Characterizing Network Explanations in Complex Systems: Patterns, Processes and Epistemic Values
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Characterizing Network Explanations in Complex Systems: Patterns, Processes and Epistemic Values
Yearbook for Philosophy of Complex Systems, Online First : pp. 1–32 | First published online: July 25, 2025
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Philippe Huneman, Institut d’Histoire et de Philosophie des Sciences et des Techniques (CNRS/Université Paris I Panthéon Sorbonne)
References
-
Bailly, F./Longo, G. (2006): Mathématiques et sciences de la nature: la singularité physique du vivant, Hermann, Paris.
Google Scholar -
Bich, L./Skillings, D. (2023): There are no intermediate stages: An organizational view on development, in: Matteo Mossio (eds.), Organization in Biology, Springer, pp. 241–262.
Google Scholar -
Canguilhem, G. (1963): Le normal et le pathologique, PUF, Paris.
Google Scholar -
Cardy, J. (1996): Scaling and Renormalization in Statistical Physics, Cambridge, Cambridge Lecture Note in Physics.
Google Scholar -
Coullet, P./Tresser, P. (1978): Itérations d’endomorphismes et groupes de renormalisation, in: Journal de Physique, Colloques, 39(C5), pp. 25–28.
Google Scholar -
Cross, M. C./Hohenberg, P. C. (1993): Pattern formation outside of equilibrium, in: Review of Modern Physics, 65, 851.
Google Scholar -
Danchin, É./Pocheville, A. (2014): Why and how is cultural transmission a biological process?, in: Biological Theory, 9, pp. 64–75.
Google Scholar -
Devaney, R. (1989): An Introduction to chaotic dynamical systems, Westview Press.
Google Scholar -
DiFrisco, J./Jaeger, J. (2019): Beyond Networks: Mechanism and Process in Evo-Devo, in: Biology & Philosophy, 34(6).
Google Scholar -
Doudna, J./Sternberg, S. (2017): A crack in creation: gene editing and the unthinkable power to control evolution, Houghton Mifflin Harcourt, Boston.
Google Scholar -
England, J. (2015): Dissipative adaptation in driven self-assembly, in: Nature Nanotechnologies, 10(11), pp. 919–923.
Google Scholar -
Friedman, N./Vardi, S./Ronen, M./Alon, U./Stavans, J. (2005): Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria, in: PLoS Biology, 3(7), e238.
Google Scholar -
Gilbert, S. (2005): Mechanisms for the environmental regulation of gene expression: ecological aspects of animal development, in: Journal of Biosciences, 30(1), pp. 65–74.
Google Scholar -
Gilbert, S. (2012): A symbiotic view of life: we have never been individuals, in: The quarterly review of biology, 87(4), pp. 325–341.
Google Scholar -
Goldenfeld, N. (1992): Lectures on phase transitions and the renormalization group, Frontiers in Physics.
Google Scholar -
Gould, S. J. (2000): The Structure of Evolutionary Theory, Harvard University Press.
Google Scholar -
Gould, S. J./Lewontin, R. (1979): The spandrels of San Marco and the panglossian paradigm: a critique of the adaptationist programme, in: Proceeding of Royal Society London, ser. B 205, pp. 581–98.
Google Scholar -
Green, B. J. et al. (2000): Mollusc-Algal Chloroplast Endosymbiosis. Photosynthesis, Thylakoid Protein Maintenance, and Chloroplast Gene Expression Continue for Many Months in the Absence of the Algal Nucleus, in: Plant Physiology, 124, pp. 331–342.
Google Scholar -
Griesemer, J. (2000): Development, culture and the units of inheritance, in: Philosophy of science, 67.
Google Scholar -
Hull, D. L. (1980): Individuality and selection, in: Annual Review of Ecology, Evolution, and Systematics, 11.
Google Scholar -
Hull, D. L. (1988): Science as a process: an evolutionary account of the social and conceptual development of science, University of Chicago Press, Chicago.
