Hostname: page-component-5d59c44645-jb2ch Total loading time: 0 Render date: 2024-03-04T09:44:07.434Z Has data issue: false hasContentIssue false

Multiple Realization in Systems Biology

Published online by Cambridge University Press:  01 January 2022

Abstract

Thomas Polger and Lawrence Shapiro claim that unlike human-made artifacts cases of multiple realization in naturally occurring systems are uncommon. Drawing on cases from systems biology, I argue that multiple realization in naturally occurring systems is not as uncommon as Polger and Shapiro initially thought. The relevant cases, which I draw from systems biology, involve generalizable design principles called network motifs, which recur in different organisms and species and perform specific functions. I show that network motifs with entirely different underlying causal structures can perform the same function of interest. The article also considers the scope problem of multiple realization.

Type
Research Article
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 am grateful to a number of friends and colleagues for feedback on early drafts of this work, including Malcolm Forster, Ying Liu, and Jiji Zhang. I am also grateful to two anonymous referees, who helped me significantly strengthen some arguments of the article, and two friends, Carl Brusse and Caitrin Donovan, who offered excellent language assistance. This study was funded by the Humanities and Social Sciences Fund for Early-Career Scholars provided by the Ministry of Education, China (grant 0300 270 0002). The author declares that he or she has no conflict of interest.

