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Research Products

Our group creates a wide variety of research products, including academic books and papers, materials for public audiences, and our blog. We also give talks to groups of specialists and the public, worldwide, and produce widely used open-source software. Check it all out below.

Note that as a group, we discourage the posting of our work on for-profit sites like Academia.edu or ResearchGate. All our articles can instead both be found here and at a variety of other open-access preprint archives.

Oliver M. Lean
Postdoctoral Fellow
Luca Rivelli
Postdoctoral Fellow
Daniel G. Swaim
Former master’s student
Under contract. Breadth: Explanatory Virtues in the Life Sciences [working title]. Cham: Springer.
A study of explanation in the life sciences, combining a theoretical treatment of breadth – an often overlooked explanatory virtue – with a number of case studies.
Under contract. The Causal Structure of Natural Selection. Cambridge: Cambridge University Press.
An opinionated introduction to the debate over probability, statistics, and causation in the foundations of evolutionary theory, to be written for Cambridge’s Elements series.
In press. “How Not to Fight About Theory: The Debate Between Biometry and Mendelism in Nature, 1890–1915.” In The Dynamics of Science: Computational Frontiers in History and Philosophy of Science, & , eds. Pittsburgh: University of Pittsburgh Press.
A book chapter looking at the network of discourse in debates over genetics in the correspondence pages of Nature at the turn of the twentieth century.
Reviewed work: Smith, D. L., ed. 2017. How Biology Shapes Philosophy: New Foundations for Naturalism. Cambridge: Cambridge Univ. Press.
Reviewed work: Uller, T. and Laland, K.N., eds. 2019. Evolutionary Causation: Biological and Philosophical Reflections. Cambridge, MA: MIT Press.
A presentation of some contemporary results from divergence time estimation and their impact on interpretations of chance in the philosophy of biology.
Reviewed work: Rosenblatt, L.B. 2018. Buckets from an English Sea: 1832 and the Making of Charles Darwin. Oxford: Oxford University Press.
& . How to Do Digital Philosophy of Science.” Philosophy of Science 85 (5): 930941.
Based on a symposium at the 2016 PSA, Grant and I offer some tips for those interested in engaging in digital projects in the philosophy of science.
Reviewed work: Archibald, J.D. 2017. Origins of Darwin’s Evolution: Solving the Species Puzzle Through Time and Place. New York: Columbia University Press.
Darwin had many influences, but perhaps the most significant on the structure of the Origin was Sir John Herschel’s Preliminary Discourse. I explore the shape and nature of that influence here.
& . The Economy of Nature: The Structure of Evolution in Linnaeus, Darwin, and the Modern Synthesis.” European Journal for Philosophy of Science 8 (3): 435454.
We consider the status of the economy of nature as a structuring concept in biological theory, from Darwin to the present, with reference to current debates over structural realism.
Reviewed work: Richards, R.J. & Ruse, M. 2016. Debating Darwin. Chicago: University of Chicago Press.
. Is Genetic Drift a Force?.” Synthese 194 (6): 19671988.
A brief paper which considers two arguments against the tenability of considering genetic drift to be analogous to a Newtonian force – that drift lacks a specifiable direction, and that it is constitutive of all evolving systems, rather than an “external” force. In defense of the force metaphor, I find both these arguments to be problematic. ERRATUM: The Lewens (2010) citation should refer to “The Natures of Selection.”
, , , , , , , & . Cognitive Phenotypes and the Evolution of Animal Decisions.” Trends in Ecology and Evolution 31 (11): 850859.
Work with a group of biologists, coordinated through the National Evolutionary Synthesis Center. Offers a new framework for understanding animal decisions which takes into account insights from human psychology. The figshare data here describes a textual analysis that was removed from the article in draft.
& . “Chance in Evolution from Darwin to Contemporary Biology.” In Chance in Evolution, & , eds. Chicago: University of Chicago Press , pp.  111.
The editors' introduction to our edited volume, covering the scope of the work and offering some thoughts on the taxonomy of chance in evolution.
& , eds. . Chance in Evolution. Chicago: University of Chicago Press.
An edited volume with contributions from philosophers, historians, biologists, and theologians on the role of “chance” in evolutionary theory.
& . evoText: A New Tool for Analyzing the Biological Sciences.” Studies in History and Philosophy of Biological and Biomedical Sciences 57: 8387.
An application note introducing the evoText project, a text-mining tool for analyzing the biological journal literature.
