Outstanding Issues in Systems and Synthetic Biology

Fu, Pengcheng; Hooker, C. A.

doi:10.1002/9780470437988.ch20

Cited by 2 publications

(2 citation statements)

References 84 publications

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“…Synthetic Biology [14,27] is an emerging discipline that aims at the rational design of artificial living systems with a predictable behaviour, either by creating new biological entities that do not exist in nature or by redesigning the existing ones. Even though important technological developments have been achieved in this field, the de-novo design of biological circuits implementing a desired behaviour results to be a very hard task, especially for large scale networks.…”

Section: Introductionmentioning

confidence: 99%

A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits

Bartocci

Bortolussi

Nenzi

2013

Computational Methods in Systems Biology

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We present a new approach for the design of a synthetic biological circuit whose behaviour is specified in terms of signal temporal logic (STL) formulae. We first show how to characterise with STL formulae the input/output behaviour of biological modules miming the classical logical gates (AND, NOT, OR). Hence, we provide the regions of the parameter space for which these specifications are satisfied. Given a STL specification of the target circuit to be designed and the networks of its constituent components, we propose a methodology to constrain the behaviour of each module, then identifying the subset of the parameter space in which those constraints are satisfied, providing also a measure of the robustness for the target circuit design. This approach, which leverages recent results on the quantitative semantics of Signal Temporal Logic, is illustrated by synthesising a biological implementation of an half-adder

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Section: Introductionmentioning

confidence: 99%

A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits

Bartocci

Bortolussi

Nenzi

2013

Computational Methods in Systems Biology

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“…For initial exploration of many of the issues, seeFu and Hooker (2008),Hooker (2008b) and references.…”

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confidence: 99%

Bio-agency and the problem of action

Skewes

Hooker

2008

Biol Philos

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The Aristotle-Kant tradition requires that autonomous activity must originate within the self and points toward a new type of causation (different from natural efficient causation) associated with teleology. Notoriously, it has so far proven impossible to uncover a workable model of causation satisfying these requirements without an increasingly unsatisfying appeal to extra-physical elements tailor-made for the purpose. In this paper we first provide the essential reason why the standard linear model of efficient causation cannot support the required model of agency: its causal thread model of efficient causation cannot support the core requirement that an action is determined by, and thus an expression of, the agent's nature. We then provide a model that corrects these deficiencies, constructed naturalistically from within contemporary biology, and argue that it provides an appropriate foundation for all the features of genuine agency. Further, we provide general characterisations of freedom and reason suitable to this bio-context (but that also capture the core classical conceptions) and show how this model reconciles them.

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Outstanding Issues in Systems and Synthetic Biology

Cited by 2 publications

References 84 publications

A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits

A Temporal Logic Approach to Modular Design of Synthetic Biological Circuits

Bio-agency and the problem of action

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