Abstract
At first sight, the empirical study of ontogenesis and the theoretical study of organismal agency seem to have little in common. In this chapter, I discuss why this initial impression is incorrect. First of all, ontogenesis and agency are indirectly connected at the level of the whole organism, because they are co-dependent on the peculiar organisation that characterises living systems. While ontogenesis is constrained by its own requirement to maintain living organisation in the form of organisational closure throughout the lifecycle, agency is grounded in the same phenomenon of organisational continuity. Secondly, cellular agency contributes more directly to various important processes of multicellular development in organisms with multiple levels of organisation. This leads to a view of ontogenesis that emphasises agency and variation in the underlying cellular dynamics and focuses on stability and reproducibility of ontogenetic processes as its main explanatory targets. I examine how these insights can help us bridge the explanatory gap between reductionist mechanistic empirical approaches and theoretical considerations regarding the organisation of an organism as a whole. I conclude that the two approaches are best used in a complementary manner. Only by placing ontogenetic mechanisms within the larger context of the evolving lifecycle can we arrive at an adequate understanding of their functionality and evolution.
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References
Arnellos, A., & Moreno, A. (2015). Multicellular agency: An organizational view. Biology & Philosophy, 30(3), 333–357.
Arnellos, A., Moreno, A., & Ruiz-Mirazo, K. (2014). Organizational requirements for multicellular autonomy: Insights from a comparative case study. Biology & Philosophy, 29(6), 851–884.
Ayad, N. M. E., Kaushik, S., & Weaver, V. M. (2019). Tissue mechanics, an important regulator of development and disease. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1779), 20180215.
Barandiaran, X. E., Di Paolo, E., & Rohde, M. (2009). Defining agency: Individuality, normativity, asymmetry, and spatio-temporality in action. Adaptive Behavior, 17(5), 367–386.
Bechtel, W. (2011). Mechanism and biological explanation. Philosophy of Science, 78(4), 533–557.
Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441.
Bechtel, W., & Abrahamsen, A. (2010). Dynamic mechanistic explanation: Computational modeling of circadian rhythms as an exemplar for cognitive science. Studies in History and Philosophy of Science Part A, 41(3), 321–333.
Bechtel, W., & Richardson, R. C. (1993). Discovering complexity: Decomposition and localization as strategies in scientific research (Original ed.). Princeton University Press.
Bich, L., & Skillings, D. (2023). There are no intermediate stages: An organizational view of development. In M. Mossio (Ed.), Organization in Biology. Springer.
Bich, L., Mossio, M., & Soto, A. M. (2020). Glycemia regulation: From feedback loops to organizational closure. Frontiers in Physiology, 11, 69.
Bickhard, M. H. (2000). Autonomy, function, and representation. Communication and Cognition – Artificial Intelligence, 17, 111–131.
Bigelow, J., & Pargetter, R. (1987). Functions. Journal of Philosophy, 84(4), 181–196.
Boorse, C. (1976). Wright on functions. The Philosophical Review, 85(1), 70–86.
Christensen, W. D., & Bickhard, M. H. (2002). The process dynamics of normative function. The Monist, 85(1), 3–28.
Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. Clarendon Press.
Craver, C., & Tabery, J. (2019). Mechanisms in science. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy (Summer 2019). Metaphysics Research Lab, Stanford University. https://plato.stanford.edu/archives/sum2019/entries/science-mechanisms
Crombach, A., & Jaeger, J. (2021). Life’s attractors continued: Progress in understanding developmental systems through reverse engineering and in silico evolution. In A. Crombach (Ed.), Evolutionary systems biology (pp. 59–88). Springer.
Crombach, A., Wotton, K. R., Jiménez-Guri, E., & Jaeger, J. (2016). Gap gene regulatory dynamics evolve along a genotype network. Molecular Biology and Evolution, 33(5), 1293–1307.
Cummins, R. (1975). Functional analysis. Journal of Philosophy, 72(20), 741–765.
DiFrisco, J. (2014). Hylomorphism and the metabolic closure conception of life. Acta Biotheoretica, 62, 499–525.
DiFrisco, J., & Jaeger, J. (2019). Beyond networks: Mechanism and process in evo-devo. Biology & Philosophy, 34, 54.
DiFrisco, J., & Jaeger, J. (2020). Genetic causation in complex regulatory systems: An integrative dynamic perspective. BioEssays, 42(6), 1900226.
