Covolution References
1. Darwinian and evolutionary foundations
Darwin, C. (1859). On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray.
Darwin, C. (1868). The Variation of Animals and Plants under Domestication. London: John Murray.
Darwin, C. (1871). The Descent of Man, and Selection in Relation to Sex. London: John Murray.
Darwin, C. (1872). The Expression of the Emotions in Man and Animals. London: John Murray.
Wallace, A. R. (1858). On the tendency of varieties to depart indefinitely from the original type. Journal of the Proceedings of the Linnean Society of London. Zoology, 3(9), 53–62.
Huxley, J. S. (1942). Evolution: The Modern Synthesis. London: Allen & Unwin.
Dobzhansky, T. (1937). Genetics and the Origin of Species. New York: Columbia University Press.
Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, 35(3), 125–129.
Mayr, E. (1942). Systematics and the Origin of Species. New York: Columbia University Press.
Mayr, E. (1961). Cause and effect in biology. Science, 134(3489), 1501–1506.
Simpson, G. G. (1944). Tempo and Mode in Evolution. New York: Columbia University Press.
Fisher, R. A. (1930). The Genetical Theory of Natural Selection. Oxford: Clarendon Press.
Wright, S. (1932). The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics, 1, 356–366.
Haldane, J. B. S. (1932). The Causes of Evolution. London: Longmans, Green.
Kimura, M. (1968). Evolutionary rate at the molecular level. Nature, 217, 624–626.
Gould, S. J., & Lewontin, R. C. (1979). The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings of the Royal Society B, 205(1161), 581–598.
Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.
Dawkins, R. (1976). The Selfish Gene. Oxford: Oxford University Press.
Dawkins, R. (1982). The Extended Phenotype. Oxford: Oxford University Press.
Lewontin, R. C. (1983). The organism as the subject and object of evolution. Scientia, 118, 63–82.
2. Information theory, computation, and communication
Hartley, R. V. L. (1928). Transmission of information. Bell System Technical Journal, 7(3), 535–563.
Gabor, D. (1946). Theory of communication. Journal of the Institution of Electrical Engineers, 93(26), 429–457.
Shannon, C. E. (1948). A mathematical theory of communication. Bell System Technical Journal, 27, 379–423, 623–656. Shannon’s paper is the canonical source for modern information theory and appeared in two parts in the 1948 Bell System Technical Journal.
Shannon, C. E., & Weaver, W. (1949). The Mathematical Theory of Communication. Urbana, IL: University of Illinois Press.
Turing, A. M. (1936–1937). On computable numbers, with an application to the Entscheidungsproblem. Proceedings of the London Mathematical Society, Series 2, 42, 230–265.
Turing, A. M. (1950). Computing machinery and intelligence. Mind, 59(236), 433–460.
Wiener, N. (1948). Cybernetics: Or Control and Communication in the Animal and the Machine. Cambridge, MA: MIT Press.
Wiener, N. (1950). The Human Use of Human Beings: Cybernetics and Society. Boston: Houghton Mifflin.
von Neumann, J. (1966). Theory of Self-Reproducing Automata. Urbana, IL: University of Illinois Press.
Kolmogorov, A. N. (1965). Three approaches to the quantitative definition of information. Problems of Information Transmission, 1(1), 1–7.
Chaitin, G. J. (1966). On the length of programs for computing finite binary sequences. Journal of the ACM, 13(4), 547–569.
Bennett, C. H. (1982). The thermodynamics of computation: A review. International Journal of Theoretical Physics, 21, 905–940.
Landauer, R. (1961). Irreversibility and heat generation in the computing process. IBM Journal of Research and Development, 5(3), 183–191.
Maturana, H. R., & Varela, F. J. (1980). Autopoiesis and Cognition: The Realization of the Living. Dordrecht: Reidel.
Varela, F. J., Thompson, E., & Rosch, E. (1991). The Embodied Mind: Cognitive Science and Human Experience. Cambridge, MA: MIT Press.
