Emile Zuckerkandl has proposed that Alu's perform some sort of
interference function with incoming viruses. I don't have
the exact reference(s) for this, but two Zuckerkandl papers
of relevance to this thread are:
Polite DNA: functional density and functional compatibility in genomes
E.Zuckerkandl J.Mol.Evol 24:12-27 1986
Maintenance of function without selection:Alu sequences as "cheap genes".
E.Zuckerkandl, G.Latter, & J.Jurka J.Mol.Evol. 29:504
Jerzy Jurka is another name worth searching on for Alu references.
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
krobison at nucleus.harvard.edu