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The theory that exons are basic modules of protein structure that can be shuffled by evolution (much like artificial methods). This does not explain why prokaryotes have no introns and eukaryotes do. The competing 'Introns Early' and 'Introns Late' hypotheses address this problem.

      ___________             _____________
_____|  EXON 1   |___________|  EXON 2     |________
     |___________|   INTRON  |_____________|

                     |  |
                     |  |
                    \|  |/
                     \  /

      ___________         _____________           _____________
_____|  EXON 1   |_______|  NEW EXON   |_________|  EXON 2     |________
     |___________|   INT |_____________|   RON   |_____________|

Arguments tend to center around the phase of the introns - that is whether they are in phase or out of phase. This concept is related to the prokaryotic tactic of gene sharing, where two different genes are coded for by the same stretch of DNA but in different reading frames.

Reasons for the existance of introns vary from viral and SINE/LINEs etc to junk.

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