3. Cybernetics, feedback, control, and perceptual control theory
Ashby, W. R. (1952). Design for a Brain. London: Chapman & Hall.
Ashby, W. R. (1956). An Introduction to Cybernetics. London: Chapman & Hall.
Powers, W. T. (1973). Behavior: The Control of Perception. Chicago: Aldine.
Powers, W. T. (2005). Behavior: The Control of Perception revised edition. New Canaan, CT: Benchmark Publications.
Marken, R. S., & Mansell, W. (2013). Perceptual Control Theory: A Model for Understanding the Mechanisms and Phenomena of Control. Review paper/resource.
Richardson, G. P. (1991). Feedback Thought in Social Science and Systems Theory. Philadelphia: University of Pennsylvania Press.
Bateson, G. (1972). Steps to an Ecology of Mind. Chicago: University of Chicago Press.
Bateson, G. (1979). Mind and Nature: A Necessary Unity. New York: Dutton.
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). Behavior, purpose and teleology. Philosophy of Science, 10(1), 18–24.
4. Morphogenesis, developmental systems, and internal architecture
Turing, A. M. (1952). The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London. Series B, 237(641), 37–72. DOI: 10.1098/rstb.1952.0012. This is a foundational work for pattern formation and reaction-diffusion morphogenesis.
Waddington, C. H. (1940). Organisers and Genes. Cambridge: Cambridge University Press.
Waddington, C. H. (1957). The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. London: George Allen & Unwin. Waddington’s book is central for epigenetic landscapes, canalization, and developmental trajectories.
Waddington, C. H. (1968). Towards a theoretical biology. Nature, 218, 525–527.
Goodwin, B. C. (1994). How the Leopard Changed Its Spots: The Evolution of Complexity. New York: Charles Scribner’s Sons.
Thom, R. (1975). Structural Stability and Morphogenesis. Reading, MA: Benjamin.
Kauffman, S. A. (1993). The Origins of Order: Self-Organization and Selection in Evolution. Oxford: Oxford University Press.
Kauffman, S. A. (1995). At Home in the Universe: The Search for Laws of Self-Organization and Complexity. Oxford: Oxford University Press.
Newman, S. A., & Müller, G. B. (2000). Epigenetic mechanisms of character origination. Journal of Experimental Zoology, 288(4), 304–317.
Müller, G. B., & Newman, S. A. (2003). Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology. Cambridge, MA: MIT Press.
Oyama, S. (1985). The Ontogeny of Information: Developmental Systems and Evolution. Cambridge: Cambridge University Press.
Oyama, S., Griffiths, P. E., & Gray, R. D. (Eds.). (2001). Cycles of Contingency: Developmental Systems and Evolution. Cambridge, MA: MIT Press.
Jablonka, E., & Lamb, M. J. (2005). Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge, MA: MIT Press.
West-Eberhard, M. J. (2003). Developmental Plasticity and Evolution. Oxford: Oxford University Press.
Kirschner, M., & Gerhart, J. (2005). The Plausibility of Life: Resolving Darwin’s Dilemma. New Haven: Yale University Press.
5. Extended evolutionary synthesis, niche construction, and organism-environment entanglement
Lewontin, R. C. (2000). The Triple Helix: Gene, Organism, and Environment. Cambridge, MA: Harvard University Press.
Odling-Smee, F. J., Laland, K. N., & Feldman, M. W. (2003). Niche Construction: The Neglected Process in Evolution. Princeton: Princeton University Press.
Laland, K. N., Odling-Smee, J., & Feldman, M. W. (2000). Niche construction, biological evolution, and cultural change. Behavioral and Brain Sciences, 23(1), 131–146.
Laland, K. N., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., & Odling-Smee, J. (2015). The extended evolutionary synthesis: Its structure, assumptions and predictions. Proceedings of the Royal Society B, 282, 20151019.
