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Ontogenesis, Organisation, and Organismal Agency

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Organismal Agency

Part of the book series: Biosemiotics ((BSEM,volume 28))

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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Bechtel, W. (2011). Mechanism and biological explanation. Philosophy of Science, 78(4), 533–557.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Bechtel, W., & Richardson, R. C. (1993). Discovering complexity: Decomposition and localization as strategies in scientific research (Original ed.). Princeton University Press.

    Google Scholar 

  • Bich, L., & Skillings, D. (2023). There are no intermediate stages: An organizational view of development. In M. Mossio (Ed.), Organization in Biology. Springer.

    Google Scholar 

  • Bich, L., Mossio, M., & Soto, A. M. (2020). Glycemia regulation: From feedback loops to organizational closure. Frontiers in Physiology, 11, 69.

    Article  PubMed  PubMed Central  Google Scholar 

  • Bickhard, M. H. (2000). Autonomy, function, and representation. Communication and Cognition – Artificial Intelligence, 17, 111–131.

    Google Scholar 

  • Bigelow, J., & Pargetter, R. (1987). Functions. Journal of Philosophy, 84(4), 181–196.

    Article  Google Scholar 

  • Boorse, C. (1976). Wright on functions. The Philosophical Review, 85(1), 70–86.

    Article  Google Scholar 

  • Christensen, W. D., & Bickhard, M. H. (2002). The process dynamics of normative function. The Monist, 85(1), 3–28.

    Article  Google Scholar 

  • Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. Clarendon Press.

    Book  Google Scholar 

  • 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

    Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cummins, R. (1975). Functional analysis. Journal of Philosophy, 72(20), 741–765.

    Article  Google Scholar 

  • DiFrisco, J. (2014). Hylomorphism and the metabolic closure conception of life. Acta Biotheoretica, 62, 499–525.

    Article  PubMed  Google Scholar 

  • DiFrisco, J., & Jaeger, J. (2019). Beyond networks: Mechanism and process in evo-devo. Biology & Philosophy, 34, 54.

    Article  Google Scholar 

  • DiFrisco, J., & Jaeger, J. (2020). Genetic causation in complex regulatory systems: An integrative dynamic perspective. BioEssays, 42(6), 1900226.

    Article  Google Scholar 

  • DiFrisco, J., & Jaeger, J. (2021). Homology of process: Developmental dynamics in comparative biology. Interface Focus, 11(3), 20210007.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Google Scholar 

  • DiFrisco, J., & Wagner, G. P. (2022). Body plan identity: A mechanistic model. Evolutionary Biology, 49, 123–141.

    Article  Google Scholar 

  • DiFrisco, J., Love, A. C., & Wagner, G. P. (2020). Character identity mechanisms: A conceptual model for comparative-mechanistic biology. Biology & Philosophy, 35, 44.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Fox Keller, E. (2002). Making sense of life: Explaining biological development with models, metaphors, and machines. Harvard University Press.

    Book  Google Scholar 

  • Gibson, J. J. (1979). The ecological approach to visual perception. Houghton Mifflin.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Glennan, S. S. (1996). Mechanisms and the nature of causation. Erkenntnis, 44, 49–71.

    Article  Google Scholar 

  • Glennan, S., & Illari, P. (Eds.). (2017). The Routledge handbook of mechanisms and mechanical philosophy. Routledge.

    Google Scholar 

  • Gold, J. I., & Shadlen, M. N. (2007). The neural basis of decision making. Annual Review of Neuroscience, 30, 535–574.

    Article  CAS  PubMed  Google Scholar 

  • Goodwin, B. C. (1982a). Biology without Darwinian spectacles. The Biologist, 29, 108–112.

    Google Scholar 

  • Goodwin, B. C. (1982b). Development and evolution. Journal of Theoretical Biology, 97(1), 43–55.

    Article  CAS  PubMed  Google Scholar 

  • Goodwin, B. C. (1985). What are the causes of morphogenesis? BioEssays, 3(1), 32–36.

    Article  CAS  PubMed  Google Scholar 

  • Goodwin, B. C., Kauffman, S., & Murray, J. D. (1993). Is morphogenesis an intrinsically robust process? Journal of Theoretical Biology, 163(1), 135–144.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Heisenberg, C.-P., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell, 153(5), 948–962.

    Article  CAS  PubMed  Google Scholar 

  • Hofmeyr, J.-H. S. (2017). Basic Biological Anticipation. In R. Poli (Ed.), Handbook of anticipation (pp. 1–15). Springer.

    Google Scholar 

  • Hofmeyr, J.-H. S. (2021). A biochemically-realisable relational model of the self-manufacturing cell. Biosystems, 207, 104463.

    Article  CAS  PubMed  Google Scholar 

  • Jaeger, J. (2018). Shift happens: The developmental and evolutionary dynamics of the gap gene system. Current Opinion in Systems Biology, 11, 65–73.

    Article  Google Scholar 

  • Jaeger, J. (2023). The fourth perspective: Evolution and organismal agency. In M. Mossio (Ed.), Organization in Biology. Springer.

    Google Scholar 

  • Jaeger, J., & Crombach, A. (2012). Life’s attractors. In O. S. Soyer (Ed.), Evolutionary systems biology (pp. 93–119). Springer.

    Chapter  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Jaeger, J., & Monk, N. (2021b). Dynamical modules in metabolism, cell and developmental biology. Interface Focus, 11, 20210011.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Kauffman, S. A. (1971b). Cellular homeostasis, Epigenesis and replication in randomly aggregated macromolecular systems. Journal of Cybernetics, 1(1), 71–96.