An application note introducing RLetters, a tool designed to allow the textual analysis of large journal article corpora.
& . Is Organismic Fitness at the Basis of Evolutionary Theory?.” Philosophy of Science 82 (5): 10811091.
It is often claimed (e.g., in a recent article by Sober (2013)) that trait fitness is where the genuine “action” can be found in evolutionary theory, and that individual fitness is theoretically secondary. We clarify this relationship by distinguishing two roles that fitness plays in biology, and arguing that individual fitness lies at the conceptual foundation of ascriptions of the fitness of traits.
. The Early History of Chance in Evolution.” Studies in History and Philosophy of Science 50: 4858.
In this paper, I argue for a new understanding of the development of chance in evolution, from the from the work of Darwin through Galton to two of Galton’s students, Karl Pearson and W.F.R. Weldon. (Invited to appear in a special issue of Studies in the History and Philosophy of Science containing selected proceedings from &HPS4.)
A commentary on a framework for ethical decision making in military genomic research by Mehlman and Li, in which I argue that significant caution is required, thanks to conceptual results from the philosophy of biology on the relationship between genotypes and phenotypes.
. The Many Chances of Charles Darwin [Essay Review].” Studies in History and Philosophy of Biological and Biomedical Sciences 53: 107110.
Essay review of: Johnson, C. 2015. Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin. Oxford: Oxford University Press.
. [Review of] Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin.” Reports of the National Center for Science Education 35 (6): 11.
Reviewed work: Johnson, C. 2015. Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin. Oxford: Oxford University Press.
Reviewed work: Wilkins, J.S. 2009. Species: A History of the Idea. Berkeley: University of California Press.
My doctoral dissertation. Most chapters from this dissertation are either other published papers or preprints available elsewhere on this website, but here it is anyway for completeness.
& . A New Foundation for the Propensity Interpretation of Fitness.” British Journal for the Philosophy of Science 64 (4): 851881.
We apply some results from mathematical biology to show that there is no reason to think that a modified formulation of the propensity interpretation of fitness cannot survive several common counterexamples to the traditional PIF.
& . Fitness: Philosophical Problems.” eLS.
An entry on the philosophical interpretation of fitness for Wiley’s Encyclopedia of the Life Sciences.
Reviewed work: Müller-Wille, S. & Rheinberger, Hans-Jörg. 2012. A Cultural History of Heredity. Chicago: University of Chicago Press.
, , , and . A Path to Success? A Review of Evolution, Development, and the Predictable Genome by David L. Stern.” Evolution and Development 15 (1): 8082.
Reviewed work: Stern, D.L. 2011. Evolution, Development, and the Predictable Genome. Greenwood Village, CO: Roberts and Company Publishers.
, & . MTBindingSim: Simulate Protein Binding to Microtubules.” Bioinformatics 28 (3): 441443.
An application note introducing MTBindingSim, a tool for classroom simulation of binding to microtubules.
& . Oyun: A New, Free Program for Iterated Prisoner’s Dilemma Tournaments in the Classroom.” Evolution: Education and Outreach 5 (3): 467476.
An application note describing Oyun, software for running iterated prisoner’s dilemma tournaments.
. ‘Describing Our Whole Experience’: The Statistical Philosophies of W.F.R. Weldon and Karl Pearson.” Studies in History and Philosophy of Biological and Biomedical Sciences 42 (4): 475485.
I argue here for a new view of the philosophy of W.F.R. Weldon, distinct in interesting and important ways from the positivism of Karl Pearson.
. Nietzsche’s Aesthetic Critique of Darwin.” History and Philosophy of the Life Sciences 33 (2): 165190.
A reinterpretation of Nietzsche’s critique of Darwin, seen in the light of his early work on aesthetics. (Several of the Nietzsche citations in the published version are missing, despite my best efforts. The preprint has them all, for those interested.)
, , , , and . [Review of] On the Origin of Stories: Evolution, Cognition, and Fiction.” The Quarterly Review of Biology 86 (2): 137138.
Reviewed work: Boyd, B. 2009. On the Origin of Stories: Evolution, Cognition, and Fiction. Cambridge, MA: Harvard University Press.
, , , , , and . [Review of] Elliott Sober: Did Darwin Write the Origin Backwards? Philosophical Essays on Darwin’s Theory.” Philosophy of Science 78 (4): 705709.
Reviewed work: Sober, E. 2011. Did Darwin Write the Origin Backwards? Philosophical Essays on Darwin’s Theory. Amherst, NY: Prometheus.
, , , and . [Review of] Darwinian Populations and Natural Selection.” The Quarterly Review of Biology 85 (4): 499500.
Reviewed work: Godfrey-Smith, P. 2009. Darwinian Popluations and Natural Selection. Oxford: Oxford University Press.

