Hostname: page-component-78c5997874-94fs2 Total loading time: 0 Render date: 2024-11-19T06:06:58.819Z Has data issue: false hasContentIssue false
  • English
  • Français

Biological Codes and Topological Causation

Published online by Cambridge University Press:  01 January 2022

Benjamin Jantzen  and
David Danks
Get access Rights & Permissions [Opens in a new window]

Abstract

Various causal details of the genetic process of translation have been singled out to account for its privileged status as a ‘code’. We explicate the biological uses of coding talk by characterizing a class of special causal processes in which topological properties are the causally relevant ones. This class contains both the process of translation and communication theoretic coding processes as special cases. We propose a formalism in terms of graphs for expressing our theory of biological codes and discuss its utility in understanding biological systems.

Type
Research Article
Information
Philosophy of Science , Volume 75 , Issue 3 , July 2008 , pp. 259 - 277
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

‡

Portions of this article first appeared in Benjamin Jantzen's M.A. thesis. Thanks to Peter Spirtes and two anonymous referees for helpful comments and suggestions. Frederick Eberhardt, Douglas Perkins, and Richard Yeh also provided valuable discussions and comments on earlier drafts.

References

Abramson, Norman (1963), Information Theory and Coding. New York: McGraw-Hill.Google Scholar
Buckley, Fred, and Lewinter, Marty (2003), A Friendly Introduction to Graph Theory. Upper Saddle River, NJ: Prentice-Hall.Google Scholar
Diudea, Mircea V., Gutman, Ivan, and Jantschi, L. (2001), Molecular Topology. Huntington, NY: Nova Science.Google Scholar
Dretske, Fred I. (1981), Knowledge and the Flow of Information. Cambridge, MA: MIT Press.Google Scholar
Eberhardt, Frederick, and Scheines, Richard (2006), “Interventions and Causal Inference”, Interventions and Causal Inference 74:981–995.Google Scholar
Gabius, H. J. (2000), “Biological Information Transfer beyond the Genetic Code: The Sugar Code”, Biological Information Transfer beyond the Genetic Code: The Sugar Code 87:108–121.Google ScholarPubMed
Gabius, H. J., and Gabius, S. (1997), Glycosciences: Status and Perspectives. London: Chapman & Hall.Google Scholar
Godfrey-Smith, Peter (2000a), “Information, Arbitrariness, and Selection: Comments on Maynard Smith”, Information, Arbitrariness, and Selection: Comments on Maynard Smith 67:202–207.Google Scholar
Godfrey-Smith, Peter (2000b), “On the Theoretical Role of `Genetic Coding’”, On the Theoretical Role of `Genetic Coding’ 67:26–44.Google Scholar
Griffiths, Paul E. (2001), “Genetic Information: A Metaphor in Search of a Theory”, Genetic Information: A Metaphor in Search of a Theory 68:394–412.Google Scholar
Maynard Smith, John (2000), “The Concept of Information in Biology”, The Concept of Information in Biology 67:177–194.Google Scholar
Pogliani, L. (2000), “From Molecular Connectivity Indices to Semiempirical Connectivity Terms: Recent Trends in Graph Theoretical Descriptors”, From Molecular Connectivity Indices to Semiempirical Connectivity Terms: Recent Trends in Graph Theoretical Descriptors 100:3827–3858.Google ScholarPubMed
Rashevsky, N. (1955), “Life, Information Theory, and Topology”, Life, Information Theory, and Topology 17:229–235.Google Scholar
Sarkar, Sahotra (1996), “Decoding ‘Coding’—Information and DNA”, Decoding ‘Coding’—Information and DNA 46:857–864.Google Scholar
Shannon, C. E. (1948), “A Mathematical Theory of Communication”, A Mathematical Theory of Communication 27:379–423.Google Scholar
Šustar, Predrag (2007), “Crick's Notion of Genetic Information and the ‘Central Dogma’ of Molecular Biology”, Crick's Notion of Genetic Information and the ‘Central Dogma’ of Molecular Biology 58:13–24.Google Scholar
Varki, Ajit, et al., eds. (1999), Essentials of Glycobiology. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Woodward, James (2003), Making Things Happen: A Theory of Causal Explanation. Oxford Studies in Philosophy of Science. New York: Oxford University Press.Google Scholar
Woodward, James, and Hitchcock, Christopher (2003), “Explanatory Generalizations, Part I: A Counterfactual Account”, Noûs 37 1:1–24.CrossRefGoogle Scholar
Yockey, Hubert P. (1992), Information Theory and Molecular Biology. Cambridge: Cambridge University Press.Google Scholar