Digital organism
Encyclopedia
A digital organism is a self-replicating
computer program
that mutates
and 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. This is closely related to the area of artificial life
.
. In Core War, it turned out that one of the winning strategies
was to replicate as fast as possible, which had the result that the opponent was deprived of all computational resources
. Programs in the Core War game are also able to mutate themselves and each other by overwriting instructions in the simulated "memory" in which this game took place. This allowed competing programs to embed damaging instructions in each other that caused errors (terminating the process that reads it), "enslave processes" (making an enemy program work for you), or even change strategies mid-game and heal themselves.
Steen Rasmussen
at Los Alamos National Laboratory
took the idea from Core War one step further in his core world system. He introduced a genetic algorithm that would automatically write 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 Tom Ray
with his Tierra
system. Tierra was similar to core world. However, 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
system, which was inspired by Tierra but had again some crucial differences. In Tierra, all programs lived in the same address space
, and could potentially overwrite or otherwise interfere with each other. In Avida, on the other hand, each program lives in its own address space. Through 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
and the Proceedings of the National Academy of Sciences
(USA).
In 1996, Andy Pargellis created a Tierra-like system called Amoeba that evolved self-replication from a randomly seeded initial condition.
Self-replication
Self-replication is any behavior of a dynamical system that yields construction of an identical copy of that dynamical system. Biological cells, given suitable environments, reproduce by cell division. During cell division, DNA is replicated and can be transmitted to offspring during reproduction...
computer program
Computer program
A computer program is a sequence of instructions written to perform a specified task with a computer. A computer requires programs to function, typically executing the program's instructions in a central processor. The program has an executable form that the computer can use directly to execute...
that mutates
Mutation (genetic algorithm)
In genetic algorithms of computing, mutation is a genetic operator used to maintain genetic diversity from one generation of a population of algorithm chromosomes to the next...
and evolves
Evolution (disambiguation)
In biology, evolution is change in traits of a population of organisms over time . In other contexts, evolution can mean any gradual directional change.Evolution may also refer to:-Companies:...
. Digital organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
s are used as a tool to study the dynamics of Darwinian evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
, and to test or verify specific hypotheses or mathematical model
Mathematical model
A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used not only in the natural sciences and engineering disciplines A mathematical model is a...
s of evolution. This is closely related to the area of artificial life
Artificial life
Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...
.
History
Digital organisms can be traced back to the game Darwin in which computer programs had to compete with each other to stop one another from executing (Aleph-Null, "Computer Recreations", Software: Practice and Experience, vol. 2, pp. 93–96, 1972). A similar implementation that followed was the game Core WarCore War
Core War is a programming game in which two or more battle programs compete for the control of the "Memory Array Redcode Simulator" virtual computer . These battle programs are written in an abstract assembly language called Redcode...
. In Core War, it turned out that one of the winning strategies
Strategy
Strategy, a word of military origin, refers to a plan of action designed to achieve a particular goal. In military usage strategy is distinct from tactics, which are concerned with the conduct of an engagement, while strategy is concerned with how different engagements are linked...
was to replicate as fast as possible, which had the result that the opponent was deprived of all computational resources
Resource (computer science)
A resource, or system resource, is any physical or virtual component of limited availability within a computer system. Every device connected to a computer system is a resource. Every internal system component is a resource...
. Programs in the Core War game are also able to mutate themselves and each other by overwriting instructions in the simulated "memory" in which this game took place. This allowed competing programs to embed damaging instructions in each other that caused errors (terminating the process that reads it), "enslave processes" (making an enemy program work for you), or even change strategies mid-game and heal themselves.
Steen Rasmussen
Steen Rasmussen
Steen Rasmussen was born in Elsinore, Denmark, in 1955. He is an Artificial Life scientist who has published numerous reviews and reports in the Journal, Artificial Life. He coined the term, complex systems dogma, which alludes to the presupposition that simple lower-level elements can give rise to...
at Los Alamos National Laboratory
Los Alamos National Laboratory
Los Alamos National Laboratory is a United States Department of Energy national laboratory, managed and operated by Los Alamos National Security , located in Los Alamos, New Mexico...
took the idea from Core War one step further in his core world system. He introduced a genetic algorithm that would automatically write programs. However, Rasmussen did not observe the evolution of complex and stable programs. It turned out that the programming language
Programming language
A programming language is an artificial language designed to communicate instructions to a machine, particularly a computer. Programming languages can be used to create programs that control the behavior of a machine and/or to express algorithms precisely....
