Evolution from Proto-Life to Metabolic Networks: Difference between revisions
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{{CSSS 2007 Santa Fe}} | {{CSSS 2007 Santa Fe}} | ||
Moved away from the projects, due to too wide a scope. | |||
'''People''' | '''People''' | ||
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* Christian Darabos | * Christian Darabos | ||
* [http://www.santafe.edu/events/workshops/index.php/Tim_Johann Tim Johann] | * [http://www.santafe.edu/events/workshops/index.php/Tim_Johann Tim Johann] | ||
* Vikas Shah | |||
* Joshua L. Payne | |||
== Idea == | |||
Given the concept of the [http://en.wikipedia.org/wiki/Origin_of_life#.22Metabolism_first.22_models:_iron-sulfur_world_and_others Metabolism First Hypothesis], how did early simple and essentially random reaction networks evolve into ones that exhibit characteristics of scale-free and small-world (sf-sw) networks? What physically meaningful rules may we find that can lead to this? | |||
== | |||
== Outline == | |||
... | |||
== Things to consider == | == Things to consider == | ||
* No predefined goal! Besides evolvability. | * No predefined goal! Besides evolvability. I.e. we don't use a fitness function based on a known goal state. | ||
* How to define fitness? Or, how to define selection without a known fitness function? | * How to define fitness? Or, how to define selection without a known fitness function? | ||
** Yes, I though it might be interesting to run simulations without fitness and selection, just based on the rules of evolution and see what comes out -- [http://www.santafe.edu/events/workshops/index.php/Amelie_Veron Amelie] | ** Yes, I though it might be interesting to run simulations without fitness and selection, just based on the rules of evolution and see what comes out -- [http://www.santafe.edu/events/workshops/index.php/Amelie_Veron Amelie] | ||
*** What to do about the explosion of possibilities? [[http://www.santafe.edu/events/workshops/index.php/Tim_Johann Tim]] | *** What to do about the explosion of possibilities? [[http://www.santafe.edu/events/workshops/index.php/Tim_Johann Tim]] | ||
* How can we get increasing complexity of metabolites? | * How can we get increasing structural complexity of metabolites? | ||
* Does structural complexity of metaboltes really imply a tendency to sf-sw? | |||
== Space for Opinions == | |||
It seemed at our first meeting, that everybody involved (but me) assumed I wanted to take the role of the leader. Actually, I wanted to have an open discussion about what WE want to achieve. -- Tim | |||
As the group of interested people is so large and the number of opinions as well, we could split into two groups with different approaches or goals. With a meeting once or twice a week. | |||
== Readings == | |||
* nearly anything by Stuart Kauffman (I just borrowed 'The Origins of Order'). | |||
* Gunter Wachtershauser has painted a detailed picture of the chemical possibilities based on geothermal vents. He has a bunch of publications that pop up on Google scholar. Steen would definitely say he has painted himself into a corner, but he has some really interesting hypotheses. | |||
Latest revision as of 01:52, 12 June 2007
| CSSS Santa Fe 2007 |
Moved away from the projects, due to too wide a scope.
People
(Just sign up yourself, if interested, or, whom I've just forgotten)
- Kathryn Cooper
- Amelie Veron
- Wenyun Zuo
- Christian Darabos
- Tim Johann
- Vikas Shah
- Joshua L. Payne
Idea
Given the concept of the Metabolism First Hypothesis, how did early simple and essentially random reaction networks evolve into ones that exhibit characteristics of scale-free and small-world (sf-sw) networks? What physically meaningful rules may we find that can lead to this?
Outline
...
Things to consider
- No predefined goal! Besides evolvability. I.e. we don't use a fitness function based on a known goal state.
- How to define fitness? Or, how to define selection without a known fitness function?
- How can we get increasing structural complexity of metabolites?
- Does structural complexity of metaboltes really imply a tendency to sf-sw?
Space for Opinions
It seemed at our first meeting, that everybody involved (but me) assumed I wanted to take the role of the leader. Actually, I wanted to have an open discussion about what WE want to achieve. -- Tim
As the group of interested people is so large and the number of opinions as well, we could split into two groups with different approaches or goals. With a meeting once or twice a week.
Readings
- nearly anything by Stuart Kauffman (I just borrowed 'The Origins of Order').
- Gunter Wachtershauser has painted a detailed picture of the chemical possibilities based on geothermal vents. He has a bunch of publications that pop up on Google scholar. Steen would definitely say he has painted himself into a corner, but he has some really interesting hypotheses.