Biology & Philosophy

, Volume 22, Issue 2, pp 293–306 | Cite as

Reports of the death of the gene are greatly exaggerated

  • Rob KnightEmail author


Cystic Fibrosis Molecular Product Developmental Resource Modern Molecular Biology Cystic Fibrosis Phenotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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I would like to thank Natalie Ahn for providing me with an overview of recent findings in cancer research, Karola Stotz for sharing related work before publication, and Amanda Birmingham for critical discussion of the manuscript.


  1. Arnheim N., Krystal M., Schmickel R., Wilson G., Ryder O., Zimmer E. (1980). Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and apes. Proc. Natl. Acad. Sci. USA 77:7323–7327CrossRefGoogle Scholar
  2. Barrell B., Air G., Hutchison C. (1976). Overlapping genes in bacteriophage phix174. Nature 264:34–41CrossRefGoogle Scholar
  3. Bateson, W. 1909. Mendel’s Principles of Heredity. Cambridge University Press.Google Scholar
  4. Beadle G.W., Tatum E. (1941). Genetic control of biochemical reactions in Neurospora. Proc. Natl. Acad. Sci. USA 27:499–506CrossRefGoogle Scholar
  5. Beurton P.J., Falk R., Rheinberger H.-J. (eds) 2000. The Concept of the Gene in Development and Evolution: Historical and Epistemological perspectives. Cambridge University Press.Google Scholar
  6. Bonen L. (1993). Trans-splicing of pre-mRNA in plants, animals, and protists. FASEB J. 7:40–46Google Scholar
  7. Borry P. (2004). Book review: Moss, Lenny. What genes can’t do. Theor Med 25:75–77CrossRefGoogle Scholar
  8. Brose N., Rosenmund C. (2002). Move over protein kinase C, you’ve got company: alternative cellular effectors of diacylglycerol and phorbol esters. J Cell Sci 115:4399–4411CrossRefGoogle Scholar
  9. Burian R.M. 2005. The Epistemology of Development, Evolution and Genetics. Cambridge University Press.Google Scholar
  10. Cantor G. 1955. Contributions to the Founding of the Theory of Transfinite Numbers. Dover PublicationsGoogle Scholar
  11. Carothers J., Oestreich S., Davis J., Szostak J. (2004). Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc. 126:5130–5137CrossRefGoogle Scholar
  12. Celotto A., Graveley B. (2001). Alternative splicing of the Drosophila DSCAM pre-mRNA is both temporally and spatially regulated. Genetics 159:599–608Google Scholar
  13. Cummins R. (1975). Functional analysis. J. Philos. 72:741–765CrossRefGoogle Scholar
  14. Elenbaas B., Spirio L., Koerner F., Fleming M., Zimonjic D., Donaher J., Popescu N., Hahn W., Weinberg R. (2001). Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev. 15:50–65CrossRefGoogle Scholar
  15. Ellington A., Szostak J. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822CrossRefGoogle Scholar
  16. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811CrossRefGoogle Scholar
  17. Fogle T. (1990). Are genes units of inheritance? Biol. Philos. 5:349–371CrossRefGoogle Scholar
  18. Fogle, T. 2001. The dissolution of protein coding genes in molecular biology. In: Beurton P., Falk R. and Rheinberger H. (eds), The Concept of the Gene in Development and Evolution. Cambridge University Press.Google Scholar
  19. Godfrey-Smith P. (1994). A modern history theory of functions. Nous 28:344–362Google Scholar
  20. Griffiths P., Neumann-Held E. (1999). The many faces of the gene. Biosciences 49:656–662CrossRefGoogle Scholar
  21. Griffiths P.E. (1993). Functional analysis and proper functions. Br. J. Philos. Sci. 44:409–422CrossRefGoogle Scholar
  22. Griffiths P.E., Gray R.D. (1994a). Developmental systems and evolutionary explanation. J. Philos. XCI:277–304CrossRefGoogle Scholar
  23. Griffiths P.E., Gray R.D. (1994b). Replicators and vehicles? or developmental systems?. Behav. Brain Sci. 17:623–624CrossRefGoogle Scholar
  24. Griffiths P.E., Gray R.D. (1997). Replicator II: judgement day. Biol. Philos. 12:471–492CrossRefGoogle Scholar
  25. Griffiths P.E., Knight R.D. (1998). What is the developmentalist challenge?. Philos. Sci. 65:253–258CrossRefGoogle Scholar
  26. Gugliotti L., Feldheim D., Eaton B. (2004). RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles. Science 304:850–852CrossRefGoogle Scholar
