Fundamentally, stratification of earth layers and the development of earth boundary surfaces is a self-organization response driven by thermally active media in the presence of gravity. Media properties such as viscosity and rigidity are controlled by atomic scales forces such as strong and electromagnetic forces that result in molecular bonding. Feedback mechanisms between media at boundary surfaces can be characterized through an analysis of each media in terms of four fundamental factors that include space, time, energy and mass (STEM). For example, convergent self-organization of fluvially mixed, transported sediment can occur through time (T) via gravitational energy (E) to move and segregate grains (M) into layers (S) to form graded bedding. Divergent self-organization can occur through weathering processes (E) that break down pre-existing bedrock, (M) disperses and reorganizes the weathered products into a different ordered state (S) over some period of time (T). The Pikes Peak Granite displays self-organization through weathering features such as corestones, grus, tors and unconsolidated granite residuum greater than 30 m below the surface. The granite medium (M) is predisposed to breakdown through the development of microfractures related to the diapiric intrusion and dilation (gravity driven)(E) and cooling (thermally driven)(E) of the Pikes Peak Batholith (S) over 1.04 Ma (T). The dynamic atmospheric medium (O2, H2O primarily)(M) in contact with the granite has interacted since the Eocene (T) by being thermally active (solar energy)(E) and reacting with biotite crystals to form hydrobiotite that expands (S) to increase permeability and cause an exponential increase in alteration rates. Other weathering phenomena include unloading fractures, case hardening and corestone complexes. Thus, self-organization at the boundary surface of the thermally agitated Pikes Peak Granite and atmosphere is “reordered” by gravity (directed energy) at macroscales and atomic forces (directed energy) at microscales to generate a new spatial/physical state (weathered granite and altered atmosphere) over 40 Ma.