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There is lively debate about whether Alu serves some larger purpose in primate genomes or is merely “selfish DNA” that has been successful in its mode of replication. Alu insertions in coding exons are implicated in a number of human diseases, including neurofibromatosis, thalassemia, cancer, and heart attack. However, the vast majority of Alus are located in introns or intergenic regions, where they appear to have no phenotypic effect. Alus in introns have had a potentially important impact on protein evolution: they provide alternative splice sites in approximately 5% of genes that produce multiple protein products. Each Alu is the “fossil” of a unique transposition event that...