Ontology, Causality, and Methodology of Evolutionary Research Programs

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 (MS), and the Extended Evolutionary Synthesis (EES). 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 this perspective, the chapter characterizes the EES research program as an attempt to introduce causal structures beyond genes as additional units of evolution, and compares its research methodology and objectives with those of the traditional MS framework

The Causal Homology Concept

This presentation proposes a new account of homology, which defines homology as a correspondence of developmental or behavioral mechanisms due to common ancestry. The idea is formally presented as isomorphism of causal graphs over lineages. The formal treatment not only clears the metaphysical skepticism regarding the homology thinking, but also provides a theoretical underpinning to the concepts like constraints, evolvability, and novelty. The novel interpretation of homology suggests a general perspective that accommodates evolutionary develop mental biology (Evo-Devo) and traditional population genetics as distinct but complementary approaches to understand evolution, facilitating further empirical and theoretical researches

Causal Foundations of Evolutionary Genetics

The causal nature of evolution is one of the central topics in the philosophy of biology. It has been discussed whether equations used in evolutionary genetics point to some causal processes or are purely phenomenological patterns. To address this question the present paper 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 adaptive evolution as a genuine causal process, where fitness and selection are both causes of evolution

Ontology, Causality, and Methodology of Evolutionary Research Programs

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 (MS), and the Extended Evolutionary Synthesis (EES). 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 this perspective, the chapter characterizes the EES research program as an attempt to introduce causal structures beyond genes as additional units of evolution, and compares its research methodology and objectives with those of the traditional MS framework

Species as models

This paper argues that biological species should be construed as abstract models, rather than biological or even tangible entities. Various (phenetic, cladistic, biological etc.) 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 model selection, scientific representation, and scientific realism

Neural correlates of implicit knowledge about statistical regularities

In this study, we examined the neural correlates of implicit knowledge about statistical regularities of temporal order and item chunks using functional magnetic resonance imaging (fMRI). In a familiarization scan, participants viewed a stream of scenes consisting of structured (i.e., three scenes were always presented in the same order) and random triplets. In the subsequent test scan, participants were required to detect a target scene. Test sequences included both forward order of scenes presented during the familiarization scan and backward order of scenes (i.e., reverse order of forward scenes). Behavioral results showed a learning effect of temporal order in the forward condition and scene chunks in the backward condition. fMRI data from the familiarization scan showed the difference of activations between the structured and random blocks in the left posterior cingulate cortex including the retrosplenial cortex. More important, in the test scan, we observed brain activities in the left parietal lobe when participants detected target scenes on temporal order information. In contrast, the left precuneus activated when participants detected target scenes based on scene chunks. Our findings help clarify the brain mechanisms of implicit knowledge about acquired regularities

Species as models

This paper argues that biological species should be construed as abstract models, rather than biological or even tangible entities. Various (phenetic, cladistic, biological etc.) 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 model selection, scientific representation, and scientific realism

The Causal Homology Concept

This presentation proposes a new account of homology, which defines homology as a correspondence of developmental or behavioral mechanisms due to common ancestry. The idea is formally presented as isomorphism of causal graphs over lineages. The formal treatment not only clears the metaphysical skepticism regarding the homology thinking, but also provides a theoretical underpinning to the concepts like constraints, evolvability, and novelty. The novel interpretation of homology suggests a general perspective that accommodates evolutionary develop mental biology (Evo-Devo) and traditional population genetics as distinct but complementary approaches to understand evolution, facilitating further empirical and theoretical researches