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In any sense in which we understand explanation, the modeling and simulations that
people like A1 and A2 are doing cannot be understood as constituting a mechanistic
explanation. In the best-case scenario – one where the modeling is actually successful – we
arrive at an understanding of the dynamical relations among the variables that comes through
the model-building process and affords control and intervention. Furthermore, this kind of
model-building is the only way to do integrated systems biology.
The problem is that mechanistic explanation is at too low a level. The understanding
that these models provide is at the high level of dynamical relations. Thus, mechanistic
understanding might not be attainable in modeling complex non-linear dynamical
phenomena. The parts and interactions in biosystems modeling are variables and their
relations are expressed abstractly in mathematics. This provides understanding but likely not
explanation, at least as currently understood.
Explanation does not subsume understanding. Researchers seek understanding of phenomena
without principally seeking to explain them. Understanding, especially in the form of skill
and judgment, plays a significant epistemic role and provides affordances for action.
Understanding is not merely psychological and should not be relegated to the context of
discovery. In all of the cases we have considered, there were really important things that
could be done once one had the understanding of the simulation model necessary for control.
Mechanistic explanation might not be attainable in biosystems modeling, but mathematical
understanding of complex non-linear dynamical relations is.
This opens up an important new area of research for philosophy: the project of
resurrecting understanding and specifying its relationship to explanation. “Living apart
together” is a lovely Dutch expression that I have borrowed from Henk de Regt (2013), who
has tried to resurrect the notion of understanding in science. As he says:
“For a long time, the marriage between explanation and understanding was taken for
granted and left unanalyzed. Do understanding and explanation need each other, or
should they go their own way? In the interest of a healthy relationship, living apart
together would seem advisable at least for the time being.”