Biological development of cell patterns: characterizing the space of cell chemistry genetic regulatory networks

Authors:
Nicholas Flann;Jing Hu;Mayank Bansal;Vinay Patel;Greg Podgorski
Affiliations:
Computer Science Department, Utah State University, Logan, UT;Computer Science Department, Utah State University, Logan, UT;Computer Science Department, Utah State University, Logan, UT;Computer Science Department, Utah State University, Logan, UT;Biology Department, Utah State University, Logan, UT
Venue:
ECAL'05 Proceedings of the 8th European conference on Advances in Artificial Life
Year:
2005

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Abstract

Genetic regulatory networks (GRNs) control gene expression and are responsible for establishing the regular cellular patterns that constitute an organism. This paper introduces a model of biological development that generates cellular patterns via chemical interactions. GRNs for protein expression are generated and evaluated for their effectiveness in constructing 2D patterns of cells such as borders, patches, and mosaics. Three types of searches were performed: (a) a Monte Carlo search of the GRN space using a utility function based on spatial interestingness; (b) a hill climbing search to identify GRNs that solve specific pattern problems; (c) a search for combinatorial codes that solve difficult target patterns by running multiple disjoint GRNs in parallel. We show that simple biologically realistic GRNs can construct many complex cellular patterns. Our model provides an avenue to explore the evolution of complex GRNs that drive development.