Talks

Upcoming engagements
  • Pence: (title TBD), McMaster University Philosophy Colloquium, Hamilton, Ontario (virtual), March 26, 2021
  • Pence: (title TBD), Summer School on Methodologies for the History of Philosophy (keynote, virtual), University of Groningen, July 5–9, 2021

The lab is always interested in talking about our work to any audiences who would like to hear about it. Send Prof. Pence an email and we’d love to set something up.

Previous talks

Sciveyor: From Corpora to Philosophy of Science

Lab Speaker(s): Pence
TU Eindhoven Philosophy and Ethics Group | Talk Date: October 6, 2020, 2:15pm

Big Data, Natural History, and Breadth

Lab Speaker(s): Pence
Biology and Integrative Genetics Seminar, Université de Lausanne | Talk Date: October 5, 2020, 4:15pm

Of Stirps and Chromosomes: Abstraction through Detail

Lab Speaker(s): Pence
PHILBIO Seminar, IHPST, Université Paris 1–Sorbonne | Talk Date: September 22, 2020, 2pm

Toward a New Picture of the Causalist/Statisticalist Debate in Evolution

Lab Speaker(s): Pence
Colloquium, Department of Logic and Philosophy of Science, UNED | Conference Date: January 17, 2020 | Talk Date: January 17, 2020, 10am

Lessons from the Case of the Life Sciences: Thinking toward Philosophy of Science as Interdisciplinarity

Lab Speaker(s): Pence
Max Planck Institute for the History of Science, Final Theory Program Seminar | Talk Date: December 2, 2019, 2pm

The Challenge of Breadth

Lab Speaker(s): Pence
Facing the Future: 21st EMBL PhD Symposium | Conference Date: November 28–30, 2019 | Talk Date: November 29, 1pm

Of Stirps and Chromosomes: Abstraction through Detail

Lab Speaker(s): Pence
New Directions in the Historiography of Genetics | Conference Date: November 18–19, 2019 | Talk Date: November 19, 10am

Analyzing the Biological Literature with evoText

Lab Speaker(s): Pence
Digital History and Philosophy of Science, Université de Québec à Montréal | Conference Date: November 1, 2019 | Talk Date: November 1, 2019, 2:40pm

Digital Humanities as Empirical Philosophy of Science

Lab Speaker(s): Pence, Lean, Rivelli
XPhiSci 2019 | Conference Date: October 15–16, 2019 | Talk Date: October 15, 2019, 3:25pm

From the Biological World to Statistical Theories: Nineteenth-Century Lessons for Twenty-First-Century Philosophy of Biology

Lab Speaker(s): Pence
EPSA 2019 | Conference Date: September 11–14, 2019 | Talk Date: September 12, 2019, 9:00am

John Herschel and Nineteenth-Century Scientific Methodology (round-table)

Lab Speaker(s): Pence
HSS 2019 | Conference Date: July 23–27, 2019 | Talk Date: July 26, 2019, 12:00pm

From the Biological World to Statistical Theories: Nineteenth-Century Lessons for Twenty-First-Century Philosophy of Biology

Lab Speaker(s): Pence
ISHPSSB 2019 | Conference Date: July 7-12, 2019 | Talk Date: July 10, 2019, 3:00pm

Reversion and Ancestry in Early Genetics

Lab Speaker(s): Pence
UK iHPS Workshop, Exeter | Conference Date: June 20–21, 2019 | Talk Date: June 20, 2019, 4:30pm

Moral Responsibility After Robots

Lab Speaker(s): Pence
Faire exister les IA-robots-cyborgs: Un nouveau projet humaniste pour l’Europe ? | Talk Date: April 30, 2019, 3:00pm

Why Should We Value Biodiversity?

