Replies

I don’t follow this stuff closely, but I must say, the concept of “junk” DNA, just because we couldn’t immediately figure out its function, seriously flunked the smell test.

It sure does, which is why the actual biologists didn't use that goofy method in order to arrive at the concept of junk DNA.

Thanks for playing, though -- come on back when you've taken a few beginner's biology classes and have the very start of what it takes to be able to critique the subject.

Then perhaps you can tell us what, if anything, is wrong with the actual methods used to conclude that large sections of most vertebrate DNA is non-functional. For example, from prior posts of mine:

Also be prepared to point out that contrary to bone-headed (and unsupported) claims that "it probably never was 'junk'", the fact remains that even though rare cases have been found of specific pieces of "junk DNA" (i.e. non-coding DNA) having some use, only an idiot would leap from that to the conclusion that "it probably never was 'junk'" on the whole, because a) the vast majority of "junk DNA" is non-conserved (e.g. "Comparative genomics has revealed that approximately 5% of the mammalian genome is under purifying selection.", leaving 95% of the genome "inconsequential" from a survival standpoint), a clear indication that it is, indeed, not used in the genome, among many other lines of general evidence supporting the same conclusion (is your correspondent ignorant of these, or just dishonest?), and b) specific tests of "junk DNA" have shown that if it's used at all, the use is extremely rare or subtle, because giant whacking swatches of it can be removed entirely without any kind of obvious harm to the animal.
For example: Megabase deletions of gene deserts result in viable mice. In short, the researchers snipped over 2.3 *million* basepairs of apparently "junk DNA" out of mouse DNA, then produced offspring mice which were entirely missing that DNA. The resulting mice were normal in all respects. As a press release states:

"In these studies, we were looking particularly for sequences that might not be essential," said Eddy Rubin, Director of the JGI, where the work was conducted. "Nonetheless we were surprised, given the magnitude of the information being deleted from the genome, by the complete lack of impact noted. From our results, it would seem that some non-coding sequences may indeed have minimal if any function."
A total of 2.3 million letters of DNA code from the 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic cells were genetically engineered to contain the newly compact mouse genome. Mice were subsequently generated from these stem cells. The research team then compared the resulting mice with the abridged genome to mice with the full-length version. A variety of features were analysed, ranging from viability, growth and longevity to numerous other biochemical and molecular features. Despite the researchers' efforts to detect differences in the mice with the abridged genome, none were found.
Another specific piece of evidence is that the genome of the fugu fish (as well as other fish in the blowfish family) is remarkably "clean" compared to that of other fish (or other vertebrates), even other fish which are rather closely related. It's *missing* most of the DNA that other fish (and vertebrates) have that are collectively known as "junk DNA", and as a result has a genome that is nearly "pure" genes (i.e. coding regions) stripped of most non-coding regions. And the fugu gets along just *fine* without them. How and why its genome got "streamlined" by "cleaning house" of most of its "junk DNA" is a fascinating question which is being looked into, but the fact remains that if this "junk DNA" is all that critical and "actually" used for something after all, on the whole, then how does the fugu do so swimmingly (sorry, bad pun) without it at all?
So I repeat -- there are very good reasons, based on testing and on the evidence, that "junk DNA" on the whole really is "junk". And that doesn't change even if a *few* specific non-coding regions end up being involved in gene expression or whatnot. Finding a few discarded items of value in the city dump doesn't magically change the whole thing into a mountain of pearls.

Another example was in an editorial I read recently:

"Even the most hard-core junkologists admit that a significant portion of human DNA is probably dispensable. For instance, Ohno, now semi-retired from City of Hope, points out several reported cases of people born with millions of bases missing from their X chromosome. And yet, these people lead perfectly healthy lives, an indication that the lost bases probably add nothing to human life."

That said, however, there has been a trend to rename such DNA to something other than "junk", since that is a somewhat misleading term, given how active some (repeat *some*) of it is, and the role it often plays in evolutionary novelty. Instead some have suggested the "genomic scrapyard" or some similar more evocative term.

A complicating factor is that evolution is adept at making use of, and building upon, things that start out as "random junk". For example, from Perspective: transposable elements, parasitic DNA, and genome evolution: "Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions."

Furthermore, it's clear that the noncoding DNA has not been "designed" as such, because the evolutionary origins of most kinds of noncoding DNA are understood, and their evolutionary histories can be traced through cross-species genome comparisons. For example: A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats .

Going to the core of the issue, however, there *are* features in the genome which actually assist in increasing the efficiency of mutational improvements in the genome, but they hardly rise to the level of "thinking" or "designing", they just do things like raise mutation rates in response to environmental stress (e.g. times when the species might need to genetically adapt or die), or keeping redundant or obsolete copies of genes around as grist for the mill of recombination. All these methods of boosting the effectiveness of evolution are themselves well within the realm of features that could themselves have evolved, they don't look at all "designed" or "preplanned" or "irreducibly complex" or whatever.