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Abstraction and the Organization of Mechanisms

Published online by Cambridge University Press:  01 January 2022

Arnon Levy  and
William Bechtel
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Abstract

Proponents of mechanistic explanation all acknowledge the importance of organization. But they have also tended to emphasize specificity with respect to parts and operations in mechanisms. We argue that in understanding one important mode of organization—patterns of causal connectivity—a successful explanatory strategy abstracts from the specifics of the mechanism and invokes tools such as those of graph theory to explain how mechanisms with a particular mode of connectivity will behave. We discuss the connection between organization, abstraction, and mechanistic explanation and illustrate our claims by looking at an example from recent research on so-called network motifs.

Type
Research Article
Information
Philosophy of Science , Volume 80 , Issue 2 , April 2013 , pp. 241 - 261
Copyright
Copyright © The Philosophy of Science Association

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Footnotes

†

For written and oral comments we wish to thank Uri Alon, Carl Craver, and Lindley Darden, as well as an anonymous referee for this journal.

References

Acar, Murat, Pando, Bernardo F., Arnold, Frances H., Elowitz, Michael B., and van Oudenaarden, Alexander. 2010. “A General Mechanism for Network-Dosage Compensation in Gene Circuits.” Science 329:1656–60.CrossRefGoogle ScholarPubMed
Alon, Uri. 2007a. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall.Google Scholar
Alon, Uri 2007b. “Network Motifs: Theory and Experimental Approaches.” Nature Reviews Genetics 8:450–61.CrossRefGoogle Scholar
Artzy-Randrup, Yael, Fleishman, Sarel J., Ben-Tal, Nir, and Stone, Lewi. 2004. “Comment on ‘Network Motifs: Simple Building Blocks of Complex Networks’ and ‘Superfamilies of Evolved and Designed Networks.’” Science 305:1107.CrossRefGoogle Scholar
Barabási, Albert-László, and Albert, Réka. 1999. “Emergence of Scaling in Random Networks.” Science 286:509–12.CrossRefGoogle ScholarPubMed
Barkai, N., and Leibler, S. 1997. “Robustness in Simple Biochemical Networks.” Nature 387:913–17.CrossRefGoogle ScholarPubMed
Bechtel, William. 2006. Discovering Cell Mechanisms: The Creation of Modern Cell Biology. Cambridge: Cambridge University Press.Google Scholar
Bechtel, William, and Abrahamsen, Adele. 2005. “Explanation: A Mechanist Alternative.” Studies in History and Philosophy of Biological and Biomedical Sciences 36:421–41.CrossRefGoogle ScholarPubMed
Bechtel, William, and Abrahamsen, Adele 2010. “Dynamic Mechanistic Explanation: Computational Modeling of Circadian Rhythms as an Exemplar for Cognitive Science.” Studies in History and Philosophy of Science A 41:321–33.CrossRefGoogle ScholarPubMed
Bechtel, William, and Abrahamsen, Adele 2011. “Complex Biological Mechanisms: Cyclic, Oscillatory, and Autonomous.” In Philosophy of Complex Systems: Handbook of the Philosophy of Science, ed. Hooker, Clifford A., 257–85. New York: Elsevier.Google Scholar
Bechtel, William, and Richardson, Robert C. 2010. Discovering Complexity: Decomposition and Localization as Strategies in Scientific Research. Repr. Cambridge, MA: MIT Press. First published in 1993 by Princeton University Press.CrossRefGoogle Scholar
Craver, Carl F. 2007. Explaining the Brain: Mechanisms and the Mosaic Unity of Neuroscience. New York: Oxford University Press.CrossRefGoogle Scholar
Craver, Carl F. 2008. “Physical Law and Mechanistic Explanation in the Hodgkin and Huxley Model of the Action Potential.” Philosophy of Science 75:1022–33.CrossRefGoogle Scholar
Cummins, Robert. 1975. “Functional Analysis.” Journal of Philosophy 72:741–65.CrossRefGoogle Scholar
Darden, Lindley. 2006. Reasoning in Biological Discoveries. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Darden, Lindley, and Craver, Carl. 2002. “Strategies in the Interfield Discovery of the Mechanism of Protein Synthesis.” Studies in History and Philosophy of Biological and Biomedical Sciences 33:1–28.CrossRefGoogle Scholar
Erdös, Paul, and Rényi, Alfréd. 1960. “On the Evolution of Random Graphs.” Proceedings of the Mathematical Institute of the Hungarian Academy of Sciences 5:17–61.Google Scholar
Ermentrout, G. B., and Kopell, N. 1984. “Frequency Plateaus in a Chain of Weakly Coupled Oscillators.” Pt. 1. Siam Journal on Mathematical Analysis 15:215–37.CrossRefGoogle Scholar
Field, Richard J., Körös, Endre, and Noyes, Richard M. 1972. “Oscillations in Chemical Systems.” Pt. 2, “Thorough Analysis of Temporal Oscillation in the Bromate-Cerium-Malonic Acid System.” Journal of the American Chemical Society 94:8649–64.CrossRefGoogle Scholar
Gervais, Raoul, and Weber, Erik. 2011. “The Covering Law Model Applied to Dynamical Cognitive Science: A Comment on Joel Walmsley.” Minds and Machines 21:33–39.CrossRefGoogle Scholar
