Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology. Academic Article uri icon

Overview

abstract

  • The technological leap of DNA sequencing generated a tension between modern metagenomics and historical microbiology. We are forcibly harmonizing the output of a modern tool with centuries of experimental knowledge derived from culture-based microbiology. As a thought experiment, we borrow the notion of Cartesian doubt from philosopher Rene Descartes, who used doubt to build a philosophical framework from his incorrigible statement that "I think therefore I am." We aim to cast away preconceived notions and conceptualize microorganisms through the lens of metagenomic sequencing alone. Specifically, we propose funding and building analysis and engineering methods that neither search for nor rely on the assumption of independent genomes bound by lipid barriers containing discrete functional roles and taxonomies. We propose that a view of microbial communities based in sequencing will engender novel insights into metagenomic structure and may capture functional biology not reflected within the current paradigm.

publication date

  • October 12, 2021

Identity

PubMed Central ID

  • PMC8510522

Scopus Document Identifier

  • 85040444802

Digital Object Identifier (DOI)

  • 10.1038/nature25172

PubMed ID

  • 34636670

Additional Document Info

volume

  • 6

issue

  • 5