Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Ankeny and Leonelli propose “repertoires” as a new way to understand the stability of certain research programs as well as scientific change in general. By bringing a more complete range of social, material, and epistemic elements into one framework, they position their work as a correction for the Kuhnian impulse in philosophy of science and other areas of science studies. I argue that this “post-Kuhnian” move is not complete, and that repertoires maintain an internalist perspective, caused partly by an asymmetrical (...) emphasis on the scientists’ side of practice. If we compare “repertoires” to alternative frameworks, like “sociotechnical imaginaries” of Jasanoff and Kim, it is evident that repertoires are missing two specific things. First, I argue that the framework needs to include the role of audience, without whom the repertoires of science are unintelligible. Second, I suggest that the framework also lacks an explicit place for ethical and political imagination, which provide meaning for otherwise mechanical promotion of particular research programs. With these modifications, Ankeny and Leonelli’s framework might fulfill its post-Kuhnian potential. (shrink)

Herbert Blumer was a key figure in what came to be identified as the Chicago School of Sociology. He invented the term ‘symbolic interactionism’ as a label for a theoretical approach that derived primarily from the work of John Dewey, George Herbert Mead and Charles Cooley. But his most influential work was methodological in character, and he is generally viewed today as a prominent critic of positivism, and of the growing dominance of quantitative method within US sociology. While this picture (...) is broadly accurate, it neglects an important strand in his methodological thinking. He was committed to the goal of a science of social life, while at the same time he was uncertain whether such a science is possible. In his Appraisal of Thomas and Znaniecki’s The Polish Peasant, he identified a serious dilemma facing this project: the problem of how a scientific approach can be made compatible with the distinctive nature of human social life. In the first chapter of his most influential book, Symbolic Interactionism, he advocates a naturalistic approach to case study, and seems to treat this as avoiding the dilemma. However, there is evidence to suggest that, even towards the end of his life, he regarded the problem as still unresolved. In this article, I examine both sides of Blumer’s dilemma, and whether his attitude towards it changed. However, my interest here is not only historiographical. I evaluate Blumer’s arguments and show that his intellectual struggle with this issue remains relevant today, despite the shifts that have taken place in social science methodology and the philosophy of science since his death. (shrink)

Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state of (...) a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege’s idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)