Below is a list of publications (for the past 5 years) authored by Theory and Method in Biosciences staff and students (current at the time of publication). Not all listed publications relate to research conducted within the team. Publications by former members are also included where the research was conducted wholly or largely within the team.


Fang, W. (Accepted). Multilevel Modeling and the Explanatory Autonomy of Psychology. Philosophy of the Social Sciences.
Fang, W. (in press). Multiple realization in systems biology. Philosophy of Science. Retrieved from
Bourrat, P. (in press). Evolutionary Transitions in Individuality: a formal analysis. Synthese.
Bourrat, P. (accepted). Evolution is about Populations, but its Causes are about Individuals. Biological Theory. Download
Bourrat, P. (in press). In what sense can there be evolution by natural selection without perfect inheritance? International Studies in the Philosophy of Science.
Bourrat, P. (in press). Natural Selection and the Reference Grain Problem. Studies in History and Philosophy of Science Part A. Download
Bourrat, P. (in press). Evolutionary transitions in heritability and individuality. Theory in Biosciences. Download



Griffiths, P. (2019). Beyond Concepts: Unicepts, Language, and Natural Information. Australasian Journal of Philosophy, 0(0), 1–4. Download
Brusse, C. (2019). Signaling theories of religion: models and explanation. Religion, Brain & Behavior, 0(0), 1–20. Download
Fang, W. (2019). Mixed-Effects Modeling and Nonreductive Explanation. Philosophy of Science, 86(5), 882–894.
Fang, W. (2019). An Inferential Account of Model Explanation. Philosophia, 47(1), 99–116.
Machery, E., Griffiths, P. E., Linquist, S., & Stotz, K. (2019). Scientists’ Concepts of Innateness: Evolution or Attraction? In R. Samuels & D. Wilkenfeld, Advances in Experimental Philosophy (pp. 172–201). Bloomsbury Academic. Download
Brusse, C. J., & Sterelny, K. (2019). Jonathan Birch, ‘The Philosophy of Social Evolution’ // Reviewed by Brusse & Sterelny. BJPS Review of Books. Retrieved from
Machery, E., Griffiths, P. E., Linquist, S., & Stotz, K. (2019). Scientists’ Concepts of Innateness: Evolution or Attraction? In D. A. Wilkenfeld & R. Samuels (Eds.), Advances in Experimental Philosophy of Science. Bloomsbury Academic. Download
Constant, A., Ramstead, M., Veissière, S., & Friston, K. (2019). Regimes of Expectations: An Active Inference Model of Social Conformity and Human Decision Making. Front. Psychol. Download
Ramstead*, M., Constant*, A., Badcock, P., & Friston, K. (2019). Variational ecology and the physics of sentient systems. Physics of Life Reviews. Download
Badcock, P., Constant, A., & Ramstead, M. (2019). Tinkering with cognitive gadgets: Cultural evolutionary psychology meets active inference. Behavioral and Brain Sciences. Download
Ramstead, M., Kirchhoff, M., Constant, A., & Friston, K. (2019). Multiscale integration: beyond internalism and externalism. Synthese. Download
Veissière, S., Constant, A., Ramstead, M., Friston, K., & Kirmayer, L. (2019). Thinking Through Other Minds: A Variational Approach to Cognition and Culture. Behavioral and Brain Sciences. Download
Lynch, K. E. (2019). Why microbes, not microbiomes, are better causal explanations in gut-brain research. Behavioral and Brain Sciences, 42.
Lynch, K. E., Parke, E. C., & O’Malley, M. A. (2019, February 28). How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers [Preprint]. Retrieved July 30, 2019, from Download
Brusse, C. (2019). Cognitive Gadgets: The Cultural Evolution of Thinking by Cecilia Heyes. The Quarterly Review of Biology, 94(2), 231–231. Download
Bourrat, P. (2019). Adaptations: Product of evolution. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Cham: Springer International Publishing.
Bourrat, P. (2019). Genetic relatedness. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Cham: Springer International Publishing. Download
Ronai, I., & Griffiths, P. E. (2019). The Case for Basic Biological Research. Trends in Molecular Medicine. Download
Bourrat, P. (2019). On Calcott’s permissive and instructive cause distinction. Biology & Philosophy, 34(1), 1. Download
Bourrat, P. (2019). Variation of information as a measure of one-to-one causal specificity. European Journal for Philosophy of Science, 9(1), 11. Download