DiFrisco, J., & Jaeger, J. (2021). Homology of process: Developmental dynamics in comparative biology. Interface Focus, 11(3), 20210007.
DiFrisco, J., & Mossio, M. (2020). Diachronic identity in complex life cycles: An organizational perspective. In A. S. Meincke & J. Dupré (Eds.), Biological identity: Perspectives from metaphysics and the philosophy of biology. Routledge.
DiFrisco, J., & Wagner, G. P. (2022). Body plan identity: A mechanistic model. Evolutionary Biology, 49, 123–141.
DiFrisco, J., Love, A. C., & Wagner, G. P. (2020). Character identity mechanisms: A conceptual model for comparative-mechanistic biology. Biology & Philosophy, 35, 44.
DiFrisco, J., Wagner, G. P., & Love, A. C. (2022). Reframing research on evolutionary novelty and co-option: Character identity mechanisms versus deep homology. Seminars in Cell & Developmental Biology, 145, 3–12.
Fox Keller, E. (2002). Making sense of life: Explaining biological development with models, metaphors, and machines. Harvard University Press.
Gibson, J. J. (1979). The ecological approach to visual perception. Houghton Mifflin.
Gilbert, S. F., & Bolker, J. A. (2001). Homologies of process and modular elements of embryonic construction. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 291(1), 1–12.
Glennan, S. S. (1996). Mechanisms and the nature of causation. Erkenntnis, 44, 49–71.
Glennan, S., & Illari, P. (Eds.). (2017). The Routledge handbook of mechanisms and mechanical philosophy. Routledge.
Gold, J. I., & Shadlen, M. N. (2007). The neural basis of decision making. Annual Review of Neuroscience, 30, 535–574.
Goodwin, B. C. (1982a). Biology without Darwinian spectacles. The Biologist, 29, 108–112.
Goodwin, B. C. (1982b). Development and evolution. Journal of Theoretical Biology, 97(1), 43–55.
Goodwin, B. C. (1985). What are the causes of morphogenesis? BioEssays, 3(1), 32–36.
Goodwin, B. C., Kauffman, S., & Murray, J. D. (1993). Is morphogenesis an intrinsically robust process? Journal of Theoretical Biology, 163(1), 135–144.
Griesemer, J. (2006). Genetics from an evolutionary process perspective. In E. M. Neumann & C. Rehmann-Sutter (Eds.), Genes in Development (pp. 199–237). Duke University Press.
Heisenberg, C.-P., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell, 153(5), 948–962.
Hofmeyr, J.-H. S. (2017). Basic Biological Anticipation. In R. Poli (Ed.), Handbook of anticipation (pp. 1–15). Springer.
Hofmeyr, J.-H. S. (2021). A biochemically-realisable relational model of the self-manufacturing cell. Biosystems, 207, 104463.
Jaeger, J. (2018). Shift happens: The developmental and evolutionary dynamics of the gap gene system. Current Opinion in Systems Biology, 11, 65–73.
Jaeger, J. (2023). The fourth perspective: Evolution and organismal agency. In M. Mossio (Ed.), Organization in Biology. Springer.
Jaeger, J., & Crombach, A. (2012). Life’s attractors. In O. S. Soyer (Ed.), Evolutionary systems biology (pp. 93–119). Springer.
Jaeger, J., & Monk, N. (2021a). Dynamical modularity of the genotype-phenotype map. In A. Crombach (Ed.), Evolutionary systems biology: Advances, questions, and opportunities (pp. 245–280). Springer.
Jaeger, J., & Monk, N. (2021b). Dynamical modules in metabolism, cell and developmental biology. Interface Focus, 11, 20210011.
Jaeger, J., Irons, D., & Monk, N. (2012). The inheritance of process: A dynamical systems approach: The inheritance of process. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 318(8), 591–612.
Kauffman, S. A. (1971a). Articulation of parts explanation in biology and the rational search for them. In R. C. Buck & R. S. Cohen (Eds.), PSA 1970 (pp. 257–272). D. Reidel Publishing Company.
Kauffman, S. A. (1971b). Cellular homeostasis, Epigenesis and replication in randomly aggregated macromolecular systems. Journal of Cybernetics, 1(1), 71–96.
