Much of the non-coding DNA may be parasitic DNA — the result of replicating elements in the eukaryotic genome reproducing themselves. As you can imagine, anything that's a parasite can't be good for the host organism, and selection would act to favor individuals with less of this parasitic DNA.
So why is it still there? Because parasitic DNA elements that are best able to reproduce themselves in the eukaryotic genome are selectively favored, even though selection is also acting to favor organisms in which they are less able to replicate. Lots of evidence exists that a large amount of your genome is really taken up by the selfish elements.
All kinds of selfish, non-coding DNA are around, but one very important kind is the retroelements. To understand the retroelements, think about retro-viruses, the most famous of which is HIV (explained in detail in Chapter 18). Retroviruses are viruses that alternate between an RNA genome and a DNA genome. They start with an RNA genome, infect their host, make a DNA copy to integrate into the host, and then replicate an RNA copy so that they can spread.
A retroelement does essentially the same thing that a retrovirus does, except that it lacks the genes that enable it to package the RNA copy into a particle that spreads. (When scientists sequence retroelements, they find that they are closely related to retroviruses but have a reduced set of genes.)
Amazingly, 95 percent of the human genome is made up of retroelement-like sequences. What's their purpose? Like everything else in evolutionary biology, their purpose is simply to make more of themselves. They replicate in your genome, and you pass them along to your kids.
Harmless — until they mess things up
For the most part, retroelements don't seem to do you any harm — until they do. Retroelements can move around in your genome and mess things up. They can insert into a new location right in the middle of an existing gene.
An example of a retroelement in action is the blue merle pattern in some breeds of dog. This coloring pattern is caused by a particular retroelement popping in and out of the pigment genes during embryonic development. At a certain point, the retroelement stops jumping around, but the dog still ends up with splotches of different colors in different places. Another, more harmful effect of retroelements may be cancer, where certain retroelements move around more actively.
Bottom line: Retroelements don't do anything beneficial, take up space, can be harmful, and may be parasitic. You'd be better off if they weren't there, but they just keep reproducing.
Transposable elements in general (pieces of DNA which pop around from one place to the next in the genome) and retroelements in particular (a subclass of transposable elements whose replication involves a reverse transcription step — that is a transcription from RNA back to DNA) are a big part of your genome, but they don't do anything of value. Why oh why are they there? That's the sixty four million dollar question of genome size.
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