Lab Speaker(s): Pence
Colloque du Cercle des Étudiants en Philosophie | Talk Date: April 23, 2019, 2:00pm

Reversion and Deep Ancestry in Early Genetics

Lab Speaker(s): Pence
Journée d'étude, Université Paris 7 — Diderot | Talk Date: April 11, 2019, 11:00am

The Boundaries of Scientific Communities

Lab Speaker(s): Pence
Ethics/Philosophy of Technology Section, TU Delft | Talk Date: April 8, 2019, 3:00pm

The Wonderful Form of Cosmic Order: Bringing Statistics to Evolution

Lab Speaker(s): Pence
UCLouvain LIBST / ELI-B / Louvain4Evolution Seminar | Talk Date: March 29, 2019, 12:30pm

Causation and Metaphysics in Evolutionary Biology

Lab Speaker(s): Pence
VUB/Ghent Seminar in Philosophy of Science | Talk Date: March 7, 2019, 3:00pm

The Wonderful Form of Cosmic Order: Bringing Statistics to Evolution

Lab Speaker(s): Pence
PhilInBioMed Seminar, ERC IDEM, Université de Bordeaux | Talk Date: March 5, 2019, 2:30pm

The Wonderful Form of Cosmic Order: Bringing Statistics to Evolution

Lab Speaker(s): Pence
UCLouvain CEFISES Work in Progress Seminar | Talk Date: February 27, 2019, 3:00pm

Causation and Metaphysics in Evolutionary Biology

Lab Speaker(s): Pence
KU Leuven, Center for Logic and Philosophy of Science | Talk Date: December 7, 2018, 3:00pm

The Development of Darwin’s Views of Chance

Lab Speaker(s): Pence
Aarhus University, Center for Science Studies | Talk Date: October 10, 2018, 2:15pm

An Introduction to Historical Explanation

Lab Speaker(s): Pence
UCLouvain Historical Explanation Seminar | Talk Date: October 3, 2018, 3:00pm

Darwin on Mind, Ethics, and Animals

Lab Speaker(s): Pence
UCLouvain GRICE Seminar | Talk Date: September 26, 2018, 3:00pm

Chance, Statistics, and Experiment in Early Evolutionary Biology

Lab Speaker(s): Pence
History of Philosophy of Science (HOPOS) 2018 | Conference Date: July 9–12, 2018 | Talk Date: July 10, 2018, 3:30pm

C'mon, Neil! Why Good Philosophy of Science is Part of Good Science Teaching and Science

Lab Speaker(s): Pence
National Science Teachers Association Regional Meeting, 2017 | Conference Date: November 30–December 2, 2017 | Talk Date: December 2, 2017, 8:00am

Darwin and Evolution: Using Historical Critiques and Responses to Address Student Misunderstandings

Lab Speaker(s): Pence
National Science Teachers Association Regional Meeting, 2017 | Conference Date: November 30–December 2, 2017 | Talk Date: December 1, 2017, 9:30am

Archives to Networks and Back Again (keynote)

Lab Speaker(s): Pence
THATCamp HSS 2017 | Talk Date: November 12, 2017, 12:00pm

Syntheses that Weren’t: W.F.R. Weldon on Chromosomes

Lab Speaker(s): Pence
ISHPSSB 2017 | Conference Date: July 16–21, 2017 | Talk Date: July 18, 2017, 9:00am

Theories Under Stress: The Evolution of Early Genetics

Lab Speaker(s): Pence
University of Leeds HPS Centre Seminar | Talk Date: May 24, 2017, 3:15pm
Later published: “How Not to Fight About Theory: The Debate Between Biometry and Mendelism in Nature, 1890–1915”

Theories Under Stress: The Evolution of Early Genetics

Lab Speaker(s): Pence
University College London | Talk Date: May 17, 2017, 5:00pm
Later published: “How Not to Fight About Theory: The Debate Between Biometry and Mendelism in Nature, 1890–1915”

What Role for Fitness?

