One of the major themes of our research into biological systems in general and immunology in particular is that these systems are by their very nature multi-scale. We propose that to understand biological control we must create an analysis which links between scales. These models must combine the underlying level where interactions occur (the microscopic scale) and the higher level where behaviors are found to emerge (the macroscopic scale). During my time at Drexel I have managed to expand my interests beyond immunology and use both the methods and sensibilities I have developed studying immunity to study other complex biological systems. These ongoing researches include: (i) Modeling and comparing patterns of cell motility and directed movement from 2D and 3D imaging experiments. (ii) Creating explicit 4D models (3D maps updated over time) of bacterial biomes and spread in urban environments. (iii) Codon usage, nucleotide distribution and the detection of selection in the genome (outside of immune genes) and in viral species competition. (iv) Developing a general model for the role of Complexity in the development and evolution of living systems.