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Biological Information as Choice and Construction

Published online by Cambridge University Press:  01 January 2022

Arnaud Pocheville
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Abstract

A causal approach to biological information is outlined. There are two aspects to this approach: information as determining a choice between alternative objects and information as determining the construction of a single object. The first aspect has been developed in earlier work to yield a quantitative measure of biological information that can be used to analyze biological networks. This article explores the prospects for a measure based on the second aspect and suggests some applications for such a measure. These two aspects are not suggested to exhaust all the facets of biological information.

Type
Research Article
Information
Philosophy of Science , Volume 85 , Issue 5 , December 2018 , pp. 1012 - 1025
Copyright
Copyright © The Philosophy of Science Association

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Footnotes

†

Maël Montévil is warmly thanked for insightful discussions and coining the language of the cell. A manuscript in preparation (Pocheville and Montévil 2018) develops the present paper. Two anonymous reviewers and the editor made numerous very helpful suggestions, and the audience at the 2016 PSA meeting provided kind feedback. Paul Griffiths and Karola Stotz mentored the project, and Maureen O’Malley provided kind encouragement. This research was supported by the Judith and David Coffey Life Lab (headed by Jean Yang), Charles Perkins Centre. This publication was made possible through the support of two grants from the Templeton World Charity Foundation (TWCF0063 to Paul Griffiths, TWCF0242 to Arnaud Pocheville). The opinions expressed in this publication are those of the author and do not necessarily reflect the views of the Templeton World Charity Foundation.

