I missed this poll by Chris Gunter yesterday, asking “If you are a non-genomicist, can you tell us if you thought/were taught much of the genome was “junk”?
Well, I’m 1) a day late and 2) not a non-genomicist, but I’ll reply anyway, because we need a little history review.
In my Eukaryotic Genomes course in grad school (in the year the draft Human Genome sequence came out), I was taught by Tom Eickbush, not so much about ‘junk DNA’, but about ‘selfish DNA’. The point is largely the same regardless of what we call it. Among the first papers we read in Eickbush’s class were the classic Doolittle and Sapienza and Orgel and Crick papers on selfish DNA.
The key argument of these papers was this: parasitic DNA that can replicate itself within the genome requires no other explanation for its existence other than is ability to replicate, period. It does not need to be functional, from the perspective of the organism. It may acquire a useful function. But in general, absent evidence of such a useful function, we don’t need to ask the question, ‘what is the function of this DNA?’ There’s no mystery why it’s there – because it can replicate.
Note here that the argument is not ‘we don’t know what this DNA does and therefore it must be junk.’
Eickbush emphasized Orgel and Crick’s argument again and again during the course of the semester. And why is this DNA still in our genomes? Wouldn’t evolution have eliminated it? No, not without either some active mechanism to eliminate this DNA (which does exist in some species), or very strong selection against these DNA parasites.
Our genomes are filled, positively stuffed with the detritus of this selfish DNA. And we’ve learned to live with it. Our cells have means of suppressing the spread of these genomic parasites. Some selfish DNA has clearly been recruited into functional roles.
This is why the ‘junk DNA is debunked’ nonsense drives me crazy. There was no mystery. The question, ‘what is the function of the 98% of genome that is non-coding’ is misleading – as Orgel and Crick pointed out, we already have an explanation for what much of that 98% of the genome is doing there, and no other explanation is required. Nobody has debunked Orgel and Crick’s argument. On top of that, there is no reason to expect that repetitive elements should be biochemically inert.
So the burden of proof is on those who are claiming that most of the genome has a crucial regulatory function.