Table 1.

Five features of a biological mechanism (adapted from [9]): a biological mechanism exhibits all five. A computational mechanism-based model may strive to do the same.

Mechanism Features	Examples	Explanations
Phenomenon		A clearly identified phenomenon is the requisite for specifying the other four features of mechanism and for developing a credible explanation of that phenomenon.
Components	entities, activities, modules, processes, underlying finer details	Working entities act in the mechanism. Activities are producers of change. Some entities and activities can be organized into a module. Inner layer phenomena can be the entities and activities responsible for the outer layer phenomenon.
Spatial arrangement of components	localization, structure orientation, connectivity, compartmentalization	Components are typically localized and organized into a structure. A component’s orientation can be a prerequisite for an activity. Producing change requires connectivity. Compartmentalization facilitates spatial arrangement within a structure.
Temporal aspects of components	order, rate, duration, frequency	Entities may play their role is a particular order. Some activities have characteristic rates. Activities can occur in stages and/or exhibit temporal organization. An activity and/or stage can repeat or exhibit frequencies. Stages can unfold in a particular order and have duration.
Contextual locations	location within a hierarchy and/or within a series	A mechanism is situated in wider context, such as within a hierarchy of mechanism levels or within a temporal series of mechanisms not directly influencing the phenomenon of interest.