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

Fang, W. (Accepted). Towards Mechanism 2.1: A Dynamic Causal Approach. Philosophy of Science. PhilSci-Archive. http://philsci-archive.pitt.edu/17435/ Download
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. 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

2020

Lynch, K. E., & Blumstein, D. T. (2020). Hidden ethical costs of conservation. Science, 370(6513), 179–180. https://doi.org/10.1126/science.abe2505 Download
Griffiths, P. E. (2020, September 21). The existence of biological sex is no constraint on human diversity. Aeon Essays. https://aeon.co/essays/the-existence-of-biological-sex-is-no-constraint-on-human-diversity
Fang, W. (2020). Multilevel Modeling and the Explanatory Autonomy of Psychology. Philosophy of the Social Sciences, 50(3), 175 –194. https://journals.sagepub.com/doi/abs/10.1177/0048393120917633
Fang, W. (2020). Multiple realization in systems biology. Philosophy of Science, 87(4), 663–684. https://www.journals.uchicago.edu/doi/abs/10.1086/709733?journalCode=phos
Murphy, D., Donovan, C., & Smart, G. L. (2020). Mental Health and Well-Being in Philosophy. In Explaining Health Across the Sciences (pp. 97–114). Springer.
Griffiths, P. E., & Matthewson, J. (2020). Diseases are Not Adaptations and Neither are Their Causes. Biological Theory, 15(3), 136–142. https://doi.org/10.1007/s13752-020-00350-x Download
Lynch, K. E., & Blumstein, D. T. (2020). Effective Conservation. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2020.07.011 Download
Brusse, C. (2020). Manipulation and Dishonest Signals. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_3616-1 Download
Brusse, C. (2020). Animal Signalling. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_2146-1 Download
Brown, R. L., Brusse, C., Huebner, B., & Pain, R. (2020). Unification at the cost of realism and precision. Behavioral and Brain Sciences, 43. https://doi.org/10.1017/S0140525X19002760 Download
Brusse, C. (2020). Signaling theories of religion: models and explanation. Religion, Brain & Behavior, 10(3), 272–291. https://doi.org/10.1080/2153599X.2019.1678514 Download
Brusse, C., & Sterelny, K. (2020). Religion and its evolution: signals, norms, and secret histories. Religion, Brain & Behavior, 10(3), 217–222. https://doi.org/10.1080/2153599X.2020.1783794 Download
Lynch, K. E., Parke, E. C., & O’Malley, M. A. (2020). Microbiome causality: further reflections (a response to our commentators). Biology & Philosophy, 35(2), 29. https://doi.org/10.1007/s10539-020-9742-7 Download
Griffiths, P. E., & Matthewson, J. (2020). Diseases are not Adaptations and Neither are their Causes. Biological Theory. Download
Chapman, R., & Veit, W. (2020). Representing the Autism Spectrum. The American Journal of Bioethics, 20(4), 46–48. https://doi.org/10.1080/15265161.2020.1730495
Donovan, C., & Murphy, D. (2020). De Haan on Sense-Making and Psychopathology. Philosophy, Psychiatry, & Psychology, 27(1), 29–30. https://doi.org/10.1353/ppp.2020.0003 Download
Lynch, K., & Blumstein, D. (2020). Conflicts and triage. Animal Sentience, 4(27). https://animalstudiesrepository.org/animsent/vol4/iss27/24
Blumstein, D., & Lynch, K. (2020). Innovative, yes: But is it rewilding? Animal Sentience, 5(28). https://animalstudiesrepository.org/animsent/vol5/iss28/8

