International Society for History, Philosophy, and Social Studies of Biology


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Program

THURSDAY, JULY 9  /  15:30 - 17:00  /  DS-1520
Organized session / standard talks
Ontology and epistemology of identifying characters and genes
Organizer(s):

Shunkichi Matsumoto (Tokai University, Japan); Alan Love (University of Minnesota, United States)

Identifying characters in organisms is a starting point of almost all biological explorations. Researches in systematics, evolutionary theory, genetics, physiology, pathology, etc. depend on the precise description of characters. However, biologists have been always puzzled about characters, not only because the discernibility of characters among closely related organisms is not always warranted but also because the factors that are responsible for bringing about those characters are intertwined. These puzzles raise many related questions: To what extent and by what approaches can we individuate characters and their variations? Are the individuated characters character types or individual characters? To what extent and by what approaches can we identify causal factors (typically, genes) that are responsible for characters? Are the identified genes gene types or individual genes? To date, biologists have been able to individuate characters and genes via different approaches. Evolutionary theory, developmental biology, classical genetics, molecular biology, and other biological sciences offer different approaches that may be separated or related. Our session aims to explore the problems of how separated or related those approaches are. Suzuki and Tanaka address the issue about how to understand homologous characters. In order to overcome the problems in each of the currently prevalent two theories about homology — the individuality theory versus the homeostatic property cluster (HPC) kind theory — they propose their own reproducible-persistent-module (RPM) theory. Matsumoto discusses the case of the discovery of the cystic fibrosis gene to examine what methodology was employed in the identification process. He especially notes the relevance of evolutionary gene concept in the modern molecular biology. Chen explores the individuation of genes from the experimental perspective. He argues that the theory of classical genetics and its attendant experiments actually individuated only some types of gene, while experiments from the biotechnology of transgenes could individuate a particular gene.


Beyond the dichotomy of individual and kind: The reproducible-persistent-module (RPM) theory of homology

Daichi Suzuki (University of Tsukuba, Japan); Senji Tanaka (Keio University, Japan)

Homology is one of the central concepts in biology, but its ontological status is still controversial. We consider it by comparing two theories: the individuality theory and the homeostatic property cluster (HPC) kind theory. According to the individuality theory, homology is a relation of correspondence between parts of individuals (Ghiselin 1990, 2005). According to the HPC kind theory, a homologous character (or a homologue) is a natural kind defined by a homeostatic property cluster (Assis & Brigandt 2009, Brigandt 2009). Both theories have not only their own advantages, but also problems. For example, it is difficult for the individuality theory to accommodate the fact that homologous characters are often genetically discontinuous, and the fact that they are often abstracted to some kind-like “types” or “body plans” even by the contemporary biologists. On the other hand, properties and underlying mechanisms of homologous characters (e.g., molecular components of vertebrate lenses, regeneration/developmental mechanisms of newt lens) are often too variable for the HPC kind theory to explain. Moreover, the HPC kind theory is likely to blur the boundary between homology and analogy (Brigandt 2009), which is important and useful for biologists. So here we propose a new conception of homology: the reproducible-persistent-module (RPM) theory. According to the theory, homologous characters are modular structures that are reproducible and persistent in evolutionary/biological (life history) processes. Homologous characters as modules are not only spatiotemporally restricted (because they are actual modular structures realized in some specific processes), but also have properties that are homeostatic to some degree (because they are persistently reproducible). Thus the RPM theory accommodates both individual-like and kind-like characteristics of homologous characters.


Cystic fibrosis as a case study for the identification of the gene

Shunkichi Matsumoto (Tokai University, Japan)

I will take up Collins, Riordan, Tsui, and colleagues’ historical feat of identifying the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989 as a case for studying the issue concerning the identification of the gene. What is noteworthy about their work is that it employed the approach of “reverse genetics,” for they had to set out for the endeavor while knowing little about the protein synthesized from it. On the other hand, discovering the mutations that give rise to pathological symptoms involved the approach of “forward genetics,” for it started with the CF phenotypes of patients and then went downward to track down the underlying genotypes (mutations). As for the causal pathways concerning how these mutations actually cause CF symptoms, the explanations available today still remain more or less sketchy although the genotype-phenotype relationships in the modern molecular biology have been described far more in detail, as compared to those counterparts in the old classical genetics. From the analysis of this case, the following points can be obtained. First, we can point out a kind of conceptual isomorphism between “the gene for X” talk emblematic of evolutionary biology and “the gene for CF” one which is one of the exemplars of molecular biology. Second, more important, in some context it is a prerequisite for an arbitrary DNA sequence to be identified as a gene (coding region) that it is an evolutionarily conserved sequence. For, the researchers eventually managed to track down the gene for CF by comparing the DNA sequences they had just decoded with DNAs from other organisms, based on the idea that evolutionarily conserved sequences across species are highly likely to encode some functional polypeptides. Thus, I will argue for the relevance of the evolutionary point of view in the modern molecular biology.


The experimental individuation of genes

Ruey-Lin Chen (National Chung Cheng University, Taiwan)

Recently, biological individuality has become a central issue in the philosophical discussion of biology. Philosophers focus on the question of what count as biological individuals and usually approach to this question via theories – evolutionary, physiological, or immunological (Godfrey-Smith 2013; Clarke 2013, Pradeu 2010, 2013). They view different biological theories as providing different principles of individuation for defining biological individuality. However, theories are not the only access to the definition of individuality; experimentation may offer an alternative approach. Even experimentation can individuate a particular object while theories can only individuate a kind or a type. In the case of the gene, for example, Gregor Mendel assumed that hereditary factors of features are unitary and corpuscular things – scientists called them genes later. The classical geneticists built up a theory of genes and performed experiments to identifying some individual genes. In this sense, one might well say that the classical geneticists experimentally individuate genes. However, I will argue the genes that the classical geneticists had individuated were no more than the gene kinds or types. Genes as particular objects had not been individuated till biotechnology of transgenes was invented. Here I presuppose a distinction between the individuation of kinds and the individuation of particular objects. I will also explore the relationship between the two kinds of individuation.