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Now You Can Try Stylus, a Computer Model for Protein Evolution, for Yourself

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We have written before about an elegant computer model for protein evolution called Stylus, for example here and here. The model draws on an amazing insight of Douglas Axe, author of the newly released book Undeniable: How Biology Confirms Our Intuition That Life Is Designed, concerning the parallels between written language and protein coding and function.

undeniable-cover.pngMany people have made the analogy between DNA’s linear coded information that specifies proteins and written human language. But proteins have a sequence to three-dimensional structure to function relationship, while most languages have only a sequence to function relationship. The analogy is incomplete, because most human languages have no real three-dimensional structure to them.

So here is Axe’s insight. Perhaps you see it already. There is a human written language with a shape to it — Chinese Han characters. Han characters preserve the structure to function relationship — in Han written language the characters have a two-dimensional structure. If each stroke is drawn on a separate plane, the characters become three-dimensional. Thus, if a linear sequence could be devised to specify how the Han characters are drawn, that linear sequence would be analogous to the linear sequence of DNA that specifies a protein’s shape. The DNA sequence specifies what protein sequence is made and thus what its structure is; similarly the Han code would specify the Han structure. Axe and colleagues wrote a code for drawing Han characters that functions in an exactly parallel way to how the DNA code specifies protein structures. The functionality of the Han character is measured by how well the drawn character matches an ideal archetype of that Han character.

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This is a brilliant system that takes a language-based linear code (the sequence) and translates it into a three-dimensional shape (the structure), resulting in a measure of similarity to the archetype (its function), just as DNA code (the sequence) translates into a three-dimensional shape (the structure), resulting in a particular function.

What use is this? It sets up a system where, using different Han characters as starting points, all kinds of evolutionary scenarios can be tested to see if random mutations of different kinds can produce Han structures that match real Han characters. It’s an elegant way to test the power of Darwinian evolution to create or optimize function.

Douglas Axe and Winston Ewert have just published a paper announcing the debut of a website where Stylus can be downloaded and installed on any laptop, so that experiments can be run by anyone. It’s intended for schools, for private individuals, and even scientists to play around with. The paper describes its use. It also provides links to the website and the first Stylus papers, so anyone can see just how elegant and analogous this computer model really is to protein evolution. For verisimilitude it beats Avida hands down.

Photo: Hong Kong street sign, by Tsength [CC BY 3.0], via Wikimedia Commons.

Ann Gauger

Senior Fellow, Center for Science and Culture
Dr. Ann Gauger is Director of Science Communication and a Senior Fellow at the Discovery Institute Center for Science and Culture, and Senior Research Scientist at the Biologic Institute in Seattle, Washington. She received her Bachelor's degree from MIT and her Ph.D. from the University of Washington Department of Zoology. She held a postdoctoral fellowship at Harvard University, where her work was on the molecular motor kinesin.

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