Google Scholar -
Jablonka, E./Lamb, M. (2005): Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. MIT Press.
Google Scholar -
Kadanoff, L. P. (1966): Scaling laws for ising models near Tc, in: Physics, 2(6), pp. 263–272.
Google Scholar -
Karsenti, E./Vernos, I. (2001): The Mitotic Spindle: A Self-Made Machine, in: Science, 294(5542), pp. 543–547.
Google Scholar -
Kauffman, S. (2000): Investigations, Oxford University Press, Oxford.
Google Scholar -
Kauffman, S. (2016): Humanity in a Creative Universe, Oxford University Press, Oxford.
Google Scholar -
Kiedrowski, G. von (1986): A Self-Replicating Hexadeoxynucleotide, Angewandte Chemie, 25(12), pp. 932–935.
Google Scholar -
Kramar, M./Alim, K. (2021): Encoding memory in tube diameter hierarchy of living flow network, in: PNAS, 118(10).
Google Scholar -
Kull, K. (2015): Semiosis stems from logical incompability in organic nature: why biophysics does not see meaning, while biosemiotics does, in: Progress in Biophysics and Molecular Biology, 119, pp. 616–621.
Google Scholar -
Lesne, A. (2008): Robustness: confronting lessons from physics and biology, in: Biological Reviews Cambridge Philosophical Society, 83(4), pp. 509–532.
Google Scholar -
Lesne, A. et al. (2008): Physique statistique. Chaos et approches multi-échelles, Belin, Paris.
Google Scholar -
Longo, G./Montévil, M. (2014): Perspectives on organisms, Biological time, Symmetries Singularities, Springer, Berlin/Heidelberg.
Google Scholar -
Lyon, P. (2015): The cognitive cell: bacterial behavior reconsidered, in: Frontiers in Microbiology, 6, Article 264.
Google Scholar -
McTaggart, J. E. (1908): The Unreality of time, in: Mind, 17(68), p. 457–474.
Google Scholar -
Miquel, P.-A. (2023): La vie est-elle naturalisable?, in: Intellectica, pp. 49–69.
Google Scholar -
Miquel, P.-A./Hwang, S.-Y. (2016): From physical to biological individuation, in: Progress in Biophysics and Molecular Biology, 122(1), pp. 51–57.
Google Scholar -
Miquel, P.-A./Soto, A. M./Sonnenschein, C. (2008): On physicalism and downward causation in developmental and cancer biology, in: Acta Biotheoretica, 56(4), pp. 257–274.
Google Scholar -
Mossio, M./Montévil, M. (2015): Biological organization as closure of constraints, in: Journal of Theoretical Biology, Elsevier, 372, pp. 179–91.
Google Scholar -
Mossio, M./Montévil, M. (2020): The identity of organisms in scientific practice: integrating historical and relational conceptions, in: Frontiers in Physiology, 11, p. 611.
Google Scholar -
Neumann, J. von (1958): The computer and the brain, Yale University Press, New Haven.
Google Scholar -
Nicoglou, A. (2009): La plasticité phénotypique: de la microévolution à la macroévolution, in: Heams, T./Huneman, P./Lecointre, G./Silberstein, M. (eds.), Les mondes darwiniens, Editions Matériologiques, Paris.
Google Scholar -
Okasha, S. (2023): The concept of agent in biology: motivations and meanings, in: Biological Theory, 19, pp. 6–10.
Google Scholar -
Perovic, S./Korenic, A./Cirkovic, M./Miquel, P. A. (2020): Symmetry breaking and functional incompleteness in biological systems, in: Progress in Biophysics and Molecular Biology, 150, pp. 1–12.
Google Scholar -
Pocheville, A. (2018): A Darwinian dream: on time, levels, and processes in evolution, in: Evolutionary Causation. Biological and philosophical reflections. Ed. by Tobias Uller and Kevin N. Laland. Vienna Series in Theoretical Biology, MIT Press, Boston.
