Avida

Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer programs (digital organisms). Avida is under active development by Charles Ofria's Digital Evolution Lab at Michigan State University; the first version of Avida was designed in 1993 by Ofria, Chris Adami and C. Titus Brown at Caltech, and has been fully reengineered by Ofria on multiple occasions since then. The software was originally inspired by the Tierra system.

Original author(s)Charles Ofria, Chris Adami
Developer(s)Charles Ofria
Stable release
2.14.0 / February 6, 2014 (2014-02-06)[1]
Written inC++, Objective-C
Operating systemMicrosoft Windows 7 or later, macOS 10.8 or later, Linux / Unix.
TypeArtificial life
LicenseLGPL

Design principles

Tierra simulated an evolutionary system by introducing computer programs that competed for computer resources, specifically processor (CPU) time and access to main memory. In this respect it was similar to Core Wars, but differed in that the programs being run in the simulation were able to modify themselves, and thereby evolve. Tierra's programs were artificial life organisms.

Unlike Tierra, Avida assigns every digital organism its own protected region of memory, and executes it with a separate virtual CPU. By default, other digital organisms cannot access this memory space, neither for reading nor for writing, and cannot execute code that is not in their own memory space.

A second major difference is that the virtual CPUs of different organisms can run at different speeds, such that one organism executes, for example, twice as many instructions in the same time interval as another organism. The speed at which a virtual CPU runs is determined by a number of factors, but most importantly, by the tasks that the organism performs: logical computations that the organisms can carry out to reap extra CPU speed as bonus.

Use in research

Adami and Ofria, in collaboration with others, have used Avida to conduct research in digital evolution, and the scientific journals Nature and Science have published four of their papers.

The 2003 paper "The Evolutionary Origin of Complex Features" describes the evolution of a mathematical equals operation from simpler bitwise operations.[2]

Use in education
Avida-ED
Original author(s)Jeff Clune
Developer(s)Diane J. Blackwood
Stable release
3 / October 10, 2021 (2021-10-10)[3]
Written inC++, JavaScript
TypeArtificial life
LicenseGPL
WebsiteMain: avida-ed.msu.edu, Mirror: avida-ed-mirror1.beacon-center.org

The Avida-ED project (Avida-ED) uses the Avida software platform within a simplified graphical user interface suitable for use in evolution education instruction at the high school and undergraduate college level, and provides freely available software, documentation, tutorials, lesson plans, and other course materials.[4][5] The Avida-ED software runs as a web application in the browser, with the user interface implemented in JavaScript and Avida compiled to JavaScript using Emscripten, making the software broadly compatible with devices commonly used in classrooms.[6] This approach has been shown to be effective in improving students' understanding of evolution.[7][8][9] The Avida-ED project was the winner of the 2017 International Society for Artificial Life Education and Outreach Award.[10]

See also

References
  1. "Avida Digital Life Platform download". sourceforge.net. Retrieved 2021-03-27.
  2. Lenski, R. E.; Ofria, C.; Pennock, R. T.; Adami, C. (2003). "The evolutionary origin of complex features" (PDF). Nature. 423 (6936): 139–144. Bibcode:2003Natur.423..139L. doi:10.1038/nature01568. PMID 12736677. S2CID 4401833. Archived from the original (PDF) on 2021-01-21. Retrieved 2012-01-30.
  3. "Avida-ED User Interface". github.com. Retrieved 2021-10-11.
  4. Smith, James J.; Johnson, Wendy R.; Lark, Amy M.; Mead, Louise S.; Wiser, Michael J.; Pennock, Robert T. (2016). "An Avida-ED digital evolution curriculum for undergraduate biology". Evolution: Education and Outreach. 9 (1). doi:10.1186/s12052-016-0060-0. ISSN 1936-6426.
  5. Anonymous (5 February 2018). "Online tool speeds up evolution education". ScienceDaily. Retrieved 3 July 2021.
  6. Taylor, Tim; Auerbach, Joshua E.; Bongard, Josh; Clune, Jeff; Hickinbotham, Simon; Ofria, Charles; Oka, Mizuki; Risi, Sebastian; Stanley, Kenneth O.; Yosinski, Jason (2016). "WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web". Artificial Life. 22 (3): 364–407. doi:10.1162/ARTL_a_00211. hdl:2241/00154082. ISSN 1064-5462.
  7. Pennock, Robert T.; Smith, James J.; Mead, Louise S.; Richmond, Gail; Lark, Amy (2018). "Exploring the Relationship between Experiences with Digital Evolution and Students' Scientific Understanding and Acceptance of Evolution". The American Biology Teacher. 80 (2): 74–86. doi:10.1525/abt.2018.80.2.74. ISSN 0002-7685.
  8. Abi Abdallah, Delbert S.; Fonner, Christopher W.; Lax, Neil C.; Babeji, Matthew R.; Palé, Fatimata A. (2020). "Evaluating the Use of Avida-ED Digital Organisms to Teach Evolution & Natural Selection". The American Biology Teacher. 82 (2): 114–119. doi:10.1525/abt.2020.82.2.114. ISSN 0002-7685.
  9. Pennock, Robert T.; Richmond, Gail; Lark, Amy (2014). "Modeling Evolution in the Classroom". The American Biology Teacher. 76 (7): 450–454. doi:10.1525/abt.2014.76.7.6. ISSN 0002-7685.
  10. Taylor, Tim (16 September 2017). "2017 ISAL Awards: Winners - Artificial Life". Artificial Life. Retrieved 3 July 2021.

Scientific publications featuring Avida
  • C. Adami and C.T. Brown (1994), Evolutionary Learning in the 2D Artificial Life Systems Avida, in: R. Brooks, P. Maes (Eds.), Proc. Artificial Life IV, MIT Press, Cambridge, MA, p. 377-381. arXiv:adap-org/9405003
  • R. E. Lenski, C. Ofria, T. C. Collier, C. Adami (1999). Genome Complexity, Robustness, and Genetic Interactions in Digital Organisms. Nature 400:661-664.
  • C.O. Wilke, J.L. Wang, C. Ofria, R.E. Lenski, and C. Adami (2001). Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest. Nature 412:331-333.
  • R.E. Lenski, C. Ofria, R.T. Pennock, and C. Adami (2003). The Evolutionary Origin of Complex Features. Nature 423:139-145.
  • S.S. Chow, C.O. Wilke, C. Ofria, R.E. Lenski, and C. Adami (2004). Adaptive Radiation from Resource Competition in Digital Organisms. Science 305:84-86.
  • J. Clune, D. Misevic, C. Ofria, R.E. Lenski, S.F. Elena, and R. Sanjuán. Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Computational Biology 4(9): 2008. doi:10.1371/journal.pcbi.1000187
  • Clune J, Goldsby HJ, Ofria C, and Pennock RT (2011) Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proceedings of the Royal Society. pdf (archive)
  • Benjamin E. Beckmann, Philip K. McKinley, Charles Ofria (2007). Evolution of an adaptive sleep response in digital organisms. ECAL 2007 pdf
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