References

Alberts, Bruce, et al. 2013. Essential Cell Biology. 4th ed. New York: Garland Science.CrossRefGoogle Scholar
Artmann, Stefan. 2008. “Biological Information.” In A Companion to the Philosophy of Biology, ed. Sarkar, Sahotra and Plutynski, Anya. New York: Wiley.Google Scholar
Ay, Nihat, and Polani, Daniel. 2008. “Information Flows in Causal Networks.” Advances in Complex Systems 11 (1): 17–41..CrossRefGoogle Scholar
Balduzzi, David. 2011. “Information, Learning and Falsification.” Preprint arXiv:1110.3592.Google Scholar
Barbieri, Marcello. 2007. Introduction to Biosemiotics: The New Biological Synthesis. Dordrecht: Springer Science & Business Media.CrossRefGoogle Scholar
Calcott, Brett, Pocheville, Arnaud, and Griffiths, Paul E.. 2018. “Signals That Make a Difference.” British Journal for the Philosophy of Science. doi:10.1093/bjps/axx022.CrossRefGoogle Scholar
Chaitin, Gregory J. 1979. “Toward a Mathematical Definition of ‘Life.’” In The Maximum Entropy Formalism, ed. Levine, R. D. and Tribus, M., 477–98. Cambridge, MA: MIT Press.Google Scholar
Chaitin, Gregory J. 2012. Proving Darwin: Making Biology Mathematical. New York: Vintage.Google Scholar
Chen, Xin, Kwong, Sam, and Li, Ming. 2000. “A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison.” In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology. New York: ACM.Google Scholar
Chen, Xin, Li, Ming, Ma, Bin, and Tromp, John. 2002. “DNACompress: Fast and Effective DNA Sequence Compression.” Bioinformatics 18 (12): 1696–98..CrossRefGoogle ScholarPubMed
Cooper, Max D., and Alder, Matthew N.. 2006. “The Evolution of Adaptive Immune Systems.” Cell 124:815–22.CrossRefGoogle ScholarPubMed
Cover, Thomas M., and Thomas, Joy A.. 2006. Elements of Information Theory. New York: Wiley.Google Scholar
Crick, Francis. 1958. On Protein Synthesis. Symposium of the Society for Experimental Biology XII. New York: Academic Press.Google ScholarPubMed
Crick, Francis 1970. “Central Dogma of Molecular Biology.” Nature 227 (5258): 561–63..CrossRefGoogle ScholarPubMed
Dretske, Fred I. 1981. Knowledge and the Flow of Information. Oxford: Blackwell.Google Scholar
Godfrey-Smith, Peter. 2000. “On the Theoretical Role of ‘Genetic Coding.’” Philosophy of Science 67:26–44.CrossRefGoogle Scholar
Griffiths, Paul E., Pocheville, Arnaud, Calcott, Brett, Stotz, Karola, Kim, Hyunju, and Knight, Rob. 2015. “Measuring Causal Specificity.” Philosophy of Science 82 (4): 529–55..CrossRefGoogle Scholar
Griffiths, Paul E., and Stotz, Karola. 2013. Genetics and Philosophy: An Introduction. New York: Cambridge University Press.CrossRefGoogle Scholar
Grünwald, Peter D., and Vitányi, Paul M. B.. 2003. “Kolmogorov Complexity and Information Theory: With an Interpretation in Terms of Questions and Answers.” Journal of Logic, Language and Information 12 (4): 497–529..CrossRefGoogle Scholar
Heams, Thomas. 2014. “Randomness in Biology.” Mathematical Structures in Computer Science 24 (3).CrossRefGoogle Scholar
Hiyama, Keiko, Hiyama, Eiso, and Shay, Jerry W.. 2009. “Telomeres and Telomerase in Humans.” In Telomeres and Telomerase in Cancer, ed. Hiyama, Keiko. New York: Springer Science & Business Media.CrossRefGoogle Scholar
Jablonka, Eva. 2002. “Information: Its Interpretation, Its Inheritance, and Its Sharing.” Philosophy of Science 69 (4): 578–605..CrossRefGoogle Scholar
Jacob, François. 1970. La logique du vivant: Une histoire de l’hérédité. Paris: Gallimard.Google Scholar
Janzing, Dominik, Balduzzi, David, Grosse-Wentrup, Moritz, and Schölkopf, Bernhard. 2013. “Quantifying Causal Influences.” Annals of Statistics 41 (5): 2324–58..CrossRefGoogle Scholar
Kay, Lily E. 2000. Who Wrote the Book of Life? A History of the Genetic Code. Stanford, CA: Stanford University Press.Google Scholar
Korb, Kevin B., Hope, Lucas R., and Nyberg, Erik P.. 2009. “Information-Theoretic Causal Power.” In Information Theory and Statistical Learning, ed. Emmert-Streib, Frank and Dehmer, Matthias, 231–65. Boston: Springer.Google Scholar
Kupiec, J. J. 1983. “A Probabilist Theory for Cell Differentiation, Embryonic Mortality and DNA C-Value Paradox.” Speculations in Science and Technology 6 (5): 471–78..Google Scholar
Li, Ming, Badger, Jonathan H., Chen, Xin, Kwong, Sam, Kearney, Paul, and Zhang, Haoyong. 2001. “An Information-Based Sequence Distance and Its Application to Whole Mitochondrial Genome Phylogeny.” Bioinformatics 17 (2): 149–54..CrossRefGoogle ScholarPubMed
Li, Ming, and Vitányi, Paul. 2008. An Introduction to Kolmogorov Complexity and Its Applications. 3rd ed. New York: Springer Science & Business Media.CrossRefGoogle Scholar
Lizier, J. T., and Prokopenko, M.. 2010. “Differentiating Information Transfer and Causal Effect.” European Physical Journal B 73 (4): 605–15..CrossRefGoogle Scholar
Maynard Smith, John, and Szathmary, Eors. 1995. The Major Transitions in Evolution. Oxford: Oxford University Press.Google Scholar
Maynard Smith, John, and Szathmary, Eors 2000. The Origins of Life: From the Birth of Life to the Origin of Language. Oxford: Oxford University Press.Google Scholar
Mayr, Ernst. 1961. “Cause and Effect in Biology.” Science 134:1501–6.CrossRefGoogle ScholarPubMed
Montévil, Maël. 2018. “Possibility Spaces and the Notion of Novelty: From Music to Biology.” Synthese. doi:10.1007/s11229-017-1668-5.CrossRefGoogle Scholar
Pearl, Judea. 2009. Causality: Models, Reasoning, and Inference. 2nd ed. New York: Cambridge University Press.CrossRefGoogle Scholar
Pocheville, Arnaud. 2018a. “New Tools for Thinking about Causation.” Manuscript, University of Sydney.Google Scholar
Pocheville, Arnaud 2018b. “Signals That Represent the World.” Manuscript, University of Sydney.Google Scholar
Pocheville, Arnaud, Griffiths, Paul E., and Stotz, Karola. 2017. “Comparing Causes—an Information-Theoretic Approach to Specificity, Proportionality and Stability.” In Proceedings of the 15th Congress of Logic, Methodology and Philosophy of Science, ed. Leitgeb, Hannes et al. London: College Publications.Google Scholar
Pocheville, Arnaud, and Montévil, Maël. 2018. “Giving Substance to Biological Information.” Manuscript, University of Sydney.Google Scholar
Sarkar, Sahotra. 1996. “Biological Information: A Skeptical Look at Some Central Dogmas of Molecular Biology.” In The Philosophy and History of Molecular Biology: New Perspectives, ed. Sarkar, Sahotra and Cohen, R. S., 187–232. Boston Studies in the Philosophy of Science, vol. 183. Dordrecht: Kluwer.CrossRefGoogle Scholar
Shannon, Claude. 1948. “A Mathematical Theory of Communication.” Bell System Technical Journal 27:379–423.CrossRefGoogle Scholar
Shea, Nicholas. 2007. “Representation in the Genome and in Other Inheritance Systems.” Biology and Philosophy 22 (3): 313–31..CrossRefGoogle Scholar
Stamos, David N. 2001. “Quantum Indeterminism and Evolutionary Biology.” Philosophy of Science 68 (2): 164–84..CrossRefGoogle Scholar
Šustar, Predrag. 2007. “Crick’s Notion of Genetic Information and the ‘Central Dogma’ of Molecular Biology.” British Journal for the Philosophy of Science 58 (1): 13–24..CrossRefGoogle Scholar
Tononi, Giulio, Sporns, Olaf, and Edelman, Gerald M.. 1999. “Measures of Degeneracy and Redundancy in Biological Networks.” Proceedings of the National Academy of Sciences 96 (6): 3257–62..CrossRefGoogle ScholarPubMed
Vinga, Susana. 2014. “Information Theory Applications for Biological Sequence Analysis.” Briefings in Bioinformatics 15 (3): 376–89..CrossRefGoogle ScholarPubMed
Walker, Sara Imari, Davies, Paul C. W., and Ellis, George F. R.. 2017. From Matter to Life: Information and Causality. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Weber, Marcel. 2017. “Discussion Note: Which Kind of Causal Specificity Matters Biologically?” Philosophy of Science 84 (3): 574–85..CrossRefGoogle Scholar
Williams, George C. 1992. Natural Selection: Domains, Levels, and Challenges. Oxford: Oxford University Press.Google Scholar
Woodward, James. 2010. “Causation in Biology: Stability, Specificity, and the Choice of Levels of Explanation.” Biology and Philosophy 25 (3): 287–318..CrossRefGoogle Scholar
Yockey, Hubert P. 2005. Information Theory, Evolution, and the Origin of Life. Cambridge: Cambridge University Press.CrossRefGoogle Scholar