Jun Otsuka
Biographic Data
| ID | 460832 |
|---|---|
| NAME | Jun Otsuka |
| GIVEN NAMES | Jun |
| FAMILY NAME | Otsuka |
| SIGNATURE | OTSUKA J |
| AFFILIATIONS | University of California, Davis |
| ORCID | 0000-0003-4774-9740 |
| VERIFIED | Yes |
| TOTAL WORKS | 7 |
| TOTAL CITATIONS | 16 |
| AUTHOR COUNT | 7 |
| EDITOR COUNT | 0 |
| FIRST PUBLICATION YEAR | 2011 |
| LATEST PUBLICATION YEAR | 2025 |
| H-INDEX | 2 |
Modeling causal processes
A Categorical Solution to the Grue Paradox
Thinking About Statistics: The Philosophical Foundations
Simply stated, this book bridges the gap between statistics and philosophy. It does this by delineating the conceptual cores of various statistical methodologies (Bayesian/frequentist statistics, model selection, machine learning, causal inference, etc.) and drawing out their philosophical implications. Portraying statistical inference as an epistemic endeavor to justify hypotheses about a probabilistic model of a given empirical problem, the boo…
Species as Models
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 vexe…
The Causal Homology Concept
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 s…
Causal Foundations of Evolutionary Genetics
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…
Why the Causal View of Fitness Survives
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)…
Causal Foundations of Evolutionary Genetics
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…
Why the Causal View of Fitness Survives
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)…
Species as Models
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 vexe…
The Causal Homology Concept
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 s…
Why the Causal View of Fitness Survives
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)…
Causal Foundations of Evolutionary Genetics
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…
The Causal Homology Concept
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 s…
Species as Models
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 vexe…
Thinking About Statistics: The Philosophical Foundations
Simply stated, this book bridges the gap between statistics and philosophy. It does this by delineating the conceptual cores of various statistical methodologies (Bayesian/frequentist statistics, model selection, machine learning, causal inference, etc.) and drawing out their philosophical implications. Portraying statistical inference as an epistemic endeavor to justify hypotheses about a probabilistic model of a given empirical problem, the boo…
A Categorical Solution to the Grue Paradox
Modeling causal processes
Computer Science (6 works) · Epistemology (6 works) · Philosophy (6 works) · Philosophy and History of Science (6 works) · Biology (3 works) · Sociology (3 works) · Artificial Intelligence (2 works) · Biomedical Text Mining and Ontologies (2 works) · Evolution and Genetic Dynamics (2 works) · Evolutionary biology (2 works)