In previous chapters, we described the cell as a robust machine that carries out complex functions through the activity of distinct functional modules. At the next level, it is important to understand how the cell accomplishes these complex functions by coordinating the activity of multiple functional modules. Clathrindependent endocytosis and plasma membrane protein synthesis are just two complex functions that result from an integrated sequence of events. For a good understanding of functions, we suggest that they should be dissected at the nanometer (protein–protein complex) level. The production of almost anything in the macroscopic world needs a plan that outlines the number of steps in its production, as well as a decision tree to provide for modifications and/or quality control. This will ensure that the final product meets all required standards. In the production of cars or computers, components are added in a series of steps that often occur in a prescribed order and depend upon the satisfactory completion of each step before subsequent steps can commence. Similarly, complex functions in cells, including clathrin-dependent endocytosis and plasma membrane protein synthesis, all occur in a series of often repetitive steps that depend upon the sequential completion of prior steps. This results in a classical ‘if/then’ decision tree that will ensure that the complex function is completed properly. In some cases, there are multiple complex functions that the cell can choose depending upon the conditions (e.g. if a cell encounters another cell, it will change its behavior). For us to understand any given integrated complex function, we need to define the steps (which are typically driven by distinct functional modules) and the critical components needed to complete the task.

To understand the multiple levels of complex functions, it is useful here to consider an easily applicable example, again using cars. To raise or lower a car window, several machine elements come into play. Only a basic understanding of the mechanism is required to raise and lower the window. However, to be able to repair a car window, the mechanism must be understood in much greater detail. Here, a complete list of the parts, right down to the screws that hold them in place, may be required.