Information Technology Reference
In-Depth Information
2
The Entities of Gene
Expression Programming
In contrast to its analogous cellular gene expression, GEP gene expression is
rather simple. The main players in gene expression programming are only
two: the chromosomes and the expression trees, the latter consisting of the
expression of the genetic information encoded in the former. The process of
information decoding (from the chromosomes to the expression trees) is called
translation. And this translation implies obviously a kind of code and a set of
rules. The genetic code is very simple: a one-to-one relationship between the
symbols of the chromosome and the functions and terminals they represent.
The rules are also quite simple: they determine the spatial organization of
the functions and terminals in the expression trees and the type of interaction
between sub-expression trees in multigenic systems.
Therefore, there are two languages in gene expression programming: the
language of the genes and the language of the expression trees, and we will
see that the sequence or structure of one of these languages is more than
sufficient to infer exactly the other. In nature, although the inference of the
sequence of proteins given the sequence of genes and vice versa is possible,
very little is known about the rules that determine the folding of the protein.
And the expression of a protein gene is not complete before the folding of
the protein, that is, strings of amino acids only become proteins when they
are correctly folded into their native three-dimensional structure. The only
thing we know for sure about protein folding is that the sequence of the
amino acids determines the folding. However, the rules that orchestrate the
folding are still unknown. Fortunately for us, in GEP, thanks to the simple
rules that determine the structure of expression trees and their interactions, it
is possible to infer immediately the phenotype (the final structure, which is
equivalent to the folded protein molecule) given the sequence of a gene, and
vice versa. This bilingual and unequivocal system is called
Karva
language.
The details of this language are explored in this chapter.
