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yoichi ishida
Department of Philosophy
Ohio University CURRICULUM VITAE
CONTACT
Department of Philosophy
Ellis Hall, Room 202
Ohio University
Athens, OH 45701
ishiday · at · ohio · dot · edu

about me

My name is Yoichi Ishida (pronounced "yo-EE-chee ee-SHEE-da"). I am an Assistant Professor of Philosophy at Ohio University. I work in the areas of philosophy of science and philosophy of biology. My philosophical and scientific articles have been published in Philosophy of Science, BioEssays, and Journal of General Physiology. My research has been supported by a grant from the National Science Foundation.

research

My research concerns epistemological and methodological issues that arise when we study the fine details of scientific practice, particularly the practice of modeling in the biological sciences. My research also brings these details to bear on topics in philosophy of science and philosophy of biology. My work is driven by a desire to understand the innovative ways in which scientists investigate the world. In collaboration with biologists I also do scientific research using computational models.
MORE ABOUT MY RESEARCH

Models in Scientific Practice (Dissertation)
My dissertation presents an account of the practice of modeling in science in which scientists' perceptual and bodily interactions with external representations take center stage. I argue that modeling is primarily a practice of constructing, manipulating, and analyzing external representations in service of cognitive and epistemic aims of research, and show that this account better captures important aspects of the practice of modeling than accounts currently popular in philosophy of science. Philosophical accounts of the practice of modeling classify models according to the categories of abstract and concrete entities developed in metaphysics. I argue that this type of account obscures the practice of modeling. In particular, using the analysis of the Lotka-Volterra model as an example, I argue that understanding mathematical models as abstract entities---non-spatiotemporally located, imperceptible entities---obscures the fact that the analysis of the Lotka-Volterra model relies primarily on visual perception of external representations, especially hand- or computer-generated graphs. Instead, I suggest that we apply the concepts of internal and external representations, developed in cognitive science, to models, including mathematical models. I then present two case studies that illustrate different aspects of modeling, understood as a practice of constructing, manipulating, and analyzing external representations. First, using Sewall Wright's long-term research on isolation by distance, I articulate the relationship between the uses of a model, the particular aims of research, and the criteria of success relevant to a given use of the model. I argue that uses of the same model can shift over the course of scientists' research in response to shifts in aim and that criteria of success for one use of a model can be different from those for another use of the same model. Second, I argue that in successful scientific research, a scientist uses a model according to the methodological principles of realism and instrumentalism despite the tension that they create among the scientist's uses of the model over time. This thesis is supported by a detailed analysis of successful scientific research done by Seymour Benzer in the 1950s and 60s.

Historical and Philosophical Analysis of the Genetic Maps in Seymour Benzer's Research on Genetic Fine Structure
This project is supported by a Doctoral Dissertation Research Improvement Grant from National Science Foundation. The project aims, among other things, to identify various uses of genetic maps (diagrammatic models) in the course of Benzer's research.

Random Sampling, Offspring Distribution, and Genetic Drift
Chris Cannings's approach to the development of drift models suggests that assumptions about stochastic mechanisms are unnecessary for developing and analyzing drift models, including the Wright-Fisher model. I argue that the stochastic mechanism of the Wright-Fisher model need not be regarded as representing a biological process. Drawing on the Cannings model, I suggest that an alternative way to think about drift is in terms of offspring distribution, the probability distribution of the number of offspring produced by an individual in a population. Offspring distribution is central to Cannings's approach, and thinking about drift in terms of offspring distribution is illuminating in many ways. I suggest that the condition of identical offspring distribution, which is closely related to the notion of exchangeability in probability theory, is the shared element of important drift models. I am working out this suggestion further, examining the epistemic significance of exchangeability and the causal structures that satisfy the condition of identical offspring distribution. This work joins the active debate in philosophy of biology over the representational content of drift models. (This is partly a joint project with Alirio Rosales (UBC). We presented a paper-in-progress at Philosophy of Biology at Madison 2012.)

teaching

I am interested in teaching a variety of courses in philosophy at undergraduate and graduate levels. My courses emphasize deep understanding of the materials and critical discussion of ideas in oral and written formats. I am committed to make my courses and materials inclusive.
MORE ABOUT MY TEACHING

Recent Courses
The syllabus for each course is available upon request. A more complete description of my teaching experience is available in my CV.

  • MODELS OF MIND AND SOCIETY (Graduate)
    Fall 2017, Ohio University
  • CAUSATION AND EXPLANATION (Graduate)
    Fall 2016, Ohio University
  • EVOLUTION OF HUMAN COGNITION AND COOPERATION (Graduate)
    Spring 2015, Spring 2017, Ohio University
  • MODELS AND REPRESENTATION (Graduate)
    Fall 2015, Ohio University
  • FUNDAMENTALS OF PHILOSOPHY
    Spring 2015, Spring 2016, Spring 2017, Ohio University
  • PRINCIPLES OF REASONING
    Fall 2014, Fall 2015, Fall 2016, Ohio University
  • PHILOSOPHY OF SCIENCE SURVEY
    Fall 2014, Ohio University

publications

  1. Sewall Wright, Shifting Balance Theory, and the Hardening of the Modern Synthesis.
    Studies in History and Philosophy of Biological and Biomedical Sciences 61 (2017): 1-10.
    JOURNAL WEBSITE PDF
  2. A Mathematical Model of Osteoclast Acidification During Bone Resorption. (With Frank V. Marcoline [first author], Joseph A. Mindell, Smita Nayak, and Michael Grabe)
    Bone 93 (2016): 167-180.
    JOURNAL WEBSITE PDF
  3. A Model of Lysosomal pH Regulation. (With Smita Nayak, Joseph A. Mindell, and Michael Grabe)
    Journal of General Physiology 141 (2013): 705-720.
    JOURNAL WEBSITE PDF
  4. Sewall Wright and Gustave Malécot on Isolation by Distance.
    Philosophy of Science 76 (2009): 784-796.
    JOURNAL WEBSITE PDF
  5. Transposable Elements and an Epigenetic Basis for Punctuated Equilibria. (With David Zeh and Jeanne Zeh)
    BioEssays 31 (2009): 715-726.
    JOURNAL WEBSITE PDF
  6. Patterns, Models, and Predictions: Robert MacArthur's Approach to Ecology.
    Philosophy of Science 74 (2007): 642-653.
    JOURNAL WEBSITE PDF

grant support

recent presentations