ion is one of the important processes in scientific modeling. It has always been implied that abstraction is an agent-centric activity that involves the cognitive processes of scientists in model building. I contend that there is an autonomous aspect of abstraction in many modeling activities. I argue that the autonomous process of abstraction is continuous with the agent-centric abstraction but capable of evolving independently from the modeler’s abstraction activity.

Physical reality as an explanatory model is an abstraction of the mind. Every perceptual system is a user interface, like the dashboard of an aeroplane or the desktop of a computer. We do not see or otherwise perceive reality but only interface with reality. The user interface concept is a starting point for a critical dialogue with those epistemic theories that present themselves as veridical and take explanatory abstractions as ontological primitives. At the heart of any scientific model are assumptions (...) about which things exist, how they are related, and how we can know them. Scientific models take our knowledge beyond ordinary experience toward explanatory abstractions. The main problem with veridical models lies in why we cannot express our theories and the explanatory abstractions associated with them other than through classical perceptual interface symbols. This study analyses the limits, possibilities and constraints of explanatory abstractions. (shrink)

New mechanical philosophy posits that explanations in the life sciences involve the decomposition of a system into its entities and their respective activities and organization that are responsible for the explanandum phenomenon. This mechanistic account of explanation has proven problematic in its application to mathematical models, leading the mechanists to suggest different ways of aligning abstract models with the mechanist program. Initially, the discussion centered on whether the Hodgkin-Huxley model is explanatory. Network models provided another complication, as they apply to (...) a wide number of materially diverse systems. In this article, we examine the various attempts to integrate abstract models within the mechanist program, also presenting a further challenge: the Heimburg-Jackson model, which was introduced as an alternative to the Hodgkin-Huxley model. We argue that although the notion of abstraction as the omission of irrelevant mechanistic details appears to give a mechanistic solution for accommodating abstract models, this notion does not suit models whose epistemic strategy is not decompositional. As a result, the mechanist has to choose whether to dilute the mechanistic approach nearly beyond recognition or to claim that many, if not most, abstract theoretical models do not deliver mechanistic explanations, or qualify as explanatory at all. (shrink)

In philosophy of science, abstraction tends to be subsumed under representation, often being described as the omission of a target’s features when it is represented. This approach to abstraction sidesteps cognitive aspects of abstraction processes. However, cognitive aspects of abstraction are important in understanding the role of historically grounded epistemic criteria supporting modeling in science. Drawing on recent work on the relation between metaphor and abstraction, we introduce the concept of paths of abstraction, and use historical and contemporary examples to (...) point to their role in guiding the development of relevance criteria which support modeling strategies in science. (shrink)

Computational modeling is one of the primary approaches to constructing protein–protein interfaces in the laboratory. The algorithm-driven computational protein design has been successfully applied to the construction of functional proteins with improved binding affinity and increased thermostability. It is intriguing how a computational protein modeling approach can construct and shape the reality of new functional proteins from scratch. I articulate an account of abstraction and exploration-driven strategies in this computational endeavor. I aim to show that how a computational modelling approach, (...) which is laden with mathematics and algorithms, can have a constructive force on the target protein. (shrink)