Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the details of the current state of our environment, agent, and reproductive models. In developing our models we have relied on a principle of using non-linear systems to model as many systems as possible including mutation and recombination, gene-environment interaction, agent metabolism, agent survival, resource gathering and sexual reproduction. In this paper we review the genetic dynamics that have emerged in our system including genotype-phenotype divergence, genetic drift, pseudogenes, and gene duplication. We conclude that emergence-focused design in complex system simulation is necessary to reproduce the multilevel emergence seen in the natural world.