The joint NAME/Alergic talk given my Chris Watkins is now available on Google Video:
http://video.google.co.uk/videoplay?docid=-3703850700473118837&hl=en-GB
Monday 19 November 2007
Saturday 20 October 2007
Next NAME/Alergic: Chris Watkins, Wed 24th Oct, ARUN401
The next NAME meeting is a combined NAME/Alergic event. Chris Watkins, Royal Holloway, will be talking about his research into information theoretic approaches to evolution and in particular the 'channel capacity' of evolution. Please see abstract below.
16:30, Wednesday 24th October
Arundel room 401
All welcome.
Abstract
This talk will consider some familiar genetic and evolutionary algorithms from a new point of view. Instead of viewing these algorithms as optimisation methods, I will consider them information-theoretically, as communication channels. After a brief introduction to Shannon's theory of communication, I will show how to view an evolutionary algorithm as a communication channel, and then show that different algorithms have very different channel capacities.
Intuitively, the channel capacity of an evolutionary algorithm is a measure of how much information -- or how much complexity -- can be put into the "genomes" as a result of selection. This seems a basic limitative computational property, which may be relevant to choosing useful regimes to get evolutionary algorithms to work effectively.
In biological evolution, in each generation genetic information is degraded by mutation, but also in some sense restored by selection. Some natural basic questions are: How much information could be encoded in a genome as a result of selection? How complex could organisms conceivably become? Does the potential complexity depend on whether the organisms are sexual? How could information be encoded most efficiently, in the sense that the greatest amount could be encoded for the lowest intensity of selection? The theoretical approach I will present may have some bearing on these questions.
New Approaches to Modelling Evolution/Ecosystems
http://newapproaches.blogspot.com
16:30, Wednesday 24th October
Arundel room 401
All welcome.
Abstract
This talk will consider some familiar genetic and evolutionary algorithms from a new point of view. Instead of viewing these algorithms as optimisation methods, I will consider them information-theoretically, as communication channels. After a brief introduction to Shannon's theory of communication, I will show how to view an evolutionary algorithm as a communication channel, and then show that different algorithms have very different channel capacities.
Intuitively, the channel capacity of an evolutionary algorithm is a measure of how much information -- or how much complexity -- can be put into the "genomes" as a result of selection. This seems a basic limitative computational property, which may be relevant to choosing useful regimes to get evolutionary algorithms to work effectively.
In biological evolution, in each generation genetic information is degraded by mutation, but also in some sense restored by selection. Some natural basic questions are: How much information could be encoded in a genome as a result of selection? How complex could organisms conceivably become? Does the potential complexity depend on whether the organisms are sexual? How could information be encoded most efficiently, in the sense that the greatest amount could be encoded for the lowest intensity of selection? The theoretical approach I will present may have some bearing on these questions.
New Approaches to Modelling Evolution/Ecosystems
http://newapproaches.blogspot.com
Monday 15 October 2007
Next meeting: Wed 17th October, 14:00, room TBC
A PDF of David's talk can be found online here.
Professor David Waxmam from the Department of Biology and Environmental Science, University of Sussex will be leading the next NAME meeting this Wednesday 14:00, room TBC. The topic for this meeting is random genetic drift in populations.
NAME meetings are biased towards group discussions rather than a single presentation with questions. Therefore they are interactive and we positively welcome contributions from all participants. Come armed with puzzles, comments and queries!
All welcome.
Professor David Waxmam from the Department of Biology and Environmental Science, University of Sussex will be leading the next NAME meeting this Wednesday 14:00, room TBC. The topic for this meeting is random genetic drift in populations.
NAME meetings are biased towards group discussions rather than a single presentation with questions. Therefore they are interactive and we positively welcome contributions from all participants. Come armed with puzzles, comments and queries!
All welcome.
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.
Thursday 21 June 2007
Next meeting: 4:40pm, Wednesday 4th July
The next NAME meeting will be held in two weeks time - 4:30pm on Wednesday, 4th July, room TBC.
The topic of the next meeting with be Chris Adami's discussion on biological complexity. I have attached Adami's 2002 review paper to this email. Please read and come armed with questions and comments!
Joel Peck will be leading the discussions. He would like us to consider the following three questions:
1 - Is the measure in this paper really a reasonable measure of biological complexity?
2 - What practical difficulties might be encountered if one tried to applied the measure described?
3 - If you have problems with the proposed measure, what alternative measure might be used to measure biological complexity?
The room may change from ARUN401 as we would prefer something more conducive to group discussion.
The topic of the next meeting with be Chris Adami's discussion on biological complexity. I have attached Adami's 2002 review paper to this email. Please read and come armed with questions and comments!
