The explosion of diversity in the Cambrian occurred in the lineage of the eukaryotes; the prokaryotes did not participate. One of the most striking genetic differences between eukaryotes and prokaryotes is that most of the genome of prokaryotes is translated into proteins, while most of the genome of eukaryotes is not. It has been estimated that typically 98% of the DNA in eukaryotes is neither translated into proteins nor involved in gene regulation, that it is simply ``junk'' DNA [93]. It has been suggested that much of this junk code is the result of the self-replication of pieces of DNA within rather than between cells [21,67].
Mobile genetic elements, transposons, have this intra-genome self-replicating property. It has been estimated that 80% of spontaneous mutations are caused by transposons [12,30]. Repeated sequences, resulting from the activity of mobile elements, range from dozens to millions in numbers of copies, and from hundreds to tens of thousands of base pairs in length. They vary widely in dispersion patterns from clumped to sparse [41].
Larger transposons carry one or more genes in addition to those necessary for transposition. Transposons may grow to include more genes; one mechanism involves the placement of two transposons into close proximity so that they act as a single large transposon incorporating the intervening code. In many cases transposons carry a sequence that acts as a promoter, altering the regulation of genes at the site of insertion [90].
Transposons may produce gene products and often are involved in gene regulation [17]. However, they may have no effect on the external phenotype of the individual [21]. Therefore they evolve through another paradigm of selection, one that does not involve an external phenotype. They are seen as a mechanism for the selfish spread of DNA which may become inactive junk after mutation [67].
DNA of transposon origin can be recognized by their palindrome endings flanked by short non-reversed repeated sequences resulting from insertion after staggered cuts. In Drosophila melanogaster approximately 5 to 10 percent of its total DNA is composed of sequences bearing these signs. There are many families of such repeated elements, each family possessing a distinctive nucleotide sequence, and distributed in many sites throughout the genome. One well known repeated sequence occurring in humans is found to have as many as a half million copies in each haploid genome [87].
Elaborate mechanisms have evolved to edit out junk sequences inserted into critical regions. An indication of the magnitude of the task comes from the recent cloning of the gene for cystic fibrosis, where it was discovered that the gene consists of 250,000 base pairs, only 4,440 of which code for protein, the remainder are edited out of the messenger RNA before translation [46,56,80,79].
It appears that many repeated sequences in genomes may have originated as transposons favored by selection at the level of the gene, favoring genes which selfishly replicated themselves within the genome. However, some transposons may have coevolved with their host genome as a result of selection at the organismal or populational level, favoring transposons which introduce useful variation through gene rearrangement. It has been stated that: ``transposable elements can induce mutations that result in complex and intricately regulated changes in a single step'', and they are ``A highly evolved macromutational mechanism'' [90].
In this manner, ``smart'' genetic operators may have evolved, through the interaction of selection acting at two or more hierarchical levels (it appears that some transposons have followed another evolutionary route, developing inter-cellular mobility and becoming viruses [41]). It is likely that transposons today represent the full continuum from purely parasitic ``selfish DNA'' and viruses to highly coevolved genetic operators and gene regulators. The possession of smart genetic operators may have contributed to the explosive diversification of eukaryotes by providing them with the capacity for natural genetic engineering.
In designing self replicating digital organisms, it would be worthwhile to introduce such genetic parasites, in order to facilitate the shuffling of the code that they bring about. Also, the excess code generated by this mechanism provides a large store of relatively neutral code that can randomly explore new configurations through the genetic operations of mutation and recombination. When these new configurations confer functionality, they may become selected for.