Formal Systems Architectures for Biology

When the word "systems" is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and "control" mechanisms, which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on the connection between top-down control mechanisms and bottom-up self-organizing mechanisms