Pigliucci, M., & Müller, G. B. (Eds.). (2010). Evolution: The Extended Synthesis. Cambridge, MA: MIT Press.
Moczek, A. P. (2015). Developmental plasticity and evolution: Concepts and mechanisms. Integrative and Comparative Biology, 55(3), 525–536.
Sultan, S. E. (2015). Organism and Environment: Ecological Development, Niche Construction, and Adaptation. Oxford: Oxford University Press.
Turner, J. S. (2000). The Extended Organism: The Physiology of Animal-Built Structures. Cambridge, MA: Harvard University Press.
6. Epigenetic inheritance, transgenerational effects, and memory
Dias, B. G., & Ressler, K. J. (2014). Parental olfactory experience influences behavior and neural structure in subsequent generations. Nature Neuroscience, 17(1), 89–96. DOI: 10.1038/nn.3594.
Dias, B. G., Maddox, S. A., Klengel, T., & Ressler, K. J. (2015). Epigenetic mechanisms underlying learning and the inheritance of learned behaviors. Trends in Neurosciences, 38(2), 96–107. DOI: 10.1016/j.tins.2014.12.003.
Dias, B. G., & Ressler, K. J. (2014). Experimental evidence needed to demonstrate inter- and trans-generational effects of ancestral experiences in mammals. BioEssays, 36(10), 919–923. DOI: 10.1002/bies.201400105.
Skinner, M. K. (2014). Endocrine disruptor induction of epigenetic transgenerational inheritance of disease. Molecular and Cellular Endocrinology, 398(1–2), 4–12.
Heard, E., & Martienssen, R. A. (2014). Transgenerational epigenetic inheritance: Myths and mechanisms. Cell, 157(1), 95–109.
Jablonka, E., & Raz, G. (2009). Transgenerational epigenetic inheritance: Prevalence, mechanisms, and implications for the study of heredity and evolution. Quarterly Review of Biology, 84(2), 131–176.
Bonduriansky, R., & Day, T. (2009). Nongenetic inheritance and its evolutionary implications. Annual Review of Ecology, Evolution, and Systematics, 40, 103–125.
Miska, E. A., & Ferguson-Smith, A. C. (2016). Transgenerational inheritance: Models and mechanisms of non-DNA sequence-based inheritance. Science, 354(6308), 59–63.
7. Teleonomy, purpose-like organization, and directionality
Pittendrigh, C. S. (1958). Adaptation, natural selection, and behavior. In A. Roe & G. G. Simpson (Eds.), Behavior and Evolution (pp. 390–416). New Haven: Yale University Press.
Mayr, E. (1974). Teleological and teleonomic: A new analysis. Boston Studies in the Philosophy of Science, 14, 91–117.
Monod, J. (1970). Le hasard et la nécessité: Essai sur la philosophie naturelle de la biologie moderne. Paris: Éditions du Seuil.
Monod, J. (1971). Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology. New York: Alfred A. Knopf. Monod’s work is one of the classic modern sources for teleonomy and the relation between chance, necessity, and biological organization.
Nagel, E. (1961). The Structure of Science: Problems in the Logic of Scientific Explanation. New York: Harcourt, Brace & World.
Jonas, H. (1966). The Phenomenon of Life: Toward a Philosophical Biology. New York: Harper & Row.
Kant, I. (1790). Critique of Judgment. Berlin: Lagarde.
Bertalanffy, L. von. (1968). General System Theory: Foundations, Development, Applications. New York: George Braziller.
8. Self-organization, complexity, and emergence
Prigogine, I. (1980). From Being to Becoming: Time and Complexity in the Physical Sciences. San Francisco: W. H. Freeman.
Prigogine, I., & Stengers, I. (1984). Order Out of Chaos: Man’s New Dialogue with Nature. New York: Bantam.
Haken, H. (1983). Synergetics: An Introduction. Berlin: Springer.
Bak, P. (1996). How Nature Works: The Science of Self-Organized Criticality. New York: Copernicus.
