Beyond the microscope: Rethinking microbial diversity measurement with the model-based account

Measuring diversity in microbial ecology and microbiome studies is fraught with challenges, rendering the assessment of its “real-world” value nearly impossible. The instability of taxonomic classification, difficulty in isolating individuals, and reliance on DNA-based methods and statistical tools all contribute to the complexity of measuring diversity reliably. This manuscript explores the underlying philosophical issues, relating them to the measurement problem in philosophy. I argue that traditional philosophical accounts of measurement, including representational, operationalist, and realist approaches, are insufficient to address these issues. Instead, I examine these challenges through the lens of a model-based perspective on measurement, which can remain agnostic about entities and property ontologies, clarify the role of assumptions in diversity measurement, and provide solutions for justifying measurement procedures. This work emphasizes the importance of calibration and clearly defining measurement purposes, providing avenues for scientists to improve their measurement procedures. Ultimately, I contribute to a deeper understanding of the challenges and opportunities in measuring microbial diversity by bridging the gap between philosophy and scientific practice.