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Jun Otsuka
Kyoto University
  1.  15
    Causal Foundations of Evolutionary Genetics.Jun Otsuka - 2016 - British Journal for the Philosophy of Science 67 (1):247-269.
    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 predict evolutionary changes. The causal reconstruction of the evolutionary principles shows (...)
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  2.  28
    Causal Foundations of Evolutionary Genetics.Jun Otsuka - 2014 - British Journal for the Philosophy of Science (1):axu039.
    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 predict evolutionary changes. The causal reconstruction of the evolutionary principles shows (...)
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  3.  56
    Using Causal Models to Integrate Proximate and Ultimate Causation.Jun Otsuka - 2015 - Biology and Philosophy 30 (1):19-37.
    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 into an “ultimate” evolutionary response, and illustrates evolutionary implications (...)
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  4.  74
    A Critical Review of the Statisticalist Debate.Jun Otsuka - 2016 - Biology and Philosophy 31 (4):459-482.
    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 shared by both sides of the debate, namely the (...)
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  5.  85
    Why the Causal View of Fitness Survives.Jun Otsuka, Trin Turner, Colin Allen & Elisabeth A. Lloyd - 2011 - Philosophy of Science 78 (2):209-224.
    We critically examine Denis Walsh’s latest attack on the causalist view of fitness. Relying on Judea Pearl’s Sure-Thing Principle and geneticist John Gillespie’s model for fitness, Walsh has argued that the causal interpretation of fitness results in a reductio. We show that his conclusion only follows from misuse of the models, that is, (1) the disregard of the real biological bearing of the population-size parameter in Gillespie’s model and (2) the confusion of the distinction between ordinary probability and Pearl’s causal (...)
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  6.  23
    The Causal Homology Concept.Jun Otsuka - 2017 - Philosophy of Science 84 (5):1128-1139.
    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 evolutionary developmental biology and traditional population genetics as distinct but complementary approaches (...)
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  7. Multi-Level Computational Methods for Interdisciplinary Research in the HathiTrust Digital Library.Jaimie Murdock, Colin Allen, Katy Börner, Robert Light, Simon McAlister, Andrew Ravenscroft, Robert Rose, Doori Rose, Jun Otsuka, David Bourget, John Lawrence & Chris Reed - 2017 - PLoS ONE 12 (9).
    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 provide a case study for the application of the methods to (...)
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  8.  23
    Species as Models.Jun Otsuka - forthcoming - Philosophy of Science.
    This paper argues that biological species should be construed as abstract models, rather than biological or even tangible entities. Various species concepts are defined as set-theoretic models of formal theories, and their logical connections are illustrated. In this view organisms relate to a species not as instantiations, members, or mereological parts, but rather as phenomena to be represented by the model/species. This sheds new light on the long-standing problems of species and suggests their connection to broader philosophical topics such as (...)
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  9.  5
    Design Problems in Life and AI生命と人工知能におけるデザイン問題.Jun Otsuka - 2019 - Journal of the Japan Association for Philosophy of Science 46 (2):71-77.
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  10.  7
    Ontology, Causality, and Methodology of Evolutionary Research Programs.Jun Otsuka - unknown
    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 prevents mutual understanding and objective evaluation in the recent contention surrounding the EES. From (...)
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  11. Causality and Probability: A View From Bayesian Networks.Jun Otsuka - 2010 - Journal of the Japan Association for Philosophy of Science 38 (1):39-47.
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  12. The Roles of Mathematics in Evolutionary Theory.Jun Otsuka - 2019 - Cambridge University Press.
    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 and as the organizing framework that integrates mathematical and (...)
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