Holland, J. H. (1995). Hidden Order: How Adaptation Builds Complexity. Reading, MA: Addison-Wesley.
Holland, J. H. (1998). Emergence: From Chaos to Order. Reading, MA: Addison-Wesley.
Gell-Mann, M. (1994). The Quark and the Jaguar: Adventures in the Simple and the Complex. New York: W. H. Freeman.
Mitchell, M. (2009). Complexity: A Guided Tour. Oxford: Oxford University Press.
Barabási, A.-L. (2002). Linked: The New Science of Networks. Cambridge, MA: Perseus.
Barabási, A.-L. (2016). Network Science. Cambridge: Cambridge University Press.
9. Origin of life, autocatalysis, and chemical evolution
Oparin, A. I. (1938). The Origin of Life. New York: Macmillan.
Haldane, J. B. S. (1929). The origin of life. Rationalist Annual, 148, 3–10.
Miller, S. L. (1953). A production of amino acids under possible primitive Earth conditions. Science, 117(3046), 528–529.
Eigen, M. (1971). Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften, 58, 465–523.
Eigen, M., & Schuster, P. (1979). The Hypercycle: A Principle of Natural Self-Organization. Berlin: Springer.
Kauffman, S. A. (1986). Autocatalytic sets of proteins. Journal of Theoretical Biology, 119(1), 1–24.
Kauffman, S. A. (2000). Investigations. Oxford: Oxford University Press.
Dyson, F. (1985). Origins of Life. Cambridge: Cambridge University Press.
Morowitz, H. J. (1992). Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. New Haven: Yale University Press.
De Duve, C. (1995). Vital Dust: Life as a Cosmic Imperative. New York: Basic Books.
Lane, N. (2015). The Vital Question: Energy, Evolution, and the Origins of Complex Life. London: Profile Books.
Walker, S. I., & Davies, P. C. W. (2013). The algorithmic origins of life. Journal of the Royal Society Interface, 10(79), 20120869.
England, J. L. (2013). Statistical physics of self-replication. Journal of Chemical Physics, 139, 121923.
10. Biosemiotics, meaning, and living information
Peirce, C. S. (1931–1958). Collected Papers of Charles Sanders Peirce. Cambridge, MA: Harvard University Press.
Uexküll, J. von. (1934). Streifzüge durch die Umwelten von Tieren und Menschen. Berlin: Springer.
Pattee, H. H. (1969). How does a molecule become a message? Developmental Biology Supplement, 3, 1–16.
Pattee, H. H. (1973). The physical basis and origin of hierarchical control. In H. H. Pattee (Ed.), Hierarchy Theory: The Challenge of Complex Systems. New York: George Braziller.
Hoffmeyer, J. (1996). Signs of Meaning in the Universe. Bloomington: Indiana University Press.
Barbieri, M. (2003). The Organic Codes: An Introduction to Semantic Biology. Cambridge: Cambridge University Press.
Kull, K. (2009). Biosemiotics: To know, what life knows. Cybernetics & Human Knowing, 16(3–4), 81–88.
Deacon, T. W. (1997). The Symbolic Species: The Co-evolution of Language and the Brain. New York: W. W. Norton.
Deacon, T. W. (2011). Incomplete Nature: How Mind Emerged from Matter. New York: W. W. Norton.
11. Cognition, prediction, active inference, and living systems
Friston, K. (2010). The free-energy principle: A unified brain theory? Nature Reviews Neuroscience, 11, 127–138.
Friston, K. (2013). Life as we know it. Journal of the Royal Society Interface, 10(86), 20130475.
Clark, A. (2013). Whatever next? Predictive brains, situated agents, and the future of cognitive science. Behavioral and Brain Sciences, 36(3), 181–204.
Clark, A. (2016). Surfing Uncertainty: Prediction, Action, and the Embodied Mind. Oxford: Oxford University Press.
Hohwy, J. (2013). The Predictive Mind. Oxford: Oxford University Press.
