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Reengineering Metaphysics: Modularity, Parthood, and Evolvability in Metabolic Engineering

Kendig, Catherine and Eckdahl, Todd T. (2017) Reengineering Metaphysics: Modularity, Parthood, and Evolvability in Metabolic Engineering. Philosophy, Theory, and Practice in Biology, 9 (8). ISSN 2475-3025

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Abstract

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline.

Part of a special issue, Ontologies of Living Beings, guest-edited by A. M. Ferner and Thomas Pradeu


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Item Type: Published Article or Volume
Creators:
CreatorsEmailORCID
Kendig, Catherinekendig@msu.edu
Eckdahl, Todd T.eckdahl@missouriwestern.edu
Keywords: BioBrick Assembly, evolvability, modularity, parts-based ontology, self-organization
Depositing User: Nora Boyd
Date Deposited: 06 Apr 2018 16:14
Last Modified: 06 Apr 2018 16:14
Item ID: 14539
Journal or Publication Title: Philosophy, Theory, and Practice in Biology
DOI or Unique Handle: https://doi.org/10.3998/ptb.6959004.0009.008
Date: 2017
Volume: 9
Number: 8
ISSN: 2475-3025
URI: https://philsci-archive-dev.library.pitt.edu/id/eprint/14539

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