Gray, P., Meek, S., Griffiths, P., Trapani, J., Small, I., Vickers, C., & Waldby, C. (2018). Synthetic biology in Australia: an outlook to 2030. Australian Council of Learned Academies. Download
Fang, W. (2018). The case for multiple realization in biology. Biology and Philosophy, 33(3).
Lynch, K. E., White, T. E., & Kemp, D. J. (2018). The effect of captive breeding upon adult thermal preference in the Queensland fruit fly (Bactrocera tryoni). Journal of Thermal Biology, 78, 290–297. Download
Constant, A., Ramstead Maxwell J. D., Veissière Samuel P. L., Campbell John O., & Friston Karl J. (2018). A variational approach to niche construction. Journal of The Royal Society Interface, 15(141), 20170685.
Bourrat, P. (2018). Have causal claims about the gut microbiome been over-hyped? BioEssays, 40(12), 1800178. Download
Bourrat, P. (2018). Natural selection and drift as individual-level causes of evolution. Acta Biotheoretica. Download
Bourrat, P., & Griffiths, P. E. (2018). Multispecies individuals. History and Philosophy of the Life Sciences, 40(2).
Lu, Q., & Bourrat, P. (2018). The evolutionary gene and the extended evolutionary synthesis. The British Journal For The Philosophy Of Science, 69(3), 775–800. Download
Wilkins, J. S., & Bourrat, P. (2018). Replication and reproduction. In E. N. Zalta (Ed.), The Stanford Encyclopedia of Philosophy (Winter 2018). Metaphysics Research Lab, Stanford University. Retrieved from
Constant, A., Bervoets, J., Hens, K., & Van de Cruys, S. (2018). Precise Worlds for Certain Minds: An Ecological Perspective on the Relational Self in Autism. Topoi. Download
Lynch, K. E., Morandini, J. S., Dar-Nimrod, I., & Griffiths, P. E. (2018). Causal Reasoning About Human Behavior Genetics: Synthesis and Future Directions. Behavior Genetics, 1–14. Download
Donovan, C., Fine, C., & Kennett, J. (2018). Reliable and Unreliable Judgments about Reasons. In D. Star (Ed.), The Oxford Handbook of Reasons and Normativity (pp. 939–963). Oxford: Oxford University Press.
Brusse, C. J., & Sterelny, K. (2018). Moral externalisation fails to scale. Behavioral and Brain Sciences, 41. Download
Brusse, C. (2018). Evolving Brains, Emerging Gods: Early Humans and the Origins of Religion by E. Fuller Torrey. The Quarterly Review of Biology, 93(3), 251–252. Download
Griffiths, P. E., & Matthewson, J. (2018). Evolution, Dysfunction, and Disease: A Reappraisal. The British Journal for the Philosophy of Science, 69(2), 301–327. Download
Stotz, K., & Griffiths, P. E. (2018). A developmental systems account of human nature. In T. Lewens & E. Hannon, Why we disagree about human nature (pp. 58–75). Oxford & New York: Oxford University Press.
Griffiths, P. E., & Stotz, K. (2018). Developmental Systems Theory as a Process Theory. In D. J. Nicholson & J. Dupre, Everything Flows: Towards a Processual Philosophy of Biology (pp. 225–245). Oxford & New York: Oxford University Press. Download
Calcott, B., Griffiths, P. E., & Pocheville, A. (2018). Signals that make a Difference. The British Journal for the Philosophy of Science. Download


