I consider three explanatory strategies from recent systems biology that are driven by mathematics as much as mechanistic detail. Analysis of differential equations drives the first strategy; topological analysis of network motifs drives the second; mathematical theorems from control engineering drive the third. I also distinguish three abstraction types: aggregations, which simplify by condensing information; generalizations, which simplify by generalizing information; and structurations, which simplify by contextualizing information. Using a common explanandum as reference point—namely, the robust perfect adaptation of (...) class='Hi'>chemotaxis in Escherichia coli—I argue that each strategy invokes a different combination of abstraction types and that each targets its abstractions to different mechanistic details. (shrink)

Organismic agency is often understood as the capacity to produce goal-directed behavior. This paper proposes a new way of modelling agency, namely as a naturalized deliberation. Deliberative action is not directed towards a particular goal, but involves a process of weighing multiple goals and a choice for a particular combination of these. The underlying causal model is symmetry breaking, where the organism breaks symmetries present in the selective environment. Deliberation is illustrated though the phenomena of mate choice and bacterial (...) class='Hi'>chemotaxis. (shrink)

We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms (...) that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. (shrink)

The epistemological situation of a single cell is considered. In chemotaxis, the relation between perception and action is found to be lawful and bidirectional. Consideration of the perception/action relation allows a characterization of the phe- nomenal world of the cell. This phenomenal world is grounded in perceptual distinctions that are relevant to the sustained vi- ability of the cell. Moving up the phylogenetic chain, this lawfulness, and its relation to the phenomenal world of ex- perience, is found to be (...) essentially unchanged in multicellular organisms. Nervous systems add some innovation, in allow- ing distal responses and the non-linear combination of infor- mation, but from cell to human, the differentiation of the phe- nomenal world is found to arise from the lawfulness of the perception/action relation, which in turn reflects the biologi- cal constitution of the organism, and not a pre-given objec- tive world. This recognition suggests that rather than looking within the nervous system for representations of pre-given, ex- ternal, entities, one might do better to explore the fit between the function of the nervous system and the phenomenal, mean- ingful, world encountered by the organism in experience. (shrink)