Maturana, H., & Mpodozis, J. (2000). The origin of species by means of natural drift. *Revista Chilena de Historia Natural*, 73(2), 261-310.

Maturana, H., & Varela, F. J. (1980). Autopoiesis: The organization of the living. In H. Maturana, & F. J. Varela, eds., *Autopoiesis and Cognition: The Realization of the Living*. Dordrecht: Reidel, pp. 59-145.

Maturana, H., & Varela, F. J. (1987). *The Tree of Knowledge*. Boston: Shambhala

McCulloch, W. (1974). Recollections of the many sources of cybernetics. *ASC Forum*, VI(2), 5-16.

McLaughlin, P. (2001). *What Functions Explain: Functional Explanation and Self-Reproducing Systems*. Cambridge: Cambridge University Press.

Menatti, L., Bich, L., & Saborido, C. (2022). Health and environment from adaptation to adaptivity: A situated relational account. *History and Philosophy of the Life Sciences*, 44(3), 38.

Militello, G., Bich, L., & Moreno, A. (2021). Functional integration and individuality in prokaryotic collective organisations. *Acta Biotheoretica*, 69(3), 391-415.

Militello, G., & Moreno, A. (2018). Structural and organisational conditions for being a machine. *Biology and Philosophy*, 33, 35.

Millikan, R. G. (1989). In defense of proper functions. *Philosophy of Science*, 56, 288-302.

Monod, J. (1970). *Les hasard et la nécessité*. Paris: Seuil.

Monod, J., Chengeux, J. P., Jacob, F. (1963). Allosteric proteins and cellular control systems. *Journal of Molecular Biology*, 6, 306-329.

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

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

Montévil, M., Speroni, L., Sonnenschein, C., & Soto, A. M. (2016). Modeling mammary organogenesis from biological first principles: Cells and their physical constraints. *Progress in Biophysics and Molecular Biology*, 122, 58-69.

Moreno, A. (2018). On minimal autonomous agency: Natural and artificial. *Complex Systems*, 27(3), 289-313.

Moreno, A., & Mossio, M. (2015). *Biological Autonomy: A Philosophical and Theoretical Enquiry*. New York: Springer.

Mossio, M. (2023). Introduction: Organization as a scientific blind spot. In M. Mossio, ed., *Organization in Biology*. New York: Springer, pp. 1-22.

Mossio, M., & Bich, L. (2017). What makes biological organisation teleological? *Synthese*, 194(4), 1089-1114.
Mossio, M., Bich, L., & Moreno, A. (2013). Emergence, closure and inter-level causation in biological systems. *Erkenntnis*, 78(2), 153–178.

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

Mossio, M., & Pontarotti, G. (2022). Conserving functions across generations: Heredity in light of biological organization. *The British Journal for the Philosophy of Science*, 73(1), 249–278.

Mossio, M., & Saborido, C. (2016). Functions, organization and etiology: A reply to Artiga and Martinez. *Acta Biotheoretica*, 64(3), 263–275.

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.

Nahas, A., & Sachs, C. (2023). What's at stake in the debate over naturalizing teleology? An overlooked metatheoretical debate. *Synthese*, 201(4), 142.

Neander, K. (1991). Functions as selected effects: The conceptual analyst's defence. *Philosophy of Science*, 58, 168–184.

Nicholson, D. (2014). The return of the organism as a fundamental explanatory concept in biology. *Philosophy Compass*, 9(5), 347–359.

Nunes-Neto, N., Moreno, A., & El Hani, C. N. (2014). Function in ecology: An organizational approach. *Biology & Philosophy*, 29(1), 123–141.

Pattee, H. (1972). The nature of hierarchical controls in living matter. In R. Rosen, ed., *Foundations of Mathematical Biology Volume I Subcellular Systems*. New York: Academic Press, pp. 1–22.

Piaget, J. (1967). *Biologie et Connaissance*. Paris: Gallimard.

Pias, C. (2016). *Cybernetics: The Macy Conferences 1946–1953: The Complete Transactions*. Zurich: Diaphanes.

Piccinini, G., & Craver, C. (2011). Integrating psychology and neuroscience: Functional analyses as mechanism sketches. *Synthese*, 183(3), 283–311.

Pickering, A. (2010). *The Cybernetic Brain: Sketches of Another Future*. Chicago: The University of Chicago Press.

