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I examine the abstraction/representation theory of computation put forward by Horsman et al., connecting it to the broader notion of modeling, and in particular, model-based explanation, as considered by Rosen. I argue that the 'representational entities' it depends on cannot themselves be computational, and that, in particular, their representational capacities cannot be realized by computational means, and must remain explanatorily opaque to them. I then propose that representation might be realized by subjective experience (qualia), through being the bearer of the structure of abstract objects that are represented. [ABSTRACT FROM AUTHOR]

In this paper we aim to give an analysis and cognitive rationalization of a common practice or strategy of modeling in systems biology known as a middle-out modeling strategy. The strategy in the cases we look at is facilitated through the construction of what can be called mesoscopic models. Many models built in computational systems biology are mesoscopic (midsize) in scale. Such models lack the sufficient fidelity to serve as robust predictors of the behaviors of complex biological systems, one of the signature goals of the field. This puts some pressure on the field to provide reasons for why and how these practices are warranted despite not meeting the stated goals of the field. Using the results of ethnographic study of problem-solving practices in systems biology, we aim to examine the middle-out strategy and mesoscopic modeling in detail and to show that these practices are rational responses to complex problem solving tasks on cognitive grounds in particular. However making this claim requires us to update the standard notion of bounded rationality to take account of how human cognition is coupled to computation in these contexts. Our account fleshes out the idea that has been raised by some philosophers on the "hybrid" nature of computational modeling and simulation. What we call "coupling" both extends modelers' capacities to handle complex systems, but also produces various cognitive and computational constraints which need to be taken into account in any computational problem solving strategy seeking to maintain insight and control over the models produced. • The application of cognitive science to philosophical questions and issues. • An account of the cognitive resources modelers use to handle complexity. • An account of the cognitive function of mesoscopic models in systems biology. • A discussion of how a cognitive account of modeling can help rationalize modeling practices in systems biology. [ABSTRACT FROM AUTHOR]