Avida (software)

Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer programs (digital organisms). Avida was originally developed by Chris Adami, Titus Brown, and Charles Ofria, and was inspired by and inherits several of its properties from the Tierra system.

Design principles

The main difference between Avida and Tierra is that in Avida, every digital organism (that is, self-replicating computer program) lives in its own protected region of memory, and is executed by its own 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 than 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: Tasks are logical computations that the organisms can carry out to reap extra CPU speed as bonus.

Use in research, and its criticism

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 several of their papers. Most controversially, it has been used in an attempt to demonstrate that Darwinian evolution can produce complexity. Nature' published "The Evolutionary Origin of Complex Features" in 2003, in which the evolution of a mathematical equals operation is constructed of at least 19 simpler, precisely ordered logical operations. Several news organizations followed with articles with dramatic headlines such as "Cyber-life obeys Darwinian theory”; philosopher Robert T. Pennock stated, "All the core parts of the Darwinian process are there. These things replicate, they mutate, and are competing with one another. The very process of natural selection is happening there."[1] Critics—particularly creationists and proponents of intelligent design—have argued that the claims were overwrought and misleading because, in the testing performed, the digital organisms were rewarded for their evolution toward a pre-specified goal; they claim that this is not a proper example of natural selection. However, natural selection in reality favours organisms better suited to an ecological niche, and is thus, in a sense, goal orientated as well.

An additional claim of the researchers has been that their research has demonstrated the evolution of irreducible complexity. Since the equals operator uses numerous simple routines, all of which are needed, Chris Adami has said, "What we show is that there are irreducibly complex things and they can evolve."[2] Proponents of intelligent design have claimed that since only functions which are capable of being constructed of simpler functions (such as the equals operator) were selected as targets, the research begs the question. They have also developed an analogous program that involves encrypted text, which is intended to make more clearly evident what they argue is a fallacious conclusion.

Further, the objection to the real evolution of irreducible complexity made by proponents of Intelligent Design is ultimately based on its improbability. The irreducible complexity expressed by the equals operator in Avida is improbable, but not so improbable as to be beyond the search capability of Avida as it generates millions of virtual organisms, and more probable than the universal probability bound. It has not been demonstrated that real irreducibly complex biochemical systems (such as the bacterial flagellum, the blood clotting cascade) are sufficiently probable for it to be reasonable to assume that they could arise by chance.

Other ALife platforms

Other Digital Organism Simulators

References

"Testing Darwin", Discover Magazine, February 2005.
"Computer Speeds Up Evolution, Produces Complexity"
"Vignere Encoded Text Evolution" from ISCID
"More about Avida", Exiled from GROGGS, October 2005

External links

Scientific publications featuring Avida

R.E. Lenski, C. Ofria, T. C. Collier, C. Adami (1999). Genomic Complexity, Robustness, and Genetic Interactions in Digital Organisms. Nature 400:661-664. abstract of this article
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 Survial 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 Organims. Science 305:84-86.