It performs a function

Maybe non-coding DNA plays some role in controlling how other DNA sections are transcribed, even though it isn't transcribed itself. In this case, the non-coding DNA is advantageous to the organism (it performs a necessary job), so natural selection maintains it. Some evidence exists that this situation actually occurs; even so, it's not enough to account for the huge amounts of non-coding DNA.

Alternatively, the non-coding DNA may serve a structural function during cell division or the production of gametes (sperm and egg). Replicating the eukaryotic genome, which is packaged in a series of chromosomes (refer to Chapter 3

for info on chromosomes), is a pretty complex process. The non-coding DNA could be involved in putting the chromosome together — pairing things up and partitioning the copied chromosome in the daughter cells, for example.

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