The derivation of protein-protein interaction networks of Saccharomyces cerevisiae, C. elegans and Drosophila has recently become a popular method for understanding the biology of these organisms. Network analysis is most advanced in the budding yeast, S. cerevisiae. The network of S. cerevisiae was developed using empirical methods such as yeast two-hybrids (e.g. Ito et al. 2001), expression profiling, identification of proteins in complexes using mass spectrometry, and systematic gene disruptions (Hazbun and Fields 2001). All of these analyses have allowed yeast to be the leading system for the study of protein networks. These networks have been found to be scale-free (Han et al. 2004). Scale-free networks are organized into a system of “hubs” and “spokes” where a few nodes (hubs) have more than five interacting partners, while most nodes (spokes) have five or fewer partners. Disruption of the hubs will cause much greater network perturbation than disruption of a spoke (Han et al. 2004). Therefore, disruption of a random node (protein) is unlikely to cause a serious disruption to function of the overall network (Han et al. 2004). This is one main argument for the ability of organisms to evolve. The protein network is robust, and the organism can still function in spite of mutations.