Hierarchy is widely observed in biological systems. In this thesis, evidence from nature is presented to show that protein interactions have became increasingly modular as evolution has proceeded over the last four billion years. The evolution of animal body plan development is considered. Results show the genes that determine the phylum and superphylum characters evolve slowly, while those genes that determine classes, families, and speciation evolve more rapidly. This result furnishes support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure that guides the evolution of aspects of the body plan. Next, the world trade network is treated as an evolving system. The theory of modularity predicts that the trade network is more sensitive to recessionary shocks and recovers more slowly from them now than it did 40 years ago, due to structural changes in the world trade network induced by globalization. Economic data show that recession-induced change to the world trade network leads to an increased hierarchical structure of the global trade network for a few years after the recession. In the study of influenza virus evolution, an approach for early detection of new dominant strains is presented. This method is shown to be able to identify a cluster around an incipient dominant strain before it becomes dominant. Recently, CRISPR has been suggested to provide adaptive immune response to bacteria. A population dynamics model is proposed that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is less diversifed. Finally, the creation of diversity of antibody repertoire is investigated. It is commonly believed that a heavy chain is generated by randomly combining V, D and J gene segments. However, using high throughput sequence data in this study, the naive VDJ repertoire is shown to be strongly correlated between individuals, which suggest VDJ recombination involves regulated mechanisms.