Biology and Philosophy

, Volume 20, Issue 2–3, pp 453–464 | Cite as

“Molecular gene”: Interpretation in the Right Context

Article

Abstract

How to interpret the “molecular gene” concept is discussed in this paper. I argue that the architecture of biological systems is hierarchical and multi-layered, exhibiting striking similarities to that of modern computers. Multiple layers exist between the genotype and system level property, the phenotype. This architectural complexity gives rise to the intrinsic complexity of the genotype-phenotype relationships. The notion of a gene being for a phenotypic trait or traits lacks adequate consideration of this complexity and has limitations in explaining the genotype-phenotype relationships. I explore ways toward an integrative interpretation of the gene in the context of multi-layered biological systems. A gene, I argue, should be interpreted as a functional unit that is responsible for the trans-generation passage of the capacity to dynamically produce a biochemical activity or biochemical activities. At the molecular level, a gene is a genetic unit, a stretch of DNA sequence, which dictates the behavior and the dynamic production of the encoded cellular component(s). Embedded in a gene’s quadruple DNA code are the regulatory signals, such as those for RNA splicing and/or editing, as well as for transcription factor binding. A regulatory signal can be recognized by the gene expression machinery in one state, but not in another. The confusion caused by RNA splicing, editing, and a gene’s selective tissue distribution pattern is addressed. Instead of a context-dependent definition of the gene, I argue for the view that it is the same gene displaying multiple meanings, subject to differential interpretation by the cellular machinery in different states. In other words, the same gene gives rise to different products and expression levels under different conditions.

Keywords

Architecture Biological system1 Gene Genetic circuit Genotype Integrative Phenotype Phenotypic trait Reductionism 

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References

  1. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J.D. 1994Molecular Biology of The Cell3Garland Publishing, Inc.New York & LondonChapter 3, Chapter 8, and Chapter 9Google Scholar
  2. Baxevanis A.D. and Ouellette B.F.F. (2001). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Wiley-Interscience, A John Wiley & Sons, Inc.Google Scholar
  3. Benzer, S. 1957

    ‘The Elementary Units of Heredity’

    McElroy, W.D.Glass, B. eds. The Chemical Basis of HeredityJohns Hopkins PressBaltimore, MD7093
    Google Scholar
  4. Beurton, P.J.Falk, R.Rheinberger, H.-J. eds. 2000The Concept of the Gene in Development and Evolution: Historical and Epistemological PerspectivesCambridge University PressCambridge and New YorkGoogle Scholar
  5. Dawkins, R. 1982The Extended PhenotypeW.H. FreemanOxfordGoogle Scholar
  6. DeRisi, J.L., Vishwanath, R.I., Brown, P.O. 1997‘Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale’Science278680686CrossRefPubMedGoogle Scholar
  7. Doyle, J. 2001‘Computational Biology: Beyond the Spherical Cow’Nature411151152CrossRefPubMedGoogle Scholar
  8. Epp, C.D. 1997‘Definition of a Gene’Nature389537CrossRefGoogle Scholar
  9. Falk, R. 2001

    ‘Can The Norm of Reaction Save the Gene Concept?’

