The novel techniques of fetal MRI and 3D,4D ultrasound recordings have now made it possible to outline the development of neurites emerging parallelly in preparatory cortices and subcortical regions toward each other, as well as the trajectories of progressing late gestation behavioral organization, originated in earlier random behaviors. Very early clocks work along a human gestational 40-week changing thermodynamic system via timewise alterations in a combinatorial manner, rather than through a simple linear progress. This progress unravels time-specific and tissue-specific functional interplay, where balances of exciting and inhibiting molecular events underlie differential rates of growth. In this chapter, recent findings on the clock genes’ control of this combinatorial time-specific and tissue-specific structural development are used to create an integrating model describing their dynamics as “times” of development. This model aims to describe the time-sensitive dynamics of clock genes across developing levels, to show how these dynamics work for morphological advance in a manner that founds the time-dependent changes in embryonic and fetal movements, behavior, and experience. The equation summarizing this model presents a synthesis of thermodynamics, electrochemical principles, and control systems. To show how clock genes determine the time of regulated transition between morphological levels by their expression-suppression ratios, logic gates were employed to show conditions of the regulatory XOR logic gates, created by more primitive Boolean functions. According to this model, to regulate the complex return to balance of their ultradian oscillations, clock genes respond to a given actual value of a structural-related electrochemical condition, following any given structural consolidation in the developing organism. The next desired value of the electrochemical condition, required for the next stage of morphological development, is triggered by the consolidation of the previous stage in a plateau condition. As such, the entire progress of transitions is reflected in a second-order step response. In turn, the electrochemical timely regulated transitions between morphological levels originate the time-sensitive changes in very early behaviors and in the first accumulation of human experiences. It is concluded that clock genes are the clock ticking behind the other very early clocks of human behaviors and experience emergence.