Past, present and future Everything you ever wanted to know about the non-coding stretches of DNA. The author is Frederick Gruber who appears to be a science writer drawing on information supplied by various researchers.
You know the article is going to be misleading as soon as you read the opening paragraph.
When the first draft of the human genome finally became available, there were many surprises, one of them being the ridiculously large amount of DNA that did not code for proteins – or anything at all. It seemed like the genome was just a huge chaotic mess sprinkled with tiny nuggets!The reason this is misleading is because it totally misrepresents the history of the human genome. It's been four decades since we first became aware of the fact that only 1-2% of the human genome encoded proteins. This was hardly a surprise—in fact it was one of the principle arguments against sequencing the human genome. (What was the point of wasting all that money on DNA sequences that were mostly junk?)
One of the unfortunate characteristics of the junk DNA deniers is that they are completely unaware of the historical arguments in favor of junk DNA (e.g. False History and the Number of Genes, Genetic Load, Neutral Theory, and Junk DNA). Everyone who understood the problem was quite happy to find verification when the first draft of the human genome was published. It's exactly what the knowledgeable experts predicted.
The article raises the standard question that seems to have only recently occurred to some researchers; namely, what is all that DNA doing? It's mostly junk—at least that's the conclusion reached by many scientists back in the 1970s and most of what we've discovered since then has supported that view.
The article points out that the term "junk DNA" was coined by Susumu Ohno back in 1972 and he identified pseudogenes as prime examples. The article goes on to say,
Today, the term ‘junk DNA’ is no longer en vogue among many genome experts. They rather prefer to talk about ‘noncoding DNA’. And this certainly includes much more than just pseudogenes, which actually represent less than 1% of the noncoding DNA. The remaining 99% are made of everything else, for which no involvement in any protein-coding function has been found so far including, for example, introns, repeated sequences, interspersed elements, telomers, transposons…Theme
& Junk DNAThis is nonsense on many levels. "Noncoding DNA" is the part of the genome (about 98%) that does not encode protein. We've known for decades that some noncoding DNA is functional; therefore, it can't be junk DNA. Examples of functional noncoding DNA include: genes that encode various RNAs, regulatory sequences, some parts of introns, 5′ leader sequences, 3′ trailer sequences, centromeres, telomeres, scaffold attachment regions (SARS), origins of replication, and recombination hot spots.
There has never, ever, been a time when a substantial number of knowledgeable experts thought that all noncoding DNA was junk and they certainly don't think so today. We know for a fact that junk DNA exists (e.g. pseudogenes) so it would be very silly to abandon the term. What we don't know for certain is how much of our genome is junk. It's extremely likely that more than half is junk in spite of what science journalists (and some unknowledgeable scientists) might think.
It's true that there are some "experts" who think that most of our DNA is functional. Some of them will put in an appearance in the comments to this posting. Naturally, those "experts" will avoid the term "junk DNA" because they reject the concept. The Lab Times article is misleading because it doesn't mention that there is a substantial number of genome experts who believe that most of our genome is junk. It may even be a majority.
In the last decades, considerable research has been carried out showing indeed some – mostly regulatory – functions for a couple of these non-coding elements. For most of the ‘junk’, however, we still have not the slightest idea why it is there, why it is maintained over time or what it is doing.It's worth noting that the existence of functional nonoding DNA dates back to the early 1960s so it's not a new phenomenon by any stretch of the imagination. It's also worth noting that substantial parts of our genome do not have any known function and that's why they are called "junk." It's not correct to say that "... we still have not the slightest idea why it is there ..." since neutral evolution and random genetic drift are perfectly adequate explanations. This is the kind of statement that can only come from someone who doesn't understand evolution.
As usual, the discussion often turns to transposable elements (TEs).
In fact, functional TEs within their sequence actually code for the enzymes needed to cut and paste themselves anywhere in the genome. However, the picture is even more ambivalent: In recent years, researchers have added a considerable amount of evidence indicating that TEs might not at all be completely ‘useless’. Thus, the question, whether still to assign TEs to ‘junk DNA’, has become ever more pressing. In the meantime, many would clearly say ‘no’.Keep in mind that almost 50% of our genome is composed of degenerate (nonfunctional) transposons and viral DNA. It's true that there are some examples of transposons that have acquired a function. At latest count this amounts to about 0.1% of the genome and that leaves a lot of explaining for the junk DNA deniers. This issue is discussed in my review of The Myth of Junk DNA by Jonathan Wells [Junk & Jonathan: Part 9—Chapter 6]. You don't discredit the existence of junk DNA by finding a few unique and exceptional sequences. That's no way to make a scientific argument.
At the population level, TEs apparently also play important roles. By jumping around the genome at a much higher rate than any known mutation rate, they create a great deal of nucleotide diversity, which, in turn, is the raw material of evolution. Therefore, these TEs may well contribute to adaptation of species to new environments and even speciation.First let's get the facts correct. Every new human zygote contains about 130 new mutations not found in the parents [Mutation Rates]. On the other hand, new transposon insertion occur at the rate of one every 20 zygotes [Transposon Insertions in the Human Genome]. By my calculations, standard errors of DNA replication create diversity at more than 2000 times the rate of transposons.
It is true that over the course of several hundred million years of evolution in a variety of well-studied species (humans, mice, Drosophila, yeast, C. elegans, Arabidopsis etc.) we have detected a few dozen examples of transposon insertions that have led to beneficial effects. It's also true that in those same species there have likely been millions of insertions that turned out to be lethal. Anyone who thinks that the existence of a few active transposons in a genome could be selected because they provide a future benefit to the species just hasn't thought hard enough. (Besides, this "explanation" doesn't explain the existence of huge amounts of defective transposon sequences.)
In conclusion, a great deal of the DNA previously described as junk DNA can be ascribed well-established functions today – there is hard evidence for it, at least. However, there are lots and lots of DNA stretches that still don’t seem to be of any function at all.It is simply not true that a "great deal" of what used to be called junk DNA has now been shown to have a "well-established function." The only way that could become a true statement is if "great deal" is taken to mean less than 1%.
Only time will tell if these sequences are, indeed, true junk or whether we are still too blind to see the real meaning of the “Dark Matter of the Genome”.
I think the real underlying problem here is that most scientists (and science writers) see evolution entirely in terms of natural selection and adaptation. This means that the existence of massive amounts of junk DNA in our genome is a "problem" because it conflicts with their view of evolution. To them, there is no explanation for the existence of junk DNA because the ideas of neutral mutations and random genetic drift are just not on their radar. They see junk DNA as a "mystery" and they continue to look for, and invent, adaptationist explanations in order to solve the mystery.