Artis


The Group The name "Artis" comes from "Natura Artis Magistra", the name of the Zoological Society founded in 1838 which opened the Artis Zoo in the centre of Amsterdam.

This project began as course work for the Master of Science degree in Computational Science at the Universiteit van Amsterdam, and continued to become two M.Sc. projects as well as a major research initiative.  The group is made up of current MSc student (UvA) Antony Antony, former MSc student (UvA), researcher (UEC) and current Ph.D. student (U. of Tokyo) Chris Salzberg, and Prof./Dr. Hiroki Sayama (Binghamton University).
The Project This project is comprised of two main themes:
  1. Investigations of self-replication and "bottom-up" evolution in cellular automata using the evoloop model. [2,3,4,5,6,7,8,9,10,11] More details on this project are available here.
  2. A new approach for visualization of evolutionary dynamics based on a graph-based conception of genealogy (using the evoloop as test case). [1,6,8,9,10,12]


There is considerable overlap between these two themes, evidenced in [6,8,9,10]. Within the first theme, the relationship between environmental conditions (in particular, hostile ones) and complexity-increase of embedded self-replicators was investigated in [3]. Modified rule-sets that realize self-protection were implemented in [7,11].

For a general overview of embedded models of self-replication and evolution, see [4].
News
  • Pre-prints for most papers in the Publications section are now available to download.
  • Growth patterns generated by replicating loop populations in open space (discussed in [2,3,4,5,6]) can be found here.
  • This page is currently being revised after 2 years of neglect... publications are now up to date.
  • We gave a presentation at the ACRI conference in Amsterdam, the Netherlands on Oct. 25, 2004 (ref. [4]). [PPT]
  • A demo version of the Evoloop simulator / analyzer is available for download from the Evoloop page as supplementary information for our recent presentation at ALIFE IX.
  • We gave a presentation at the recent ALIFE IX conference in Boston, USA, on Sept. 15, 2004. See the publications section (ref. [5]) for details. [PPT]
  • Chris received his Master of Science degree at the University of Amsterdam on August 29th, 2003. [PPT]
  • We gave a talk at the NVTB Conference (Netherlands Conference on Theoretical Biology) abstract is here, powerpoint presentation is here.
  • New results from a 6k x 6k grid here.
  • We gave a presentation of current results at the SCS meeting Friday, Jan. 17, 2003 (abstract). [PPT]
Publications [1] Chris Salzberg, Antony Antony and Hiroki Sayama, Visualizing Evolutionary Dynamics of Self-Replicators: A Graph-based Approach, Artificial Life 12(2):275-288, 2006. [PDF]

[2] Chris Salzberg and Hiroki Sayama, Complex genetic evolution of artificial self-replicators in cellular automata, Complexity 10(2):33-39, 2004. [PDF]

[3] Chris Salzberg, Antony Antony and Hiroki Sayama, Evolutionary dynamics of cellular automata-based self-replicators in hostile environments, BioSystems 78: 119-134, 2004. [PDF]

[4] Chris Salzberg and Hiroki Sayama, Heredity, complexity and surprise: Embedded self-replication and evolution in CA, Cellular Automata: Proceedings of the Sixth International Conference on Cellular Automata for Research and Industry (ACRI 2004), P.M.A. Sloot, B. Chopard, and A.G. Hoekstra, eds., 161-171, Amsterdam, The Netherlands, 2004, Springer-Verlag. [PDF]

[5] Chris Salzberg, Antony Antony and Hiroki Sayama, Complex genetic evolution of self-replicating loops, Artificial Life IX: Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems, J. Pollack, M. Bedau, P. Husbands, T. Ikegami, and R. A. Watson, eds., 262-267, Boston, MA, 2004, MIT Press. [PDF]

[6] Chris Salzberg, Antony Antony, and Hiroki Sayama, Complex genetic evolution of self-replicating loops in cellular automata, Proceedings of the Sixth Annual Meeting of the Society of Evolutionary Studies, Japan, 26 (for workshop session, in Japanese) / 119 (for poster presentation, in English), Tokyo, Japan, 2004.

[7] Hiroki Sayama, Self-protection and diversity in self-replicating cellular automata, Artificial Life 10:83-98, 2004. [PDF]

[8] Chris Salzberg, Antony Antony and Hiroki Sayama, Genetic diversification and complex genealogy of self-replicators discovered in simple cellular automata: A preliminary report, Journal of Three Dimensional Images, 17(4):103-109, 3D Forum, Japan, 2003. [PDF]

[9] Chris Salzberg, Emergent Evolutionary Dynamics of Self-Reproducing Cellular Automata, M.Sc. Thesis, Section Computational Science, Universiteit van Amsterdam, August 2003. [PDF]

[10] Chris Salzberg, Antony Antony and Hiroki Sayama, Genetic diversification and adaptation of self-replicators discovered in simple cellular automata, Proceedings of the Sixth International Conference on Humans and Computers (HC-2003), 194-199, University of Aizu, Japan, 2003.

[11] Hiroki Sayama, Self-protection maintains diversity of artificial self-replicators evolving in cellular automata, Proceedings of the 2003 NASA/DoD Conference on Evolvable Hardware (EH2003), 252-255, Chicago, Illinois, 2003, IEEE Press.

[12] Chris Salzberg, Antony Antony and Hiroki Sayama, Visualizing Evolutionary Dynamics of Self-Replicators Using Graph-based Genealogy, Proceedings of the Seventh International Conference on Artificial Life (ECAL 2003), W. Banzhaf, T. Christaller, P. Dittrich, J. T. Kim, and J. Ziegler, eds., 387-394, Dortmund, Germany, 2003, Springer-Verlag. [PDF]
Movies
screenshot
 This is the full-length QuickTime movie (50 Mb) of our main run on a 3000 by 3000 grid.  The simulation was run for 29 days on DAS II.  Species are coloured differently based on their genotype + phenotype (note some species are difficult to differentiate due to lack of colours - there are over 5000 species!).
Phenotype
 This is the same movie but with species coloured only by phenotype (130 Mb).  The colouring scheme is:

Yellow - 4 (smallest), Red - 5, Blue - 6, Light Blue - 7, Purple - 8
No identification
 This is the original data set (160 Mb), without colouring for identification.
If these movies are too big, try the following animated GIF's:
First 30K iterations
 Evolutionary Bottleneck
 Return of the Giants
Links

Last updated Mar. 28, 2006