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Towards a processual microbial ontology.

Eric Bapteste1, John Dupré

  • 1UMR CNRS 7138, Université Pierre et Marie Curie, 75005 Paris, France.

Biology & Philosophy
|March 15, 2013
PubMed
Summary
This summary is machine-generated.

Microbial evolution ontology needs updating beyond vertical inheritance. A network-based approach reveals diverse processes driving microbial diversity and the emergence of new entities.

Keywords:
Microbial evolutionNetworkOntologyProcess philosophyTree of life

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Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Systems Biology

Background:

  • Traditional microbial evolutionary ontology relies on nested hierarchies and vertical inheritance, focusing on stable entities.
  • This limited perspective underestimates microbial diversity by overlooking complex dynamics and interactions.
  • Advances in microbiology reveal that vertical descent alone does not explain microbial evolution.

Purpose of the Study:

  • To propose a network-based ontology for microbial entities that incorporates diverse evolutionary processes.
  • To evaluate existing ontological assumptions in microbial evolution.
  • To identify novel classes of microbial entities crucial for understanding microbial dynamics.

Main Methods:

  • Considering microbial entities as stabilized functional wholes.
  • Developing a network-based ontology to represent phylogenetic relations, interactions, spatial relations, ecological connections, and genetic exchanges.
  • Utilizing a pluralistic framework to analyze existing ontological assumptions and identify hidden ontological kinds.

Main Results:

  • The limitations of traditional, hierarchy-based ontologies in capturing microbial diversity are highlighted.
  • A network-based approach reveals that microbial entities are shaped by various processes beyond vertical inheritance.
  • New entity classes like "processually equivalent," "processually versatile," and "stabilized" entities are proposed.

Conclusions:

  • A shift towards a network-based, pluralistic ontology is necessary for a comprehensive understanding of microbial evolution.
  • Recognizing diverse processes and novel entity types enhances our view of microbial diversity and dynamics.
  • This revised ontological framework provides new insights into the structure and evolution of the microbial world.