NKS in Computational Biology and Bioinformatics

Christian Jacob
University of Calgary

We are surrounded by a natural world of massively parallel, decentralized biological information processing systems, a world that exhibits fascinating emergent properties in many ways. In fact, our very own bodies are the result of emergent patterns, as the development of any multi-cellular organism is determined by localized interactions among an enormous number of cells, carefully orchestrated by enzymes, signalling proteins and other molecular agents. What is particularly striking about these highly distributed developmental processes is that a centralized control agency is completely missing. This is also the case for many other biological systems, such as termites which build their nests without an architect that draws a plan, or brain cells evolving into a complex “mind machine” without an explicit blueprint of a network layout.

Obviously, being able to understand, build, and harness the emergent properties of such systems would be highly beneficial. Designers of complex systems could utilize their adaptability and robustness. Such systems would construct themselves, through self-organization. However, system designers and programmers are facing an enormous challenge. How can we actually build highly distributed systems of which we have only limited understanding? Would we have to invent new ways of building, maintaining, and controlling such systems? It seems to be necessary to explore a completely new mindset for programming and system control. I intend to discuss computational biology models my Evolutionary & Swarm Design Group has investigated and built. I will give examples of these models and discuss the specific aspects related to NKS. In particular, I will demonstrate how these systems can be designed through evolutionary techniques. The models to be presented are:
• A swarm-based traffic simulation, with cars that communicate through “pheromones”.
• A rule-based and an agent-based 3D simulation of the Lactose Operon as a classical gene regulatory system.
• Agent-based 3D simulation of the Lambda Switch, a gene regulation system used by the bacterial phage.
• Agent-based 3D simulations of the human immune system.
• Genetic programming of dynamic swarm behaviors.

Created by Mathematica  (April 20, 2004)