References

Aizawa, Kenneth. 2009. “Neuroscience and Multiple Realization: A Reply to Bechtel and Mundale.” Synthese 167 (3): 493510..CrossRefGoogle Scholar
Aizawa, Kenneth. 2013. “Multiple Realization by Compensatory Differences.” European Journal for Philosophy of Science 3 (1): 6986..CrossRefGoogle Scholar
Aizawa, Kenneth, and Gillett, Carl. 2011. “The Autonomy of Psychology in the Age of Neuroscience.” In Causality in the Sciences, Vol. 6, ed. Phyllis McKay Illari, Federica Russo, and Jon Williamson, 202–23. Oxford: Oxford University Press.Google Scholar
Alberghina, Lilia, and Westerhoff, Hans V.. 2005. Systems Biology: Definitions and Perspectives. vol. 13. Dordrecht: Springer.CrossRefGoogle Scholar
Alon, Uri. 2007a. An Introduction to Systems Biology: Design Principles of Biological Circuits. London: Chapman & Hall.Google Scholar
Alon, Uri. 2007b. “Network Motifs: Theory and Experimental Approaches.” Nature Reviews Genetics 8 (6): 450–61..CrossRefGoogle Scholar
Arias, Alfonso Martinez. 2003. “Wnts as Morphogens? The View from the Wing of Drosophila.Nature Reviews Molecular Cell Biology 4 (4): 321–25..Google Scholar
Babu, M. Madan, Luscombe, Nicholas M., Aravind, L., Gerstein, Mark, and Teichmann, Sarah A.. 2004. “Structure and Evolution of Transcriptional Regulatory Networks.” Current Opinion in Structural Biology 14 (3): 283–91..CrossRefGoogle ScholarPubMed
Batterman, Robert. 2000. “Multiple Realizability and Universality.” British Journal for the Philosophy of Science 51 (1): 115–45..CrossRefGoogle Scholar
Batterman, Robert. 2018. “Autonomy of Theories: An Explanatory Problem.” Noûs 52 (4): 858–73..CrossRefGoogle Scholar
Bechtel, William, and Mundale, Jennifer. 1999. “Multiple Realizability Revisited: Linking Cognitive and Neural States.” Philosophy of Science 66 (2): 175207..CrossRefGoogle Scholar
Becskei, Attila, and Serrano, Luis. 2000. “Engineering Stability in Gene Networks by Autoregulation.” Nature 405 (6786): 590–93..CrossRefGoogle ScholarPubMed
Bickle, John. 2003. Philosophy and Neuroscience: A Ruthlessly Reductive Account. Dordrecht: Springer.CrossRefGoogle Scholar
Bickle, John. 2010. “Has the Last Decade of Challenges to the Multiple Realization Argument Provided Aid and Comfort to Psychoneural Reductionists?Synthese 177 (2): 247–60..CrossRefGoogle Scholar
Block, Ned J., and Fodor, Jerry A.. 1972. “What Psychological States Are Not.” Philosophical Review 81 (2): 159–81..CrossRefGoogle Scholar
Boogerd, Fred, Bruggeman, Frank J., Hofmeyr, Jan-Hendrik S., and Westerhoff, Hans V.. 2007. Systems Biology: Philosophical Foundations. Amsterdam: Elsevier.Google Scholar
Braillard, Pierre-Alain. 2010. “Systems Biology and the Mechanistic Framework.” History and Philosophy of the Life Sciences 32 (1): 4362..Google ScholarPubMed
Brigandt, Ingo. 2018. “Explanation of Molecular Processes without Tracking Mechanism Operation.” Philosophy of Science 85 (5): 984–97..CrossRefGoogle Scholar
Camas, Francisco M., Blázquez, Jesús, and Poyatos, Juan F.. 2006. “Autogenous and Nonautogenous Control of Response in a Genetic Network.” Proceedings of the National Academy of Sciences 103 (34): 12718–23..CrossRefGoogle Scholar
Chirimuuta, Mazviita. 2018. “Marr, Mayr, and MR: What Functionalism Should Now Be About.” Philosophical Psychology 31 (3): 403–18..CrossRefGoogle Scholar
Clapp, Lenny. 2001. “Disjunctive Properties: Multiple Realizations.” Journal of Philosophy 98 (3): 111–36..Google Scholar
Conant, Gavin C., and Wagner, Andreas. 2003. “Convergent Evolution of Gene Circuits.” Nature Genetics 34 (3): 264–66..CrossRefGoogle ScholarPubMed
Couch, Mark B. 2004. “Discussion: A Defense of Bechtel and Mundale.” Philosophy of Science 71 (2): 198204..CrossRefGoogle Scholar
Couch, Mark B.. 2005. “Functional Properties and Convergence in Biology.” Philosophy of Science 72 (5): 1041–51..CrossRefGoogle Scholar
Couch, Mark B.. 2009. “Multiple Realization in Comparative Perspective.” Biology and Philosophy 24 (4): 505–19..CrossRefGoogle Scholar
Couch, Mark B.. 2018. “Some Concerns with Polger and Shapiro’s View.” Philosophical Psychology 31 (3): 419–30..CrossRefGoogle Scholar
Doncic, Andreas, and Skotheim, Jan M.. 2013. “Feedforward Regulation Ensures Stability and Rapid Reversibility of a Cellular State.” Molecular Cell 50 (6): 856–68..CrossRefGoogle ScholarPubMed
Eldar, Avigdor, Dorfman, Ruslan, Weiss, Daniel, Ashe, Hilary, Shilo, Ben-Zion, and Barkai, Naama. 2002. “Robustness of the BMP Morphogen Gradient in Drosophila Embryonic Patterning.” Nature 419 (6904): 304–8..CrossRefGoogle ScholarPubMed
