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((Short description|Self-replicating computer program that mutates and evolves))
((more citations needed|date=November 2013))
((Evolutionary biology))
A '''digital organism''' is a [[Self-replication|self-replicating]] [[computer program]] that [[Mutation (genetic algorithm)|mutates]] and [[Evolutionary algorithm|evolves]].  Digital [[organism]]s are used as a tool to study the dynamics of Darwinian [[evolution]], and to test or verify specific hypotheses or [[mathematical model]]s of evolution.  The study of digital organisms is closely related to the area of [[artificial life]].

== History ==
Digital organisms can be traced back to the game [[Darwin (programming game)|Darwin]], developed in 1961 at Bell Labs, in which computer programs had to compete with each other by trying to stop others from [[Execution (computing)|executing]] .<ref>Aleph-Null, "Computer Recreations", Software: Practice and Experience, vol. 2, pp.&nbsp;93–96, 1972</ref> A similar implementation that followed this was the game [[Core War]]. In Core War, it turned out that one of the winning [[strategy|strategies]] was to replicate as fast as possible, which deprived the opponent of all [[resource (computer science)|computational resources]].  Programs in the Core War game were also able to mutate themselves and each other by overwriting instructions in the simulated "memory" in which the game took place.  This allowed competing programs to embed damaging instructions in each other that caused errors (terminating the process that read it), "enslaved processes" (making an enemy program work for you), or even change strategies mid-game and heal themselves.

[[Steen Rasmussen (physicist)|Steen Rasmussen]] at [[Los Alamos National Laboratory]] took the idea from Core War one step further in his core world system by introducing a genetic algorithm that automatically wrote programs. However, Rasmussen did not observe the evolution of complex and stable programs. It turned out that the [[programming language]] in which core world programs were written was very brittle, and more often than not mutations would completely destroy the functionality of a program.

The first to solve the issue of program brittleness was [[Thomas S. Ray]] with his [[Tierra (computer simulation)|Tierra]] system, which was similar to core world. Ray made some key changes to the programming language such that mutations were much less likely to destroy a program. With these modifications, he observed for the first time computer programs that did indeed evolve in a meaningful and complex way.

Later, [[Chris Adami]], Titus Brown, and [[Charles Ofria]] started developing their [[Avida (software)|Avida]] system,<ref>((Cite web|url=http://avida.devosoft.org/|title=Avida by devosoft|website=avida.devosoft.org))</ref> which was inspired by Tierra but again had some crucial differences. In Tierra, all programs lived in the same [[address space]] and could potentially execute or otherwise interfere with each other's code. In Avida, on the other hand, each program lives in its own address space. Because of this modification, experiments with Avida became much cleaner and easier to interpret than those with Tierra. With Avida, digital organism research has begun to be accepted as a valid contribution to evolutionary biology by a growing number of evolutionary biologists.  Evolutionary biologist [[Richard Lenski]] of [[Michigan State University]] has used Avida extensively in his work.  Lenski, Adami, and their colleagues have published in journals such as ''[[Nature (journal)|Nature]]''<ref name="LenskiOfria2003">((cite journal|last1=Lenski|first1=Richard E.|last2=Ofria|first2=Charles|last3=Pennock|first3=Robert T.|last4=Adami|first4=Christoph|title=The evolutionary origin of complex features|journal=Nature|volume=423|issue=6936|year=2003|pages=139–144|issn=0028-0836|doi=10.1038/nature01568|pmid=12736677|bibcode=2003Natur.423..139L|s2cid=4401833|url=https://authors.library.caltech.edu/56142/2/nature01568-s1.pdf))</ref> and the ''[[Proceedings of the National Academy of Sciences]]'' (USA).<ref name="AdamiOfria2000">((cite journal|last1=Adami|first1=C.|last2=Ofria|first2=C.|last3=Collier|first3=T. C.|title=Evolution of biological complexity|journal=Proceedings of the National Academy of Sciences|volume=97|issue=9|year=2000|pages=4463–4468|issn=0027-8424|arxiv=physics/0005074 | doi=10.1073/pnas.97.9.4463|pmid=10781045|pmc=18257|doi-access=free))</ref>

In 1996, Andy Pargellis created a Tierra-like system called ''Amoeba'' that evolved self-replication from a randomly seeded initial condition. More recently ''REvoSim'' - a [https://github.com/palaeoware/revosim/releases software package] based around binary digital organisms - has allowed evolutionary simulations of large populations that can be run for geological timescales.<ref name="GarwoodSpencer2019">((cite journal|last1=Garwood|first1=Russell J.|last2=Spencer|first2=Alan R. T.|last3=Sutton|first3=Mark D.|last4=Smith|first4=Andrew|title=REvoSim: Organism-level simulation of macro and microevolution|journal=Palaeontology|volume=62|issue=3|year=2019|pages=339–355|issn=0031-0239|doi=10.1111/pala.12420|doi-access=free|bibcode=2019Palgy..62..339G |hdl=10044/1/68991|hdl-access=free))</ref>

== Physical form ==
((See also|Energy being|Holography#Tactile_holograms|label 2 = Tactile holograms))

== See also ==
===Related topics and overviews===
((Portal|Evolutionary biology))
* [[Artificial life]]
* [[Evolutionary computation]]
* [[Genetic algorithm]]s
* [[Combinatorial optimization]]
* [[Cellular automaton]]

===Specific programs===
* [[List of digital organism simulators]]
* [[Evolution@Home]]
* [[Polyworld]]

== References ==
<references />

== Further reading ==
* ((cite journal | last=O'Neill | first=Bill | title=Digital Evolution | journal=PLOS Biology | publisher=Public Library of Science (PLoS) | volume=1 | issue=1 | date=2003-10-13 | issn=1545-7885 | doi=10.1371/journal.pbio.0000018 | page=e18| pmid=14551915 | pmc=212697 | doi-access=free ))
* ((cite journal | last1=Wilke | first1=Claus O. | last2=Adami | first2=Christoph | title=The biology of digital organisms | journal=Trends in Ecology & Evolution | publisher=Elsevier BV | volume=17 | issue=11 | year=2002 | doi=10.1016/s0169-5347(02)02612-5 | pages=528–532))
* ((cite journal | last=Pargellis | first=A.N. | title=The spontaneous generation of digital "Life" | journal=Physica D: Nonlinear Phenomena | publisher=Elsevier | volume=91 | issue=1–2 | year=1996 | issn=0167-2789 | doi=10.1016/0167-2789(95)00268-5 | pages=86–96| bibcode=1996PhyD...91...86P ))
* ((cite journal | last1=Misevic | first1=Dusan | last2=Ofria | first2=Charles | last3=Lenski | first3=Richard E | title=Sexual reproduction reshapes the genetic architecture of digital organisms | journal=Proceedings of the Royal Society B: Biological Sciences | publisher=The Royal Society | volume=273 | issue=1585 | date=2005-11-08 | issn=0962-8452 | doi=10.1098/rspb.2005.3338 | pages=457–464 |pmid=16615213 |pmc=1560214))

((Computer science))

[[Category:Artificial life]]
[[Category:Evolutionary biology]]
[[Category:Digital organisms| ]]
[[Category:Evolutionary computation]]

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