Ciliated protozoa represent some of the most diverse microbial eukaryotes on our planet. They have two types of genomes in one single-cell: a somatic nucleus that encodes all proteins and a germ-line nucleus used only in conjugation. The somatic genomes of some ciliates are composed of short "nano-chromosomes", each encoding just one or a few genes. In Oxytricha trifallax approximately 95% of the germ-line genome is destroyed in the process of forming these nanochromosomes. This illustrates one creative real-time solution to two basic problems in biology -- gene-finding and "junk DNA": throw away almost everything that is not a gene. Furthermore, a large fraction of all Oxytricha genes appears to be scrambled, that is, segments of genes can be both interrupted and present in a permuted or inverted order. For example, the segments for two independent genes may be intertwined on two separate germ-line loci that together construct the functional somatic versions. I will describe our current understanding of this phenomenon, based on experiments in our lab that survey the origin, evolution, and developmental processing of scrambled genes.