Optimality is a property of a process
Even if you know the optimal state of individual enzymes, their function as a group, may be far from optimal. Which is a good example that a whole is more than the sum of its parts. Nevertheless our metabolism is always optimal. Optimality is the hallmark of life.
In order to model optimality with CA you need several prerequisites:
1. Enzymes are processes, that operate in interacting chains.
2. The context of an enzymatic reaction is the set of enzymes involved in it.
3. Optimization involves the entire context.
Take the citric acid cycle, which actually is a vortex whose optimality depends on all enzymes involved.
How to model it? You start with a small CA set, let them
interact and evolve, and try to adjust their state parameters so as to optimize
an attribute. By trial and error. Such an experimentation
helps you to grasp intuitively what’s involved and how to proceed. Hopefully
you will find out how to grow a CA ensemble which will optimize itself. Which is precisely what I am looking for.
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