Goals

The aim of our project is to investigate the emergence of complexity and how we can deal with complexity in general. Our project addresses this goal in two ways.

First, we follow a biomimetic approach. This approach corresponds to the motto "What I cannot create, I cannot understand" (Richard Feynman). We are inspired by Sierpinski triangle patterns present on sea snail shells, and engineer the same kind of emergent patterns on grids of bacterial colonies. These patterns are emergent because they arise directly from one logic gate implemented in all bacteria. This project that combines modeling and wet-lab work will enable us to answer some questions such as how complexity can emerge from simple rules, whether it can be predicted from simple rules, how we can deal with crosstalk and leakiness of biological systems to enable a good predictability.

Second, we widen the scope of our investigation to other projects and disciplines, from scientific fields to philosophy, sociology or art. We address the issue of how to deal with complexity, by interviewing experts in several fields and conducting a larger scale study with a survey. Do these people consider that parts are strictly ordered, and try to reduce complexity to simple parts strictly following a set of deterministic rules, or do they accept that complexity comprises a mix of order and disorder, that a part of uncertainty cannot be neglected and that complex systems should be studied as a whole? Both approaches have their advantages and their drawbacks, which one should we choose to deal with the increasing complexity of our world?

Here is a more detailed list of subgoals:

• Make a Sierpinski triangle pattern appear on a grid of bacteria
• Conjugate quorum sensing and logic gates in bacterial colonies
• Implement an XOR gate in an E. coli
• Characterize integrases (retrieve missing parameters)
• Lower the leakiness in quorum sensing systems
• Study quorum sensing crosstalk in order to implement orthogonal communication
• Be able to predict accurately the system’s behavior
• Conduct a survey about how to deal with complexity
• Gather interviews of experts from different fields
• Find our own answer to this question thanks to our Mosaicoli

Applications and outlook

Future development of synthetic biological systems will require the implementation of reliable synthetic circuits. These gene circuits will be designed to program new biological behaviour, dynamics, and logic control^[1]. A crucial part to coordinate and control the biological computation needed to perform their tasks can be seen in multichannel orthogonal communication. In order to achieve the goals of our project we need to thoroughly characterize available components, improve their performance, and develop novel constructs that get closer to actual multichannel orthogonal communication and subsequent logic processing. With our findings we will try to make a contribution to the field of biological computation by enabling further development of complex systems that rely on the interaction between its subparts.

These biological computers in turn also need to find a way to be implemented in patients, if they are developed to perform therapeutic tasks. A promising application of such synthetic biological systems is cell based therapy by alginate-microencapsulated implants^[2][3]. We will try to achieve communication and input integration in a grid of alginate beads and thus producing a more complex behavior than a single bead could show. This can be seen as a step towards the development of artificial organs composed of multiple alginate-microencapsulated implants, that work together to tackle tasks a single implant, which is not communicating with its neighbors, could not solve.