Experimental measurements of shale permeability are normally conducted under conditions of constant effective stresses. Based on the theory of poroelasticity, shale permeability in non-sorbing media is determined by the effective stress alone and remains unchanged if the effective stress does not change. This theoretical conclusion contradicts some experimental observations in sorbing media. These enigmatic phenomena are analyzed through a model accommodating gas slippage. This approach can explain why shale permeability is significant at low gas pressure but does not explain the contradiction with poromechanics. In this work, we develop and apply an alternative approach to resolve this dilemma. The model comprises flow within a nanotube capillary embedded within the shale matrix (discrete approach) and allows the evolution of shale permeability to be followed during the processes of shale gas flow. In the formulation, we define four strains: global strain of the shale, fracture-local strain, matrix-global strain, and pore-local strain. Shale permeability is defined as a function of these strains that are, in turn, a consequence of effective stress transfer between the matrix and the fracture systems. This behavior is regulated by the differential compliance of the various components and by gas diffusion from the fracture system to the matrix. We use the strain evolution to define how shale permeability changes with time or gas pressure in the matrix system. We apply the new model to generate a series of shale permeability profiles. These profiles are consistent with experimental observations reported in the literature. Through this study, we demonstrate that the experimental observations can indeed be explained through the inclusion of explicit interactions between shale microstructures and gas transport processes.