Causal Concepts in Biology: How Pathways Differ from Mechanisms and Why It Matters

Abstract

Over the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term ‘mechanism’ in their explanations of biological phenomena. Of course, biologists use a variety of causal concepts in their explanations, including concepts like pathways, cascades, triggers, and processes. Despite this variety, mainstream philosophical views interpret all of these concepts with the single notion of mechanism. In using the mechanism concept interchangeably with other causal concepts, it is not clear that these accounts well capture the diversity of causal structures in biology. This article analyses two causal concepts in biology—the notions of ‘mechanism’ and ‘pathway’—and how they figure in biological explanation. I argue that these concepts have unique features, that they are associated with distinct strategies of causal investigation, and that they figure in importantly different types of explanation. 1Introduction2Mechanisms: The Basics3The Pathway Concept 3.1Main features3.2Investigative strategy4Explanation: Pathways and Mechanisms5Conclusion: Mechanism and Pathway as Analogy

Viral Infection and Stress Affect Protein Levels of Dicer 2 and Argonaute 2 in Drosophila melanogaster

“…Biological systems are composed of two features: pathways and mechanisms (22). Pathways describe the flow of entities or information along space and time; mechanisms describe indirectly the reason these pathways exist.…”

“…In the case of RNAi, if we consider the hierarchical scale that includes the entire RNAi phenomenon, studying the pathway means to study the components of such pathway, the causal way they interact and the flow of these interactions until reaching the "interference" event, which it is relevant to a variety of outcomes. Studying the mechanism means to study how such a pathway works, how it is controlled and regulated, how it is induced or repressed, and for what specific outcome (22). Dcr-2 and Ago-2 are the best characterized enzymes involved in the insect antiviral siRNA pathway.…”

Distinguishing topological and causal explanation

“…13 Although these species are all located in the same body of water, scientists identify that fish species C has extremely high levels of Selenium, which is toxic to this fish and causes various pathologies. Meanwhile, fish species D and E have normal levels of Selenium and lack these issues (Ross 2019). Scientists want to know what explains these differences in toxic levels of Selenium across different species of fish.…”

“…This allows them to be interpreted with an interventionist framework. For more on this see(Ross 2019). 14 It is easy to imagine ordinary life examples that are similar to this case.…”

Data science and molecular biology: prediction and mechanistic explanation

“…http://www.nature.com/tcga/ 36 The reason for doing this is that, when mechanistic sketches in this field are outlined, usually genes and mutations at the genetic level are considered central, and hence we decided to focus only on this important level because the epistemic processes applied to it are similar to the ones applied to other levels. Hence the analysis of other levels may be redundant 37 On the difference between 'pathways' and 'mechanisms' see(Ross 2018) and(Boniolo and Campaner 2018) …”