Eldar, Avigdor, Rosin, Dalia, Shilo, Ben-Zion, and Barkai, Naama. 2003. “Self-Enhanced Ligand Degradation Underlies Robustness of Morphogen Gradients.” Developmental Cell 5 (4): 635–46..CrossRefGoogle ScholarPubMed
Eldar, Avigdor, Shilo, Ben-Zion, and Barkai, Naama. 2004. “Elucidating Mechanisms Underlying Robustness of Morphogen Gradients.” Current Opinion in Genetics and Development 14 (4): 435–39..CrossRefGoogle ScholarPubMed
Ellis, George F. R. 2008. “On the Nature of Causation in Complex Systems.” Transactions of the Royal Society of South Africa 63 (1): 6984..CrossRefGoogle Scholar
Ellis, George F. R.. 2011. “Top-Down Causation and Emergence: Some Comments on Mechanisms.” Interface Focus 2 (1): 126–40..Google Scholar
Fang, Wei. 2018. “The Case for Multiple Realization in Biology.” Biology and Philosophy 33 (1): 3.CrossRefGoogle Scholar
Fodor, Jerry A. 1974. “Special Sciences; or, The Disunity of Science as a Working Hypothesis.” Synthese 28 (2): 97115..CrossRefGoogle Scholar
Ghosh, Bhaswar, Karmakar, Rajesh, and Bose, Indrani. 2005. “Noise Characteristics of Feed Forward Loops.” Physical Biology 2 (1): 3645..CrossRefGoogle ScholarPubMed
Gillett, Carl. 2003. “The Metaphysics of Realization, Multiple Realizability, and the Special Sciences.” Journal of Philosophy 100 (11): 591603..Google Scholar
Green, Sara. 2015. “Revisiting Generality in Biology: Systems Biology and the Quest for Design Principles.” Biology and Philosophy 30 (5): 629–52..CrossRefGoogle Scholar
Green, Sara. 2017. “Philosophy of Systems and Synthetic Biology.” In Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N.. Stanford, CA: Stanford University. https://plato.stanford.edu/entries/systems-synthetic-biology/#DesiPrinBiol.Google Scholar
Kim, Dongsan, Kwon, Yung-Keun, and Cho, Kwang-Hyun. 2008. “The Biphasic Behavior of Incoherent Feed-Forward Loops in Biomolecular Regulatory Networks.” Bioessays 30 (11–12): 1204–11.CrossRefGoogle ScholarPubMed
Kitano, Hiroaki. 2002. “Systems Biology: A Brief Overview.” Science 295 (5560): 1662–64..CrossRefGoogle ScholarPubMed
Kitano, Hiroaki. 2004. “Biological Robustness.” Nature Reviews Genetics 5 (11): 826–37..CrossRefGoogle ScholarPubMed
Kitano, Hiroaki. 2007. “Towards a Theory of Biological Robustness.” Molecular Systems Biology 3 (1): 137.CrossRefGoogle ScholarPubMed
Kitcher, Philip. 1984. “1953 and All That: A Tale of Two Sciences.” Philosophical Review 93 (3): 335–73..CrossRefGoogle Scholar
Kollmann, Markus, L⊘vdok, Linda, Bartholomé, Kilian, Timmer, Jens, and Sourjik, Victor. 2005. “Design Principles of a Bacterial Signalling Network.” Nature 438 (7067): 504–7..CrossRefGoogle ScholarPubMed
Koskinen, Rami. 2017. “Synthetic Biology and the Search for Alternative Genetic Systems: Taking How-Possibly Models Seriously.” European Journal for Philosophy of Science 7 (3): 493506..CrossRefGoogle Scholar
Latchman, David S. 1997. “Transcription Factors: An Overview.” International Journal of Biochemistry and Cell Biology 29 (12): 1305–12..CrossRefGoogle ScholarPubMed
Levy, Arnon, and Bechtel, William. 2013. “Abstraction and the Organization of Mechanisms.” Philosophy of Science 80 (2): 241–61..CrossRefGoogle Scholar
Mangan, Shmoolik, and Alon, Uri. 2003. “Structure and Function of the Feed-Forward Loop Network Motif.” Proceedings of the National Academy of Sciences 100 (21): 11980–85..CrossRefGoogle ScholarPubMed
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 (5): 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 (2): 197204..CrossRefGoogle ScholarPubMed
Milo, Ron, Shen-Orr, Shai, Itzkovitz, Shalev, Kashtan, Nadav, Chklovskii, Dmitri, and Alon, Uri. 2002. “Network Motifs: Simple Building Blocks of Complex Networks.” Science 298 (5594): 824–27..CrossRefGoogle ScholarPubMed
Molina, Carlos A., Foulkes, Nicholas S., Lalli, Enzo, and Sassone-Corsi, Paolo. 1993. “Inducibility and Negative Autoregulation of CREM: An Alternative Promoter Directs the Expression of ICER, an Early Response Repressor.” Cell 75 (5): 875–86..CrossRefGoogle ScholarPubMed
Moreno-Risueno, Miguel A., and Benfey, Philip N.. 2011. “Time-Based Patterning in Development: The Role of Oscillating Gene Expression.” Transcription 2 (3): 124–29..CrossRefGoogle ScholarPubMed
Morishita, Yoshihiro, and Hironaka, Ken-ichi. 2013. “Systems Approach to Developmental Biology: Designs for Robust Patterning.” IET Systems Biology 7 (2): 3849..CrossRefGoogle ScholarPubMed