  27. Hahn W., Counter C., Lundberg A., Beijersbergen R., Brooks M., Weinberg R. (1999). Creation of human tumour cells with defined genetic elements. Nature 400:464–468CrossRefGoogle Scholar
  28. Hahn W., Dessain S., Brooks M., King J., Elenbaas B., Sabatini D., DeCaprio J., Weinberg R. (2002). Enumeration of the simian virus 40 early region elements necessary for human cell transformation. Mol. Cell. Biol. 22:2111–2123CrossRefGoogle Scholar
  29. Hanahan D., Weinberg R. (2000). The hallmarks of cancer. Cell 100:57–70CrossRefGoogle Scholar
  30. Hillis D. (1991). Co-evolving parasites improve simulated evolution as an optimization procedure. Artif. Life II, SFI Stud. Sci. Complex. 10:313–324Google Scholar
  31. Holland J. 1975. Adaptation in Natural and Artificial Systems. University of Michigan Press.Google Scholar
  32. Huang F., Yarus M. (1997). Versatile 5’ phosphoryl coupling of small and large molecules to an RNA. Proc. Natl. Acad. Sci. USA 94:8965–8969CrossRefGoogle Scholar
  33. Ideker T., Galitski T., Hood L. (2001). A new approach to decoding life: systems biology. Annu. Rev. Genom. Hum. Genet. 2:343–372CrossRefGoogle Scholar
  34. Iida M., Anna C., Hartis J., Bruno M., Wetmore B., Dubin J., Sieber S., Bennett L., Cunningham M., Paules R., Tomer K., Houle C., Merrick A., Sills R., Devereux T. (2003). Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and wyeth-14,643. Carcinogenesis 24:757–770CrossRefGoogle Scholar
  35. Illangasekare M., Sanchez G., Nickles T., Yarus M. (1995). Aminoacyl-rna synthesis catalyzed by an RNA. Science 267:643–647CrossRefGoogle Scholar
  36. Jablonka E. 1995. Epigenetic Inheritance and Evolution: The Lamarckian Dimension. Oxford University Press.Google Scholar
  37. Kaneko M., Morimura K., Nishikawa T., Wanibuchi H., Takada N., Osugi H., Kinoshita H., Fukushima S. (2002). Different genetic alterations in rat forestomach tumors induced by genotoxic and non-genotoxic carcinogens. Carcinogenesis 23:1729–1735CrossRefGoogle Scholar
  38. Karlik C., Fyrberg E. (1985). An insertion within a variably spliced drosophila tropomyosin gene blocks accumulation of only one encoded isoform. Cell 41:57–66CrossRefGoogle Scholar
  39. Kay L.E. 2000. Who Wrote the Book Of Life? A History of the Genetic Code. Stanford University Press.Google Scholar
  40. Keller E.F. 2000. The Century of the Gene. Harvard University Press.Google Scholar
  41. Knight R., De Sterck H., Markel R., Smit S., Oshmyansky A., Yarus M. (2005). Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res. 33:5924–5935CrossRefGoogle Scholar
  42. Knight R., Yarus M. (2003). Finding specific RNA motifs: function in a zeptomole world?. RNA 9:218–230CrossRefGoogle Scholar
  43. Kuperwasser C., Chavarria T., Wu M., Magrane G., Gray J., Carey L., Richardson A., Weinberg R. (2004). Reconstruction of functionally normal and malignant human breast tissues in mice. Proc. Natl. Acad. Sci. USA 101:4966–4971CrossRefGoogle Scholar
  44. Legiewicz M., Lozupone C., Knight R., Yarus M. (2005). Size, constant sequences, and optimal selection. RNA 11:1701–1709CrossRefGoogle Scholar
  45. Lipson H., Pollack J.B. (2000). Automatic design and manufacture of robotic lifeforms. Nature 406(6799):974–978CrossRefGoogle Scholar
  46. Lusis A.J. (2003). What genes can’t do, by Lenny Moss. Nature Med 9:501CrossRefGoogle Scholar
  47. MacLaurin J. (1998). Reinventing molecular Weismannism: information in evolution. Biol. Philos. 13:37–59CrossRefGoogle Scholar
  48. Mally A., Chipman J. (2002). Non-genotoxic carcinogens: early effects on gap junctions, cell proliferation and apoptosis in the rat. Toxicology 180:233–248CrossRefGoogle Scholar
  49. Moss L. 2001. Deconstructing the gene and reconstructing molecular developmental systems. In: Oyama S., Griffiths P.E. and Gray R.D. (eds), Cycles of Contingency: Developmental Systems and Evolution, MIT Press, pp. 85–97.Google Scholar
  50. Moss L. (2002). From representational preformationism to the epigenesis of openness to the world? reflections on a new vision of the organism. Ann. NY. Acad. Sci. 981:219–229CrossRefGoogle Scholar
  51. Moss L. (2003a). One, two (too?), many genes?. Quart. Rev. Biol. 78:57–67CrossRefGoogle Scholar
