Perspectives
The Microbiome Through a Systems Architect's Eyes
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…
I approach the microbiome with an occupational habit: I want to draw boxes and arrows. That habit is useful because architecture forces questions about state, boundaries, interfaces, resources and failure. It is dangerous because natural systems were not designed to respect our diagrams.
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.
Where does state live?
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.
Software gives us the expectation that important state should have an owner. Natural systems often distribute state across structure, concentrations, relationships and history. A snapshot can therefore tell us less than the process that produced it.
Where are the interfaces?
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.
Engineered interfaces are declarations. Natural boundaries are often material: membranes, tissues, ecological borders, channels, gradients or social conventions. They can leak, adapt and participate in the behavior they constrain.
What is the failure model?
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.
Failure analysis is useful because normal operation hides assumptions. A healthy component can coexist with an unhealthy whole. A local optimization can damage the larger system. Robustness at one level can create fragility at another.
History is part of the architecture
After germ theory transformed medicine through the study of pathogens, microbiome research made coexistence and ecological interaction equally important questions.
In a designed system, legacy structure may be accidental baggage. In an evolved or historically accumulated system, legacy structure can be the reason the current architecture exists at all. The path is not documentation around the system; sometimes it is part of the system.
The zoom test
A good architectural description should survive zooming. Going down a level should reveal mechanisms capable of implementing the higher-level pattern. Going up should reveal regularities that justify discussing the larger entity in its own vocabulary.
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?
Reading trail
These links are starting points for the scientific and historical ideas. The systems interpretation, analogies and conclusions here are my own.