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Intelligent Design Lab is Going Where no Evolution Simulation has Gone Before

Over the past decade or so there has been much hype about computer simulations of Darwinian evolution. The most hyped is Avida at the MSU Digital Evolution Laboratory. Avida researchers claim their work is not a simulation, but actually is Darwinian evolution in action. They describe it like this:

In Avida, a population of self-replicating computer programs is subjected to external pressures (such as mutations and limited resources) and allowed to evolve subject to natural selection. This is not a mere simulation of evolution — digital organisms in Avida evolve to survive in a complex computational environment and will adapt to perform entirely new traits in ways never expected by the researchers, some of which seem highly creative.

According to MSU’s Robert Pennock: “Avida is not a simulation of evolution; it is an instance of it.”
You can’t ignore the fact that …

… previous computer simulations of evolution, such as Avida, were carefully proscribed and tightly constrained by the environment created by its programmers. For example Avida shows how organisms can advance in an environment where they are solving problems, but problems that were set up for them to solve. The digital organisms produced there can only do so much or go so far as they are constrained by the environment the programmer has designed.

Should the Avida team be working in quarantine? Lenski argues that Avida itself acts as a quarantine, because its organisms can exist only in its computer language. “They’re living in an alien world,” Lenski says. “They may be nasty predators from Mars, but they’d drop dead here.” Life is a different environment than that programmed for Avida’s digital organisms.

Enter the new evolution computational software just released by Biologic Institute. The program, Stylus, was developed by molecular biologist Douglas Axe and software engineer Brendan Dixon, and announced last week in a peer-reviewed publication at PLos One.

Stylus however goes way beyond previous computer simulations. Axe describes it this way:

Like the structures of life, the structures of language are used to solve real problems at a high level. And the high level solutions in both worlds depend on a succession of solutions at lower levels.
In life, body plans serve the needs of particular modes of life, organs serve the needs of particular body plans, tissues serve the needs of particular organs, cells serve the needs of particular tissues, protein functions serve the needs of particular cells, protein structures serve the needs of particular protein functions, protein sequences serve the needs of particular structures, and genes serve the needs of these particular protein sequence requirements.

In a similarly hierarchical way, texts of various kinds serve the needs of particular communication objectives, sections serve the needs of particular texts, paragraphs serve the needs of particular sections, sentences serve the needs of particular paragraphs, phrases serve the needs of particular sentences, and words serve the needs of particular phrases.

What about letters serving the needs of words? Well, the problem with letter-based texts is that they are only sequences, whereas structures figure prominently in the functions of proteins. Protein sequences must form functional three-dimensional structures in order to work, whereas alphabetic sequences function directly as sequences.

But not all written languages are alphabetic. Chinese writing, in particular, employs structural characters that are analogous in some interesting ways to protein structures. Like folded proteins, these written characters perform the low level functions from which higher functions can be achieved.

Why is this important? Well, for one thing, if realism is important it shows how far Avida falls short as an “instance of evolution.” And for another thing, it is going to open new avenues of research into how much or how little organisms can evolve and whether it really is possible to go from the simplest building blocks of life to the more complex and necessary functions of life without any guiding intelligence at all.

Avida, Stylus. Stylus, Avida. Out with the old, in with the new.