Prediction is more than testing established theory by examining whether the prediction matches the data. To show this, I examine the practices of a community of scientists, known as threaders, who are attempting to predict the final, folded structure of a protein from its primary structure, i.e., its amino acid sequence. These scientists employ a careful and deliberate methodology of prediction. A key feature of the methodology is calibration. They calibrate in order to construct better models. The construction leads to (...) knowledge of how to construct or build an object. Thus, prediction serves a cognitive goal of model construction and not just model or theory testing. The kind of knowledge that results is relevantly different than theoretical knowledge. (shrink)

Usually within the context of computer simulations in quantum chemistry practices, there is a distinction between ab initio and semi-empirical methods. Related to this, a controversy within the scientific and philosophical communities came about regarding the superiority of the ab initio methods due to their theoretical rigor. In this article we re-evaluate the condition of the semi-empirical simulations in this area of research. We examine some of the aspects of this debate that have been considered in philosophy and provide additional (...) elements to the analysis. (shrink)

In this rejoinder to Eric Scerri's response to my first comment on his paper on the reduction of chemistry to physics, the main point concerns laws in chemistry. But other themes touched upon include the assumptions involved in ab initio calculations, the question of what is reduced to what on Scerri's view, and the significance he attaches to the term "naturalism".

Focusing on computational studies of pericyclic reactions from the late twentieth century into the twenty-first century, this paper argues that computational diagnostics is a key methodological development that characterize the management and coordination of plural approximation methods in computational organic chemistry. Predictive divergence between semi-empirical and ab initio approximation methods in the study of pericyclic reactions has issued in epistemic dissent. This has resulted in the use of diagnostics to unpack computational greyboxes in order to critically assess the effect of (...) specific misrepresentations on predictive accuracy given that approximations and idealizations must be made to render computational models tractable. Furthermore, benchmarking is used to determine the applicability of approximation methods depending on how accurate the results need to be in a given research context. The epistemology of benchmarking consists of the co-generation of data sets in a hybrid computational–experimental form used to standardize computational methods but does not determine a unique quantitative method to be used across computational organic chemistry. (shrink)

Arguably no concept is more fundamental to science than that of causality, for investigations into cases of existence, persistence, and change in the natural world are largely investigations into the causes of these phenomena. Yet the metaphysics and epistemology of causality remain unclear. For example, the ontological categories of the causal relata have been taken to be objects (Hume 1739), events (Davidson 1967), properties (Armstrong 1978), processes (Salmon 1984), variables (Hitchcock 1993), and facts (Mellor 1995). (For convenience, causes and effects (...) will usually be understood as events in what follows.) Complicating matters, causal relations may be singular (Socrates’s drinking hemlock caused Socrates’s death) or general (Drinking hemlock causes death); hence the relata might be tokens (e.g., instances of properties) or types (e.g., types of events) of the category in question. Other questions up for grabs are: Are singular causes metaphysically and/or epistemologically prior to general causes or vice versa (or neither)? What grounds the intuitive asymmetry of the causal relation? Are macro-causal relations reducible to micro-causal relations? And perhaps most importantly: Are causal facts (e.g., the holding of causal relations) reducible to non-causal facts (e.g., the holding of certain spatiotemporal relations)? (shrink)