Figure 1. Common approaches in the study of design principles in metabolic networks.

In general, one is interested in mapping molecular design to fitness. How can this be done? One route is to define a hypothesis about what system specifications confer a fitness contribution in the system under study (process 2). For example, the hypothesis could be that growth rate is the main (or only) determinant for fitness under constant environments. With this hypothesis in mind, engineering models can be used to test what molecular design of the system specification (e.g., a genome-scale metabolic network) would be optimal with respect to growth rate (process 1). The results can then be compared to the actual behavior of cells. Although suggestive, this does not strictly prove that the molecular design was actually selected for that trait, because the hypothesis about fitness cannot be independently proven. Therefore, process 3 is very important, i.e., show either by fitness measurements of alternative forms of the molecular design, by comparative studies between organisms with well-defined environmental niches, or by adaptive evolution studied under well-defined conditions that the molecular design in question can be directly shaped by natural selection instead of merely being a by-product of other evolutionary processes.