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.
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.
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.
On the Successful Practice of Modeling in Science
Philosophers generally understand a scientific model to be an object with parts or properties that a scientist interprets as representing parts or properties of the real-world system of interest. To illuminate the complex ways in which scientists interpret and use parts and properties of their models, I develop this idea further by following scientists' interpretations and uses of models over time---in their notebooks, letters, and papers. I argue that some interpretations of parts or properties of a model are more fixed and stable over the course of research than others in the sense that certain parts or properties of a model are interpreted as representing the same parts or properties of the real-world system over the course of research. The relative fixity and stability of these interpretations help maintain the identity of the model over time and enable a scientist to determine and explore the representational content of the model. I also argue that within the constraints imposed by the relatively fixed and stable interpretations, other parts or properties of the model are given relatively flexible and transient interpretations: some parts or properties of a model are interpreted at one point as representing parts or properties of the real-world system of interest but at another point as representing things other than the parts or properties of that system. These interpretations are given in response to theoretical, empirical, or technological developments and a variety of practical needs that arise over the course of research.
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.
Realism, Instrumentalism, and Uses of Models in Science
Realism and instrumentalism are widely understood as incompatible views about scientific theories and models. But this is importantly mistaken. I argue that in successful scientific research, a scientist uses a model according to the methodological principles of both realism and instrumentalism despite the tension that they create among the scientist's uses of the model over time. A scientist profits from embracing the counterintuitive position that a single model should be used both as a representation of reality and as a mere instrument for solving practical problems. Dominant realist and instrumentalist views cannot make sense of this position and thus do not agree with a key feature of successful scientific practice.
What Makes a Useful Model?
My account of successful modeling practice clarifies the relationship between the realistic and instrumental uses of a model. The realistic uses of a model depend on fixed and stable interpretations of some parts and properties of the model, whereas the instrumental uses of the same model depend on flexible and transient interpretations. This provides a more cogent alternative to the common view that instrumental as well as realistic uses of a model depend on the representational relation between the model and the world, a view that has resulted from philosophers' nearly exclusive focus on the representational content of a model. Based on this account, I analyze what makes a useful scientific model. If most parts and properties of the model were given fixed and stable interpretations, the model would be less useful in practice because there would be fewer parts and properties to which a scientist could give flexible and transient interpretations. For a working scientist, a model would be more useful if it had parts and properties that admit flexible and transient interpretations as well.
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.)
Sewall Wright's Analysis of the Distribution of Flower Color in Linanthus parryae, 1941-1978
This project reconstructs the details of Wright's research on Linanthus using his research notes, correspondence, unpublished manuscripts, and published works. So far I have analyzed Wright's resistance to the hardening of the Modern Synthesis, his uses of various models at different periods of research, and a radical shift in his assumption about the spatial distributions of evolutionary parameters of interest. I have presented tentative results of this project at two ISHPSSB meetings.
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.
The syllabus for each course is available upon request. A more complete description of my teaching experience is available in my CV.
The full list of my presentations is available in my CV.