Evolutionary Algorithms - Self-Adaptive Heuristics for Evolutionary Computation - page 11

2.1.4 A Short Excursus to Molecular Biology and Genetics

Carrier of the genetic information of organisms is the DNA, deoxyribonucleic
acid [156]. Nucleic acids are linear unbranched polymers, i.e. chain molecules, of
nucleotides. Nucleotides are divided into purines (adenine - A, guanine - G) and
pyrimidines (thymine - T, cytosine - C). The DNA is organized into a double helix
structure. Complementary nucleotides (bases) are pitted against each other: A
and T, as well as G and C. The next level of structure are the codons. A sequence
of three nucleotides is a codon, also called triplet. Because a codon consists of
three bases, 4 3 = 64 different codons exist. With three exceptions all codons
code one of 20 amino acids. The synonyms code identical amino acids. The DNA
macro molecules are wrapped around large protein molecules, the histones. Such
a structure is called nucleosome, the histone molecule is the nucleosome core.
The chain of nucleosomes is called chromatin. The rewind of the DNA results
in a compression of 1:7. A further compression into chromatin chains achieves a
space reduction by 10 − 4 . The human genome is about 3 billion base pairs long,
arranged in 23 pairs of homologous chromosomes. All base pairs would have an
overall length of 2 . 6 m, but are compressed in the core to size of 200 μm .
Now, what is a gene? In fact, the definition has not satisfactorily been given
until now. The most popular definition is: A gene as a DNA sequence that codes
for a particular protein. But several thousands of genes have been found that
do not code for proteins, but seem to have other tasks. A recent estimation of
the number of human genes is 20488 [107]. The transformation from genotype
to phenotype is called gene expression. In the first phase, the transcription, the
DNA is translated into the RNA. In the second phase, the translation, the RNA
synthesizes proteins. Proteins are polypeptide chains consisting of 20 types of
amino acids. Amino acids consist of a carboxyl and an amino group and differ
in their rest group that may also be aromatic, i.e. contain the famous hexagonal
benzene molecule. The peptide bound of the long polypeptide chains happens
between the amino and the carboxyl group of the neighbored molecule. Proteins
are the basis modules of all cells. They build characteristic three dimensional
structures, e.g. the alpha helix molecule.

2.1.5 Concepts of the Evolutionary Computation Framework

The essential idea of EC is the randomized exploration of the search space with
a population of candidate solutions, which are improved during each iteration
of the algorithm. These iterations are called generations in terms of EC. The
improvement of the candidate solutions is achieved in two steps. In the first
step, the existing solutions are diversified with random variation. In the second
step, the best solutions are selected and provide a direction for the search. There
exist various kinds of genetic operators which are designed for the various types
of representations, as well as search space features. In chapters 4 and 6 the
most important types of genetic variation operators, mutation and crossover,
are presented. The EC methods are supposed to find solutions which satisfy
certain quality criteria.