of the Gene in Development and Evolution. Cambridge University Press, Cambridge, pp 317–48.Google Scholar
  16. Falk Raphael (1986) What Is a Gene? Studies in the History and Philosophy of Science 17:133–73.CrossRefGoogle Scholar
  17. Finta C. and Zaphiropoulos P.G. (2001) A Statistical View of Genome Transcription. Journal of Molecular Evolution 53:160–62.Google Scholar
  18. Fogle Thomas (2001) The Dissolution of Protein Coding Genes in Molecular Biology In: P. Beurton., Falk R., Rheinberger H.-J. (eds) The Concept of the Gene in Development and Evolution. Cambridge University Press, Cambridge, pp 3–25.Google Scholar
  19. Holmes Frederic L. (2000) Seymour Benzer and the Definition of the Gene. In: Beurton P., Falk R., Rheinberger H.-J. (eds) The Concept of the Gene in Development and Evolution. Cambridge University Press, Cambridge, 115–55.Google Scholar
  20. Gray M.W. (2003) “Diversity and evolution of mitochondrial RNA editing systems.” IUBMB Life 55(4–5):227–233.CrossRefGoogle Scholar
  21. Kampa D., Cheng J., Kapranov P., Yamanaka M., Brubaker S., Cawley S., Drenkow J., Piccolboni A., Bekiranov S., Helt G., Tammana H. and Gingeras T.R. (2004) Novel Rnas Identified from an in-Depth Analysis of the Transcriotome of Human Chromosomes 21 and 22. Genome Research 14:331–342.CrossRefGoogle Scholar
  22. Kapranov P., Drenkow J., Cheng J., Long J., Gregg H., Dike S. and Gingeras T.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 Scholar
  23. Kuhn Thomas (1962) The Structure of Scientific Revolutions. 1 ed. University of Chicago Press, Chicago.Google Scholar
  24. Morange Michael (1998) A History of Molecular Biology. Harvard University Press, Cambridge, MA.Google Scholar
  25. Morgan Thomas Hunt (1917) The Theory of the Gene. American Naturalist 51:513–44.CrossRefGoogle Scholar
  26. Moss Lenny (2003) What Genes Can’t Do. MIT Press, Cambridge, MA.Google Scholar
  27. Neumann-Held E.M. (1998) The Gene Is Dead - Long Live the Gene: Conceptualising the Gene the Constructionist Way. In: P. Koslowski (Eds) Sociobiology and Bioeconomic: The Theory of Evolution in Biological and Economic Theory. Springer-Verlag, Berlin, 105–37.Google Scholar
  28. Olby Robert C. (1974) The Path to the Double Helix. University of Washington Press, Seattle.Google Scholar
  29. Oyama S., Griffiths P.E. and Gray R.D. (eds) (2001) Cycles of Contingency: Developmental Systems and Evolution. MIT Press, Cambridge, MA.Google Scholar
  30. Portin Petter (1993) The Concept of the Gene: Short History and Present Status. The Quarterly Review of Biology 68(2):173–223.CrossRefGoogle Scholar
  31. Stent G. (1977) You Can Take the Ethics out of Altruism but You Can’t Take the Altruism out of Ethics. Hastings Center Report 7(6):33–36.CrossRefGoogle Scholar
  32. Sterelny K. and Griffiths P.E. (1999) Sex and Death: An Introduction to the Philosophy of Biology. University of Chicago Press, Chicago.Google Scholar
  33. Stotz Karola, Bostanci A. and Griffiths Paul E. (2006) Tracking the Shift to ‘Postgenomics’,” Community Genetics 9(3):190–196.CrossRefGoogle Scholar
  34. Stotz K. and Griffiths P.E. (2004) Genes: Philosophical Analyses Put to the Test. History and Philosophy of the Life Sciences 26(1):5–28.CrossRefGoogle Scholar
  35. Waters C. Kenneth (1994) Genes Made Molecular. Philosophy of Science 61:163–85.CrossRefGoogle Scholar
  36. Waters C. Kenneth (2000) Molecules Made Biological. Rev. Int. de Philosophie 4(214):539–64.Google Scholar
  37. Waters C. Kenneth (2004) What Was Classical Genetics? Studies in History and Philosophy of Science 35(4):783–809.Google Scholar
  38. Waters, C. Kenneth. “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. Edited by A. Fine, M. Forbes and L. Wessells. 125–139. Columbia, SC: Philosophy of Science Association, 1990.Google Scholar
  39. Weber Marcel (2004) Philosophy of Experimental Biology. Cambridge University Press, Cambridge, New York.CrossRefGoogle Scholar
  40. Williams G.C. (1966) Adaptation & Natural Selection. Princeton University Press, Princeton.Google Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Biohumanities ProjectUniversity of QueenslandBrisbaneAustralia
  2. 2.Cognitive Science ProgramIndiana UniversityBloomingtonUSA

Personalised recommendations