ABSTRACT
We focus on the preliminary steps and processes of knowledge production which are prerequisite to the construction or identification of ontologies of parts within synthetic biology. Biological parts repositories serve as a common resource where synthetic biologists can go to obtain physical samples of DNA associated with descriptive data about those samples. Perhaps the best example of a biological parts repository is the iGEM Registry of Standard Biological Parts. These parts have been classified into collections, some labeled with engineering terms (e.g. chassis, receiver) some labeled with biological terms (e.g., proteindomain, binding), and some labeled with vague generality (e.g., classic, direction). Descriptive catalogues appear to furnish part-specific knowledge and individuation criteria that allow us to individuate them as parts. Repositories catalogue parts. It seems straightforward enough to understand what is contained within the repository in terms of the general concept: part. But what are we doing when we describe something as being a part? In this paper, we investigate some problems arising from the varied descriptions of parts contained in different repositories. Following this, we outline problems that arise with naming and tracking parts within and across repositories and explore how the comparison of parts across different databases might be facilitated. This focuses on computational models currently being sought that would allow practitioners to capture information and meta-information relevant to answering particular questions through the construction of similarity measures for different biological ontologies. We conclude by discussing the social and normative aspects of part-making and kind-making in synthetic biology.