Godfrey-Smith, Peter. 2009. “Abstractions, Idealizations, and Evolutionary Biology.” In Mapping the Future of Biology: Evolving Concepts and Theories, ed. Barberousse, Anouk, Morange, Michel, and Pradeu, Thomas, 47–55. Boston: Springer.CrossRefGoogle Scholar
He, Hao, Sui, Jing, Yu, Qingbao, Turner, Jessica A., Ho, Beng-Choon, Sponheim, Scott R., Manoach, Dara S., Clark, Vincent P., and Calhoun, Vince D. 2012. “Altered Small-World Brain Networks in Schizophrenia Patients during Working Memory Performance.” PLoS ONE 7:e38195.CrossRefGoogle ScholarPubMed
Jones, Martin R. 2005. “Idealization and Abstraction: A Framework.” In Idealization 12: Correcting the Model, ed. Thomson-Jones, Martin and Cartwright, Nancy, 173–217. Amsterdam: Rodopi.CrossRefGoogle Scholar
Kalir, Shiraz, Mangan, Shmoolik, and Alon, Uri. 2005. “A Coherent Feed-Forward Loop with a Sum Input Function Prolongs Flagella Expression in Escherichia Coli.” Molecular Systems Biology 1:2005.0006.CrossRefGoogle ScholarPubMed
Kitcher, Philip. 1981. “Explanatory Unification.” Philosophy of Science 48:507–31.CrossRefGoogle Scholar
Kopell, Nancy, and Ermentrout, G. Bard. 1988. “Coupled Oscillators and the Design of Central Pattern Generators.” Mathematical Biosciences 90:87–109.CrossRefGoogle Scholar
Levy, Arnon. 2013. “Causal Organization and Strategies of Abstraction.” Working paper, Van Leer Jerusalem Institute.Google Scholar
Levy, Arnon Forthcoming. “What Was Hodgkin and Huxley’s Achievement.” British Journal for the Philosophy of Science.Google Scholar
Lewis, David. 1986. On the Plurality of Worlds. Malden, MA: Blackwell.Google Scholar
Machamer, Peter, Darden, Lindley, and Craver, Carl F. 2000. “Thinking about Mechanisms.” Philosophy of Science 67:1–25.CrossRefGoogle Scholar
Mangan, Shmoolik, Itzkovitz, Shalev, Zaslaver, Alon, and Alon, Uri. 2006. “The Incoherent Feed-Forward Loop Accelerates the Response-Time of the gal System of Escherichia Coli.” Journal of Molecular Biology 356:1073–81.CrossRefGoogle ScholarPubMed
Mangan, Shmoolik, Zaslaver, Alon, and Alon, Uri. 2003. “The Coherent Feedforward Loop Serves as a Sign-Sensitive Delay Element in Transcription Networks.” Journal of Molecular Biology 334:197–204.CrossRefGoogle ScholarPubMed
Maxwell, James Clerk. 1868. “On Governors.” Proceedings of the Royal Society of London 16:270–83.Google Scholar
Newman, Mark E. J. 2003. “The Structure and Function of Complex Networks.” SIAM Review 45:167–256.CrossRefGoogle Scholar
Pearl, Judea. 2000. Causality: Models, Reasoning, and Inference. Cambridge: Cambridge University Press.Google Scholar
Power, Jonathan D., Cohen, Alexander L., Nelson, Steven M., Wig, Gagan S., Barnes, Kelly Anne, Church, Jessica A., Vogel, Alecia C., Laumann, Timothy O., Miezin, Fran M., Schlaggar, Bradley L., and Petersen, Steven E. 2011. “Functional Network Organization of the Human Brain.” Neuron 72:665–78.CrossRefGoogle ScholarPubMed
Rosen, Gideon. 2001. “Abstract Objects.” In The Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N. Palo Alto, CA: Stanford University.Google Scholar
Solé, Ricard V., and Valverde, Sergi. 2006. “Are Network Motifs the Spandrels of Cellular Complexity?” Trends in Ecology and Evolution 21:419–22.CrossRefGoogle ScholarPubMed
Spirtes, Peter, Glymour, Clark N., and Scheines, Richard. 2000. Causation, Prediction, and Search. 2nd ed. Cambridge, MA: MIT Press.Google Scholar
Sporns, Olaf. 2010. Networks of the Brain. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Strevens, Michael. 2008. Depth: An Account of Scientific Explanation. Cambridge, MA: Harvard University Press.Google Scholar
Sun, Junfeng, Tong, Shanbao, and Yang, Guo-Yang. 2012. “Reorganization of Brain Networks in Aging and Age-Related Diseases.” Aging and Disease 3:181–93.Google ScholarPubMed
Ward, Jonathan J., and Thornton, Janet M. 2007. “Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network.” PLoS Computational Biology 3:e198.CrossRefGoogle ScholarPubMed
Watts, Duncan, and Strogatz, Steven. 1998. “Collective Dynamics of Small Worlds.” Nature 393:440–42.CrossRefGoogle Scholar
Wiener, Norbert. 1948. Cybernetics; or, Control and Communication in the Animal and the Machine. New York: Wiley.Google ScholarPubMed
Wimsatt, William C. 1986. “Forms of Aggregativity.” In Human Nature and Natural Knowledge, ed. Donagan, Alan, Perovich, Anthony N., and Wedin, Mmichael V., 259–93. Dordrecht: Reidel.Google Scholar
Winfree, Arthur T. 1967. “Biological Rhythms and the Behavior of Populations of Coupled Oscillators.” Journal of Theoretical Biology 16:15–42.CrossRefGoogle ScholarPubMed
Woodward, James. 2003. Making Things Happen: A Theory of Causal Explanation. Oxford: Oxford University Press.Google Scholar
Yook, Soon-Hyung, Oltvai, Zoltán N., and Barabási, Albert-László. 2004. “Functional and Topological Characterization of Protein Interaction Networks.” Proteomics 4:928–42.CrossRefGoogle ScholarPubMed