Publications

Edited Books

• Cooperation and Its Evolution (2013). MIT Press. Edited by Kim Sterelny, Richard Joyce, Brett Calcott and Ben Fraser.
• The Major Transitions in Evolution Revisited (2011). MIT Press. Edited by Brett Calcott and Kim Sterelny.

Journal Articles

• Calcott, B. (2019). Further Clarification on Permissive and Instructive Causes. Biology & Philosophy 34. ↓PDF
• Parke, Emily C., Calcott, B., and O’Malley, Maureen A. (2018). A Cautionary Note for Claims about the Microbiome’s Impact on the ‘Self’ PLOS Biology 16 (9): e2006654.
• Calcott, B., Griffiths, P. E., Pocheville, A. (2018). Signals that make a Difference. British Journal Philosophy for the Philosophy of Science. ↓PDF
• Calcott, B. (2017). Causal Specificity and the Instructive–Permissive Distinction Biology & Philosophy, May, 1–25. ⬇︎PDF
• 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 ⬇︎PDF
• Griffiths, P. E., Pocheville, A., Calcott, B., Stotz, K., Kim, H., Knight, Rob. (2015). Measuring causal specificity. Philosophy of Science. ⬇︎PDF
• Calcott, B., Levy, A. Siegal, M.L., Soyer O.S., Wagner, A. (2015). Engineering and Biology: Counsel for a Continued Relationship. Biological Theory.⬇︎PDF
• 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.⬇︎PDF
• Calcott, B. (2014). The Creation and Reuse of Information in Gene Regulatory Networks. Philosophy of Science 81: 1–12. ⬇︎PDF
• Misof, Bernhard et al. (2014). Phylogenomics Resolves the Timing and Pattern of Insect Evolution. Science 346(6210): 763–67. ⬇︎PDF
• Calcott, B. (2014). Evolvability and Engineering. Biology and Philosophy. 29(3), 293-313. ⬇︎PDF
• Lanfear, R., Calcott, B., Kainer, D., Mayer, C., & Statmatakis, A. (2014). Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14(82)⬇︎PDF
• Calcott, B. (2013). Why How and Why Aren’t Enough: More Problems with Mayr’s Proximate-Ultimate Distinction. Biology and Philosophy. 28(5), 767-780⬇︎PDF
• Lanfear, R., Calcott, B., Ho, S. Y., & Guindon, S. (2012). PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.Molecular Biology and Evolution, 29, 1695–1701.⬇︎PDF
• Matthewson, John & Calcott, Brett (2011). Mechanistic models of population-level phenomena.Biology and Philosophy, 26 (5), 737-756.⬇︎PDF
• Calcott, B. (2009). Lineage Explanations: Explaining How Biological Mechanisms Change. British Journal for the Philosophy of Science, 60, 51-78.⬇︎PDF
• Calcott, B. (2008). The Other Cooperation Problem: Generating Benefit. Biology and Philosophy, 23(2), 179-203.⬇︎PDF
• Calcott, B. (2008). Assessing the Fitness Landscape Revolution.Biology & Philosophy, 23(5), 639-657.⬇︎PDF
• Calcott, B., Balcan, D. & Hohenlohe, P. (2008) A publish-subscribe model of gene-regulation. PloS One, 3(9): e3245.⬇︎PDF

Book Chapters

• Calcott, B. (Forthcoming). A Roomful of Robovacs: How to think about Genetic Programs, in Sune Holm (ed.) Living Machines? Philosophical Perspectives on the Engineering Approach in Biology. Routledge. ⬇︎PDF
• Calcott, B., Levy, A. Modeling and Simulation. Laura Nuño de la Rosa and Gerd B. Müller (eds)In Evolutionary Developmental Biology - A Reference Guide⬇︎PDF
• Calcott, B. (2013). Why the Proximate–Ultimate Distinction is Misleading, and Why it Matters For Understanding the Evolution of Cooperation. In Sterelny, K., Joyce, R., Calcott, B., Fraser B (Eds.), Cooperation and Its Evolution, MIT Press.⬇︎PDF
• Calcott, B., Sterelny, K. (2011). A Dynamic View of Evolution. In B. Calcott & K. Sterelny (Eds.), The Major Transitions in Evolution Revisited. MIT Press.. ⬇︎PDF
• Calcott, B. (2011). Alternative Patterns of Explanation for Major Transitions. In B. Calcott & K. Sterelny (Eds.), The Major Transitions in Evolution Revisited. MIT Press⬇︎PDF

Reviews, Communications, & Proceedings

• Calcott, B. (2013). Engineering: Biologists borrow more than words. Nature, 502, 170–170.⬇︎PDF
• Calcott, B (2010). Wimsatt and the Robustness Family—review of Re-engineering Philosophy of Limited Beings. Biology and Philosophy, 26 (2), 281-293.⬇︎PDF
• Calcott, B (2009). Review of “Modeling Biology: Structures, Behaviors, Evolution”.Acta Biotheoretica, 57(3), 383-387⬇︎PDF
• Gardner, J., Marsack, P., Trueman, J., Calcott, B., & Heinsohn, R. (2007). Story-telling: an essential part of science.Trends in Ecology and Evolution, 22(10), 510.⬇︎PDF
• Calcott, B. (2005). Review of “Fitness Landscapes and the Origin of Species”.Austral Ecology, 30(5), 610-611.⬇︎PDF
• Calcott, B., Balcan, D., & Hohenlohe, P. (2005). Modeling the Evolution of Development. Collected Papers from the Santa Fe Summer School 2005.

Academic Publications

• Calcott, B (2007). Transitions in Biological Organisation. PhD Thesis, Australian National University.⬇︎PDF