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Modelling gene regulation: (De)compositional and template-based strategies.

Tarja Knuuttila1, Vivette García Deister2

  • 1University of South Carolina, University of Helsinki, 901 Sumter St., Byrnes Suite, Columbia, SC, 29208, USA.

Studies in History and Philosophy of Science
|November 9, 2019
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Summary
This summary is machine-generated.

Engineering network methods are increasingly used in biology. This study contrasts two labs using different approaches to gene regulatory networks, questioning how mechanistic philosophy accommodates new modeling techniques.

Keywords:
Gene regulationInterdisciplinarityModel transferModellingSynthetic biology

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Area of Science:

  • Integrative biology
  • Philosophy of science
  • Systems biology

Background:

  • Interdisciplinary approaches are common in biology.
  • The application of engineering concepts and methods in biology requires further examination.
  • Mechanistic philosophy of science provides a framework for analyzing scientific practice.

Purpose of the Study:

  • To examine the transfer of engineering network methods into biological research.
  • To analyze two distinct laboratory approaches to studying gene regulatory networks at Caltech.
  • To explore the implications of different modeling strategies for mechanistic explanation.

Main Methods:

  • Analysis of two biology laboratories (Davidson and Elowitz) at Caltech.
  • Application of mechanistic philosophy of science as an analytic tool.
  • Comparative study of network methods in gene regulatory network research.

Main Results:

  • The Davidson lab employs a traditional mechanistic approach, focusing on decomposition and reconstruction of gene regulatory networks.
  • The Elowitz lab utilizes minimal, template-based models for studying gene regulation principles, independent of specific biological circuits.
  • Distinct strategies highlight differing applications of engineering methods in biology.

Conclusions:

  • The study calls for a re-evaluation of mechanistic philosophy to encompass diverse modeling approaches in biology.
  • It questions whether template-based modeling aligns with traditional mechanistic explanation.
  • This work prompts consideration of modifications to the mechanistic paradigm for broader applicability to modeling.