Béla, Novák, and Tyson, John J.. 2008. “Design Principles of Biochemical Oscillators.” Nature Reviews Molecular Cell Biology 9 (12): 981–91..Google Scholar
O’Malley, Maureen A., and Dupré, John. 2005. “Fundamental Issues in Systems Biology.” BioEssays 27 (12): 1270–76..Google ScholarPubMed
Polger, Thomas W. 2002. “Putnam’s Intuition.” Philosophical Studies 109 (2): 143–70..CrossRefGoogle Scholar
Polger, Thomas W.. 2008. “Two Confusions Concerning Multiple Realization.” Philosophy of Science 75 (5): 537–47..CrossRefGoogle Scholar
Polger, Thomas W.. 2009. “Evaluating the Evidence for Multiple Realization.” Synthese 167 (3): 457–72..CrossRefGoogle Scholar
Polger, Thomas W.. 2015. “Realization and Multiple Realization, Chicken and Egg.” European Journal of Philosophy 23 (4): 862–77..CrossRefGoogle Scholar
Polger, Thomas W., and Shapiro, Lawrence A.. 2008. “Understanding the Dimensions of Realization.” Journal of Philosophy 105 (4): 213–22..CrossRefGoogle Scholar
Polger, Thomas W., and Shapiro, Lawrence A.. 2016. The Multiple Realization Book. Oxford: Oxford University Press.CrossRefGoogle Scholar
Polger, Thomas W., and Shapiro, Lawrence A.. 2018. “Responses to Critics.” Philosophical Psychology 31 (3): 446–57..CrossRefGoogle Scholar
Putnam, Hilary. 1967. “Psychological Predicates.” In Art, Mind, and Religion, ed. Capitan, William H. and Merrill, Daniel D., 1:3748. Pittsburgh: University of Pittsburgh Press.Google Scholar
Richardson, Robert C. 2008. “Autonomy and Multiple Realization.” Philosophy of Science 75 (5): 526–36..CrossRefGoogle Scholar
Rosenberg, Alex. 2001. “On Multiple Realization and the Special Sciences.” Journal of Philosophy 98 (7): 365–73..CrossRefGoogle Scholar
Rosenfeld, Nitzan, Elowitz, Michael B., and Alon, Uri. 2002. “Negative Autoregulation Speeds the Response Times of Transcription Networks.” Journal of Molecular Biology 323 (5): 785–93..CrossRefGoogle ScholarPubMed
Savageau, Michael A. 1976. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Reading, MA: Addison-Wesley.Google Scholar
Shapiro, Lawrence A. 2000. “Multiple Realizations.” Journal of Philosophy 97 (12): 635–54..CrossRefGoogle Scholar
Shapiro, Lawrence A.. 2004. The Mind Incarnate. Cambridge, MA: MIT Press.Google Scholar
Shapiro, Lawrence A.. 2008. “How to Test for Multiple Realization.” Philosophy of Science 75 (5): 514–25..CrossRefGoogle Scholar
Shapiro, Lawrence A., and Polger, Thomas W.. 2012. “Identity, Variability, and Multiple Realization in the Special Sciences.” In New Perspectives on Type Identity: The Mental and the Physical, ed. Gozzano, Simone and Hill, Christopher S., 264–88. Cambridge: Cambridge University Press.Google Scholar
Shen-Orr, Shai S., Milo, Ron, Mangan, Shmoolik, and Alon, Uri. 2002. “Network Motifs in the Transcriptional Regulation Network of Escherichia Coli.” Nature Genetics 31 (1): 6468..CrossRefGoogle ScholarPubMed
Singh, Abhyudai, and Hespanha, Joao P.. 2009. “Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks.” Biophysical Journal 96 (10): 4013–23..CrossRefGoogle ScholarPubMed
Sober, Elliott. 1999. “The Multiple Realizability Argument against Reductionism.” Philosophy of Science 66 (4): 542–64..CrossRefGoogle Scholar
Sullivan, Jacqueline Anne. 2008. “Memory Consolidation, Multiple Realizations, and Modest Reductions.” Philosophy of Science 75 (5): 501–13..CrossRefGoogle Scholar
Wall, Michael E., Dunlop, Mary J., and Hlavacek, William S.. 2005. “Multiple Functions of a Feed-Forward-Loop Gene Circuit.” Journal of Molecular Biology 349 (3): 501–14..CrossRefGoogle ScholarPubMed
Walter, Sven, and Eronen, Markus. 2014. “Reduction, Multiple Realizability, and Levels of Reality.” In The Bloomsbury Companion to the Philosophy of Science, ed. French, Steven, and Saatsi, Juha, 138–56. London: Bloomsbury.Google Scholar
Wilson, Robert A., and Craver, Carl F.. 2007. “Realization: Metaphysical and Scientific Perspectives.” In Philosophy of Psychology and Cognitive Science, ed. Thagard, Paul, 81104. Amsterdam: North-Holland.CrossRefGoogle Scholar
Wolpert, Lewis. 2011. “Positional Information and Patterning Revisited.” Journal of Theoretical Biology 269 (1): 359–65..CrossRefGoogle ScholarPubMed
Zabet, Nicolae Radu. 2011. “Negative Feedback and Physical Limits of Genes.” Journal of Theoretical Biology 284 (1): 8291..CrossRefGoogle ScholarPubMed
Zerilli, John. 2019. “Multiple Realization and the Commensurability of Taxonomies.” Synthese 196:3337–53.CrossRefGoogle Scholar