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© C. FERREIRA, 2002 (Terms of Use) ISBN: 9729589054

Gene Expression Programming: Mathematical Modeling by an Artificial Intelligence

Transposable genetic elements consist of genes that can move from place to place within the genome. There are three classes of transposable elements with different structures and mechanisms of transposition. They exist both in eukaryotes and prokaryotes and cause different effects on the chromosome they move to. For instance, they can inactivate genes by interrupting the coding sequence of a gene; they can activate an adjacent gene by providing a promoter or transcriptional activator; or they can restructure a chromosome by producing homologous sequences that might afterwards be used in homologous recombination. The existence of these “jumping genes” which move from one chromosome to another without respect for boundaries, including species boundaries, greatly altered our views of evolution, as something smoothly driven by neutral mutations alone. The effects of transposition are too drastic to be apparently of any use. And so are the effects of non-homologous recombination or the effects of nonsense or frameshift mutations. Nonetheless, transposition (and non-homologous recombination) is not only fairly frequent but also widely distributed throughout the living world, and many are the marks it left behind in living organisms. Notwithstanding, most of the times the effect of transposition and some kinds of non-homologous recombination is deleterious. Very occasionally, though, some “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 a computer system like GEP. The transposable elements used in GEP are an oversimplification of those found in nature. First, in GEP, transposable elements were chosen 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 identifying 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 GEP, simple and repetitive sequences are created using transposition.

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