Copenhagen, Denmark, 24 July 2024, 15:00 CET (Hybrid Format)
organized by
Pasquale Stano, Michael Barros, Malcolm Egan, Murat Kuscu, Yutetsu Kuruma, and Tadashi Nakano
A satellite workshop of
The 2024 Conference on Artificial Life (ALIFE 2024), Copenhagen, Denmark,
22-26 July 2024
Recent advances in systems and synthetic biology constitute a basis for the realization of the wetware approach to Artificial Life (AL), in addition to hardware and software approaches. Developing AL systems in wetware domains requires the use of chemical and biological materials to construct tools, devices, and systems capable of displaying life-like behaviors such as growth, division, adaptation, plasticity, evolution, autonomy, and other bio-inspired patterns.
While thermodynamic and kinetic laws governing (bio)chemical processes provide a basis to attack the complex tasks of devising systems that significantly contribute to AL, it is also important to understand the organizational structure of AL systems. It is often noted that the governing principles of organizational structures rely on a characterization of information flow. As a consequence, it is natural to suspect that models and characterizations from information theory and communication theory will be useful in the study of organization in AL.
The combination of areas such as synthetic biology, systems chemistry, chemical reaction network theory, and chemical organization have already impacted AL, as is often reported within the AL community. On the other hand, the exploration of the so-called “bio-them-ICTs” (bio-chem-information and communication technologies), and the theories behind them, known as “Molecular Communications”, have received—to date—limited attention from the AL community.
The workshop Molecular Communication Approaches for Wetware Artificial Life aims to fill this gap, providing an arena for discussing how current interest in chemical information and chemical communication can converge with AL, especially in the context of synthetic biology and systems chemistry approaches. The field of Molecular Communications, recently developed from an engineering perspective, can provide valuable tools for achieving a higher degree of complexity in AL systems, including: (i) Synthetic/Artificial Cells or Protocells and their assemblies; and (ii) hybrid biological/artificial systems (e.g., Synthetic Cells that can communicate with biological cells; hardware/software microsystems interfaced to biological systems; networks made of both artificial and biological entities).
Some of the questions that we would like to address in this workshop are:
What are the principles and models of molecular information and communication in wetware AL systems? How can we measure and compare the information content and flow in such biochemical systems?
How can engineering of molecular communication enhance the functionality and complexity of AL systems?
How can we create synthetic/artificial cells or protocells that can communicate with each other or with natural cells using MC? What are the design principles and mechanisms for generating emergent behaviors in synthetic/artificial cell populations or networks towards AL?
How can we model and analyze the network structure and dynamics of artificial and biological components that communicate via MC? What are the effects of noise, interference, feedback, adaptation, evolution, etc. on network behavior?
We invite all interested researchers to join us at the second version of this workshop at ALIFE 2024, and to contribute to the discussions on MC for wetware AL, including but not limited to those topics outlined above.
Date: 24 July 2024; 15:00-16.40 CET, Hybrid Format (in presence + Zoom)
15:00 - 15:10 Introduction. Organizers.
15:10 - 15:20 Jitka Čejková. Innovative Methods for Selective Silencing of Microbial Signals Using Micro-Scavengers in Artificial Life Systems
15:20 - 15:45 Marco Villani and Roberto Serra. Asymmetrical Division in Populations of Protocells
15:45 - 16:10 Thomas Gorochowski. Programming Biological Systems with Synthetic Biology
16:10 - 16:40 Discussion and Closing Remarks
Innovative Methods for Selective Silencing of Microbial Signals Using Micro-Scavengers in Artificial Life Systems
Jitka Čejková, University of Chemistry and Technology, Prague, Czechia
The aim of our project is to develop innovative methods to modulate microbial communication by selectively silencing specific signalling substances within microbial environments. This approach, akin to silencing certain words in a conversation to observe the resulting changes, involves using micro-scavengers (MSSs) equipped with an active core, gating mechanism, and magnetic particles for remote manipulation. These MSSs will absorb signalling substances through mechanisms such as complexation of metal ions, adsorption of low-molecular-weight organic substances, and catalytic degradation. By periodically regenerating the scavengers via photocatalytic degradation, we will maintain their capacity for signal removal. This methodology allows for the investigation of phenomena such as quorum sensing (QS), where microorganisms gauge population size through signal concentration. The ability to disrupt QS can mitigate pathogenic behaviours or induce dormancy in microorganisms, offering potential applications in antifouling and preservation. Additionally, selective signal scavenging will enable the study of chemotaxis and can facilitate active microbial control, paving the way for unconventional applications like biocomputing. Our work aligns with the goals of the Molecular Communication Approaches for Wetware Artificial Life workshop, providing insights into the engineering of molecular communication to enhance the functionality and complexity of artificial life systems.
Asymmetrical Division in Populations of Protocells
Marco Villani [1,2] (speaker), Roberto Serra [1,2,3]
[1] University of Modena and Reggio Emilia, Italy; [2] European Centre for Living Technology, Venice, Italy; [3] Institute of Advanced Studies, University of Amsterdam, Netherlands
The growth of a protocell population that divides symmetrically requires the synchronization between the two processes of duplication of the genetic material and of fission of the lipid container. However, uneven division, where daughter protocells are of different sizes, often occurs. This work examines asymmetrical division, where each protocell produces two daughters of different sizes, making true synchronization impossible. The concept of homogeneous growth is introduced to ensure sustainable population growth. Various models of protocell growth and reproduction are considered, showing through simulations that homogeneous growth can occur in both Surface Reaction Models (where replicators are in the membrane) and Internal Reaction Models (where replicators are in the internal water phase) under different kinetic equations. The study suggests that the “chemical signature” of a protocell, defined by the ratios of replicators at fission time, is conserved through generations when linear kinetic equations are involved.
Programming Biological Systems with Synthetic Biology
Thomas Gorochowski, Royal Society University Research Fellow & Associate Professor of Biological Engineering,
School of Biological Sciences, University of Bristol, UK
I have always been fascinated by the possibility of reprogramming biology across scales using synthetic biology as a foundation. In this talk, I'll cover some of the diverse projects my lab has been working on in this area, covering the characterisation of genetic parts and regulatory circuits using sequencing technologies, to the spatial control of living collectives using light. I hope this scattering of science will give you a feeling for my broad scientific interests and demonstrate some of the exciting possibilities that synthetic biology approaches offer to harness biology in new ways.
1st Workshop on Molecular Communication Approaches for Wetware Artificial Life
Sapporo, Hokkaido, Japan, 25 July 2023