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“promising monsters” are formed and a completely new protein is created. In
nature, in fact, very different proteins - both in structure and functionality -
share the same construction motifs (domains) probably due to these kinds of
genetic modification.
Both the structural details and the varied mechanisms of the different classes
of transposons are of little importance in an artificial evolutionary system
such as gene expression programming. The transposable elements used in
gene expression programming are an oversimplification of those found in
nature. First, in GEP, transposable elements were designed to transpose only
within the same chromosome. Second, GEP transposable elements might be
entire genes or fragments of a gene. Third, any gene or fragment is eligible to
become a transposable element, without requirements for particular identi-
fying sequences. Fourth, the transposable element is copied in its entirety at
the target site. Finally, in gene transposition, the donor sequence is deleted in
the place of origin, whereas in fragment transposition the donor sequence
stays unchanged, usually producing two homologous sequences resident in
the same chromosome. We will see that, in gene expression programming,
simple and repetitive sequences might be created using transposition.
Gene Duplications
Gene duplication plays an important role in protein evolution. Although the
mechanism of gene duplication is unknown, occasionally a gene is copied
twice during replication. This kind of transformation is potentially harmless
and may be advantageous if the protein produced is needed in large amounts.
On the other hand, with time, the two copies of the gene might start to evolve
independently. One copy may continue to express the original protein, but
the other may evolve into an entirely different protein.
In gene expression programming, occasionally, genes are also duplicated.
Although there is no special operator for gene duplication, a gene might get
duplicated through the combined effects of gene transposition and recombi-
nation. Interestingly, chromosomes with duplicated genes are commonly found
among the best individuals of GEP populations.
1.2.3 Transcription
The expression of the genetic information into proteins does not proceed
directly from DNA. For the language of DNA to be transferred into the lan-
guage of proteins, an intermediate molecule is necessary. This molecule is a
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