Where the compiled binaries Analogy Breaks

Calling proteins a compiled binaries 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.

An engineer can think about proteins as active components with interfaces and state, but their interfaces are molecular surfaces whose shapes, charge and energies change with conditions.

What the metaphor gets right

An engineer can think about proteins as active components with interfaces and state, but their interfaces are molecular surfaces whose shapes, charge and energies change with conditions.

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

A compiled binary assumes a comparatively stable machine model. Proteins are part of a medium in which machine, component and environment are all physical and mutually modifying.

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

Proteins begin as amino-acid chains, but their biological roles depend on folding, chemical modification, concentration, location, binding partners and the surrounding physical conditions. Sequence constrains function without specifying every event that will occur.

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

1. What mechanism does this comparison help me see?
2. Which engineering assumption does the natural system not share?
3. 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

Structural biology connected linear sequence to three-dimensional molecular form and made it clear that sequence alone is not a complete description of function.

Proteins remind us that information must become physical organization before it can do work.

At what point does encoded possibility become physical function?

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

• Aeon — We are not machines
• Aeon — The cell is not a factory

These links are starting points for the scientific and historical ideas. The systems interpretation, analogies and conclusions here are my own.