Are bio-ontologies metaphysical theories?

Abstract

Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community's ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of science that some philosophers have envisaged. However, I argue that the local, practical, social and technological factors that influence their design prevent us from straightforwardly reading metaphysical conclusions from them. I discuss these complications and suggest how they can be overcome, revealing more general lessons for the development of a well-founded scientific metaphysics.

Explaining ambiguity in scientific language

“…Even basic information about an observation is subject to major transformations, such as in ecology where scientists seeking long-term data have to reconcile contemporary latitude-longitude measurements of location with historical landmarks used in observations a century ago (Shavit & Griesemer, 2011). In response, scientists in many disciplines have adopted the strategy of standardizing and formalizing the language they use to communicate and reason about their research, for example by using computer ontologies (Leonelli, 2012;Poirier, 2019;Sterner et al, 2020b;Lean, 2021).…”