Applied Statistics Requires Scientific Context

TL;DR

This paper emphasizes that applying and interpreting statistical methods in science critically depends on understanding nuanced foundational and practical context, challenging the idea of universal significance thresholds.

Contribution

It argues for the importance of considering scientific context in statistical practice and critiques the pursuit of universal significance thresholds.

Findings

Reformulation of p-value as divergence measure highlights context importance.

Contextual considerations improve validity in randomized trials.

Low significance thresholds are effective due to validation, not the thresholds themselves.

Abstract

Statistical methods are indispensable to scientific inference. However, there exists a longstanding tension across a wide range of scientific disciplines about the role that ``context'' should play in the application of statistical methods and the interpretation of statistical results. Though frequently invoked, the notion of ``scientific context'' refers to at least two distinct concepts: a set of foundational nuanced and elusive background assumptions and substantive features of a given area of study that shape the validity and reliability of statistical methods; and more quantifiable contextual issues that affect the performance of statistical methods and interpretation of statistical results. I argue here that the application and interpretation of statistical methods requires careful consideration of foundational contextual issues. To motivate the arguments, I review a recent re-formulation of the $p$-value as a measure of divergence between an observed dataset and a set of assumptions used to construct statistical measures. I use this framework to illustrate the role that context plays in two randomized trials: on low-dose aspirin for pregnancy loss, and a new inhibitor of a key biochemical pathway affecting ankylosing spondylitis. Finally, I note that the adoption of low significance thresholds in genome-wide association studies and high energy particle physics has been successful more so because of extensive validity-checking gauntlets and contextual considerations that have accompanied these low thresholds, not because of the low thresholds themselves. I use these illustrations and arguments to suggest that (i) the adoption of a universal threshold for significance testing should be abandoned as a goal of statistics reform; and (ii) the validity and optimal use of applied statistical tools requires careful consideration of nuanced scientific context.