Molecular pathways and the contextual explanation of molecular functions

Abstract

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed up in the notion of 'pathway', which is far from being just equivalent to that of 'mechanism' and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway.

The logic of explanation in molecular biology: historical-processual and logical-procedural aspects

“…As pointed out in a few loci in the recent philosophical literature (e.g. Duprè, 2013;Ioannidis & Psillos, 2017;Nicholson & Dupré, 2018;Boniolo & Campaner, 2018;Ross, 2018Ross, , 2020, molecular pathways should be most properly conceived as processes that bring about certain effects by virtue of a number of intermediate steps, causally related to one another. The current debate on processes and pathways has partly expressed metaphysical stancesas in the case of works by Dupré and colleaguesand partly strictly epistemological ones, stressing the role such notions play in causal investigations, and, in particular, how they figure in explanatory accounts (e.g.…”

“…The current debate on processes and pathways has partly expressed metaphysical stancesas in the case of works by Dupré and colleaguesand partly strictly epistemological ones, stressing the role such notions play in causal investigations, and, in particular, how they figure in explanatory accounts (e.g. Boniolo & Campaner, 2018;Ross, 2020). Our take on processes is the latter.…”

Complexity and integration. A philosophical analysis of how cancer complexity can be faced in the era of precision medicine

“…Our current focus is on the epistemological impact of the adoption of iCluster in dealing with cancer complexity, especially from a classificatory and a prognostic standpoint. 20 Against the reductionism concerning molecular mechanisms and in favour of a more holist approach based on pathways, see Boniolo, Campaner (2018). Russnes et al (2017).…”

Molecular Biology Meets Logic: Context-Sensitiveness in Focus

“…The aim of this paper is to describe and discuss the context sensitiveness phenomenon, as it emerges in molecular reactions and processes, through the lenses of our logical approach. This means we shall be touching issues such as biological networks-in particular those concerning molecular interactions-as well as control mechanisms (Boniolo and Campaner 2018). Needless to say, context sensitiveness is an aspect of utmost relevance, since all biochemical reactions and processes always occur in specific molecular environments.…”