Perspectives
Where the dependency ecosystem Analogy Breaks
Software dependencies have package boundaries. Host and microbial systems exchange metabolites and influence one another in ways that make the system/environment boundary much less…
Calling the microbiome a dependency ecosystem is useful for about five minutes. The comparison can expose structure that ordinary language hides. The problem begins when the comparison stops behaving like a tool and starts behaving like a claim about what the thing literally is.
A software product depends on services and libraries it does not fully own. The microbiome similarly complicates the picture of an organism as a completely self-contained unit.
What the metaphor gets right
A software product depends on services and libraries it does not fully own. The microbiome similarly complicates the picture of an organism as a completely self-contained unit.
This is why engineering metaphors are so attractive. They compress a complicated relationship into something we can manipulate mentally. In the best case, the metaphor produces predictions and sharper questions.
What it smuggles in
Software dependencies have package boundaries. Host and microbial systems exchange metabolites and influence one another in ways that make the system/environment boundary much less tidy.
Engineering words often carry hidden assumptions: a designer, a specification, modular ownership, explicit goals, a stable machine underneath the program. Those assumptions must be tested rather than inherited.
Return to the physical story
Humans live with large communities of microorganisms on and inside the body. These communities interact with digestion, immune development, metabolism and environmental exposure, and they change with diet, age, medication and surroundings.
Once the mechanism is back in view, the analogy can be kept on a short leash. We can state which relation is genuinely similar and which difference would make the analogy generate a wrong prediction.
My three tests for a metaphor
- What mechanism does this comparison help me see?
- Which engineering assumption does the natural system not share?
- What would I predict incorrectly if I took the comparison literally?
The third test is the most important. An analogy that cannot fail is decoration, not explanation.
Beyond the borrowed language
After germ theory transformed medicine through the study of pathogens, microbiome research made coexistence and ecological interaction equally important questions.
The microbiome makes individuality porous: a human body is also habitat.
Where should we draw the boundary of an organism whose normal life depends on other organisms?
A good metaphor should eventually make itself less necessary. It gets us close enough to the real system that we can see where the scaffolding ends.
Reading trail
These links are starting points for the scientific and historical ideas. The systems interpretation, analogies and conclusions here are my own.