Lab Speaker(s): Pence
Deep South Philosophy of Biology, University of Alabama Birmingham | Conference Date: March 31–April 1, 2017 | Talk Date: April 1, 2017, 8:45am

Evolution and Chance

Lab Speaker(s): Pence
Darwin Day, Stephen F. Austin State University | Talk Date: February 10, 2017, 12:00pm

Fitness and Prediction in Evolutionary Theory

Lab Speaker(s): Pence
London School of Economics | Talk Date: January 25, 2017, 5:00pm

evoText and Philosophy of Science

Lab Speaker(s): Pence
Philosophy of Science Association 2016 | Conference Date: November 3–5, 2016 | Talk Date: November 4, 2016, 1:30pm
Later published: “How to Do Digital Philosophy of Science”

Theories Under Stress: The Evolution of Early Genetics

Lab Speaker(s): Pence
The Science of Evolution and the Evolution of the Sciences | Conference Date: October 12–13, 2016 | Talk Date: October 13, 2016, 2:00pm
Later published: “How Not to Fight About Theory: The Debate Between Biometry and Mendelism in Nature, 1890–1915”

The Economy of Nature and Structure in Evolution

Lab Speaker(s): Pence
KU Leuven Centre for Logic and Analytic Philosophy Seminar | Talk Date: October 11, 2016, 4:00pm
Later published: “The Economy of Nature: The Structure of Evolution in Linnaeus, Darwin, and Toward the Extended Synthesis”

The Economy of Nature: Structure in Biology from Linnaeus, to Darwin, to the Modern Synthesis

Lab Speaker(s): Pence, Swaim
The History of Science and Scientific Realism | Conference Date: February 19–21, 2016 | Talk Date: February 19, 2016, 2:30pm
Later published: “The Economy of Nature: The Structure of Evolution in Linnaeus, Darwin, and Toward the Extended Synthesis”

What is Evolutionary Fitness For?

Lab Speaker(s): Pence
Mississippi State University Philosophy Department | Talk Date: November 6, 2015, 1:30pm

Charles Darwin and Sir John F.W. Herschel

Lab Speaker(s): Pence
EPSA 2015 | Conference Date: September 23–26, 2015 | Talk Date: September 23, 2015, 6:00pm
Later published: “Sir John F. W. Herschel and Charles Darwin: Nineteenth-Century Science and its Methodology”

Charles Darwin and Sir John F.W. Herschel

Lab Speaker(s): Pence
CLMPS 2015 | Conference Date: August 3–8, 2015 | Talk Date: August 7, 2015, 6:30pm
Later published: “Sir John F. W. Herschel and Charles Darwin: Nineteenth-Century Science and its Methodology”

Prediction, Optimization, Chaos: The Role of Fitness

Lab Speaker(s): Pence
ISHPSSB 2015 | Conference Date: July 5–10, 2015 | Talk Date: July 6, 2015, 9:00am

evoText: A New Text Analysis Tool for the History and Philosophy of Biology

Lab Speaker(s): Pence
American Philosophical Association Pacific Division Meeting, 2015 | Conference Date: April 1–4, 2015 | Talk Date: April 4, 2015, 1:00pm
Later published: “evoText: A New Tool for Analyzing the Biological Sciences”

Is Organismic Fitness at the Basis of Evolutionary Theory?

Lab Speaker(s): Pence
Philosophy of Science Association 2014 | Conference Date: November 6–9, 2014 | Talk Date: November 7, 2014, 1:30pm
Later published: “Is Organismic Fitness at the Basis of Evolutionary Theory?”

Background: Attribution & Repression (in Cyberwarfare)

Lab Speaker(s): Pence
Cyberwarfare, Ethics, and International Humanitarian Law, International Committee of the Red Cross | Conference Date: May 21–22, 2014 | Talk Date: May 21, 2014, 2:00pm

Models, Probability, and the Deep Past

Lab Speaker(s): Pence
Models and Simulations 6 | Conference Date: May 9–11, 2014 | Talk Date: May 10, 2014, 2:30pm
Later published: “Locating Uncertainty in Stochastic Evolutionary Models: Divergence Time Estimation”

Coming to Terms with Chance in Evolution

Lab Speaker(s): Pence
Louisiana State University | Talk Date: February 3, 2014, 11:00am