Joel Peck will be leading the discussions. He would like us to consider the following three questions:
1 - Is the measure in this paper really a reasonable measure of biological complexity?
2 - What practical difficulties might be encountered if one tried to applied the measure described?
3 - If you have problems with the proposed measure, what alternative measure might be used to measure biological complexity?
The room may change from ARUN401 as we would prefer something more conducive to group discussion.
Wednesday 20 June 2007
Meeting Report: 20th June 2007
The first NAME meeting was held today. We plan to post meeting reports for all meetings. These will vary as some meetings will essentially be presentation / question sessions, some round table discussions and perhaps other formats.
The meeting today consisted of:
With regards the next meeting, Joel Peck from the Centre for the Study of Evolution will be leading a discusion on information theory and it applications to population genetics - in particular the work of Chris Adami. James and Nathaniel will be emailing out the paper before the meeting.
The next meeting is provisionally scheduled for Wednesday 4th July - in TWO weeks time, not the originally stated ONE week. James and Nathaniel plan to have weekly NAME meetings in the very near future.
Inman Harvey drew people's attention to the workshop on mathematical models in evolution that will be held in Sussex on 20-21 September. The website for this event is in the "links" section of this blog.
James compiled a long list of attendees research interests. He will post this to this blog shortly.
James and Nathaniel will be contacting a number of people who were not aware of todays meeting, but may be interested in attending.
The meeting today consisted of:
- Nathaniel and James restating their motivations for creating the group
- Introductions and research interests of those attending
- List of those not attending, but who we feel may be interested in attending
- Discussion of possible meeting format
- List of future meeting topics
With regards the next meeting, Joel Peck from the Centre for the Study of Evolution will be leading a discusion on information theory and it applications to population genetics - in particular the work of Chris Adami. James and Nathaniel will be emailing out the paper before the meeting.
The next meeting is provisionally scheduled for Wednesday 4th July - in TWO weeks time, not the originally stated ONE week. James and Nathaniel plan to have weekly NAME meetings in the very near future.
Inman Harvey drew people's attention to the workshop on mathematical models in evolution that will be held in Sussex on 20-21 September. The website for this event is in the "links" section of this blog.
James compiled a long list of attendees research interests. He will post this to this blog shortly.
James and Nathaniel will be contacting a number of people who were not aware of todays meeting, but may be interested in attending.
Friday 15 June 2007
First Meeting: 20th June, 16:30, ARUN401
This first meeting will allow us to introduce ourselves, state our research interests and what we hope to get out of the group.
Please bring along any lists of publications that you would like to discuss in future. We are very interested in having members of the group lead discussions on a particular topic, or present their own work.
Please bring along any lists of publications that you would like to discuss in future. We are very interested in having members of the group lead discussions on a particular topic, or present their own work.
Tuesday 1 May 2007
NAME is a new reading and discussion group at Sussex University that will be conducted via regular weekly meetings, a mailing list and a blog.
It is designed to foster collaboration between the mathematical, physical and life sciences and artificial life, primarily with application to evolutionary theory and ecology.
NAME can stand for "New Approaches to Modelling Ecosystems" or "New Approaches to Modelling Evolution".
We envisage discussions that will span the fields of ecology, evolutionary theory, artificial life, biology, mathematics, physics and computational modelling. We believe these domains are ripe for cross-fertilization. We are particularly interested in models that include feedback between populations and their environment. Proposed topics include:
* niche construction
* ecosystem thermodynamics
* levels of selection
* homeostatic models
* network approaches
* information theory in evolution
We will meet on a regular (weekly) basis with a program of invited speakers presenting research or leading discussions. We hope to pursue both abstract models and real world issues.
Please contact us if you have an interest in joining our group; we will add you to the mailing list.
James Dyke & Nathaniel Virgo
j.g.dyke@sussex.ac.uk
nathanielvirgo@gmail.com
It is designed to foster collaboration between the mathematical, physical and life sciences and artificial life, primarily with application to evolutionary theory and ecology.
NAME can stand for "New Approaches to Modelling Ecosystems" or "New Approaches to Modelling Evolution".
We envisage discussions that will span the fields of ecology, evolutionary theory, artificial life, biology, mathematics, physics and computational modelling. We believe these domains are ripe for cross-fertilization. We are particularly interested in models that include feedback between populations and their environment. Proposed topics include:
* niche construction
* ecosystem thermodynamics
* levels of selection
* homeostatic models
* network approaches
* information theory in evolution
We will meet on a regular (weekly) basis with a program of invited speakers presenting research or leading discussions. We hope to pursue both abstract models and real world issues.
Please contact us if you have an interest in joining our group; we will add you to the mailing list.
James Dyke & Nathaniel Virgo
j.g.dyke@sussex.ac.uk
nathanielvirgo@gmail.com
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