Evolutionary Cellular Computing for Environmental Synthetic Biology

Introduction

This project will build living evolutionary cellular computers and showcase them as intelligent bioremediation agents. Current synthetic genetic networks that perform human-defined computations must remain unchanged—as initially designed—in order to perform well. This is a problem since biological substrates adapt and evolve, compromising durability, robustness, and computing power.

Objectives

We will exploit the intrinsic dynamic features of living systems. ECCO’s biocomputers will be able to self-adapt and reconfigure at run-time. They will show unprecedented levels of robustness and efficiency—far beyond current technological limits.

Intra-Cellular Evolvability

To this end, we will tackle intra-cellular evolvability and multi-cellular reconfigurability. At the intra-cellular level, we will upgrade current genetic circuitry with pre-defined mutation, evaluation, and selection dynamics. Circuits will optimize themselves.

Multi-Cellular Reconfigurability

At the multi-cellular level, we will design cellular consortia able to reconfigure their structure—therefore changing their functionality—according to environmental needs, thus adaptive.

Integration of Theory and Experimentation

The ECCO project will integrate theoretical developments with in-vivo experimentation. The soil bacteria Pseudomonas putida will be used as a host to illustrate the capabilities of evolutionary genetic circuits.

Demonstration of Efficiency

To demonstrate long-run efficiency, bacteria will be used to colonize the root of the plant Arabidopsis thaliana—a much more complex environment than the pristine laboratory conditions where circuits are often characterized.

Reconfigurability and Pollution

Reconfigurability will be achieved by building a multicellular computer able to switch between metal and aromatic removal circuits—two important pollutants.

Conclusion

Evolution, adaptation, and reconfigurability are elusive to conventional computers; conveniently, these are intrinsic properties of living organisms. The ECCO will benefit from this in order to engineer living computers that unlock applications in novel domains—from synthetic agriculture to precision bioremediation.