It appears that one of my previous posts was rather confusing for some readers (see this and this, also this for rebuttal). In the post “The Junk DNA myth strikes again (next up: media hype)“, I lamented the painfully cliched tendency for authors to start every paper reporting functions for some small segment of non-coding DNA with reference to the supposed long-running neglect of such DNA as “useless junk”. About all I had to say, really, was that this is historically inaccurate — “junk DNA” was never dismissed in any major way in the scientific literature. So, the idea that it was is a myth. Does this mean that the concept of non-functional DNA is a myth? Of course not. But let me clarify:
“Junk DNA myth”, interpretation #1: There is no “junk DNA”, where “junk DNA” is defined as non-functional DNA. That is, there is no non-functional DNA. I do not think this is a myth — lots of non-coding DNA is probably non-functional. However, lots isn’t. It’s not either-or.
“Junk DNA myth”, interpretation #2: That non-coding DNA was “long dismissed as useless junk but now we’re finding functions”. This is a myth. There was no such period of dismissal. Even if there was, it could only have been between about 1985 and 1995, which is less time than the period since this claim started being made. I have tried to show this by referring directly to the primary literature of the 1970s, 1980s, and 1990s.
So, to clarify, I do not particularly like the term “junk DNA” because a) it has changed since its original meaning, and b) it clearly is too loaded to be used effectively in objective discourse. I do think there is a large amount of DNA in most animal genomes that does not have any function at the organism level, but I also think some of it has been co-opted for very important roles. The originators of the “selfish DNA” idea thought so too:
“It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another.”
– Orgel and Crick 1980
How much is functional? I don’t know, but I can say that since there very beginning — in the first detailed discussion of “junk DNA” ever published — the proposed figure was higher than the current data suggest:
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.
– Comings (1972)
I don’t know how to state it any more clearly than this.