Publications

The following is a list of all publications by staff and/or students of the Theory and Method in Biosciences team for the past five years.

Forthcoming

Stotz, K., & Griffiths, P. E. (Under review). When is a biological cause a source of information? Biology and Philosophy.
Stotz, K., & Griffiths, P. E. (In Press). Biological Information, causality and specificity – an intimate relationship. In S. I. Walker, P. Davies, & G. Ellis, From Matter to Life: Information and Causality. Cambridge and New York: Cambridge University  Press. Download
Stotz, K., & Griffiths, P. E. (In Press). Genetic, epigenetic and exogenetic information. In R. Joyce, Routledge Handbook of Evolution and Philosophy. London & New York: Routledge. Download
Griffiths, P. E., & Stotz, K. (In Press). Developmental Systems Theory as a Process Theory. In D. J. Nicholson & J. Dupre, Everything Flows: Towards a Processual Philosophy of Biology. Oxford & New York: Oxford University Press.
Griffiths, P. E., & Stotz, K. (In Press). How DST Became a Process Theory. In D. J. Nicholson & J. Dupre, Everything Flows: Towards a Processual Philosophy of Biology. Oxford and New York: Oxford University Press.
Calcott, B., Griffiths, P. E., & Pocheville, A. (In Press). Signals that make a Difference. The British Journal for the Philosophy of Science. Download
Pocheville, A. (under review). Causal specificity, information flow, and causal independence.
Pocheville, A., Griffiths, P. E., & Stotz, K. (In Press). 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. London: College Publications. Download
Matthewson, J., & Griffiths, P. E. (In Press). Biological Criteria of Disease. Journal of Medicine and Philosophy.

2016

Griffiths, P. E., & Matthewson, J. (2016). Evolution, dysfunction and disease: a reappraisal. British Journal For The Philosophy of Science.
Stotz, K., & Griffiths, P. E. (2016). Epigenetics: ambiguities and implications. History and Philosophy of the Life Sciences, 38(4). Retrieved from http://rdcu.be/mJjE
Dagaeff, A.-C., Pocheville, A., Nöbel, S., Loyau, A., Isabel, G., & Danchin, E. (2016). Drosophila mate copying correlates with atmospheric pressure in a speed learning situation. Animal Behaviour, 121, 163–174. https://doi.org/10.1016/j.anbehav.2016.08.022
Fang, W. (2016). Holistic modeling: an objection to Weisberg’s weighted feature-matching account. Synthese, 1–22. https://doi.org/10.1007/s11229-016-1018-z
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.

2015

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/10.1016/j.shpsc.2015.08.002
Griffiths, P. E., & Hochman, A. (2015, October 15). 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
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/10.1086/682914
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/10.1016/j.jinsphys.2015.06.014
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/10.1093/molbev/msv202
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/10.1016/j.puhe.2015.08.007
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/10.1016/j.puhe.2015.07.035
Bourrat, P. (2015). Distinguishing Natural Selection from Other Evolutionary Processes in the Evolution of Altruism. Biological Theory, 1–11. https://doi.org/10.1007/s13752-015-0210-6
Bourrat, P. (2015). Levels of Selection Are Artefacts of Different Fitness Temporal Measures. Ratio, 28(1), 40 – 50. https://doi.org/10.1111/rati.12053
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
Bourrat, P. (2015). Levels, Time and Fitness in Evolutionary Transitions in Individuality. Philosophy & Theory in Biology, 7. https://doi.org/http://dx.doi.org/10.3998/ptb.6959004.0007.001
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. Retrieved from http://link.springer.com/article/10.1007/s13752-014-0198-3
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/10.1186/s12862-015-0283-7
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., & 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.
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/10.1113/JP270438