    Article  Google Scholar 

  • Kauffman, S. A. (1986). Autocatalytic sets of proteins. Journal of Theoretical Biology, 119(1), 1–24.

    Article  CAS  PubMed  Google Scholar 

  • Kauffman, S. A. (1993). The origins of order: Self-organization and selection in evolution (1st ed.). Oxford University Press.

    Book  Google Scholar 

  • Kauffman, S. A. (2000). Investigations. Oxford University Press.

    Book  Google Scholar 

  • Koestler, A. (1982). The ghost in the machine. Hutchinson.

    Google Scholar 

  • Lewontin, R. (2000). The triple helix: Gene, organism, and environment. Harvard University Press.

    Google Scholar 

  • Love, A. C. (2007). Functional homology and homology of function: Biological concepts and philosophical consequences. Biology & Philosophy, 22, 691–708.

    Article  Google Scholar 

  • Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25.

    Article  Google Scholar 

  • Maturana, H. R., & Varela, F. J. (1980). Autopoiesis and cognition: The realization of the living. Springer.

    Book  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Montévil, M., & Mossio, M. (2015). Biological organisation as closure of constraints. Journal of Theoretical Biology, 372, 179–191.

    Article  PubMed  Google Scholar 

  • Montévil, M., & Soto, A. M. (2023). Modeling organogenesis from biological first principles. In M. Mossio (Ed.), Organization in Biology. Springer.

    Google Scholar 

  • Montévil, M., Mossio, M., Pocheville, A., & Longo, G. (2016a). Theoretical principles for biology: Variation. Progress in Biophysics and Molecular Biology, 122(1), 36–50.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Moreno, A., & Etxeberria, A. (2005). Agency in natural and artificial systems. Artificial Life, 11(1–2), 161–175.

    Article  PubMed  Google Scholar 

  • Moreno, A., & Mossio, M. (2015). Biological autonomy. Springer.

    Book  Google Scholar 

  • Mossio, M., & Bich, L. (2017). What makes biological organisation teleological? Synthese, 194, 1089–1114.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Mossio, M., Montévil, M., & Longo, G. (2016). Theoretical principles for biology: Organization. Progress in Biophysics and Molecular Biology, 122(1), 24–35.

    Article  PubMed  Google Scholar 

  • Nijhout, H. F. (1990). Metaphors and the role of genes in development. BioEssays, 12(9), 441–446.

    Article  CAS  PubMed  Google Scholar 

  • Noble, D. (2008). The music of life: Biology beyond genes. Oxford University Press.

    Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Oyama, S. (2000). The ontogeny of information: Developmental systems and evolution (Revised ed.). Duke University Press.

    Google Scholar 

  • Peluffo, A. E. (2015). The “genetic program”: Behind the genesis of an influential metaphor. Genetics, 200(3), 685–696.

    Article  PubMed  PubMed Central  Google Scholar 

  • Piaget, J. (1967). Biologie et connaissance. Idées/Gallimard.

    Google Scholar 

  • Pigliucci, M. (2008). Is evolvability evolvable? Nature Reviews Genetics, 9, 75–82.

    Article  CAS  PubMed  Google Scholar 

  • Rescher, N. (2009). Unknowability: An inquiry into the limits of knowledge. Lexington Books.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Rosen, R. (1991). Life itself: A comprehensive inquiry into the nature, origin, and fabrication of life. Columbia University Press.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Szathmáry, E., & Maynard Smith, J. (1993). The origin of genetic systems. Abstracta Botanica, 17(1–2), 197–206.

    Google Scholar 

  • Varela, F. J. (1979). Principles of biological autonomy. North Holland.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Verd, B., Monk, N. A., & Jaeger, J. (2019). Modularity, criticality, and evolvability of a developmental gene regulatory network. eLife, 8, e42832.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Wagner, A. (2005a). Distributed robustness versus redundancy as causes of mutational robustness. BioEssays, 27(2), 176–188.

    Article  CAS  PubMed  Google Scholar 

  • Wagner, A. (2005b). Robustness and Evolvability in living systems. Princeton University Press.

    Google Scholar 

  • Wagner, A. (2011). The origins of evolutionary innovations: A theory of transformative change in living systems. Oxford University Press.

    Book  Google Scholar 

  • Wagner, G. P., & Altenberg, L. (1996). Complex adaptations and the evolution of Evolvability. Evolution, 50(3), 967–976.

    Article  PubMed  Google Scholar 

  • Wagner, G. P., & Laubichler, M. D. (2000). Character identification in evolutionary biology: The role of the organism. Theory in Biosciences, 119, 20–40.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Walsh, D. (2015). Organisms, agency, and evolution. Cambridge University Press.

    Book  Google Scholar 

  • Webster, G., & Goodwin, B. C. (1982). The origin of species: A structuralist approach. Journal of Social and Biological Structures, 5(1), 15–47.

    Article  Google Scholar 

  • Webster, G., & Goodwin, B. C. (1996). Form and transformation: Generative and relational principles in biology. Cambridge University Press.

    Google Scholar 

  • Wimsatt, W. C. (1974). Complexity and organization. In K. F. Schaffner & R. S. Cohen (Eds.), PSA 1972 (pp. 67–86). D. Reidel Publishing Company.

    Chapter  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Wimsatt, W. C. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Harvard University Press.

    Book  Google Scholar 

  • Wright, L. (1973). Functions. Philosophical Review, 82(2), 139–168.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

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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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