Bourrat, P. (2017). Review of Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives by Scott Lidgard and Lynn K. Nyhart. Notre Dame Philosophical Reviews. Retrieved from
Bourrat, P. (2017). Explaining drift from a deterministic setting. Biological Theory, 12(1), 27–38.
Lynch, K. E., & Bourrat, P. (2017). Interpreting heritability causally. Philosophy of Science, 84(1).
Bourrat, P. (2017). Review of Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. Notre Dame Philosophical Reviews. Retrieved from
Bourrat, P. (2017). Review of Evolution by Natural Selection: Confidence, Evidence and the Gap, by Michaelis Michael. Australasian Journal of Philosophy, 95(4), 816–819.
Stotz, K., & Griffiths, P. E. (2017). Genetic, epigenetic and exogenetic information. In R. Joyce, Routledge Handbook of Evolution and Philosophy. London & New York: Routledge. Download
Stotz, K. (2017). Why developmental niche construction is not selective niche construction: and why it matters. Interface Focus, 7(5), 2–10. Download
Bourrat, P., & Lu, Q. (2017). Dissolving the missing heritability problem. Philosophy of Science, 84(5), 1055–1067.
Griffiths, P. E. (2017). Communicating genomic complexity. Journal and Proceedings of the Royal Society of New South Wales, 150(463/464), 93–103. Retrieved from;dn=075903482941369;res=IELHSS Download
Calcott, B. (2017). Causal Specificity and the Instructive-Permissive Distinction. Biology and Philosophy, 32(4), 481–505. Retrieved from Download
Lynch, K. E. (2017). Heritability and causal reasoning. Biology & Philosophy, 32(1), 25–49. Download
Bourrat, P., Lu, Q., & Jablonka, E. (2017). Why the missing heritability might not be in the DNA. BioEssays, 39(7), n/a-n/a. Download
Fang, W. (2017). Holistic modeling: an objection to Weisberg’s weighted feature-matching account. Synthese, 194(5), 1743–1764. Download
Stotz, K., & Griffiths, P. E. (2017). Biological Information, causality and specificity – an intimate relationship. In S. I. Walker, P. Davies, & G. Ellis (Eds.), From Matter to Life: Information and Causality (pp. 366–390). Cambridge and New York: Cambridge University  Press. Download
Pocheville, A., & Danchin, É. (2017). Genetic assimilation and the paradox of blind variation. In D. M. Walsh & P. Huneman (Eds.), Challenging the Modern Synthesis. Oxford: Oxford University Press. Retrieved from
Pocheville, A., Griffiths, P. E., & Stotz, K. (2017). Comparing causes – an information-theoretic approach to specificity, proportionality and stability. In H. Leitgeb, I. Niiniluoto, E. Sober, & Seppälä, Päivi (Eds.), Proceedings of the 15th Congress of Logic, Methodology and Philosophy of Science (pp. 260–275). London: College Publications. Retrieved from Download
Matthewson, J., & Griffiths, P. E. (2017). Biological Criteria of Disease: Four Ways of Going Wrong. The Journal of Medicine and Philosophy: A Forum for Bioethics and Philosophy of Medicine, 42(4), 447–466. Download
Brusse, C. (2017). Making do without selection—review essay of “Cultural Evolution: Conceptual Challenges” by Tim Lewens. Biology & Philosophy, 32(2), 307–319. Download
Bruner, J. P., Brusse, C., & Kalkman, D. (2017). Cost, expenditure and vulnerability. Biology & Philosophy, 32(3), 357–375. Download
Brusse, C., & Bruner, J. (2017). Responsiveness and Robustness in the David Lewis Signaling Game. Philosophy of Science, 84(5), 1068–1079. Download
Griffiths, P. E. (2017). Genetic, epigenetic and exogenetic information in development and evolution. Interface Focus, 7(5). Download
Bourrat, P. (2017). Review of Michaelis Michael “Evolution by Natural Selection.” Australasian Journal of Philosophy, 95(4).
Griffiths, P. E. (2017). Mechanisms can be complex: Talia Morag: Emotion, Imagination, and the Limits of Reason. Abingdon, Oxon & New York: Routledge, 2016, 288 pp, £88.00 HB. Metascience, 26(3), 387–391. Download


Lynch, K. (2016). Gene-Environment Correlation. In V. Zeigler-Hill & T. K. Shackelford (Eds.), Encyclopedia of Personality and Individual Differences (pp. 1–4). Cham: Springer International Publishing. Download
Bourrat, P. (2016). Generalizing contextual analysis. Acta Biotheoretica, 64(2), 197–217. Download
Bourrat, P., & Viciana, H. (2016). Supernatural beliefs and the evolution of cooperation. In J. Liddle & T. K. Shackelford (Eds.), Oxford Handbook of the Evolutionary Perspectives on Religion.
Stotz, K., & Griffiths, P. (2016). A niche for the genome. Biology & Philosophy, 31(1), 143–157.
Griffiths, P. E. (2016). Proximate and Ultimate Information in Biology. In M. Couch & J. Pfeifer (Eds.), The Philosophy of Philip Kitcher (pp. 74–91). New York and Oxford: Oxford University Press. Download
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2016). PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Molecular Biology and Evolution, msw260. Download
Pocheville, A., Calcott, B., Stotz, K., & Griffiths, P. E. (2016, November). New tools for thinking about causation. Poster presented at the PSA Biennal Meeting, Atlanta.
Brusse, C. (2016). Planets, pluralism, and conceptual lineage. Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics, 53, 93–106. Download
Stotz, K., & Griffiths, P. E. (2016). Epigenetics: ambiguities and implications. History and Philosophy of the Life Sciences, 38(4), 1–22. Download