Computational Chemistry as Voodoo Quantum Mechanics : Models, Parameterization, and Software

TL;DR

This paper examines the epistemic transparency issues in computational chemistry, focusing on how parameterization and software contribute to opacity and the tensions among scientists, using discussions from a professional mailing list as a case study.

Contribution

It highlights the interconnectedness of models, parameterization, and software in creating epistemic opacity in computational chemistry.

Findings

Parameterization leads to epistemic opacity in models and software.

Discussions reveal tensions and lack of transparency among scientists.

Models and software should be addressed together to understand epistemological issues.

Abstract

Computational chemistry grew in a new era of "desktop modeling", which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous enterprise, and we argue that this activity leads, in this specific context, to tensions among scientists regarding the lack of epistemic transparency of parameterized methods and the software implementing them. To explicit these tensions, we rely on a corpus which is suited for revealing them, namely the Computational Chemistry mailing List (CCL), a professional scientific discussion forum. We relate one flame war from this corpus in order to assess in detail the relationships between modeling methods, parameterization, software and the various forms of their enclosure or disclosure. Our claim is that parameterization issues are a source of epistemic opacity and that this opacity is entangled in methods and software alike. Models and software must be addressed together to understand the epistemological tensions at stake.