On Nov 2, 2023, the core team of the project met with our external guest and collaborator Christoph Flamm for a day-long workhop.
This workshop was intended to take stock of our project almost one year after its initiation. It features five talks by PhD students & core members of the project team, plus our guest speaker.
Among other things, the workshop will explore:
Here is an outline of the program:
Among other things, the workshop will explore:
- the kind of emergence involved in complexification during biological evolution & the kind of possibility spaces that arise from it,
- the organization of living matter, and how to model it,
- how this relates to research efforts in far-from-equilibrium thermodynamics, combinatorial chemistry, theoretical computer science, AI, etc.
Here is an outline of the program:
Yogi opened the meeting with an introduction to our project, focusing on the self-manufacturing (autopoietic or teleodynamic) organization of organismic agents and how it can be described and analyzed using relational models (Rosen, Louie, Hofmeyr). We will use these models as a starting point for our research. The main idea is to establish a connection between the abstract level of relational biology, and the more concrete methodological frameworks of far-from-equilibrium thermodynamics and the theory of computation (especially in the form of Church's lambda calculus). Basically, we are asking to what extent the behavior and evolution of organisms can be captured by such formalized approaches, and why such formalization must forever remain incomplete. In the end, this will amount to a new account of the emergence of new levels of complexity, and a rigorous characterization of co-evolving possibility space, which Stuart Kauffman has called "the adjacent possible."
The next two talks were given by the PhD students on the core team of the project. Paul Poledna spoke about constraint-based approaches to organizational emergence, starting with the work of Ross Ashby, Robert Rosen, Howard Pattee, and Terrence Deacon. His thesis will be focused around constraint-based higher-level dynamics, which must form the basis for any rigorous processual account of organismic organization. Kevin Purkhauser focused on the concept of emergence itself, looking at its recent resurgence and the confusion between computational and organizational definitions of the term. His thesis will attempt to link organizational accounts of the organism with simulation-based approaches from physics and computer science/computational biology.
Our guest speaker, Christoph Flamm, started the afternoon session by introducing his hypergraph-based methodology to simulate and explore open-ended chemical reaction networks, based on experimentally verified thermodynamic and kinetic principles and measurements. His framework amounts to a flexible rewrite system that (unlike lambda-based models) can exhibit the spontaneous emergence of higher-level constraints as the simulation proceeds. This kind of framework is of special interest in the context of our project because of its potential applicability to biological instead of chemical evolution. We also discussed evolving possibility spaces in chemistry during Christoph's talk. Hopefully, this discussion will lead to further collaborations in the future.
Moritz Kriegleder, PhD student in Tarja Knuuttila's research group, then took us on a philosophical journey into the free-energy principle and its application to study the organization of living systems. Karl Friston's Bayesian approach to predictive processing in perception has been claimed to apply more broadly, as a characterization of life itself. Moritz critically examined these claims (and the worldview of Markovian monism that comes with it), concluding that the whole framework is best considered instrumentally, as a powerful tool to study organismic perception and behavior, rather than an account of the organism (or reality) itself.
Andrea Loettgers finished the meeting presenting work she is doing in collaboration with Tarja Knuttila on the possibility spaces associated with the practice of synthetic biology, and its changing claims over the past couple of decades. She argued that synthetic biology is not able to implement arbitrary possibilities left inaccessible to evolution, but rather needs to be anchored in combinations of factors that exist in actual evolved organisms. For this purpose, she used Armstrong's combinational account of possibilities to map out the realizable possibility space of what she calls potential biology. It suggests a pragmatic combinatorial exploration instead of abstract rational design as a realistic path to success for synthetic biology. Again, this pragmatic notion of evolving possibility spaces will be used in our project to come up with a more systematic understanding of Kauffman's adjacent possible and the nature of open-ended evolution in general.
You can find the abstracts of the talks below.
The next two talks were given by the PhD students on the core team of the project. Paul Poledna spoke about constraint-based approaches to organizational emergence, starting with the work of Ross Ashby, Robert Rosen, Howard Pattee, and Terrence Deacon. His thesis will be focused around constraint-based higher-level dynamics, which must form the basis for any rigorous processual account of organismic organization. Kevin Purkhauser focused on the concept of emergence itself, looking at its recent resurgence and the confusion between computational and organizational definitions of the term. His thesis will attempt to link organizational accounts of the organism with simulation-based approaches from physics and computer science/computational biology.
Our guest speaker, Christoph Flamm, started the afternoon session by introducing his hypergraph-based methodology to simulate and explore open-ended chemical reaction networks, based on experimentally verified thermodynamic and kinetic principles and measurements. His framework amounts to a flexible rewrite system that (unlike lambda-based models) can exhibit the spontaneous emergence of higher-level constraints as the simulation proceeds. This kind of framework is of special interest in the context of our project because of its potential applicability to biological instead of chemical evolution. We also discussed evolving possibility spaces in chemistry during Christoph's talk. Hopefully, this discussion will lead to further collaborations in the future.
Moritz Kriegleder, PhD student in Tarja Knuuttila's research group, then took us on a philosophical journey into the free-energy principle and its application to study the organization of living systems. Karl Friston's Bayesian approach to predictive processing in perception has been claimed to apply more broadly, as a characterization of life itself. Moritz critically examined these claims (and the worldview of Markovian monism that comes with it), concluding that the whole framework is best considered instrumentally, as a powerful tool to study organismic perception and behavior, rather than an account of the organism (or reality) itself.
Andrea Loettgers finished the meeting presenting work she is doing in collaboration with Tarja Knuttila on the possibility spaces associated with the practice of synthetic biology, and its changing claims over the past couple of decades. She argued that synthetic biology is not able to implement arbitrary possibilities left inaccessible to evolution, but rather needs to be anchored in combinations of factors that exist in actual evolved organisms. For this purpose, she used Armstrong's combinational account of possibilities to map out the realizable possibility space of what she calls potential biology. It suggests a pragmatic combinatorial exploration instead of abstract rational design as a realistic path to success for synthetic biology. Again, this pragmatic notion of evolving possibility spaces will be used in our project to come up with a more systematic understanding of Kauffman's adjacent possible and the nature of open-ended evolution in general.
You can find the abstracts of the talks below.
