The second thing to understand is that natural selection is a process by which nature filters organisms in a population.
But this process is not done by choice, but rather by chance due to different selective pressures and traits affecting rates of reproduction.
The simplifying assumptions mean that while the model predicts the space occupied by the protein in the cellular membrane, and how far into the membrane the retinal sits, it does not help predict the time it takes for the protein to transport protons.
How did scientists discover this?
In fashion, it can be said that style evolves. In biology, life and, in particular, reproducing populations of organisms with different traits evolve.