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Thinking Dynamically About Biological Mechanisms: Networks of Coupled Oscillators

Bechtel, William and Abrahamsen, Adele (2012) Thinking Dynamically About Biological Mechanisms: Networks of Coupled Oscillators. [Preprint]

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Abstract

Explaining the complex dynamics exhibited in many biological mechanisms requires extending the recent philosophical treatment of mechanisms that emphasizes sequences of operations. To understand how nonsequentially organized mechanisms will behave, scientists often advance what we call dynamic mechanistic explanations. These begin with a decomposition of the mechanism into component parts and operations, using a variety of laboratory-based strategies. Crucially, the mechanism is then recomposed by means of computational models in which variables or terms in differential equations correspond to properties of its parts and operations. We provide two illustrations drawn from research on circadian rhythms. Once biologists identified some of the components of the molecular mechanism thought to be responsible for circadian rhythms, computational models were used to determine whether the proposed mechanisms could generate sustained oscillations. Modeling has become even more important as researchers have recognized that the oscillations generated in individual neurons are synchronized within networks; we describe models being employed to assess how different possible network architectures could produce the observed synchronized activity.


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Item Type: Preprint
Creators:
CreatorsEmailORCID
Bechtel, Williambill@mechanism.ucsd.edu
Abrahamsen, Adeleadele@crl.ucsd.edu
Keywords: dynamics, dynamic mechanistic explanation, decomposition, recomposition, computational modeling, circadian rhythms
Subjects: Specific Sciences > Biology > Molecular Biology/Genetics
General Issues > Explanation
General Issues > Models and Idealization
General Issues > Reductionism/Holism
Depositing User: Professor William Bechtel
Date Deposited: 26 Sep 2012 12:27
Last Modified: 26 Sep 2012 12:27
Item ID: 9344
URI: http://philsci-archive.pitt.edu/id/eprint/9344

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