Publications

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.

Forthcoming

Bourrat, P. (accepted). Evolution is about Populations, but its Causes are about Individuals. Biological Theory. Download
Bourrat, P. (in press). Evolutionary Transitions in Individuality: a formal analysis. Synthese.
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. https://doi.org/10.1016/j.shpsa.2019.03.003 Download
Bourrat, P. (in press). Evolutionary transitions in heritability and individuality. Theory in Biosciences. https://doi.org/10.1007/s12064-019-00294-2 Download

2019

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. https://doi.org/https://doi.org/10.3389/fpsyg.2019.00679 Download
Ramstead*, M., Constant*, A., Badcock, P., & Friston, K. (2019). Variational ecology and the physics of sentient systems. Physics of Life Reviews. https://doi.org/https://doi.org/10.1016/j.plrev.2018.12.002 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. https://doi.org/https://doi.org/10.1007/s11229-019-02115-x 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. https://doi.org/https://doi.org/10.1017/S0140525X19001213 Download
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. Bloomsbury Academic. Download
Lynch, K. E. (2019). Why microbes, not microbiomes, are better causal explanations in gut-brain research. Behavioral and Brain Sciences, 42. https://doi.org/10.1017/S0140525X18002820
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 http://philsci-archive.pitt.edu/15777/ Download
Brusse, C. (2019). Cognitive Gadgets: The Cultural Evolution of Thinking by Cecilia Heyes. The Quarterly Review of Biology, 94(2), 231–231. https://doi.org/10.1086/703622 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. https://doi.org/10.1007/978-3-319-16999-6_2106-1 Download
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. https://doi.org/10.1007/978-3-319-16999-6_1358-1 Download
Ronai, I., & Griffiths, P. E. (2019). The Case for Basic Biological Research. Trends in Molecular Medicine. https://doi.org/10.1016/j.molmed.2018.12.003 Download
Bourrat, P. (2019). On Calcott’s permissive and instructive cause distinction. Biology & Philosophy, 34(1), 1. https://doi.org/10.1007/s10539-018-9654-y 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. https://doi.org/10.1007/s13194-018-0224-6 Download

2018

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. https://doi.org/10.1016/j.jtherbio.2018.10.005 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. https://doi.org/10.1098/rsif.2017.0685 Download
Bourrat, P. (2018). Have causal claims about the gut microbiome been over-hyped? BioEssays, 40(12), 1800178. https://doi.org/10.1002/bies.201800178 Download
Bourrat, P. (2018). Natural selection and drift as individual-level causes of evolution. Acta Biotheoretica. https://doi.org/10/gd2zfp Download
Bourrat, P., & Griffiths, P. E. (2018). Multispecies individuals. History and Philosophy of the Life Sciences, 40(2). https://doi.org/10/gd2zft
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. https://doi.org/10.1093/bjps/axw035 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 https://plato.stanford.edu/archives/win2018/entries/replication/
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. https://doi.org/10.1007/s11245-018-9546-4 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. https://doi.org/10/gd2zfn 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. https://doi.org/10.1017/S0140525X18000055 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. https://doi.org/10.1086/699412 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. https://doi.org/10/gd2zfr 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. Download
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. https://doi.org/10.1093/bjps/axx022 Download

2017

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 http://ndpr.nd.edu/news/biological-individuality-integrating-scientific-philosophical-and-historical-perspectives/
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). https://doi.org/10.1086/688933
Bourrat, P. (2017). Review of Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. Notre Dame Philosophical Reviews. Retrieved from https://ndpr.nd.edu/news/biological-individuality-integrating-scientific-philosophical-and-historical-perspectives/
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. https://doi.org/10/gd2zfq Download
Bourrat, P., & Lu, Q. (2017). Dissolving the missing heritability problem. Philosophy of Science, 84(5), 1055–1067. https://doi.org/10/gd2zfv
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 http://search.informit.com.au/documentSummary;dn=075903482941369;res=IELHSS Download
Calcott, B. (2017). Causal Specificity and the Instructive-Permissive Distinction. Biology and Philosophy, 32(4), 481–505. Retrieved from https://link.springer.com/article/10.1007/s10539-017-9568-0 Download
Lynch, K. E. (2017). Heritability and causal reasoning. Biology & Philosophy, 32(1), 25–49. https://doi.org/10.1007/s10539-016-9535-1 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. https://doi.org/10.1002/bies.201700067 Download
Fang, W. (2017). Holistic modeling: an objection to Weisberg’s weighted feature-matching account. Synthese, 194(5), 1743–1764. https://doi.org/10.1007/s11229-016-1018-z 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 https://arnaud.pocheville.science/publication/pocheville_genetic_2017/
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 https://arnaud.pocheville.science/publication/pocheville_comparing_2017/
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. https://doi.org/10/gbtpb2 Download
Brusse, C. (2017). Making do without selection—review essay of “Cultural Evolution: Conceptual Challenges” by Tim Lewens. Biology & Philosophy, 32(2), 307–319. https://doi.org/10.1007/s10539-016-9560-0 Download
Bruner, J. P., Brusse, C., & Kalkman, D. (2017). Cost, expenditure and vulnerability. Biology & Philosophy, 32(3), 357–375. https://doi.org/10.1007/s10539-017-9563-5 Download
Brusse, C., & Bruner, J. (2017). Responsiveness and Robustness in the David Lewis Signaling Game. Philosophy of Science, 84(5), 1068–1079. https://doi.org/10.1086/694156 Download
Griffiths, P. E. (2017). Genetic, epigenetic and exogenetic information in development and evolution. Interface Focus, 7(5). https://doi.org/10/gd2zfk 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. https://doi.org/10/gd2zfm Download

