Wednesday, 10 October 2007
Alergic meeting Wed 10 October, 16:30, ARUN 401
The first meeting of the term for Alergic (Artificial Life Reading Group in Cogs) is today. The NAME group can be seen as a spin off from Alergic and used the 'Alergic slot' on Wednesday afternoons. In today's meeting we will introduce the NAME group and discuss where and when to hold NAME meetings this term.
Thursday, 16 August 2007
Next meeting: Wed 22nd August, 16:00, room TBC
James Dyke will be presenting at the next NAME meeting, this coming Wednesday 22nd August at 16:00, room TBC. The talk will be approximately 30 minutes long in order to allow discussion afterwards. Those interested in niche construction and ecosystems engineering as well as ecosystems complexity/stability may find the presentation and discussion of use.
Title:
Increasing complexity can increase stability in a self-regulating ecosystem
Abstract:
A long standing debate within ecology is to what extent ecosystem complexity and stability are related. Landmark theoretical studies claimed that the more complex an ecosystem, the more unstable it is likely to be. Stability in an ecosystems context can be assessed in different ways. In this paper we measure stability in terms of a model ecosystem's ability to regulate environmental conditions. We show how increasing biodiversity in this model can result in the regulation of the environment over a wider range of external perturbations. This is achieved via changes to the ecosystem's resistance and resilience. This result crucially depends on the feedback that the organisms have on their environment.
Title:
Increasing complexity can increase stability in a self-regulating ecosystem
Abstract:
A long standing debate within ecology is to what extent ecosystem complexity and stability are related. Landmark theoretical studies claimed that the more complex an ecosystem, the more unstable it is likely to be. Stability in an ecosystems context can be assessed in different ways. In this paper we measure stability in terms of a model ecosystem's ability to regulate environmental conditions. We show how increasing biodiversity in this model can result in the regulation of the environment over a wider range of external perturbations. This is achieved via changes to the ecosystem's resistance and resilience. This result crucially depends on the feedback that the organisms have on their environment.
Friday, 27 July 2007
Next meeting: Wed 1st August, 16:30, ARUN401
The next NAME meeting will see Chris Gordon-Smith present his research into the origins of life with his SimSoup software.
Abstract:
Network dynamics may have played a key role in the Origin of Life. ‘Smart’ molecules such as template replicators and enzymes may not have been necessary in the first evolving entities. This paper shows evolution of a metabolic network using the SimSoup artificial chemistry simulation. The context and conceptual background for SimSoup is first outlined. The model is then described, and differences with other models are highlighted. SimSoup has network elements that correspond directly to the unimolecular and bimolecular elementary reaction schemes of physical chemistry. These network elements can be combined in very general ways to produce ‘compound interactions’ which can be catalytic.The model includes mass conservation, reaction rates based on considerations of energy and thermodynamics, and cycle detection. A run of the model is presented showing an evolutionary process with selection for high entropy production. The network includes a large number of cyclic flows. It evolves through a series of persistent states, each of which can be regarded as a different ‘species’.
Abstract:
Network dynamics may have played a key role in the Origin of Life. ‘Smart’ molecules such as template replicators and enzymes may not have been necessary in the first evolving entities. This paper shows evolution of a metabolic network using the SimSoup artificial chemistry simulation. The context and conceptual background for SimSoup is first outlined. The model is then described, and differences with other models are highlighted. SimSoup has network elements that correspond directly to the unimolecular and bimolecular elementary reaction schemes of physical chemistry. These network elements can be combined in very general ways to produce ‘compound interactions’ which can be catalytic.The model includes mass conservation, reaction rates based on considerations of energy and thermodynamics, and cycle detection. A run of the model is presented showing an evolutionary process with selection for high entropy production. The network includes a large number of cyclic flows. It evolves through a series of persistent states, each of which can be regarded as a different ‘species’.
Wednesday, 18 July 2007
Next meeting: Wed 18th July, 14:00, ARUN401
The NAME next meeting will be held in Arundel 401, Wednesday 18th July at 14:00. Previous CCNRer Alex Penn will be talking about her research into group selection and niche construction at Southampton University.
Monday, 9 July 2007
Next meeting: Wed 11th July, 16:30, ARUN203
The NAME next meeting will be held in Arundel 203, Wednesday 11th July at 16:30. We will continue the discussions on biological complexity. Inman Harvey will give a brief presentation on Worden's "Speed Limit for Evolution" paper - available here:
http://dspace.dial.pipex.com/jcollie/sle
http://dspace.dial.pipex.com/jcollie/sle
Thursday, 5 July 2007
Meeting Report: 4th July 2007
Yesterday's meeting was very productive. Joel kicked things off with a presentation on Adami's biological complexity review paper. The slides (in pdf format) can be found here:
http://www.sussex.ac.uk/Users/jgd20/data/NAME_4Jul2007_Adami_presentation.pdf
The discussion ranged far and wide and whilst I attempted to make notes during the meeting, reviewing them today clearly shows that they are not sufficient for me to be sure of not misrepresenting ideas. I can confidently state that there was broad agreement that Adami's paper had a number of fundamental problems/issues and one clear error.
There was also some discussion as to whether the application of a measure of biological complexity can make any real sense or have any utility. David Waxman cited a paper that considers the complexity of phenotypes rather than genotypes. The paper can be found here:
http://www.sussex.ac.uk/Users/jgd20/data/mcshea_1993.pdf
With regards alternative accounts of genome complexity and the utility of biological complexity as a concept, Inman Harvey cited Worden's "Speed Limit for Evolution" paper:
http://dspace.dial.pipex.com/jcollie/sle
Time was running out, so it was decided that Inman would start next weeks meeting with a brief presentation of Worden and we can then continue the discussion.
The room is TBC - I will send out details later.
The discussion ranged far and wide and whilst I attempted to make notes during the meeting, reviewing them today clearly shows that they are not sufficient for me to be sure of not misrepresenting ideas. I can confidently state that there was broad agreement that Adami's paper had a number of fundamental problems/issues and one clear error.
There was also some discussion as to whether the application of a measure of biological complexity can make any real sense or have any utility. David Waxman cited a paper that considers the complexity of phenotypes rather than genotypes. The paper can be found here:
http://www.sussex.ac.uk/Users/jgd20/data/mcshea_1993.pdf
With regards alternative accounts of genome complexity and the utility of biological complexity as a concept, Inman Harvey cited Worden's "Speed Limit for Evolution" paper:
http://dspace.dial.pipex.com/jcollie/sle
Time was running out, so it was decided that Inman would start next weeks meeting with a brief presentation of Worden and we can then continue the discussion.
The room is TBC - I will send out details later.
Monday, 2 July 2007
Next meeting in different room - Pev1 1A01
The next NAME meeting will be held in a different room - Pevensey 1, 1A01, 16:30, Wednesday 4th July.
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