you are mixing up models and simulations. A simulation can be a great way of exploring something unknown if you understand the rules in enough granularity. Models can be judged by their ability to make accurate predictions. Electrical engineering depends on both a great deal, I expect you agree that it is useful as a field given the method of communication we're using.

For chemotaxis, while they can't observe the underlying processes directly, they result in phenomena that are observable, which can be compared with the same phenomena predicted by simulations and models (the same is true of all scientific fields).