Commentary on Kate E. Lynch, Emily C. Parke, and Maureen A. O’Malley: ‘How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers’
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This commentary focuses on the authors’ treatment of Koch’s postulates. It argues in favour of a modification of Koch’s postulates and their analysis in terms of necessary and sufficient conditions. This leads to a criticism of the authors’ treatment of the C. difficile case, and to query the need for the criteria of specificity and proportionality.
KeywordsMicrobiomes Causality Koch’s postulates Helicobacter pylori C. difficile
Let me begin by saying that there is a great deal in this paper with which I agree, especially the central parts of the paper (pp. 10–15) criticizing current attempts to explain obesity and some mental health conditions in terms of microbiomes. My commentary then will be mainly focussed on those parts of the paper which deal with Koch’s postulates and related issues.
Now this is a productive action based on causality, that is to say an action which produces the disease. However, for medicine, it is much more important to have avoidance actions based on causality, that is to say actions which prevent or cure the disease rather than producing it. Koch’s mistake, on this account, was to have a postulate corresponding to productive actions, but not one corresponding to the more crucial avoidance actions. This is easily remedied by replacing postulate 3 by the postulate either 3a or 3b, where 3a is the old 3, and 3b is
3. After being fully isolated and repeatedly grown in pure culture, the microorganism can induce the disease by being introduced into a healthy animal host.
Both the cholera and the helicobacter pylori cases do satisfy Koch’s postulates modified in this way. This modification also has the advantage that it makes the kind of risky self-experimentation carried out by Marshall quite unnecessary.
3b. If the microorganisms are prevented from multiplying in the patient’s body, then the patient will not have the disease.
where the cause here is understood as a necessary, but not sufficient, condition for the effect. Moreover (*) is a causal law of just the kind which is most useful for medicine.
An unhealthy microbiome causes clostridium difficile infections (*)
This example seems to me to show that the criteria of specificity and proportionality do not need to be satisfied to establish satisfactory causal laws in medicine. Of course these criteria might be useful heuristics for further research in the field. For example, if we could replace (*) by a more specific causal law, this might lead to a treatment which could be easier, cheaper, less invasive, etc. than FMT. However, such a development would not show that (*) is invalid, or that it is wrong to regard the whole microbiome as being causally efficacious.
The success has been interpreted as evidence in favour of the whole microbiome being causally efficacious in curing C. difficile. But does this treatment indicate specificity and proportionality?
- Gillies D (2019) Causality, probability, and medicine. Routledge, LondonGoogle Scholar
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