Embryonic stem cells (ESCs) serve as a model for development and as a potential source of
cells for the treatment of a variety of human conditions. ESCs can undergo differentiation to each of the
3 germ layers and, upon successive elaboration, can generate all of the cell types of the developing
embryo and adult. Multiple interconnected layers of regulatory networks/circuits control ESC self
renewal, pluripotency, and differentiation. This complex biological system can only be partially
understood and manipulated to advantage using reductive experimental approaches. Instead, complex
systems analysis tools, which inherently take into consideration the nonlinear, non-intuitive, and highly
interconnected nature of the system must be applied. In recent years, a combination of the development
of high-throughput screening methods for measuring gross system properties, array technologies for
measuring global system changes at various molecular levels, and mathematical algorithms and
computer software for data handling and modelling has brought complex systems analysis to the fore.
This Chapter highlights recent examples of complex systems applications to ESCs undergoing the
earliest stages of differentiation to the germ layers via intermediate pluripotent populations.
Keywords: Complex systems, systems biology, regulatory networks, molecular circuits, emergent
properties, bioinformatics, lineage commitment.
