Let me say it one more time.
The term “junk DNA” was not coined on the basis of not knowing what it does. It was not a cop-out or a surrender. Susumu Ohno coined the term in 1972 in reference to a specific mechanism of non-coding DNA formation that he thought accounted for the discrepancies in genome size among species: gene duplication and pseudogenization. That is, a gene is duplicated and one of the copies becomes degraded by mutation to the point of being non-functional with regard to protein coding. (Sometimes the second copy takes on a new function through “neofunctionalization”, or the two copies may split the original function through “subfunctionalization”). “Junk” meant “something that was functional (a gene) but now isn’t (a pseudogene)”.
It has turned out that non-coding DNA is far more complex than just pseudogenes. It also includes transposable elements, introns, and highly repetitive sequences (e.g., microsatellites). For the most part, the mechanisms by which these form are reasonably well understood, and as a result there is good reason to expect that many or even most of them are not functional for the organism. Many authors argue that most non-coding DNA is non-functional, not because of a lack of imagination, but on the basis of a large amount of information regarding its mechanisms of accumulation.
Some non-coding DNA is proving to be functional, to be sure. Gene regulation, structural maintenance of chromosomes, alternative splicing, etc., all involve sequences other than protein-coding exons. But this is still a minority of the non-coding DNA, and there is always the issue of the onion test when considering all non-coding DNA to be functional.
And finally, it needs to be pointed out again that evolutionary biologists and geneticists held a variety of views on functionality, some claiming that it was all functional, some saying very little (but few, if any, saying it was all totally non-functional). Strict adaptationist (“ultra-Darwinian”) thinking had led many authors to assume that non-coding DNA must be doing something useful or it would have been eliminated by selection long ago. The proponents of the “selfish DNA” approach to non-coding DNA wrote their papers in direct response to this overly adaptationist interpretation and argued that much of it could be explained simply by the existence of mechanisms that put it there, independent of organism-level function. But even they expected that some would turn out to play a role in regulation. At the same time, most researchers for the past half century have noted the link between DNA amount and cell size, which means that total non-coding DNA content is not irrelevant biologically. This could, however, be an effect instead of a function, which is why there has for decades been discussion about this issue.
You can tell someone who knows very little about the science or history of “junk DNA” when they make one or more of the following claims: 1) All scientists have always thought it was all totally irrelevant to the organism. 2) New evidence is suggesting that it is all functional. 3) “Darwinism” led to the assumption that non-coding DNA is non-functional. The opposite is true in each case.
One can discuss possible functions for non-coding DNA — that’s not a problem, and it makes for an interesting topic if data are used to back up claims — but please stop distorting the views of scientists both past and present in the process.
- A word about “junk DNA”.
- Function, non-function, some function: a brief history of junk DNA.
- The onion test.
- An opportunity for ID to be scientific.
- Human gene number: surprising (at first) but not paradoxical.
- Ultraconserved non-coding regions must be functional… right?
- Gene number and complexity.
- What’s wrong with this figure?
- Dog’s Ass Plots (DAPs).
- Genome size and gene number.