Piekarski, M. (2023). Incorporating (variational) free energy models into mechanisms: The case of predictive processing under the free energy principle. *Synthese*, 202(2), 58.

Pouvreau, D., & Drack, M. (2007). On the history of Ludwig von Bertalanffy's "General Systemology," and on its relationship to cybernetics. *International Journal of General Systems*, 36(3), 281–337.

Rampioni, G., Mavelli, F., Damiano, L., et al. (2014). A synthetic biology approach to bio-chem-ICT: First moves towards chemical communication between synthetic and natural cells. *Natural Computing*, 13, 333–349.
Rashevsky, N. (1954). *Topology and life*. *Bulletin of Mathematical Biophysics*, 16, 317–348.

Rasmussen, S., Bedau, M., Hen, L., et al. (2008). *Protocells: Bridging Nonliving and Living Matter*. Cambridge, MA: MIT Press.

Rosen, R. (1970). *Dynamical System Theory in Biology: Stability Theory and Its Applications*. New York: Wiley-Interscience.

Rosen, R. (1972). Some relational cell models: The metabolism-repair systems. In R. Rosen, ed., *Foundations of Mathematical Biology: Volume II Cellular Systems*. New York: Academic Press, pp. 217–253.

Rosen, R. (1985). *Anticipatory Systems*. Oxford: Pergamon Press.

Rosen, R. (1991). *Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life*. New York: Columbia University Press.

Rosenblueth, A., Wiener, N., & Bigelow, J. (1943). Behaviour, purpose and teleology. *Philosophy of Science*, 10(1), 18–24.

Ruiz-Mirazo, K., Briones, C., & De la Escosura, A. (2014). Prebiotic systems chemistry: New perspectives for the origins of life. *Chemical Reviews*, 114, 285–366.

Ruiz-Mirazo, K., & Mavelli, F. (2007). Simulation model for functionalized vesicles: Lipid-peptide integration in minimal protocells. In F. Almeida e Costa, L. M. Rocha, E. Costa, I. Harvey, A. Coutinho, eds., *Advances in Artificial Life, ECAL 2007*. Berlin: Springer, pp. 32–41.

Ruiz-Mirazo, K., & Moreno, A. (2004). Basic autonomy as a fundamental step in the synthesis of life. *Artificial Life*, 10(3), 235–259.

Saborido, C., & Moreno, A. (2015). Biological pathology from an organizational perspective. *Theoretical Medicine and Bioethics*, 36(1), 83–95.

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.

Sachs, C. (2023). Naturalized Teleology: Cybernetics, Organization, Purpose. *Topoi*, 42(3), 781–791.

Scott-Phillips, T. C. (2009). The quest for a general account of communication: A review of sociobiology of communication. *Journal of Evolutionary Psychology*, 7(3), 245–249.

Shirt-Ediss, B., Solé, R., & Ruiz-Mirazo, K. (2013). Steady state analysis of a vesicle bioreactor with mechanosensitive channels. In P. Liò ed., *Advances in Artificial Life, ECAL 2013*. Cambridge, MA: The MIT Press, pp. 1162–1169.

Skillings, D. (2016). Holobionts and the ecology of organisms – Multi-species communities or integrated individuals? *Biology and Philosophy*, 31, 875–892.
Skillings, D. (2019). Trojan horses and black queens: “Causal core” explanations in microbiome research. *Biology & Philosophy*, 34(6), 60.

Stano, P., & Luisi, P. L. (2016). Theory and construction of semi-synthetic minimal cells. In D. L. Nesbeth, ed., *Synthetic Biology Handbook*. Boca Raton: CRC Press, pp. 209–258.

Varela, F. J. (1979). *Principles of Biological Autonomy*. New York: North-Holland.

Varela, F. J., & Maturana, H. (1972). Mechanism and biological explanation. *Philosophy of Science*, 39(3), 378–382.

Varela, F. J., Maturana, H., & Uribe, R. (1974). Autopoiesis: The organization of living systems, its characterization and a model. *Biosystems*, 5(4), 187–196.

Von Bertalanffy, L. (1968). *General System Theory*. New York: Braziller.

Walsh, D. (2015). *Organisms, Agency, and Evolution*. Cambridge: Cambridge University Press.

Weber, A., & Varela, F. J. (2002). Life after Kant: Natural purposes and the autopoietic foundations of biological individuality. *Phenomenology and the Cognitive Sciences*, 1(2), 97–125.