2016

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. https://doi.org/10.1007/978-3-319-28099-8_1470-1 Download
Bourrat, P. (2016). Generalizing contextual analysis. Acta Biotheoretica, 64(2), 197–217. https://doi.org/10.1007/s10441-016-9280-5 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. https://doi.org/10.1007/s10539-015-9507-x
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. https://doi.org/10.1093/molbev/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. https://doi.org/10.1016/j.shpsb.2015.11.002 Download
Stotz, K., & Griffiths, P. E. (2016). Epigenetics: ambiguities and implications. History and Philosophy of the Life Sciences, 38(4), 1–22. https://doi.org/10/gd2zfw

2015

Bourrat, P. (2015). Distinguishing natural selection from other evolutionary processes in the evolution of altruism. Biological Theory. https://doi.org/10.1007/s13752-015-0210-6 Download
Bourrat, P. (2015). How to read‘ heritability’ in the recipe approach to natural selection. The British Journal for the Philosophy of Science, 66(4), 883–903. https://doi.org/10.1093/bjps/axu015 Download
Bourrat, P. (2015). Levels of selection are artefacts of different fitness temporal measures. Ratio, 28(1), 40–50. https://doi.org/10/gdp82g Download
Bourrat, P. (2015). Levels, time and fitness in evolutionary transitions in individuality. Philosophy & Theory in Biology, 7. https://doi.org/10/gd2zgb
Bourrat, P. (2015). Origins and evolution of religion from a Darwinian point of view: synthesis of different theories. In T. Heams, P. Huneman, G. Lecointre, & M. Silberstein (Eds.), Handbook of Evolutionary Thinking in the Sciences (pp. 761–780). Springer Netherlands. Retrieved from http://link.springer.com.ezproxy2.library.usyd.edu.au/chapter/10.1007/978-94-017-9014-7_36
Magnusson, R. S., & Griffiths, P. E. (2015). Who’s afraid of the nanny state? Introduction to a symposium. Public Health, 129(8), 1017–1020. https://doi.org/10/gd2zfc Download
Griffiths, P. E., Pocheville, A., Calcott, B., Stotz, K., Kim, Hyunju, & Knight, R. (2015). Measuring Causal Specificity. Philosophy of Science, 82(4), 529–555. https://doi.org/10/gd2zfh Download
Ronai, I., Oldroyd, B. P., Barton, D. A., Cabanes, G., Lim, J., & Vergoz, V. (2015). Anarchy Is a Molecular Signature of Worker Sterility in the Honey Bee. Molecular Biology and Evolution, msv202. https://doi.org/10/f79kp7 Download
Stotz, K., & Griffiths, P. (2015). Dissecting Developmental Biology. Review of “Towards a Theory of Development.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. https://doi.org/10/gd2zfz Download
Griffiths, P. E., & Magnusson, R. S. (2015, October 13). Good laws create freedom, not a nanny state. Sydney Morning Herald. Retrieved from http://www.smh.com.au/comment/good-laws-create-freedom-not-a-nanny-state-20151012-gk7k71.html
Frandsen, P. B., Calcott, B., Mayer, C., & Lanfear, R. (2015). Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates. BMC Evolutionary Biology, 15(1), 13. https://doi.org/10/f6x8xs
Calcott, B., Levy, A., Siegal, M. L., Soyer, O. S., & Wagner, A. (2015). Engineering and biology: counsel for a continued relationship. Biological Theory, 10(1), 50–59. https://doi.org/10/gd2zf6
Ronai, I., Barton, D. A., Oldroyd, B. P., & Vergoz, V. (2015). Regulation of oogenesis in honey bee workers via programed cell death. Journal of Insect Physiology, 81, 36–41. https://doi.org/10/f7sbj2 Download
Pocheville, A. (2015). The Ecological Niche: History and Recent Controversies. In Handbook of Evolutionary Thinking in the Sciences (pp. 547–586). Springer. Retrieved from http://link.springer.com/chapter/10.1007/978-94-017-9014-7_26
Pocheville, A., & Danchin, E. (2015). Physiology and evolution at the crossroads of plasticity and inheritance. J Physiol, 593, 2243–2243. https://doi.org/10/gd2zf8
Griffiths, P. E., & Wilkins, J. S. (2015). Crossing the Milvian Bridge: When Do Evolutionary Explanations of Belief Debunk Belief? In P. Sloan, G. McKenny, & K. Eggelson (Eds.), Darwin in the 21st Century: Nature, Humanity, and God (pp. 201–231). Notre Dame, IN: Notre Dame University Press.
Griffiths, P. E. (2015). Conceptual change and conceptual diversity contribute to progress in science. In G. Bammer (Ed.), Change! Combining Analytic Approaches with Street Wisdom (pp. 163–176). Acton, ACT: Australian National University Press.
Griffiths, P. E., & Hochman, A. (2015). Developmental Systems Theory. In John Wiley & Sons Ltd (Ed.), eLS (pp. 1–7). Chichester, UK: John Wiley & Sons, Ltd. Retrieved from http://doi.wiley.com/10.1002/9780470015902.a0003452.pub2 Download
Griffiths, P. E., & West, C. (2015). A balanced intervention ladder: promoting autonomy through public health action. Public Health, 129(8), 1092–1098. https://doi.org/10/gd2zff Download