Kauffman, S. A. (1986). Autocatalytic sets of proteins. Journal of Theoretical Biology, 119(1), 1–24.
Kauffman, S. A. (1993). The origins of order: Self-organization and selection in evolution (1st ed.). Oxford University Press.
Kauffman, S. A. (2000). Investigations. Oxford University Press.
Koestler, A. (1982). The ghost in the machine. Hutchinson.
Lewontin, R. (2000). The triple helix: Gene, organism, and environment. Harvard University Press.
Love, A. C. (2007). Functional homology and homology of function: Biological concepts and philosophical consequences. Biology & Philosophy, 22, 691–708.
Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25.
Maturana, H. R., & Varela, F. J. (1980). Autopoiesis and cognition: The realization of the living. Springer.
Maynard Smith, J., Burian, R., Kauffman, S., Alberch, P., Campbell, J., Goodwin, B., Lande, R., Raup, D., & Wolpert, L. (1985). Developmental constraints and evolution. The Quarterly Review of Biology, 60(3), 265–287.
Montévil, M., & Mossio, M. (2015). Biological organisation as closure of constraints. Journal of Theoretical Biology, 372, 179–191.
Montévil, M., & Soto, A. M. (2023). Modeling organogenesis from biological first principles. In M. Mossio (Ed.), Organization in Biology. Springer.
Montévil, M., Mossio, M., Pocheville, A., & Longo, G. (2016a). Theoretical principles for biology: Variation. Progress in Biophysics and Molecular Biology, 122(1), 36–50.
Montévil, M., Speroni, L., Sonnenschein, C., & Soto, A. M. (2016b). Modeling mammary organogenesis from biological first principles: Cells and their physical constraints. Progress in Biophysics and Molecular Biology, 122(1), 58–69.
Moreno, A., & Etxeberria, A. (2005). Agency in natural and artificial systems. Artificial Life, 11(1–2), 161–175.
Moreno, A., & Mossio, M. (2015). Biological autonomy. Springer.
Mossio, M., & Bich, L. (2017). What makes biological organisation teleological? Synthese, 194, 1089–1114.
Mossio, M., & Pontarotti, G. (2020). Conserving functions across generations: Heredity in light of biological organization. The British Journal for the Philosophy of Science, 73(1), axz031.
Mossio, M., Saborido, C., & Moreno, A. (2009). An organizational account of biological functions. The British Journal for the Philosophy of Science, 60(4), 813–841.
Mossio, M., Montévil, M., & Longo, G. (2016). Theoretical principles for biology: Organization. Progress in Biophysics and Molecular Biology, 122(1), 24–35.
Nijhout, H. F. (1990). Metaphors and the role of genes in development. BioEssays, 12(9), 441–446.
Noble, D. (2008). The music of life: Biology beyond genes. Oxford University Press.
Nunes, M. D. S., Arif, S., Schlötterer, C., & McGregor, A. P. (2013). A perspective on Micro-Evo-Devo: Progress and potential. Genetics, 195(3), 625–634.
Oyama, S. (2000). The ontogeny of information: Developmental systems and evolution (Revised ed.). Duke University Press.
Peluffo, A. E. (2015). The “genetic program”: Behind the genesis of an influential metaphor. Genetics, 200(3), 685–696.
Piaget, J. (1967). Biologie et connaissance. Idées/Gallimard.
Pigliucci, M. (2008). Is evolvability evolvable? Nature Reviews Genetics, 9, 75–82.
Rescher, N. (2009). Unknowability: An inquiry into the limits of knowledge. Lexington Books.
Roli, A., Jaeger, J., & Kauffman, S. A. (2022). How organisms come to know the world: Fundamental limits on artificial general intelligence. Frontiers in Ecology and Evolution, 9, 806283.
Rosen, R. (1991). Life itself: A comprehensive inquiry into the nature, origin, and fabrication of life. Columbia University Press.
Saborido, C., Mossio, M., & Moreno, A. (2011). Biological organization and cross-generation functions. The British Journal for the Philosophy of Science, 62(3), 583–606.
Salazar-Ciudad, I. (2006). Developmental constraints vs. variational properties: How pattern formation can help to understand evolution and development. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 306B(2), 107–125.
Sonnenschein, C., & Soto, A. M. (2016). Carcinogenesis explained within the context of a theory of organisms. Progress in Biophysics and Molecular Biology, 122(1), 70–76.