    Singh, R.Krimbas, C.Paul, D.B.Beatty, J. eds. Thinking about Evolution: Historical, Philosophical and Political PerspectivesCambridge University PressNew York119140
    Google Scholar
  10. Godfrey-Smith, P. 1994‘A Modern History Theory of Function’NOÛS28344362Google Scholar
  11. Godfrey-Smith, P. 2000‘OnThe TheoreticalRole of “Genetic Coding”’Philosophyof Science672644CrossRefGoogle Scholar
  12. Griffiths, P.E. 2002‘Lost:OneGeneConceptRewardto Finder’Biology andPhilosophy14235252Google Scholar
  13. Griffiths, P.E., Neumann-Held, E.M. 1999‘The Many Faces of the Gene’BioScience49656663Google Scholar
  14. Hua, J., Meyerowitz, E.M. 1998‘Ethylene Responses are Negatively Regulated by a Receptor Gene Family in Arabidopsis Thaliana’Cell94261271CrossRefPubMedGoogle Scholar
  15. Hughes, T.R., Marton, M.J., Jones, A.R. 2000‘Functional Discovery via a Compendium of Expression ProfilesCell102109126CrossRefPubMedGoogle Scholar
  16. Hutchison, C.A.,III, Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O., Venter, J.C. 1999‘Global Transposon Mutagenesis and a Minimal Mycoplasma Genome’Science28621652169CrossRefPubMedGoogle Scholar
  17. Ihle, J.N. 2000‘The Challenges of Translating Knockout Phenotypes into Gene Function’Cell102131134CrossRefPubMedGoogle Scholar
  18. Kaplan, J.M., Pigliucci, M. 2001‘Genes “for” Phenotypes: A Modern History View’Biology and Philosophy16189213CrossRefGoogle Scholar
  19. Kitcher, P. 1982‘Genes’Br. J. Phil. Sci.33337359Google Scholar
  20. Nowak, M.A., Boerlijst, M.C., Cooke, J., Smith, J.M. 1997Evolution of Genetic RedundancyNature388167171CrossRefPubMedGoogle Scholar
  21. Palsson, B. 2000‘The Challenges of in silico BiologyNature Biotechnol.1811471150CrossRefGoogle Scholar
  22. Palson, B.O. 1997‘What Lies beyond Bioinfomatics?’Nature Biotechnol.1534CrossRefGoogle Scholar
  23. Rieger, D.K., Reichenberger, E., McLean, W., Sidow, A., Olsen, B.R. 2001‘A Double-deletion Mutation in the Pitx3Gene Causes Arrested LensDevelopment inAphakiaMiceGenomics726172CrossRefPubMedGoogle Scholar
  24. Sandgren, E.P., Luetteke, N.C., Palmiter, RD., Brinster, R.L., Lee, D.C. 1990‘Overexpression of TGF Alpha in Transgenic Mice: Induction of Epithelial Hyperplasia, Pancreatic Metaplasia, and Carcinoma of the BreastCell6111211135CrossRefPubMedGoogle Scholar
  25. Sarkar, S. 1999‘From the Reaktionsnorm to the Adaptive Norm: The Norm of Reaction 1909–1960Biology and Philosophy14235252CrossRefGoogle Scholar
  26. Semina, E.V., Murray, J.C., Reiter, R., Hrstka, R.F., Graw, J. 2000‘Deletion in the Promoter Region and Altered Expression of Pitx3 Homeobox Gene in Aphakia Mice’Human Molecular Genetics915751585CrossRefPubMedGoogle Scholar
  27. Sibilia, M., Wagner, E.F. 1995‘Strain-dependent Epithelial Defects in Mice Lacking the EGF Receptor’Science269234238PubMedGoogle Scholar
  28. Tanenbaum, A.S. 1999Structured Computer Organization4Prentice Hall UpperSaddle River, NJGoogle Scholar
  29. Thomas, H., Jaschkowitz, K., Bulman, M., Frayling, T.M., Roosen, S.M., Mitchell, S., Lingott-Frieg, A., Tack, C.J., Ellard, S., Ryffel, G.U., Hattersley, A.T. 2001‘A Distant Upstream Promoter of the HNF-4alpha Gene Connects the Transcription Factors Involved in Maturity-onset Diabetes of the Young’Hum Mol Genet1020892097CrossRefPubMedGoogle Scholar
  30. Threadgill, D.W., Dlugosz, A.A., Hansen, L.A., Teneenbaum, T., Lichti, U., Yee, D., LaMantia, C., Mourton, T., Herrup, K., Harris, R.C. 1995‘Targeted Disruption of Mouse EGF Receptor: Effect of Genetic Background on Mutant Phenotype’Science269230234PubMedGoogle Scholar
  31. Waters, C.K. 1994‘Genes Made Mo1ecular’Philosophy of Science61163185Google Scholar
  32. Williams, G.C. 1966Adaptation & Natural SelectionPrinceton University PressPrinceton, NJ464Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  1. 1.San Diego Supercomputer CenterUniversity of California, San DiegoLa JollaUSA

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