  52. Moss L. 2003b. What Genes Can’t Do. MIT Press.Google Scholar
  53. Neander K. (1991). Function as selected effects: The conceptual analyst’s defense. Philos. Sci. 58:168–184CrossRefGoogle Scholar
  54. Neumann-Held E.M. 1997. The gene is dead – long live the gene: Conceptualising the gene the constructionist way. In: Koslowski P. (ed.), Developmental Systems, Competition and Cooperation in Sociobiology and Economics. Springer-Verlag.Google Scholar
  55. Oyama S. 1985. The Ontogeny of Information. Cambridge University Press.Google Scholar
  56. Pereira M., Wang W., Kramer P., Tao L. (2004). Dna hypomethylation induced by non-genotoxic carcinogens in mouse and rat colon. Cancer Lett. 212:145–151CrossRefGoogle Scholar
  57. Portin P. (1993). The concept of the gene: Short history and present status. Quart Rev Biol 68:173–223CrossRefGoogle Scholar
  58. Portin P. (2000). The origin, development and present status of the concept of the gene: a short historical account of the discoveries. Current Genom. 1:29–40CrossRefGoogle Scholar
  59. Rakitsky V., Koblyakov V., Turusov V. (2000). Nongenotoxic (epigenetic) carcinogens: pesticides as an example. A critical review. Teratog. Carcinog. Mutagen. 20:229–240CrossRefGoogle Scholar
  60. Riordan J., Rommens J., Kerem B., Alon N., Rozmahel R., Grzelczak Z., Zielenski J., Lok S., Plavsic N., Chou J. (1989). Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245:1066–1073CrossRefGoogle Scholar
  61. Robertson D., Joyce G. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467–468CrossRefGoogle Scholar
  62. Roux P., Ballif B., Anjum R., Gygi S., Blenis J. (2004). Tumor-promoting phorbol esters and activated ras inactivate the tuberous sclerosis tumor suppressor complex via p90 ribosomal s6 kinase. Proc. Natl. Acad. Sci. USA 101:13489–13494CrossRefGoogle Scholar
  63. Rudnick E.M., Holm J.G., Saab D.G. and Patel J.H. 1994. Application of simple genetic algorithms to sequential circuit test generation. In: EDAC-ETC-EUROASIC, pp. 40–45.Google Scholar
  64. Sabeti P., Unrau P., Bartel D. (1997). Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 4:767–774CrossRefGoogle Scholar
  65. Schroedinger E. 1944. What is Life? The Physical Aspect of the Living Cell. Cambridge University Press.Google Scholar
  66. Shannon C.E. 1949. The Mathematical Theory of Communication. University of Illinois Press.Google Scholar
  67. Shimada T., Fujii-Kuriyama Y. (2004). Inhibition of human cytochrome P450 1a1-, 1a2-, and 1b1-mediated activation of polycyclic aromatic hydrocarbons to carcinogens by cytochromes P450 1a1 and 1b1. Cancer Sci 95:1–6CrossRefGoogle Scholar
  68. Sterelny K., Smith K.C., Dickison M. (1996). The extended replicator. Biol. Philos. 11:377–403CrossRefGoogle Scholar
  69. Stotz K., Griffiths P. (2004). Genes: philosophical analyses put to the test. Hist. Philos. Life Sci. 26:5–28CrossRefGoogle Scholar
  70. Stotz K., Griffiths P.E., Knight R.D. (2004). How biologists conceptualize genes: an empirical study. Stud. Hist. Philos. Biol. Sci. C Biomed. Sci. 35:647–673CrossRefGoogle Scholar
  71. Tarasow T., Tarasow S., Eaton B. (1997). RNA-catalysed carbon-carbon bond formation. Nature 389:54–57CrossRefGoogle Scholar
  72. Tuerk C., Gold L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510CrossRefGoogle Scholar
  73. Waters C.K. (1994). Genes made molecular. Philos. Sci. 61:163–185Google Scholar
  74. Waters C.K. (2004). What was classical genetics?. Stud. Hist. Philos. Sci. C Med. Sci. 35:783–809Google Scholar
  75. Weber M. 2004. Philosophy of Experimental Biology. Cambridge University Press.Google Scholar
  76. Williams G.C. 1966. Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought. Princeton University Press.Google Scholar
  77. Yarus M., Caporaso J., Knight R. (2005). Origins of the genetic code: the escaped triplet theory. Annu. Rev. Biochem. 74:179–198CrossRefGoogle Scholar
  78. Zimonjic D., Brooks M., Popescu N., Weinberg R., Hahn W. (2001). Derivation of human tumor cells in vitro without widespread genomic instability. Cancer Res. 61:8838–8844Google Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of ColoradoBoulderUSA

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