Wiener, N. (1948). *Cybernetics, or Control and Communication in the Animal and in the Machine*. Cambridge MA: The MIT Press.

Winning, J., & Bechtel, W. (2018). Rethinking causality in neural mechanisms: Constraints and control. *Minds and Machines*, 28(2), 287–310.

Woese, C. (2004). A new biology for a new century. *Microbiology and Molecular Biology Reviews*, 68(2),173–186.

Wolfe, C. (2014). Holism, organicism and the risk of biochauvinism. *Verifiche: Rivista di scienze umane*, 43, 39–57.

Zepik, H. H., Blöchliger, E., & Luisi, P. L. (2001). A chemical model of homeostasis. *Angewandte Chemie*, 113, 205–208.
Acknowledgments

I thank Laura Menatti for her love and support, for our discussions and collaborations, and for so many other things that listing them would easily exceed the space of an Element. The idea of writing this Element came out in a conversation with Derek Skillings, who was trying to keep me awake while I was driving during a long car trip in the south of France. I am grateful to him for encouraging me, for discussing many ideas in philosophy of biology, and for supporting me with his friendship. A substantial part of this Element was written during my guest fellowship at the KLI – Konrad Lorenz Institute for Evolution and Cognition Research (from Fall 2022 to Spring 2023). I thank the director Guido Caniglia, and all its members and fellows for the kind hospitality and for providing a very serene and stimulating research environment. I wish to thank William Bechtel for the many helpful suggestions and, together with Andrew Bollhagen and Matteo Mossio, for the very helpful feedback on a previous version of the manuscript. I thank Alvaro Moreno and all my other co-authors for the very stimulating conversations and the collaborative work, which over the years have contributed to shaping my way of thinking about living systems.
## Funding

This research was supported by grant Ramón y Cajal RYC-2016-19798 funded by MCIN/AEI /10.13039/501100011033 and by ESF "Investing in your future"; by grant PID2019-104576GB-I00 for project Outonomy funded by MCIN/AEI/10.13039/501100011033; and by grant IT1668-22 funded by the Basque Government. The open access publication of this book was funded by the John Templeton Foundation (grant #62220). I deeply thank Alvaro Moreno and Derek Skillings for making these funds available from their subawards. The viewpoints expressed in this Element are those of the author and not those of the John Templeton Foundation.

## Conflict of Interest

The author has no conflict of interest to declare.
# Philosophy of Biology

## Grant Ramsey

KU Leuven

Grant Ramsey is a BOFZAP research professor at the Institute of Philosophy, KU Leuven, Belgium. His work centers on philosophical problems at the foundation of evolutionary biology. He has been awarded the Popper Prize twice for his work in this area. He also publishes in the philosophy of animal behavior, human nature and the moral emotions. He runs the Ramsey Lab (theramseylab.org), a highly collaborative research group focused on issues in the philosophy of the life sciences.

## Michael Ruse

Florida State University

Michael Ruse is the Lucyle T. Werkmeister Professor of Philosophy and the Director of the Program in the History and Philosophy of Science at Florida State University. He is Professor Emeritus at the University of Guelph, in Ontario, Canada. He is a former Guggenheim fellow and Gifford lecturer. He is the author or editor of over sixty books, most recently *Darwinism as Religion: What Literature Tells Us about Evolution; On Purpose; The Problem of War: Darwinism, Christianity, and their Battle to Understand Human Conflict; and A Meaning to Life*.

## About the Series

This Cambridge Elements series provides concise and structured introductions to all of the central topics in the philosophy of biology. Contributors to the series are cutting-edge researchers who offer balanced, comprehensive coverage of multiple perspectives, while also developing new ideas and arguments from a unique viewpoint.
Philosophy of Biology

Elements in the Series

*Evolution, Morality and the Fabric of Society*

R. Paul Thompson

*Structure and Function*

Rose Novick

*Hylomorphism*

William M. R. Simpson

*Biological Individuality*

Alison K. McConwell

*Human Nature*

Grant Ramsey

*Ecological Complexity*

Alkistis Elliott-Graves

*Units of Selection*

Javier Suárez and Elisabeth A. Lloyd

*Evolution and Development: Conceptual Issues*

Alan C. Love

*Inclusive Fitness and Kin Selection*

Hannah Rubin

*Animal Models of Human Disease*

Sara Green

*Cultural Selection*

Tim Lewens

*Biological Organization*

Leonardo Bich

A full series listing is available at: www.cambridge.org/EPBY