2014

Stotz, K. (2014). Extended evolutionary psychology: the importance of transgenerational developmental plasticity. Frontiers in Psychology, 5. https://doi.org/10.3389/fpsyg.2014.00908
Calcott, B. (2014). The Creation and Reuse of Information in Gene Regulatory Networks. Philosophy of Science, 81(5), 879–890. https://doi.org/10.1086/677687
Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., … Zhou, X. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science, 346(6210), 763–767. https://doi.org/10.1126/science.1257570
Bourrat, P. (2014). How to Read “Heritability” in the Recipe Approach to Natural Selection. The British Journal for the Philosophy of Science, axu015. https://doi.org/10.1093/bjps/axu015
Lanfear, R., Calcott, B., Kainer, D., Mayer, C., & Stamatakis, A. (2014). Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology, 14(1), 82. https://doi.org/10.1186/1471-2148-14-82
Calcott, B. (2014). Engineering and evolvability. Biology & Philosophy, 29(3), 293–313. Retrieved from http://link.springer.com/article/10.1007/s10539-014-9425-3
Danchin, E., & Pocheville, A. (2014). Inheritance is where physiology meets evolution. J Physiol, 592, 2307–2317. https://doi.org/10.1113/jphysiol.2014.272096
Griffiths, P. E., & Stotz, K. (2014). Conceptual Barriers to Interdisciplinary Communication. In M. O’Rourke Crowley,Stephen, Eigenbrode, Sanford D. .. Wulfhorst, J. . (Ed.), Enhancing Communication & Collaboration in Interdisciplinary Research. Sage.
Longo, G., Montévil, M., & Pocheville, A. (2014). L’incompressible complexité du réel et la construction évolutive du simple. Retrieved from http://www.di.ens.fr/users/longo/files/PhilosophyAndCognition/IncompressReel.pdf
Pocheville, A., & Montévil, M. (2014). Ecological Models for Gene Therapy. I. Models for Intraorganismal Ecology. Biol Theory, 9, 401–413. https://doi.org/10.1007/s13752-014-0191-x
Pocheville, A., Montévil, M., & Ferrière, R. (2014). Ecological Models for Gene Therapy. II. Niche Construction, Nongenetic Inheritance, and Ecosystem Perturbations. Biol Theory, 9, 414–422. https://doi.org/10.1007/s13752-014-0190-y

2013

Bourrat, P. (2013). From survivors to replicators: evolution by natural selection revisited. Biology & Philosophy, 29(4), 517–538. https://doi.org/10.1007/s10539-013-9383-1
Calcott, B. (2013). Why how and why aren’t enough: more problems with Mayr’s proximate-ultimate distinction. Biology & Philosophy, 28(5), 767–780. https://doi.org/10.1007/s10539-013-9367-1
Calcott, B. (2013). Why the Proximate–Ultimate Distinction Is Misleading, and Why It Matters for Understanding the Evolution of Cooperation. In K. Sterelny, R. Joyce, B. Calcott, & B. Fraser (Eds.), Cooperation and its Evolution (pp. 1–31). MIT Press.
Duncan, M. J., Bourrat, P., DeBerardinis, J., & O’Malley, M. A. (2013). Small Things, Big Consequences: Microbiological Perspectives on Biology. In K. Kampourakis (Ed.), The Philosophy of Biology (pp. 373–394). Springer Netherlands. Retrieved from http://link.springer.com.ezproxy2.library.usyd.edu.au/chapter/10.1007/978-94-007-6537-5_18
Griffiths, P. E. (2013). What is Innateness? In S. M. Downes & E. Machery, Arguing About Human Nature: Contemporary Debates. Routledge.
Griffiths, P. E. (2013). Lehrman’s dictum: Information and explanation in developmental biology. Developmental Psychobiology, 55(1), 22–32.
Griffiths, P. E. (2013). Rand on concepts, definitions, and the advance of science: Comments on Gotthelf and Lennox. In A. Gotthelf & J. G. Lennox (Eds.), Concepts and their Role in Knowledge: Reflections on objectivist epistemology (pp. 139–147). Pittsburgh, PA: University of Pittsburgh Press.
Griffiths, P. E. (2013). Current emotion research in philosophy. Emotion Review, 5(2), 1–8.
Griffiths, P. E., & Stotz, K. (2013). Genetics and Philosophy: An introduction. New York: Cambridge University Press.
Griffiths, P. E., & Tabery, J. G. (2013). Developmental Systems Theory: What Does it Explain, and How Does It Explain It? In R. M. Lerner & J. B. Benson (Eds.), Embodiment and Epigenesis: Theoretical and Methodological Issues in Understanding the Role of Biology within the Relational Developmental System Part A: Philosophical, Theoretical, and Biological Dimensions (Vol. 45, pp. 65–94). Elsevier.
Griffiths, P. E., & Walsh, E. (2013). Emotion and Expression. In International Encyclopedia of the Social and Behavioral Sciences. Pergamon/Elsevier Science.
Vallat, L., Kemper, C., Jung, N., Maumy-Bertrand, M., Bertrand, F., Meyer, N., … Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. PNAS, 110, 459–464. https://doi.org/10.1073/pnas.1211130110
Walsh, E., & Griffiths, P. E. (2013). Emotion, Evolution of. In International Encyclopedia of the Social and Behavioral Sciences. Pergamon/Elsevier Science.
Wilkins, J. S., & Griffiths, P. E. (2013). Evolutionary debunking arguments in three domains: Fact, value, and religion. In G. Dawes & J. Maclaurin (Eds.), A New Science of Religion (pp. 133–146). New York: Routledge.