Maureen A. O’Malley, Emily C. Parke (2020), Stanford Encyclopedia of Philosophy — https://plato.stanford.edu/entries/microbiology/
Key takeaways
- Philosophy of biology’s animal-centred habits distort its conclusions: taking microbes seriously changes debates over species concepts, the tree of life, major transitions, model systems, and — through microbiome research — biological individuality and causal explanation.
Seeded from the abstract and a skim, before the reading in NOTE-159. What follows is what the work says about itself.
The entry asks why philosophers should pay attention to microbes, given philosophy’s focus on humans and philosophy of biology’s historical focus on animals. It argues in four steps: microbes do most of the planet’s biological work and underlie every major transition; microbiology gave rise to fields such as modern medicine, molecular biology and genomics; microbes serve as material models of general phenomena; and microbiome research bears on human nature, individuality and causality.
Standing in the record
Filed from the 2026-09-26 sweep of the papers-feed tracker for philosophy: 20 seconds of active reading over 2 sessions. It was filed Deferred, unread. NOTE-159 is the close reading of 2026-09-26, and it placed the work: Active — worth reading as a short, current (April 2026) orientation to where microbes change philosophy of biology, with a useful deflationary check on microbiome-and-self claims. It is a survey with no thesis beyond “pay attention to microbes”; for individuality it points onward to the Biological Individuals (LIT-168) and Units and Levels of Selection (LIT-160) entries.
When seeded, before the reading in NOTE-159, the entry gave a priority for a deeper reading: low — short visits (t = 20 s over 2 sessions); a survey whose map the skim captures, with §5 the only part worth a closer read.
What the seeding asked a deeper reading to check (NOTE-159 is that reading):
- Connects the biological-individuality cluster (LIT-168, LIT-142) to units of selection (LIT-160) through holobionts and host–microbe units.
- §5.2’s use of microbiome science to test interventionist causation links to the reciprocal-causation debate (LIT-110, LIT-156).
Access when seeded: Full SEP entry fetched directly and read by section (openings of all sections; §§5.1, 5.2 and 6 in more depth). First published Wed Aug 12, 2020; substantive revision Fri Apr 10, 2026 (the version read); citation metadata lists Maureen A. O’Malley and Emily C. Parke.