Fred Gould in American Scientist:
Although many of us have gotten used to the idea that our bodies serve the needs of a variety of viruses, bacteria, mites and other parasitic species, it comes as a surprise to most people when they hear that their bodies are also hosting alien parasitic DNA.
Analysis of output from the Human Genome Project makes it clear that just one form of such alien DNA, transposons, makes up about 50 percent of our genome. Every time one of your cells divides, it uses time and energy to replicate this parasitic DNA. There is even evidence that the size of your cells is set to accommodate this extra genetic load. In return, this type of DNA typically does nothing useful for you or any of the other organisms it inhabits.
So why do humans and the vast majority of other species serve as homes for parasitic DNA? This is one of many questions about selfish genetic elements that Austin Burt and Robert Trivers address in their scholarly, thought-provoking new book, Genes in Conflict. As can be gleaned from the title, the authors don’t envision an easy alliance between selfish genes and the rest of the genome.
As background, it is worth noting that all specific sequences of DNA manage to persist over time by causing their host organisms to keep passing them on to their progeny. There are two basic evolutionary mechanisms that DNA sequences use to improve their odds of getting into that next generation. The first method involves increasing the number of viable offspring produced by the host relative to competing individuals. This process fits within our typical understanding of adaptation and natural selection.
The second evolutionary mechanism is for a DNA sequence somehow to increase the percentage of the host’s offspring in which it is contained.
More here.