Kirchhoff, M. D., Parr, T., Palacios, E., Friston, K., & Kiverstein, J. (2018). The Markov blankets of life: Autonomy, active inference and the free energy principle. Journal of the Royal Society Interface, 15, 20170792.
Parr, T., Pezzulo, G., & Friston, K. J. (2022). Active Inference: The Free Energy Principle in Mind, Brain, and Behavior. Cambridge, MA: MIT Press.
12. Symbiosis, holobionts, and co-constructed individuality
Sagan, L. L. (1967). On the origin of mitosing cells. Journal of Theoretical Biology, 14(3), 255–274. https://doi.org/10.1016/0022-5193(67)90079-
Margulis, L. (1970). Origin of Eukaryotic Cells. New Haven: Yale University Press.
Margulis, L. (1998). Symbiotic Planet: A New Look at Evolution. New York: Basic Books.
Sapp, J. (1994). Evolution by Association: A History of Symbiosis. Oxford: Oxford University Press.
Bordenstein, S. R., & Theis, K. R. (2015). Host biology in light of the microbiome: Ten principles of holobionts and hologenomes. PLOS Biology, 13(8), e1002226.
Rosenberg, E., & Zilber-Rosenberg, I. (2013). The Hologenome Concept: Human, Animal and Plant Microbiota. Cham: Springer.
Gilbert, S. F., Sapp, J., & Tauber, A. I. (2012). A symbiotic view of life: We have never been individuals. Quarterly Review of Biology, 87(4), 325–341.
McFall-Ngai, M. et al. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), 3229–3236.
13. Aging, entropy, repair, and biological maintenance
Medawar, P. B. (1952). An Unsolved Problem of Biology. London: H. K. Lewis.
Williams, G. C. (1957). Pleiotropy, natural selection, and the evolution of senescence. Evolution, 11(4), 398–411.
Kirkwood, T. B. L. (1977). Evolution of ageing. Nature, 270, 301–304.
Kirkwood, T. B. L. (2005). Understanding the odd science of aging. Cell, 120(4), 437–447.
Harman, D. (1956). Aging: A theory based on free radical and radiation chemistry. Journal of Gerontology, 11(3), 298–300.
López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M., & Kroemer, G. (2013). The hallmarks of aging. Cell, 153(6), 1194–1217.
López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M., & Kroemer, G. (2023). Hallmarks of aging: An expanding universe. Cell, 186(2), 243–278.
Kennedy, B. K. et al. (2014). Geroscience: Linking aging to chronic disease. Cell, 159(4), 709–713.
Gladyshev, V. N. (2016). Aging: Progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes. Aging Cell, 15(4), 594–602.
Gladyshev, V. N. (2021). The ground zero of organismal life and aging. Trends in Molecular Medicine, 27(1), 11–19.
Horvath, S. (2013). DNA methylation age of human tissues and cell types. Genome Biology, 14, R115.
Horvath, S., & Raj, K. (2018). DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nature Reviews Genetics, 19, 371–384.
Levine, M. E. et al. (2018). An epigenetic biomarker of aging for lifespan and healthspan. Aging, 10(4), 573–591.
Lu, A. T. et al. (2019). DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging, 11(2), 303–327.
14. Selection before birth, embryo quality, and organismal filtering
Teklenburg, G., Salker, M., Molokhia, M., Lavery, S., Trew, G., Aojanepong, T., Mardon, H. J., Lokugamage, A. U., Rai, R., Landles, C., Roelen, B. A. J., Quenby, S., Kuijk, E. W., Kavelaars, A., Heijnen, C. J., Regan, L., Macklon, N. S., & Brosens, J. J. (2010). Natural selection of human embryos: Decidualizing endometrial stromal cells serve as sensors of embryo quality upon implantation. PLOS ONE, 5(4), e10258.
Macklon, N. S., Geraedts, J. P. M., & Fauser, B. C. J. M. (2002). Conception to ongoing pregnancy: The “black box” of early pregnancy loss. Human Reproduction Update, 8(4), 333–343.
