Catherine Kendig (Michigan State University)
The naming, coding, and tracking of parts and modules is pervasive in all fields of biology. However, these activities seem to play a particular role in synthetic biology where discovering something is the same part is crucial to ideas of identity as well as successful construction.
Synthetic biology is frequently defined as the application of engineering principles to the design, construction, and analysis of biological systems. For example, biological functions such as metabolism may now be genetically reengineered to produce new chemical compounds. Designing, modifying, and manufacturing new biomolecular systems and metabolic pathways draws upon analogies from engineering such as standardized parts, circuits, oscillators, and digital logic gates. These engineering techniques and computational models are then used to understand, rewire, and reengineer biological networks. But is that all there is to synthetic biology? Is this descriptive catalogue of bricolage wholly explanatory of the discipline? Do these descriptions impact scientific metaphysics? If so, how might these parts descriptions inform us of what it is to be a biological kind? Attempting to answer these questions requires investigations into the nature of these biological parts as well as what role descriptions of parts play in the identification of them as the same sort of thing as another thing of the same kind.
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 (igem.org). 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 informational specificity 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 understanding what we mean by “part”, how we individuate parts, or how we attribute the property of parthood to something seems to rely on assumptions about the nature of part-whole relationships.
My aim is to tease out these underlying concepts in an attempt to understand the process of what has been called “ontology engineering” (Gruber 2009). To do this, I focus on the preliminary processes of knowledge production which are prerequisite to the construction or identification of ontologies of parts. I investigate the activities of naming and tracking parts within and across repositories and highlight the ineliminable normativity of part-making and kind-making. I will then sketch some problems arising from the varied descriptions of parts contained in different repositories. Lastly, I will critically discuss some recent computational models currently in use that promise to offer practitioners a means of capturing information and meta-information relevant to answering particular questions through the construction of similarity measures for different biological ontologies.
