. 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 epistemic opacity transparency of parameterized methods and the software implementing them. We relate one flame war from the Computational Chemistry mailing List 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 an important and often neglected 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. (shrink)

The main question of this article is given by its title: how inclusive is European philosophy of science? Phrased in this way, the question presupposes that, as a mature discipline, philosophy of science should provide an inclusive account of its subject area. I first provide an explanation of the notion of an inclusive philosophy of science. This notion of an inclusive philosophy of science is specified by discussing three general topics that seem to be missing from, or are quite marginal (...) in, restricted philosophy of science. These topics are the philosophy of historical inquiry, the role of technology in science, and the socio-political and moral dimensions of science. On this basis, I address the question whether European philosophy of science qualifies as more inclusive as compared with Anglo-American philosophy of science. (shrink)

The five studies of this special section investigate the role of models and similar representational tools in interdisciplinarity. These studies were all written by philosophers of science, who focused on interdisciplinary episodes between disciplines and sub-disciplines ranging from physics, chemistry and biology to the computational sciences, sociology and economics. The reasons we present these divergent studies in a collective form are three. First, we want to establish model-exchange as a kind of interdisciplinary event. The five case studies, which are summarized (...) in Section 2 below, show the relevance of this kind. Arguing for the relative unity of these cases will, we hope, re-orient the current debate over interdisciplinarity so as to reflect more appropriately the importance of this kind. We discuss our view of the current state of the debate in Section 3. The evidence from these cases also helps us to develop a taxonomy of interdisciplinary model exchanges in Section 4da taxonomy, we would like to add, that might be useful for the discussion of interdisciplinary exchanges beyond the context of models and their transfer. The second reason for presenting these studies together is that they provide an important source of evidence for the philosophy of science. Over the last three decades, philosophy of science has increasingly differentiated into philosophies of various disciplines. This differentiation in our view has greatly increased our understanding of the scientific practices of the respective disciplines, including the epistemological and methodological standards and conventions on which these practices are based and by which they are evaluated. But it has also made it harder to compare these practices and standards across disciplines. The studies we present here are case studies of interdisciplinary exchange: they focus on the transfer, collaborative construction or parallel use of models and similar representational tools. They therefore provide a unique opportunity to investigate various disciplinary treatments of the same or at least similar representational tools. This allows the identification and comparison of different disciplinary practices and their underlying conventions as well as of the respective normative standards of their evaluation. By tracing the paths along which models travel between disciplines and research fields we can observe to which extent discipline-external practices associated with an adopted tool are retained or replaced by disciplineinternal practices. This generates invaluable information about both disciplinarity and interdisciplinarity. We develop this argument further in Section 5. The third reason for presenting these studies in collective form is that their philosophical analysis also has important normative implications for the notion of interdisciplinarity itself. Too often in the current (non-philosophical) discourse is interdisciplinarity cast as an exclusively integrative project: interdisciplinary exchange is often claimed to be successful only if the involved disciplines become mutually more integrated as a consequence of this process. In contrast to this, many of the cases presented here show that interdisciplinary exchange can be scientifically highly successful, even if at the end of the exchange disciplinary borders remain fully intact. Indeed, borders can be fruitfully crossed without any integration across these borders. Such considerations of divergence in scientific practices and tools offer arguments against a naïve plea for unitarian or non-pluralist versions of interdisciplinarity. Disciplinary divergences may have their justifications, and attempting exchanges that require the reduction of these divergences may consequently not be justified. We pursue this argument further in Section 6. (shrink)

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)

Many philosophical accounts of scientific models fail to distinguish between a simulation model and other forms of models. This failure is unfortunate because there are important differences pertaining to their methodology and epistemology that favor their philosophical understanding. The core claim presented here is that simulation models are rich and complex units of analysis in their own right, that they depart from known forms of scientific models in significant ways, and that a proper understanding of the type of model simulations (...) are fundamental for their philosophical assessment. I argue that simulation models can be distinguished from other forms of models by the many algorithmic structures, representation relations, and new semantic connections involved in their architecture. In this article, I reconstruct a general architecture for a simulation model, one that faithfully captures the complexities involved in most scientific research with computer simulations. Furthermore, I submit that a new methodology capable of conforming such architecture into a fully functional, computationally tractable computer simulation must be in place. I discuss this methodology—what I call recasting—and argue for its philosophical novelty. If these efforts are heading towards the right interpretation of simulation models, then one can show that computer simulations shed new light on the philosophy of science. To illustrate the potential of my interpretation of simulation models, I briefly discuss simulation-based explanations as a novel approach to questions about scientific explanation. (shrink)

This paper argues that a significant focus in computational organic chemistry, alongside the construction and deployment of models, is the “deconstruction” of computational models. This practice has arisen in response to difficulties and controversies resulting from the use of plural methods and computational models to study organic reaction mechanisms. Diagnostic controllability is the capacity of cognitive agents to gain epistemic access to grey-boxed computational models, to identify and explain the impact of specific idealizations on results, and to demonstrate the applicability (...) of computational methods to target systems. (shrink)

Both thought experiments and simulation experiments apparently belong to the family of experiments, though they are somewhat special members because they work without intervention into the natural world. Instead they explore hypothetical worlds. For this reason many have wondered whether referring to them as “experiments” is justified at all. While most authors are concerned with only one type of “imagined” experiment – either simulation or thought experiment – the present chapter hopes to gain new insight by considering what the two (...) types of experiment share, and what they do not. A close look reveals at least one fundamental methodological difference between thought and simulation experiments: while thought experiments are a cognitive process that employs intuition, simulation experiments rest on automated iterations of formal algorithms. It will be argued that this difference has important epistemological ramifications. (shrink)