[ecoherb]

In biological Boolean Networks, this is a long standing form of debate, particularly the last line: "And without the correct context, the statement might not make sense at all."

Should we build Boolean networks that represent biological systems that have specific configurational requirements or should the model itself encode the limited context?

Often we choose something in-between, where the Boolean model of our biological system has some configurational choices (the context), but we can modify the context to see how the system operates in non-standard conditions.

All of this is with the hope that the ways that the model produces contradictions and unexpected behaviors can inform how our reality produces contradictions and unexpected behaviors (most commonly cancers). The states of the representative system, the Boolean network, may make no sense, and we can diagnose why with a Boolean network, when it would be neigh impossible to understand that odd state in the real system.