One of the main aims in Systems Chemistry research deals with the development of complex synthetic systems displaying emergent properties; i. e., properties that go beyond the sum of the characteristics of the molecular constituents of the system. In comparison to the frequently applied synthetic biology tools, the systems chemistry approach may sometimes appear to be challenging with respect to design and synthesis; however, it often facilitates better control over a desired function and subtle manipulations, together with widening the range of experimental conditions. For more than 10 years now, my group at Ben-Gurion University has focused on the development of such systems using peptide-based replication networks. Our studies were first conducted to shine light on basic principles of catalysis and to probe scenarios relevant to the Origin of Life. These experiments have been recently expanded for finding new tools to control complex reaction networks and to synthesize structures that might be useful for nanotechnology. We apply common biophysical methods and tools to characterize the structures of peptide-based assemblies and we furthermore develop and exploit experimental and computational kinetic assays to express the function of the peptide networks under variable environmental and experimental conditions. Among other interesting features, we have disclosed how competition and cooperation at the molecular level affect the network behavior, and how replication out of chemical equilibrium leads to life-like emergent behavior, such as bistability, multistability and oscillatory functions.