Junk DNA Hypotheses of origin and function

There are some hypotheses, none conclusively established, from the most academic to the less expected, for how junk DNA arose and why it persists in the genome:

• These chromosomal regions could be composed of the now-defunct remains of ancient genes, known as pseudogenes, which were once functional copies of genes but have since lost their protein-coding ability (and, presumably, their biological function). After non-functionalization, pseudogenes are free to acquire genetic noise in the form of random mutations.
• 8% of human junk DNA has been shown to be formed by retrotransposons of Human Endogenous Retroviruses (HERVs)^[5], although as much as 25% is recognisably formed of retrotransposons^[6]. This is a lower limit on how much of the genome is retrotransposons because older remains might not be recognizable having accumulated too much mutation. New research suggests that genome size variation in at least two kinds of plants is mostly because of retrotransposons.^[7]
• In 1997, Steven Sparks proposed that "The end purpose of this "excess DNA" must be to reduce the probability of transcribable genes being cut by chromosomal crossover. Gametes can survive only when their important, transcribed genes are saved from meiotic cutting by being surrounded with "buffer DNA"."^[8]
• Junk DNA might provide a reservoir of sequences from which potentially advantageous new genes can emerge. In this way, it may be an important genetic basis for evolution^[9].
• Some junk DNA could simply be spacer material that allows enzyme complexes to form around functional elements more easily. In this way, the junk DNA could serve an important function even though the actual sequence information it contains is irrelevant.
• Some portions of junk DNA could serve presently unknown regulatory functions, controlling the expression of certain genes, the development of an organism from embryo to adult^[10], and/or development of certain organs/organelles^[11].
• More and more scientists believe that in fact regulatory layer(s) in the "junk DNA", such as through non-coding RNAs, altogether contain genetic programming at least on par with, and possibly much more important than protein coding genes.^[12] But still how much of the 98% would be involved in such activity is unknown.
• Junk DNA may have no function. For example, recent experiments removed 1% of the mouse genome and were unable to detect any effect on the phenotype^[13]. This result suggests that the DNA is, in fact, non-functional. However, it remains a possibility that there is some function that the experiments performed on the mice were merely insufficient to detect.

http://en.wikipedia.org/wiki/Junk_DNA