Modelling Molecular Mechanisms: A Framework of Scientific Reasoning to Construct Molecular-Level Explanations for Cellular Behaviour

Abstract

Although molecular-level details are part of the upper-secondary biology curriculum in most countries, many studies report that students fail to connect molecular knowledge to phenomena at the level of cells, organs and organisms. Recent studies suggest that students lack a framework to reason about complex systems to make this connection. In this paper, we present a framework that could help students to reason back and forth between cells and molecules. It represents both the general type of explanation in molecular biology and the research strategies scientists use to find these explanations. We base this framework on recent work in the philosophy of science that characterizes explanations in molecular biology as mechanistic explanations. Mechanistic explanations describe a phenomenon in terms of the entities involved, the activities displayed and the way these entities and activities are organized. We conclude that to describe cellular phenomena scientists use entities and activities at multiple levels between cells and molecules. In molecular biological research, scientists use heuristics based on these intermediate levels to construct mechanistic explanations. They subdivide a cellular activity into hypothetical lower-level activities (top-down approaches) and they predict and test the organization of macromolecules into functional modules that play a role in higherlevel activities (bottom-up approaches). We suggest including molecular mechanistic reasoning in biology education and we identify criteria for designing such education. Education using molecular mechanistic reasoning can build on common intuitive reasoning about mechanisms. The heuristics that scientists use can help students to apply this intuitive notion to the levels in between molecules and cells.

Molecular Mechanistic Reasoning: Toward Bridging the Gap Between the Molecular and Cellular Levels in Life Science Education

“…The design presented in this paper builds on the theoretical analysis presented previously by Van Mil et al (2013) and is informed by empirical evidence from one previous research cycle with a similar setup to the case study presented here. To be able to determine whether the design was indeed a proof of principle, we first describe and justify the features that we incorporated into the design and explain how we expected these principles to shape and guide the learning process.…”

“…The upward question: "What is its role or function, or how does it contribute to the larger whole?" Figure 2 is a schematic representation of the general mechanistic reasoning structure (adapted from Van Mil et al, 2013). The structure directs one to search for relationships between entities and activities at different levels (parts and wholes), as well as to search for causal connections within one level (cause and effect).…”

From Theory to Data: The Process of Refining Learning Progressions

“…The heuristic guiding our decision here was that levels should be added when the new ideas are directly related to the construct, represent an important conceptual shift, and/or afford instructional leverage. Given that the transition from a non-information-based to an information-based view of genes is a particularly challenging one (Duncan & Reiser, 2007;Lewis & Kattmann, 2004;van Mil, Boerwinkel, & Waarlo, 2011;Venville & Treagust, 1998), we decided that capturing this understanding as a distinct and separate level was merited. Cognitively speaking, this understanding reflects an ontological shift in students' understandings of genes, in essence the beginning of an important conceptual change (Venville & Treagust, 1998 recognize this understanding as bridging across ontologically distinct understandings of genes and leverage it in their instruction.…”

Using Primary Literature in an Undergraduate Assignment: Demonstrating connections among cellular processes

“…Together, these issues make the learning of cell biology rather uninspiring for students. Moreover, previous studies have reported that students fail to make connections across different topics, leading them to only partially appreciate how nature functions (Mil, Boerwinkel, and Waarlo 2011;Newman, Catavero, and Wright 2012). From my previous experience, I have noted that students tend to study topics in isolation, with little or no regard for functional interactions among them.…”