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How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers

Lynch, Kate E and Parke, Emily C. and O'Malley, Maureen A. (2019) How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers. [Preprint]

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Abstract

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made.


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Item Type: Preprint
Creators:
CreatorsEmailORCID
Lynch, Kate Ekateemmalynch@gmail.com
Parke, Emily C.e.parke@auckland.ac.nz
O'Malley, Maureen A.maureen.omalley@sydney.edu.au0000-0003-0367-7079
Additional Information: Preprint of target article for future commentaries in Biology and Philosophy.
Keywords: microbiome; causal explanation; Helicobacter pylori; Koch’s postulates, interventionism
Subjects: General Issues > Explanation
Depositing User: Maureen O'Malley
Date Deposited: 02 Mar 2019 01:10
Last Modified: 02 Mar 2019 01:10
Item ID: 15777
Subjects: General Issues > Explanation
Date: 28 February 2019
URI: http://philsci-archive.pitt.edu/id/eprint/15777

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