Hostname: page-component-84b7d79bbc-2l2gl Total loading time: 0 Render date: 2024-08-01T08:14:32.621Z Has data issue: false hasContentIssue false
  • English
  • Français

A Defense of Syntax-Based Gene Concepts in Postgenomics: Genes as Modular Subroutines in the Master Genomic Program

Published online by Cambridge University Press:  01 January 2022

Tudor M. Baetu
Get access Rights & Permissions [Opens in a new window]

Abstract

The purpose of this article is to update and defend syntax-based (conserved DNA-sequence motifs) gene concepts. I show how syntax-based concepts have been and can be extended to accommodate complex cases of genome expression, regulation, and processing. In response to difficult cases and causal parity objections, I argue that the syntax-based approach fleshes out a deflationary concept that defines genes in terms of sequences and organizational features of the genome that contribute to a phenotype.

Type
Research Article
Information
Philosophy of Science , Volume 78 , Issue 5 , December 2011 , pp. 712 - 723
Copyright
Copyright © The Philosophy of Science Association

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.)

Footnotes

‡

I would like to thank Lindley Darden, Erika Milam, Eric Saidel, Pamela Henson, Joan Straumanis, Lane DesAutels, Christophe DiTeresi, and the DC History and Philosophy of Biology group for helpful discussion and comments on earlier drafts. This work is supported by Fonds de la recherche sur la société et la culture, Québec, Canada (grant 127231).

References

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J.. 1990. “Basic Local Alignment Search Tool.” Journal of Molecular Biology 215 (3): 403–10.CrossRefGoogle ScholarPubMed
Black, D. L. 2003. “Mechanisms of Alternative Pre-messenger RNA Splicing.” Annual Reviews of Biochemistry 72 (1): 291–336.CrossRefGoogle ScholarPubMed
Callebaut, W., and Rasskin-Gutman, D.. 2005. Modularity: Understanding the Development and Evolution of Natural Complex Systems. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Caudevilla, C., Serra, D., Miliar, A., Codony, C., Asins, G., Bach, M., and Hegardt, F. G.. 1998. “Natural Trans-Splicing in Carnitine Octanoyltransferase Pre-mRNAs in Rat Liver.” Proceedings of the National Academy of Science 95 (21): 12185–90.CrossRefGoogle ScholarPubMed
Crick, F. H. 1958. “On Protein Synthesis.” Symposia of the Society for Experimental Biology 12:138–63.Google ScholarPubMed
Falk, R. 1986. “What Is a Gene?” Studies in History and Philosophy of Science 17:133–70.CrossRefGoogle ScholarPubMed
Falk, R.. 2003. “Linkage: From Particulate to Interactive Genetics.” Journal of the History of Biology 36 (1): 87–117.CrossRefGoogle ScholarPubMed
Finta, C., and Zaphiropoulos, P. G.. 2002. “Intergenic mRNA Molecules Resulting from Trans-Splicing.” Journal of Biological Chemistry 277 (8): 5882–90.CrossRefGoogle ScholarPubMed
Fox-Keller, E. 2000. The Century of the Gene. Cambridge, MA: Harvard University Press.Google Scholar
Fox-Keller, E.. 2001. “Beyond the Gene but Beneath the Skin.” In Cycles of Contingency: Developmental Systems and Evolution, ed. Oyama, S., Griffiths, P., and Gray, R., 299–312. Cambridge, MA: MIT Press.Google Scholar
Fox-Keller, E., and Harel, D.. 2007. “Beyond the Gene.” PLoS ONE 2 (11): e1231, doi:10.371/journal.pone.0001231.CrossRefGoogle Scholar
Gerstein, M. B., Bruce, C., Rozowsky, J. S., Zheng, D., Du, J., Korbel, J. O., Emanuelsson, O., Zhang, Z. D., Weissman, S., and Snyder, M.. 2007. “What Is a Gene, Post-ENCODE? History and Updated Definition.” Genome Research 17 (6): 669–81.CrossRefGoogle ScholarPubMed
Griffiths, P., and Neumann-Held, E.. 1999. “The Many Faces of the Gene.” Bioscience 49:656–63.CrossRefGoogle Scholar
Griffiths, P. E., and Stotz, K.. 2006. “Genes in the Postgenomic Era.” Theoretical Medicine and Bioethics 27 (6): 499–521.CrossRefGoogle ScholarPubMed
Griffiths, P. E., and Stotz, K.. 2007. “Gene.” In The Cambridge Companion to the Philosophy of Biology, ed. Ruse, M. and Hull, D.. Cambridge: Cambridge University Press.Google Scholar
Lauffenburger, D. A. 2000. “Cell Signaling Pathways as Control Modules: Complexity for Simplicity?” Proceedings of the National Academy of Science 97:5031–33.CrossRefGoogle ScholarPubMed
Levine, M., and Davidson, E.. 2005. “Gene Regulatory Networks for Development.” Proceedings of the National Academy of Science 102 (14): 4936–42.CrossRefGoogle ScholarPubMed
Mandoiu, I., and Zelikovsky, A.. 2008. Bioinformatics Algorithms: Techniques and Applications. Hoboken, NJ: Wiley.CrossRefGoogle ScholarPubMed
Mazumder, B., Seshadri, V., and Fox, P. L.. 2003. “Translational Control by the 3′-UTR: The Ends Specify the Means.” Trends in Biochemical Sciences 28 (2): 91–98.CrossRefGoogle ScholarPubMed
Morgan, T. H. 1935. “The Relation of Genetics to Physiology and Medicine.” Scientific Monthly 41 (1): 5–18.Google Scholar
Portin, P. 2002. “Historical Development of the Concept of the Gene.” Journal of Medicine and Philosophy 27 (3): 257–86.CrossRefGoogle ScholarPubMed
Stotz, K. 2006. “With ‘Genes’ Like That, Who Needs an Environment? Postgenomics's Argument for the ‘Ontogeny of Information.’” Philosophy of Science 73:905–17.CrossRefGoogle Scholar
Stotz, K.. 2011. “2001 and All That: A Tale of a Third Science.” Biology and Philosophy, forthcoming.Google Scholar
Stotz, K., Bostanci, A., and Griffiths, P.. 2006. “Tracking the Shift to ‘Postgenomics.’” Community Genetics 9:190–96.Google Scholar
Turner, B. 2001. Chromatin and Gene Regulation: Mechanisms in Epigenetics. Oxford: Blackwell.CrossRefGoogle Scholar
Wain, H. M., Bruford, E. A., Lovering, R. C., Lush, M. J., Wright, M. W., and Povey, S.. 2002. “Guidelines for Human Gene Nomenclature.” Genomics 79 (4): 464–70.CrossRefGoogle ScholarPubMed
Waters, C. K. 1994. “Genes Made Molecular.” Philosophy of Science 61:163–85.CrossRefGoogle Scholar
Watson, J. D., and Crick, F. H.. 1953. “Genetical Implications of the Structure of Deoxyribonucleic Acid.” Nature 171 (4361): 964–67.CrossRefGoogle ScholarPubMed