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 Tom Ray
Tom Ray
Thomas Archer Ray was an American animator.-Career:Ray was born in Williams, Arizona. He began work at Warner Bros. Cartoons in 1937. Over the first two decades of his career, he was a junior animator who received no screen credit until Destination Earth in 1956. In 1958, he became a master...
with his Tierra
Tierra (computer simulation)
Tierra is a computer simulation developed by ecologist Thomas S. Ray in the early 1990s in which computer programs compete for central processing unit time and access to main memory...
system. Tierra was similar to core world. However, 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
Chris Adami
Christoph Carl Herbert Adami is a professor at Michigan State University. He is best known for his work on Avida, an artificial life simulator used to study evolutionary biology. He received the NASA Exceptional Achievement Medal while serving at JPL...
, Titus Brown, and Charles Ofria
Charles Ofria
Dr. Charles A. Ofria is currently an Associate Professor in the Department of Computer Science and Engineering, the director of the Digital Evolution Lab at Michigan State University and a co-founder of the BEACON Center for the Study of Evolution in Action. Ofria's research focuses on the...
started developing their Avida
Avida
Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer programs . Avida is under active development by Charles Ofria's Digital Evolution Lab at Michigan State University and was originally designed by Ofria, Chris Adami and C. Titus...
system, which was inspired by Tierra but had again some crucial differences. In Tierra, all programs lived in the same address space
Address space
In computing, an address space defines a range of discrete addresses, each of which may correspond to a network host, peripheral device, disk sector, a memory cell or other logical or physical entity.- Overview :...
, and could potentially overwrite or otherwise interfere with each other. In Avida, on the other hand, each program lives in its own address space. Through 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
Richard Lenski
Richard E. Lenski is an American evolutionary biologist. He is the son of sociologist Gerhard Lenski. He earned his BA from Oberlin College in 1976, and his PhD from the University of North Carolina in 1982...
of Michigan State University
Michigan State University
Michigan State University is a public research university in East Lansing, Michigan, USA. Founded in 1855, it was the pioneer land-grant institution and served as a model for future land-grant colleges in the United States under the 1862 Morrill Act.MSU pioneered the studies of packaging,...
has used Avida extensively in his work. Lenski, Adami, and their colleagues have published in journals such as Nature
Nature (journal)
Nature, first published on 4 November 1869, is ranked the world's most cited interdisciplinary scientific journal by the Science Edition of the 2010 Journal Citation Reports...
and the Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
The Proceedings of the National Academy of Sciences of the United States of America, usually referred to as PNAS, is the official journal of the United States National Academy of Sciences...
(USA).
In 1996, Andy Pargellis created a Tierra-like system called Amoeba that evolved self-replication from a randomly seeded initial condition.
See also
- List of digital organism simulators
- Artificial lifeArtificial lifeArtificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...
- Evolution@HomeEvolution@HomeEvolution@Home is the first parallel computing project for evolutionary biology. The aim of Evolution@Home is to improve understanding of evolutionary processes. This is achieved by simulating individual-based models. The first such model targets the accumulation of mutations in asexual populations...
- Genetic algorithmGenetic algorithmA genetic algorithm is a search heuristic that mimics the process of natural evolution. This heuristic is routinely used to generate useful solutions to optimization and search problems...
s - Combinatorial optimizationCombinatorial optimizationIn applied mathematics and theoretical computer science, combinatorial optimization is a topic that consists of finding an optimal object from a finite set of objects. In many such problems, exhaustive search is not feasible...
- Cellular automatonCellular automatonA cellular automaton is a discrete model studied in computability theory, mathematics, physics, complexity science, theoretical biology and microstructure modeling. It consists of a regular grid of cells, each in one of a finite number of states, such as "On" and "Off"...
Further reading
- O'Neill, B. (2003). Digital Evolution. PLoS Biology 1, 011-014.
- Wilke, C.O. & Adami, C. (2002). The biology of digital organisms. Trends in Ecology and Evolution 17, 528-532.
- Pargellis, A.N. (1996). The spontaneous generation of digital "Life". Physica D 91 86-96
- Misevic, Dusan & Ofria, Charles & Lenski, Richard E. Sexual reproduction reshapes the genetic architecture of digital organisms Proc Biol Sci. 2006 February 22; 273(1585): 457–464.