Avida (software)

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.{{citation needed|date=February 2012}}

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.

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.{{cite journal|last1=Lenski|first1=R. E.|last2=Ofria|first2=C.|last3=Pennock|first3=R. T.|last4=Adami|first4=C.|date=2003|author1-link=Richard Lenski|author2-link=Charles Ofria|author3-link=Robert T. Pennock|author4-link=Chris Adami|title=The evolutionary origin of complex features|journal=Nature|volume=423|pages=139–144|url=http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf|doi=10.1038/nature01568|pmid=12736677|issue=6936|bibcode=2003Natur.423..139L|s2cid=4401833|access-date=2012-01-30|archive-date=2021-01-21|archive-url=https://web.archive.org/web/20210121232710/http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf|url-status=dead}}

{{Infobox software

| name = Avida-ED

| author = Jeff Clune

| developer = Diane J. Blackwood

| latest release version = 3

| latest release date = {{start date and age|2021|10|10}}{{cite web

| url = https://github.com/DBlackwood/AvidaED_user_interface

| title = Avida-ED User Interface

| website = github.com

| access-date = 2021-10-11

}}

| programming language = C++, JavaScript

| genre = Artificial life

| license = GPL

| website = Main: {{url|avida-ed.msu.edu}}, Mirror: {{url|avida-ed-mirror1.beacon-center.org}}

}}

The Avida-ED project ([https://avida-ed.msu.edu/app/AvidaED.html 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, [https://avida-ed.msu.edu/curriculum/ lesson plans], and other course materials.{{cite journal|last1=Smith|first1=James J.|last2=Johnson|first2=Wendy R.|last3=Lark|first3=Amy M.|last4=Mead|first4=Louise S.|last5=Wiser|first5=Michael J.|last6=Pennock|first6=Robert T.|title=An Avida-ED digital evolution curriculum for undergraduate biology|journal=Evolution: Education and Outreach|volume=9|issue=1|year=2016|issn=1936-6426|doi=10.1186/s12052-016-0060-0|doi-access=free}}{{Cite web

| title = Online tool speeds up evolution education

| author = Anonymous

| work = ScienceDaily

| date = 5 February 2018

| access-date = 3 July 2021

| url = https://www.sciencedaily.com/releases/2018/02/180205113043.htm

| quote =

}} 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.{{cite journal|last1=Taylor|first1=Tim|last2=Auerbach|first2=Joshua E.|last3=Bongard|first3=Josh|last4=Clune|first4=Jeff|last5=Hickinbotham|first5=Simon|last6=Ofria|first6=Charles|last7=Oka|first7=Mizuki|last8=Risi|first8=Sebastian|last9=Stanley|first9=Kenneth O.|last10=Yosinski|first10=Jason|title=WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web|journal=Artificial Life|volume=22|issue=3|year=2016|pages=364–407|issn=1064-5462|doi=10.1162/ARTL_a_00211|pmid=27472416 |hdl=2241/00154082|s2cid=12092129 |url=https://tsukuba.repo.nii.ac.jp/record/48596/files/AL_22-3.pdf |hdl-access=free}} This approach has been shown to be effective in improving students' understanding of evolution.{{cite journal|last1=Pennock|first1=Robert T.|last2=Smith|first2=James J.|last3=Mead|first3=Louise S.|last4=Richmond|first4=Gail|last5=Lark|first5=Amy|title=Exploring the Relationship between Experiences with Digital Evolution and Students' Scientific Understanding and Acceptance of Evolution|journal=The American Biology Teacher|volume=80|issue=2|year=2018|pages=74–86|issn=0002-7685|doi=10.1525/abt.2018.80.2.74|s2cid=52260399 }}{{cite journal|last1=Abi Abdallah|first1=Delbert S.|last2=Fonner|first2=Christopher W.|last3=Lax|first3=Neil C.|last4=Babeji|first4=Matthew R.|last5=Palé|first5=Fatimata A.|title=Evaluating the Use of Avida-ED Digital Organisms to Teach Evolution & Natural Selection|journal=The American Biology Teacher|volume=82|issue=2|year=2020|pages=114–119|issn=0002-7685|doi=10.1525/abt.2020.82.2.114|doi-access=free}}{{cite journal|last1=Pennock|first1=Robert T.|last2=Richmond|first2=Gail|last3=Lark|first3=Amy|title=Modeling Evolution in the Classroom|journal=The American Biology Teacher|volume=76|issue=7|year=2014|pages=450–454|issn=0002-7685|doi=10.1525/abt.2014.76.7.6|s2cid=83720929 }}

The Avida-ED project was the winner of the 2017 International Society for Artificial Life Education and Outreach Award.{{Cite web

| title = 2017 ISAL Awards: Winners - Artificial Life

| last = Taylor | first = Tim

| work = Artificial Life

| date = 16 September 2017

| access-date = 3 July 2021

| url = https://alife.org/2017-isal-awards-winners/

| quote =

}}

• [http://carlzimmer.com/articles/2005.php?subaction=showfull&id=1177184710&ucat=8 "Testing Darwin"], Discover Magazine, February 2005.

{{reflist}}

• [https://github.com/devosoft/avida Avida Software - GitHub]
• [http://avida-ed.msu.edu Avida-ED Project - Robert T. Pennock]
• [https://web.archive.org/web/20071101065234/http://www.programerror.com/software/avida/ An Avida Developer's Site]
• [https://devolab.org/?s=AVida MSU Devolab website]

• 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. [https://www.msu.edu/~jclune/webfiles/publications/Clune-2011-InclusiveFitness-Proc.Royal.Society.pdf pdf] ([https://web.archive.org/web/20111207001544/https://www.msu.edu/~jclune/webfiles/publications/Clune-2011-InclusiveFitness-Proc.Royal.Society.pdf archive])
• Benjamin E. Beckmann, Philip K. McKinley, Charles Ofria (2007). Evolution of an adaptive sleep response in digital organisms. ECAL 2007 [https://web.archive.org/web/20100213012528/http://www.cse.msu.edu/notables/images/ecal-2007-sleep.pdf pdf]

Category:Artificial life

Category:Artificial life models

Category:Digital organisms