Brosens, J. J., Salker, M. S., Teklenburg, G., Nautiyal, J., Salter, S., Lucas, E. S., Steel, J. H., Christian, M., Chan, Y.-W., Boomsma, C. M., Moore, J. D., Hartshorne, G. M., Sućurović, S., Mulac-Jericevic, B., & Quenby, S. (2014). Uterine selection of human embryos at implantation. Scientific Reports, 4, 3894.
15. Physics, entropy, and thermodynamic context
Boltzmann, L. (1877). Über die Beziehung zwischen dem zweiten Hauptsatze der mechanischen Wärmetheorie und der Wahrscheinlichkeitsrechnung. Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften, 76, 373–435.
Schrödinger, E. (1944). What Is Life? The Physical Aspect of the Living Cell. Cambridge: Cambridge University Press.
Brillouin, L. (1956). Science and Information Theory. New York: Academic Press.
Jaynes, E. T. (1957). Information theory and statistical mechanics. Physical Review, 106(4), 620–630.
Prigogine, I. (1967). Introduction to Thermodynamics of Irreversible Processes. New York: Wiley.
Atlan, H. (1972). L’organisation biologique et la théorie de l’information. Paris: Hermann.
Brooks, D. R., & Wiley, E. O. (1988). Evolution as Entropy: Toward a Unified Theory of Biology. Chicago: University of Chicago Press.
Chaisson, E. J. (2001). Cosmic Evolution: The Rise of Complexity in Nature. Cambridge, MA: Harvard University Press.
Chaisson, E. J. (2011). Energy Rate Density as a Complexity Metric and Evolutionary Driver. Complexity, 16(3), 27–40.
16. Adam Smith, invisible hand, and selection-like processes
Smith, A. (1759). The Theory of Moral Sentiments. London: A. Millar.
Smith, A. (1776). An Inquiry into the Nature and Causes of the Wealth of Nations. London: W. Strahan and T. Cadell.
Hayek, F. A. (1945). The use of knowledge in society. American Economic Review, 35(4), 519–530.
Hayek, F. A. (1967). Studies in Philosophy, Politics and Economics. Chicago: University of Chicago Press.
Hodgson, G. M., & Knudsen, T. (2010). Darwin’s Conjecture: The Search for General Principles of Social and Economic Evolution. Chicago: University of Chicago Press.
17. Useful online or secondary resources from your original list
Sensuous Curmudgeon. Adam Smith’s invisible hand and Charles Darwin’s natural selection.
https://sensuouscurmudgeon.wordpress.com/2008/12/16/adam-smiths-invisible-hand-and-charles-darwins-natural-selection/
National Center for Science Education. Predictive power of evolutionary biology: Discovery of eusociality.
https://ncse.com/library-resource/predictive-power-evolutionary-biology-discovery-eusociality
Perceptual Control Theory resource.
http://www.pctweb.org/PCTunderstanding-2.pdf
PLOS ONE embryo selection paper.
http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0010258&type=printable
Most important references for covolution specifically
For your covolution theory, I would treat these as the core reference backbone:
- Darwin, 1859 — natural selection and descent
- Shannon, 1948 — information theory
- Turing, 1936/1952 — computation and morphogenesis
- Wiener, 1948 — cybernetics
- Waddington, 1957 — developmental landscapes and canalization
- Ashby, 1956 — cybernetic regulation
- von Neumann, 1966 — self-reproducing automata
- Prigogine, 1980 — dissipative systems and irreversible order
- Kauffman, 1993 — self-organization and selection
- Lewontin, 1983/2000 — organism-environment reciprocity
- Odling-Smee et al., 2003 — niche construction
- Jablonka & Lamb, 2005 — multidimensional inheritance
- Friston, 2010 — predictive/active inference
- Maturana & Varela, 1980 — autopoiesis
- Monod, 1970/1971 — teleonomy, chance, and necessity
댓글 0