Studying the transition between single-celled organisms and multicellular ones is vital for the understanding of the complexification of life on earth. During that major transition in evolution, the notion of individual changed, as the unit of selection, hence of fitness, switched from the single cell to the higher level multicellular organism. One characteristic which is believed to be closely related to this transition is the emergence of cooperation in colonies of closely related microorganisms. We developed during our research a new type of Boolean Artificial Developmental Genetic Regulatory Network, which is used to control artificial agents which are evolved in a two-level fitness driven genetic algorithm. This evolution is used to study the particular trade-offs in the transition to higher level individuality during the emergence of cooperation in cell colonies as against competition with the selfish tendencies of their simpler constituent cells, as well as the potential for emergence of higher level cooperation despite the competition between two levels of selection in evolutionary dynamics.