•  3
    This article explores the intersection of philosophy and statistics by examining the philosophical assumptions underlying modern mathematical statistics from ontological and epistemological perspectives. Statistics holds interest for philosophers engaged with the problem of induction, as its mathematical apparatus serves as models for philosophical ideas. For instance, the much-discussed concepts of the uniformity of nature and natural kinds correspond to probability models and statistical model…Read more
  •  34
    The Roles of Mathematics in Evolutionary Theory
    Cambridge University Press. 2019.
    The central role of mathematical modeling in modern evolutionary theory has raised a concern as to why and how abstract formulae can say anything about empirical phenomena of evolution. This Element introduces existing philosophical approaches to this problem and proposes a new account according to which evolutionary models are based on causal, and not just mathematical, assumptions. The novel account features causal models both as the Humean 'uniform nature' underlying evolutionary induction an…Read more
  •  26
    Design Problems in Life and AI生命と人工知能におけるデザイン問題
    Journal of the Japan Association for Philosophy of Science 46 (2): 71-77. 2019.
  •  61
    Species as Models
    Philosophy of Science 86 (5): 1075-1086. 2019.
    This article characterizes various species concepts in terms of set-theoretic models that license biological inferences and illustrates the logical connections among different species concepts. Species in this construal are abstract models, rather than biological or even tangible entities, and relate to individual organisms via representation, rather than the membership or mereological whole/part relationship. The proposal sheds new light on vexed issues of species and situates them within broad…Read more
  •  23
    Ontology, Causality, and Methodology of Evolutionary Research Programs
    In Evolutionary Causation: Biological and Philosophical Reflections, . pp. 247-264. 2019.
    Scientific conflicts often stem from differences in the conceptual framework through which scientists view and understand their own field. In this chapter, I analyze the ontological and methodological assumptions of three traditions in evolutionary biology, namely, Ernst Mayr’s population thinking, the gene-centered view of the Modern Syn thesis, and the Extended Evolutionary Synthesis. Each of these frameworks presupposes a different account of "evolutionary causes," and this discrepancy preven…Read more
  •  426
    Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library
    with Jaimie Murdock, Colin Allen, Katy Börner, Robert Light, Simon McAlister, Andrew Ravenscroft, Robert Rose, Doori Rose, David Bourget, John Lawrence, and Chris Reed
    PLoS ONE 12 (9). 2017.
    We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We…Read more
  •  43
    The Causal Homology Concept
    Philosophy of Science 84 (5): 1128-1139. 2017.
    I propose a new account of homology, according to which homology is a correspondence of developmental mechanisms due to common ancestry, formally defined as an isomorphism of causal graphs over lineages. The semiformal definition highlights the role of homology as a higher-order principle unifying evolutionary models and also provides definite meanings to concepts like constraints, evolvability, and novelty. The novel interpretation of homology suggests a broad perspective that accommodates evol…Read more
  •  10
    Causality and Probability: A View from Bayesian Networks
    Journal of the Japan Association for Philosophy of Science 38 (1): 39-47. 2010.
  •  92
    Using causal models to integrate proximate and ultimate causation
    Biology and Philosophy 30 (1): 19-37. 2015.
    Ernst Mayr’s classical work on the nature of causation in biology has had a huge influence on biologists as well as philosophers. Although his distinction between proximate and ultimate causation recently came under criticism from those who emphasize the role of development in evolutionary processes, the formal relationship between these two notions remains elusive. Using causal graph theory, this paper offers a unified framework to systematically translate a given “proximate” causal structure i…Read more
  •  150
    A critical review of the statisticalist debate
    Biology and Philosophy 31 (4): 459-482. 2016.
    Over the past decade philosophers of biology have discussed whether evolutionary theory is a causal theory or a phenomenological study of evolution based solely on the statistical features of a population. This article reviews this controversy from three aspects, respectively concerning the assumptions, applications, and explanations of evolutionary theory, with a view to arriving at a definite conclusion in each contention. In so doing I also argue that an implicit methodological assumption sha…Read more
  •  50
    Causal Foundations of Evolutionary Genetics
    British Journal for the Philosophy of Science 67 (1): 247-269. 2016.
    The causal nature of evolution is one of the central topics in the philosophy of biology. The issue concerns whether equations used in evolutionary genetics point to some causal processes or purely phenomenological patterns. To address this question the present article builds well-defined causal models that underlie standard equations in evolutionary genetics. These models are based on minimal and biologically plausible hypotheses about selection and reproduction, and generate statistics to pred…Read more