Santa Fe Institute Events Wiki - User contributions [en]

CSSS 2008 Beijing-Photos

2008-07-25T07:56:53Z

Altenber: /* Photos */

== Photos ==
[[Image:Afterduck.jpg]]
[[Image:LookingUp.jpg]]
[[Image:Gw1.jpg]]

2007-07-16T16:18:44Z

Altenber: /* Additional Reading */

Lee Altenberg

2007-07-15T14:35:51Z

Altenber:

My research focus is the dynamics of evolutionary systems, which now include not only organic evolution, but evolutionary computation. I am interested in the mathematical analysis of systems that evolve under selection and genetic operators, and in higher order phenomena that can emerge, such as robustness, evolvability, modularity, and genetic systems.

I will be staying on an additional week at the CSSS after my lectures, and will be available to advise students on their CSSS projects.

Other areas I have pursued outside of research include Hawaiian conservation (I am the Chair of the Native Hawaiian Plant Society, Maui), Swing, Salsa, and Tango dance (note: by 7/14 there is already some dance self-organization going on among CSSS participants! Join the annealing).

For more information on me, please visit [http://dynamics.org/Altenberg/ my home page].

CSSS 2007 Beijing-Readings-Week-Two

2007-07-10T08:22:53Z

Altenber: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional Reading===
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.

*Altenberg, L. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.

*Erik van Nimwegen, James P. Crutchfield, and Martijn Huynen [http://www.santafe.edu/~evca/Papers/nemr.pdf Neutral Evolution of Mutational Robustness.] Proceedings of the National Academy of Science U.S.A. 96:9716-9720 (1999).

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

*Erik van Nimwegen and James P. Crutchfield. [http://www.santafe.edu/~evca/Papers/med.pdf Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?] Bulletin of Mathematical Biology 62:5:799-848 (Sep 2000)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
===Additional Reading===

==Dan Hruschka==

===Lecture Notes===
===Additional Reading===

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-10T08:17:07Z

Altenber: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation]
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics]
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena]

===Additional Reading===
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.

*Altenberg, L. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.

*Erik van Nimwegen, James P. Crutchfield, and Martijn Huynen [http://www.santafe.edu/~evca/Papers/nemr.pdf Neutral Evolution of Mutational Robustness.] Proceedings of the National Academy of Science U.S.A. 96:9716-9720 (1999).

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

*Erik van Nimwegen and James P. Crutchfield. [http://www.santafe.edu/~evca/Papers/med.pdf Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?] Bulletin of Mathematical Biology 62:5:799-848 (Sep 2000)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
===Additional Reading===

==Dan Hruschka==

===Lecture Notes===
===Additional Reading===

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

2006-07-09T22:52:17Z

Altenber: /* Readings Associated with Particular Lecturers */

{{CSSS 2006 Beijing}}

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. These readings are ''not'' required. I will be updating this list fairly frequently. --[[User:Dpf|Dpf]] 19:15, 26 June 2006 (MDT)

=== General Background ===

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|What Lies between Order and Chaos?]], in ''Art and Complexity'', J. Casti, editor, Oxford University Press (2002). An interesting, non-technical essay discussing how new patterns are discovered, and how complexity arises from the interplay between order and chaos. This is an excellent introduction to the notions of complexity and emergence, and history of one strand of the study of complex systems.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|Methods and Techniques of Complex Systems Science: An Overview]]. Chapter 1 (pp. 33--114) in Thomas S. Deisboeck and J. Yasha Kresh (eds.), ''Complex Systems Science in Biomedicine'' (New York: Springer, 2006.) This is an excellent, thorough review of the "field" -- to the extent that there is such a thing -- of complex systems. Covers many tools: statistical learning and model selection; time series analysis; cellular automata; agent-based models; the evaluation of complex-systems models; information theory; and ways of measuring complexity. Contains over 250 references. Also available [http://arxiv.org/abs/nlin.AO/0307015 here].

----

=== Readings Associated with Particular Lecturers ===

Lecturers are listed in order of appearance.

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 2 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Guila_Naquitz_A.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]] [[Media:chaos.1.4.pdf|Part I]] [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]]
* Lecture 3: Computation Theory.

'''Cosma Shalizi'''

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

CSSS 2006 Beijing-Readings

2006-07-09T22:18:26Z

Altenber: /* General Background */

CSSS 2006 Beijing-Readings

2006-07-09T22:17:44Z

Altenber: /* General Background */

{{CSSS 2006 Beijing}}

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. These readings are ''not'' required. I will be updating this list fairly frequently. --[[User:Dpf|Dpf]] 19:15, 26 June 2006 (MDT)

=== General Background ===

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|What Lies between Order and Chaos?]], in ''Art and Complexity'', J. Casti, editor, Oxford University Press (2002). An interesting, non-technical essay discussing how new patterns are discovered, and how complexity arises from the interplay between order and chaos. This is an excellent introduction to the notions of complexity and emergence, and history of one strand of the study of complex systems.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|Methods and Techniques of Complex Systems Science: An Overview]]. Chapter 1 (pp. 33--114) in Thomas S. Deisboeck and J. Yasha Kresh (eds.), ''Complex Systems Science in Biomedicine'' (New York: Springer, 2006.) This is an excellent, thorough review of the "field" -- to the extent that there is such a thing -- of complex systems. Covers many tools: statistical learning and model selection; time series analysis; cellular automata; agent-based models; the evaluation of complex-systems models; information theory; and ways of measuring complexity. Contains over 250 references. Also available [http://arxiv.org/abs/nlin.AO/0307015 here].

[http://dynamics.org/Altenberg/ Lee Altenberg], [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework to evolutionary optimization and its unsolved problems. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

----

=== Readings Associated with Particular Lecturers ===

Lecturers are listed in order of appearance.

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 2 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Guila_Naquitz_A.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]] [[Media:chaos.1.4.pdf|Part I]] [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]]
* Lecture 3: Computation Theory.

'''Cosma Shalizi'''

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.