Soto, A. M., Longo, G., Miquel, P.-A., Montevil, M., Mossio, M., Perret, N., Pocheville, A., & Sonnenschein, C. (2016a). Toward a theory of organisms: Three founding principles in search of a useful integration. Progress in Biophysics and Molecular Biology, 122(1), 77–82.
Soto, A. M., Longo, G., Montévil, M., & Sonnenschein, C. (2016b). The biological default state of cell proliferation with variation and motility, a fundamental principle for a theory of organisms. Progress in Biophysics and Molecular Biology, 122(1), 16–23.
Szathmáry, E., & Maynard Smith, J. (1993). The origin of genetic systems. Abstracta Botanica, 17(1–2), 197–206.
Varela, F. J. (1979). Principles of biological autonomy. North Holland.
Varela, F. G., Maturana, H. R., & Uribe, R. (1974). Autopoiesis: The organization of living systems, its characterization and a model. Biosystems, 5(4), 187–196.
Verd, B., Monk, N. A., & Jaeger, J. (2019). Modularity, criticality, and evolvability of a developmental gene regulatory network. eLife, 8, e42832.
von Dassow, G., & Munro, E. (1999). Modularity in animal development and evolution: Elements of a conceptual framework for EvoDevo. The Journal of Experimental Zoology, 285(4), 307–325.
Wagner, A. (2005a). Distributed robustness versus redundancy as causes of mutational robustness. BioEssays, 27(2), 176–188.
Wagner, A. (2005b). Robustness and Evolvability in living systems. Princeton University Press.
Wagner, A. (2011). The origins of evolutionary innovations: A theory of transformative change in living systems. Oxford University Press.
Wagner, G. P., & Altenberg, L. (1996). Complex adaptations and the evolution of Evolvability. Evolution, 50(3), 967–976.
Wagner, G. P., & Laubichler, M. D. (2000). Character identification in evolutionary biology: The role of the organism. Theory in Biosciences, 119, 20–40.
Wagner, G. P., Chiu, C.-H., & Laubichler, M. (2000). Developmental evolution as a mechanistic science: The inference from developmental mechanisms to evolutionary processes. American Zoologist, 40(5), 819–831.
Walsh, D. (2015). Organisms, agency, and evolution. Cambridge University Press.
Webster, G., & Goodwin, B. C. (1982). The origin of species: A structuralist approach. Journal of Social and Biological Structures, 5(1), 15–47.
Webster, G., & Goodwin, B. C. (1996). Form and transformation: Generative and relational principles in biology. Cambridge University Press.
Wimsatt, W. C. (1974). Complexity and organization. In K. F. Schaffner & R. S. Cohen (Eds.), PSA 1972 (pp. 67–86). D. Reidel Publishing Company.
Wimsatt, W. C. (1976). Reductive explanation: A functional account. In R. S. Cohen, C. A. Hooker, A. C. Michalos, & J. W. Van Evra (Eds.), PSA 1974 (pp. 671–710). D. Reidel Publishing Company.
Wimsatt, W. C. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Harvard University Press.
Wright, L. (1973). Functions. Philosophical Review, 82(2), 139–168.
Zakirov, B., Charalambous, G., Thuret, R., Aspalter, I. M., Van-Vuuren, K., Mead, T., Harrington, K., Regan, E. R., Herbert, S. P., & Bentley, K. (2021). Active perception during angiogenesis: Filopodia speed up Notch selection of tip cells in silico and in vivo. Philosophical Transactions of the Royal Society of London B, 376(1821), 20190753.
Acknowledgments
I thank my late mentor and supervisor, Brain Goodwin, whose spirit can strongly be felt in this manuscript. Matteo Mossio, Denis Walsh, and James Griesemer provided moral and intellectual support on various occasions and came up with key ideas that I use in my argument, which is based on numerous extensive discussions with my philosophical collaborator James DiFrisco, who provided detailed feedback on the manuscript, even though the views presented here and the responsibility for potential errors remain exclusively mine.
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Jaeger, J. (2024). Ontogenesis, Organisation, and Organismal Agency. In: Švorcová, J. (eds) Organismal Agency. Biosemiotics, vol 28. Springer, Cham. https://doi.org/10.1007/978-3-031-53626-7_10
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