In the second chapter, Wagner discusses the variability of metabolic networks. How do metabolic networks evolve? How many reactions can I remove or add to a metabolic network, without altering its phenotype? How much the phenotype of a metabolic network is robust to changes?
A possible source of confusion in this chapter is the definitions used. The “metabolic network” is the set of all the reactions that an organism can catalyze; while the “genotype network” is the concept defined in the previous chapter. So, this chapter explains how “genotypes networks of metabolic networks” evolve; be careful to not confuse the two terms. The following figure from  can clarify the definitions:
1. Matias Rodrigues, J., & Wagner, A. (2009). Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks PLoS Computational Biology, 5 (12) DOI: 10.1371/journal.pcbi.1000613