RLetters

Lab Speaker(s): Pence
NESCent Lunch Talk | Talk Date: December 5, 2013, 12:00pm
Later published: “RLetters: A Web-Based Application for Text Analysis of Journal Articles”

Putting Process and Product Conceptions of Natural Selection and Genetic Drift to the Test

Lab Speaker(s): Pence
European Philosohy of Science Association 2013 | Conference Date: August 28–31, 2013 | Talk Date: August 30, 2013, 9:30am

Putting Process and Product Conceptions of Natural Selection and Genetic Drift to the Test

Lab Speaker(s): Pence
ISHPSSB 2013 | Conference Date: July 7–12, 2013 | Talk Date: July 12, 2013, 9:00am

It’s Okay to Call Genetic Drift a ‘Force’

Lab Speaker(s): Pence
American Philosophical Association Eastern Division Meeting, 2012 | Conference Date: December 27–30, 2012 | Talk Date: December 29, 2012, 9:00am
Later published: “Is Genetic Drift a Force?”

It’s Okay to Call Genetic Drift a ‘Force’

Lab Speaker(s): Pence
Philosophy of Science Association 2012 | Conference Date: November 15–17, 2012 | Talk Date: November 15, 2012, 2:00pm
Later published: “Is Genetic Drift a Force?”

Oyun: Prisoner’s Dilemma Tournaments in the Philosophy of Science

Lab Speaker(s): Pence
American Association of Philosophy Teachers 19th Biennial Workshop/Conference | Conference Date: July 25–29, 2012 | Talk Date: July 27, 2012, 10:45am
Later published: “Oyun: A New, Free Program for Iterated Prisoner’s Dilemma Tournaments in the Classroom.”

The Early History of Chance in Evolution: Causal and Statistical in the 1890s

Lab Speaker(s): Pence
History of Philosophy of Science (HOPOS) 2012 | Conference Date: June 21–24, 2012 | Talk Date: June 22, 2012, 2:15pm
Later published: “The Early History of Chance in Evolution.”

Software Demo: RLetters

Lab Speaker(s): Pence
Digital Humanities Summer Institute | Conference Date: June 3–10, 2012 | Talk Date: June 6, 2012, 8am
Later published: “RLetters: A Web-Based Application for Text Analysis of Journal Articles”

Four Conflated ‘Chance’-Like Concepts in Evolutionary Theory

Lab Speaker(s): Pence
Indiana Philosophical Association | Conference Date: April 20–21, 2012 | Talk Date: April 21, 2012, 2pm

Biology Meets Metaphysics? The Causalist/Statisticalist Debate

Lab Speaker(s): Pence
PhiloSTEM-3 | Conference Date: April 13–14, 2012 | Talk Date: April 14, 2012, 1pm

The Early History of Chance in Evolution

Lab Speaker(s): Pence
Integrated History and Philosophy of Science (&HPS4) | Conference Date: March 15–18, 2012 | Talk Date: March 17, 2012, 11am
Later published: “The Early History of Chance in Evolution.”

evoText: Digital Humanities Meets Evolutionary Biology

Lab Speaker(s): Pence
Notre Dame Graduate Research Symposium (received two awards) | Conference Date: 24th February 2012, 2pm–5pm
Later published: “evoText: A New Tool for Analyzing the Biological Sciences”

The Conflation of “Chance” in Evolution

Lab Speaker(s): Pence
ISHPSSB 2011 | Conference Date: July 10–15, 2011 | Talk Date: July 11, 2011, 11am

The Statistical Philosophy of W.F.R. Weldon

Lab Speaker(s): Pence
ISHPSSB 2009 | Conference Date: July 12–16, 2009 | Talk Date: July 13, 2009
Later published: “‘Describing Our Whole Experience’: The Statistical Philosophies of W.F.R. Weldon and Karl Pearson.”

Outreach

Code

  • RLetters — A web application for text mining on a collection of journal articles   Git
  • Oyun — An evolutionary game-theory simulator   Git
  • AFormula — A mathematical formula evaluation library   Git
  • MTBindingSim — Plot polymer binding curves   Git
  • StickyFlag — Tag your files, search by tags (works on PDF, MMD, PNG, etc.)   Git
  • get_comments — Extract comments from Word and PDF documents (e.g., for grading)   Git