A physical standard for time

I've now completed Chapter 2 of Cook's "The Observational Foundations of Physics," my current lunchtime reading. In this chapter, Cook describes a thought experiment in which a beam of caesium atoms is polarized by a strong magnetic field, then enters a region where a strong RF field is applied. Following the RF region, the beam passes through another magnetic field such that atoms whose magnetic dipole moments are not flipped by the RF field are deflected into a beam block. Those atoms that do undergo an electronic transition that is accompanied by a flip of the magnetic dipole moment reach a detector that reports the intensity of the beam. A feedback mechanism adjusts the frequency of the RF field so that the beam intensity at the detector is maximized; in this way, a quantum standard of time is established through the frequency of the RF field that maximizes the atomic beam intensity (you may note the similarity to the Stern-Gerlach appartus).

Cook then proceeds to argue for his thesis, namely that the experiments and observations that are available to us dictate the form of our physical theories. He starts first with the theory. The time-evolution of the caesium atoms is described by the Schroedinger equation. This equation contains a first order time derivative which is a consequence of the wavefunction containing all information about the system at any one point in time. If only one initial condition is required to establish the wavefunction, then it must be first order in time (this is in contrast to the wave equation which is second order in time and whose solution requires an initial condition on the wavefunction and its derivative).

Cook next mathematically defines the operations of the experiment described above, postulating that the two magnetic states of the atoms are described by stationary states of a wavefunction. Using only mathematical arguments derived from the nature of the experiment, he obtains the form of the equations governing the time evolution of the system; the wavefunction is affected by a first order time derivative. This suggests that how we perform experiments determines the form of our theories. The time standard need not be quantum in nature as he repeats the argument for a classical, mechanical oscillator. Again he stresses that once the time standard is set, it is meaningless to ask whether or not its period remains invariant with time, since the standard defines time itself. It is recognized that differences between the same apparatus for establishing the standard exist when the apparatus are spatially separated due to the geometry of spacetime.

These are some of the thoughts I had while reading this chapter:

1. Many times physical theories are developed first and then experiments follow that verify their predictions. Does this fact weaken Cook's argument that experiments shape our theories? If the purpose of theory is to predict experimental outcomes, then why argue for the reverse? Which came first, the chicken or the egg?
2. Cook was careful to explain that his arguments are based on a physical world that is independent of a subjective observer. Still, I wonder how the human perception of time can be reconciled with these arguments. As stated earlier, it makes no sense to ask whether or not the time standard is invariant within the context of observation and theory. But a human can perceive large changes in the period of a slow mechanical oscillator. What is it that acts as an internal time standard for a subjective observer and can it be related to the physical standard?
3. Cook only obtains the form of the equations of motion for the systems he describes. On the other hand, the theories give meaning to his unspecified parameters, such as energy and the unit of electronic charge. What determines how these mental concepts are developed? Energy is a relatively easy concept to understand. Was this why the fathers of thermodynamics used it as a core concept in physics as opposed to some other mental construct?