Computer Science and Engineering, Department of


Date of this Version

Spring 4-21-2016


J. Firestone (2016). A Roadmap to Safe and Reliable Engineered Biological Nano-communication Networks. Master's thesis, University of Nebraska - Lincoln.


A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Computer Science, Under the Supervision of Professors Myra Cohen and Massimiliano Pierobon. Lincoln, Nebraska: May, 2016

Copyright © 2016 Justin Firestone


Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell's core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened to self-adaptive programs that read inputs, process them, and produce outputs, reacting differently to different environmental conditions. With the increasing complexity of potential programs for SBOs, as in any new technology, there will be both beneficial as well as malicious uses. Although there has been much discussion about the potential safety and security risks of SBOs, and some research on predicting whether engineered life will be harmful, there has been little research on how to validate or verify safety of SBOs.

In this thesis, we lay a foundation for validating and verifying safety for SBOs. We first present two case studies where we give insight into the difficulties of determining whether novel SBOs will be harmful given the vast combinatorial search space available for their engineering. Second, we explain how the current U.S. regulatory environment is fragmented with respect to the multiple dimensions of SBOs. Finally, we present a way forward for formalizing the architecture of SBOs and present a case study to show how we might utilize assurance cases to reason about SBO safety.

Advisors: Myra Cohen and Massimiliano Pierobon