I had a series of posts on Ye Olde Genomicron about what people actually said regarding "junk DNA" and non-function in the 1970s, 80s, and 90s. I have been meaning to repackage this material for a revised and more synthetic series here, but I haven't gotten around to that as yet. For the moment, here are some quotes I came across while reading a few sources for a paper I am writing.
Remember, a significant number of creationists, science writers, and molecular biologists want us to believe that non-coding DNA was totally ignored after the term "junk DNA" was published in 1972, that the authors of the "junk DNA" and "selfish DNA" papers denied any possible functions for non-coding elements, and, in the case of creationists, that "Darwinism" is to blame for this oversight. The latter of these is nonsensical as the very ideas of "junk DNA" and "selfish DNA" were postulated as antidotes to excessive adaptationist expectations based on too strong a focus on Darwinian natural selection at the organism level.
For those of you who didn't read the earlier posts, see if you can guess when these statements were made.
There is a strong and widely held belief that all organisms are perfect and that everything within them is there for a function. Believers ascribe to the Darwinian natural selection process a fastidious prescience that it cannot possibly have and some go so far as to think that patently useless features of existing organisms are there as investments for the future.
I have especially encountered this belief in the context of the much larger quantity of DNA in the genomes of humans and other mammals than in the genomes of other species.
Even today, long after the discovery of repetitive sequences and introns, pointing out that 25% of our genome consists of millions of copies of one boring sequence, fails to move audiences. They are all convinced by the argument that if this DNA were totally useless, natural selection would already have removed it. Consequently, it must have a function that still remains to be discovered. Some think that it could even be there for evolution in the future -- that is, to allow the creation of new genes. As this was done in the past, they argue, why not in the future?
A survey of previous literature reveals two emerging traditions of argument, both based on the selectionist assumption that repetitive DNA must be good for something if so much of it exists. One tradition ... holds that repeated copies are conventional adaptations, selected for an immediate role in regulation (by bringing previously isolated parts of the genome into new and favorable combinations, for example, when repeated copies disperse among several chromosomes). We do not doubt that conventional adaptation explains the preservation of much repeated DNA in this manner.
But many molecular evolutionists now strongly suspect that direct adaptation cannot explain the existence of all repetitive DNA: there is simply too much of it. The second tradition therefore holds that repetitive DNA must exist because evolution needs it so badly for a flexible future--as in the favored argument that "unemployed," redundant copies are free to alter because their necessary product is still being generated by the original copy.
These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn't mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.
There is a hierarchy of types of explanations we use in efforts to rationalize, in neo-darwinian terms, DNA sequences which do not code for protein. Untranslated messenger RNA sequences which precede, follow or interrupt protein-coding sequences are often assigned a phenotypic role in regulating messenger RNA maturation, transport or translation. Portions of transcripts discarded in processing are considered to be required for processing. Non-transcribed DNA, and in particular repetitive sequences, are thought of as regulatory or somehow essential to chromosome structure or pairing. When all attempts to assign a given sequence or class of DNA functions of immediate phenotypic benefit to the organism fail, we resort to evolutionary explanations. The DNA is there because it facilitates genetic rearrangements which increase evolutionary versatility (and hence long-term phenotypic benefit), or because it is a repository from which new functional sequences can be recruited or, at worst, because it is the yet-to-be eliminated by-product of past chromosomal rearrangements of evolutionary significance.
This is what I emphasized earlier, that this DNA must have a functional value since nothing is known so widespread and universal in nature that has proven useless.
I've stopped using the term ['junk'] ...Think about it the way you think about stuff you keep in your basement. Stuff you might need some time. Go down, rummage around, pull it out if you might need it.
Answers to be provided in the comments.