My presentation for this symposium follows a "practice-first" approach. This approach starts with one scientific practice, analyzes it in terms of the epistemic activities that form it, and sees what philosophical issues emerge from such an analysis. I analyze the practice of amplicon sequencing (AS), a widely used method in microbiology and microbial ecology. The principle is the analysis of environmental DNA to assess the composition of microorganisms in a given environment. Decomposing the technique in terms of epistemic activities highlights the choices available to scientists impacting the form or the content of the knowledge produced. I propose two new aspects of philosophical issues from the practice analysis.
The first one is a novel definition of biological samples. Samples have been overlooked in the philosophy of science compared to the concept of data. Using the relational framework of data developed by Leonelli (2016), I argue that samples have a specific epistemic function in the AS context. In particular, I argue that samples are necessarily transformed to be considered evidence, portable in the limit of the situation where they endure this transformation, and act as material/world anchors for data claims about a phenomenon.
The second is a new angle on model-based accounts of measurement. AS is used to measure biological diversity. It is a substitution for natural observation. Model-based accounts of measurement (Mari, Frigerio, Tal) are rooted in scientific practice but lack a convincing biological example. Analyzing AS is a way of breaching this gap. It remains unclear whether modifying these accounts will be needed at this investigation stage. Moreover, exploring AS in terms of measurements highlights the ontological commitments required to perform this activity. This sheds light on the role (if any) and the content of the species concept in this measurement practice.
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