2019

Calcott, B. (2019). Further Clarification on Permissive and Instructive Causes. Biology and Philosophy, 34(5), 1–11. https://doi.org/10.1007/s10539-019-9700-4
Ronai, I., & Griffiths, P. E. (2019). The Case for Basic Biological Research. Trends in Molecular Medicine, 25(2), 65–69. https://doi.org/10.1016/j.molmed.2018.12.003 Download
Griffiths, P. (2019). Beyond Concepts: Unicepts, Language, and Natural Information. Australasian Journal of Philosophy, 0(0), 1–4. https://doi.org/10.1080/00048402.2019.1618885 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 (pp. 172–201). Bloomsbury Academic. Download
Donovan, C. (2019). Biological Function. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_2097-1
Donovan, C. (2019). Biological Function. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_2097-1
O’Neill, S. J., White, T. E., Lynch, K. E., & Kemp, D. J. (2019). Male guppies differ in daily frequency but not diel pattern of display under daily light changes. Behavioral Ecology and Sociobiology, 73(11), 157. https://doi.org/10.1007/s00265-019-2768-7 Download
Lynch, K. E. (2019). Heritability. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–6). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_41-1 Download
Lynch, K. E. (2019). Gut Microbiome. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–6). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_2782-1 Download
Takacs, Peter. (2019, March 19). Macquarie Uni_Work in Progress Seminar_Assessing Fitness Functions for Selected Effects Accounts of Dysfunction. Download
Takacs, Peter. (2019, October 28). Assessing Fitness Functions for Selected Effects Accounts of Dysfunction. Download
Takacs, Peter, & Christie, J. R. (2019, August 15). Selected Effects Accounts of Dysfunction. Download
Takacs, Peter. (2019, May 12). Current Research for Australian Academy of Science (5-12-2019). Download
Fang, W. (2019). Mixed-Effects Modeling and Nonreductive Explanation. Philosophy of Science, 86(5), 882–894. https://doi.org/https://doi.org/10.1086/705449
Fang, W. (2019). An Inferential Account of Model Explanation. Philosophia, 47(1), 99–116. https://doi.org/https://doi.org/10.1007/s11406-018-9958-9
Brusse, C. J., & Sterelny, K. (2019). Jonathan Birch, ‘The Philosophy of Social Evolution’ // Reviewed by Brusse & Sterelny. BJPS Review of Books. http://www.thebsps.org/2019/08/brusseandsterelnyonbirch/
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. https://doi.org/10.5040/9781350068896 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. 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
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]. 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). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_2106-1
Bourrat, P. (2019). Genetic relatedness. In T. K. Shackelford & V. A. Weekes-Shackelford (Eds.), Encyclopedia of Evolutionary Psychological Science (pp. 1–4). Springer International Publishing. https://doi.org/10.1007/978-3-319-16999-6_1358-1 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

Pocheville, A. (2018). Biological Information as Choice and Construction. Philosophy of Science, 85(5), 1012–1025. https://doi.org/10.1086/699832
Donovan, C., Fine, C., & Kennett, J. (2018). Reliable and unreliable judgments about reasons. The Oxford Handbook of Reasons and Normativity, 939–963. https://doi.org/10.1093/oxfordhb/9780199657889.013.41
Dar-Nimrod, I., MacNevin, G., Godwin, A., Lynch, K., Magory Cohen, T., Ganesan, A., & Morandini, J. (2018). Genetic Knowledge within a National Australian Sample: Comparisons with Other Diverse Populations. Public Health Genomics, 21(3–4), 133–143. https://doi.org/10.1159/000496381
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). https://doi.org/https://doi.org/10.1007/s10539-018-9613-7
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 Download
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. 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 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 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 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

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
Calcott, B. (2017). Causal Specificity and the Instructive-Permissive Distinction. Biology and Philosophy, 32(4), 481–505. https://link.springer.com/article/10.1007/s10539-017-9568-0 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. 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. 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. 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. http://search.informit.com.au/documentSummary;dn=075903482941369;res=IELHSS 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
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 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 University Press. 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). College Publications. https://arnaud.pocheville.science/publication/pocheville_comparing_2017/ 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. 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

Griffiths, P. E. (2016). Proximate and Ultimate Information in Biology. In M. Couch & J. Pfeifer (Eds.), The Philosophy of Philip Kitcher (pp. 74–97). Oxford University Press. Download
Lynch, K. (2016). Gene-Environment Correlation. In V. Zeigler-Hill & T. K. Shackelford (Eds.), Encyclopedia of Personality and Individual Differences (pp. 1–4). 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
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 4). New tools for thinking about causation [Poster]. 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 Download