Google Scholar -
Pontarotti, G./Mossio, M./Pocheville, A. (2022): The genotyp-phenotype distinction: from mendelian genetics to 21st century biology, in: Genetica, 150, pp. 223–234.
Google Scholar -
Prigogine, I./Nicolis, G. (1977): Self- organization in non-equilibrium systems, Willey, New York.
Google Scholar -
NY, Prokopenko, M. et al. (2025): Biological arrow of time: emergence of tangled information hierarchies and self-modelling dynamics, in: Journal of Physics: Complexity, 6.
Google Scholar -
Rogers, T. (2024): A formal model of primitive aspects of cognition and learning in cell biology as a generalizable case study of the threefold logic of Peircean semiotics in natural system, in: Sign System Studies, 52(1/2), pp. 8–48.
Google Scholar -
Simondon, G. (1964): L’individu et sa genèse physico-biologique, PUF, Paris.
Google Scholar -
Tahar, M. (2022): Biological constraints as norms in evolution, in: HPLS, 44, 9.
Google Scholar -
Varela, F. J. (1980): Principles of Biological Autonomy, North Holland/Elsevier, New York.
Google Scholar -
Varela, F. J. (1981): Autonomy and autopoiesis, in: Roth, G./Schwegler, H. (eds.), Self-organizing systems: An interdisciplinary approach, Campus Verlag, Frankfurt/New York, pp. 14–24.
Google Scholar -
Vogel, D./Dussutour, A. (2016): Direct transfer of learned behaviours via cell fusion in non-neural organisms, in: Proceedings of the Royal Society Biological Sciences, 283(1845).
Google Scholar -
Wilson, K. G. (1971): Renormalization group and critical phenomena, in: Physical Review B, 4, pp. 3174–3183.
Google Scholar -
Wilson, K. G./Kogut, J. (1974): The renormalization group and the ε expansion, in: Physics Reports, 12(2), pp. 75–199.
Google Scholar -
Woodward, J. (2003): Making things happen: A theory of causal explanation, Oxford University Press, Oxford.
Google Scholar
Abstract
Network modeling is pervasive in the sciences that address complex systems, especially when they require big data. In the philosophical literature some argued that network analysis in some cases gives rise to explanations, often termed topological. In this paper I use several classical distinctions used in the scientist’s talk about modeling in order to characterize such purported explanations. I show that the distinctions between phenomenological and mechanistic models, as well as the claim that topological explanations are abstractions to be connected to genuine mechanistic explanations, don’t capture what’s at stake with these purported explanations. Finally, I consider the distinctions between epistemic values inspired by Levins (1966) and show that, contrary to what may seem intuitive, the difference between topological and mechanistic explanations is not one between genericity and realism. I call for the recognition of the plurality of uses of network modeling and explanation.
Table of Contents
Section Title | Page | Action | Price |
---|---|---|---|
Philippe Hunemann: Characterizing Network Explanations in Complex Systems:Patterns, Processes and Epistemic Values | 1 | ||
Abstract | 1 | ||
I. Network Explanation: Some Distinctive Features | 3 | ||
II. Network Topologies: The Pattern vs. Process Approach | 7 | ||
1. Patterns and Processes, Phenomenological vs. Mechanistic Modeling | 7 | ||
2. What About Network Modeling? | 10 | ||
III. Looking for Very Abstract Mechanisms? | 12 | ||
1. Network Analysis and Abstract Mechanisms | 13 | ||
2. Network Explanations as a Class of Very Generaland Unrealistic Explanations | 15 | ||
IV. Realism and Genericity as Epistemic Values:Another Look at Network Models | 18 | ||
1. Epistemic Values and the Realism Issue | 18 | ||
2. A Realism Gradient Among the Class of Networks | 20 | ||
3. Recovering Functional Roles from Within Networks | 21 | ||
4. Realism and Genericity: The Case of Functional Ecology | 25 | ||
5. Wrapping up | 27 | ||
V. Conclusion | 27 | ||
References | 28 |