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The structure of engineered infrastructure systems can be represented by a layered architecture. The relationship between physical components of many types of these systems has been well studied and modelled. The engineered design of these systems can account for some of their characteristics such as robustness, flexibility, reliability. We believe that the resilience, or adaptive capacity, of these systems cannot be described merely by studying the engineered components of such systems. This requires studying what we refer to as the protocol layers. The protocol layer is where humans interact with the engineered elements of the system through the collection and processing of information with the aim of producing a control activity on the system. In the first part of this study we look at several formulations of a generic layered transportation system, to discuss the importance of protocols in adaptive capability. In the second part, we take a brief historical look at an important American intermodal inland waterway transportation system, The Tennessee Valley Authority. From this system we extract some basic protocol layers and discuss how the success or failure of this system has resulted from these protocol layers.