More and more research is turning up uses of junk or non-coding DNA. At one time, it was an axiom that this DNA was useless, but the term, coined in 1972, is falling out of favor as more and more uses turn up. A recent Cold Spring Harbor-University of Chicago study suggests that at least 30% of non-coding DNA may be functional.

Scientists from Cold Spring Harbor Laboratory (CSHL) and the University of Chicago now report that one of the steps in turning genetic information into proteins leaves genetic fingerprints, even on regions of the DNA that are not involved in coding for the final protein. They estimate that such fingerprints affect at least a third of the genome, suggesting that while most DNA does not code for proteins, much of it is nonetheless biologically important – important enough, that is, to persist during evolution.

The assumption, of course, is that if the non-coding DNA wasn't important, it would not persist over long periods of time because a human or mouse (the two types of study subject) would be no more or less likely to survive without it. According to Cold Spring Harbour,

The scientists found a preference for some “letters” across intron regions, and the opposite preference in coding regions. Together, these regions make up at least a third of the genome, which is thus under selective pressure during evolution. The result supports other recent studies that suggest that, although most DNA does not code for proteins, much of it is nonetheless biologically important.

British physicist David Tyler explains

Without getting into details, this finding is potentially of great importance. Introns comprise about 30% of the genome, and the fingerprint of functionality is pervasive. The rest of the genome awaits further research, and we may find that most of that has some functionality also. We still have a lot to find out about how the splicing-regulatory elements work, and we can predict some interesting tests of contrasting hypotheses.

Junk DNA as evidence for the course of evolution - whatever it is!

The history of "junk DNA replicates, in some ways, the history of beliefs about "vestigial organs" in humans. Vestigial organs - organs that allegedly once had a use but don't any more - were thought to be common in the human body. A frequently cited example was the appendix. The explanation offered was that the progress of evolution eliminated their function. However, the appendix for example was found, like almost all supposed human vestigial organs, to have a function. One popular misunderstanding is the fact that many organs in the human body are redundant - that is, they do some of the same jobs as another organ. But redundant parts should not necessarily be considered vestigial or unnecessary. Redundancy is a feature of a stable system. It prevents crises provoked by the failure of a single essential part. However, one difficulty in interpreting research into non-coding DNA is that unwarranted and unsupported assumptions about how evolution works are often mingled with valid findings from an actual study. Biophysicist Cornelius Hunter addresses the problem in connection with this paper (April 15, 2008):

Did you know that most of the evidence claimed for evolution is actually not evidence for evolution? That's right. Remember the mountain of evidence that evolutionists say is supposed to make evolution a fact? Well, most of it consists of biological findings that merely have been interpreted according to evolution.

Here is an example: a prestigious scientific journal, the Proceedings of the National Academy of Sciences, published last week detailed findings about how DNA information is used to make proteins in our cells. The research team, led by Cold Spring Harbor Laboratory professor Michael Zhang, discovered subtle signals in the DNA that help guide incredibly complex molecular machinery when editing the DNA information. The findings are not in any way evidence for evolution, yet the headlines proclaimed, "Scientists Find a Fingerprint of Evolution Across the Human Genome."

This was not merely a case of journalistic naivete. One can hardly blame the science writer when the journal paper itself presented the results as elucidating the evolutionary process. The paper's title alone ("RNA landscape of evolution for optimal exon and intron discrimination") suggests a new finding about evolution, and the paper concludes that human genes seem to have been optimized "during evolution."

But the "during evolution" part is gratuitous. The key findings are about how the genetic signals work, not that they evolved. There is, in fact, nothing in the findings to indicate evolution. The science writer concluded that "the researchers found signs that evolution rejects some types of mutations," but there simply was no such finding. What the researchers actually found was the presence of certain subtle signals in the genome. They found no evidence that the signals were produced by evolution. 

At least one science editor wants to hang on to the term "junk DNA" because it persuades the public that the conventional picture of evolution is correct ("helps frame the debate"). David Tyler addresses his proposal in strongly in "Framing the debate about Junk DNA" (070907),

In his July editorial in The Scientist, Richard Gallagher marks the 35th anniversary of the term "Junk DNA" by asking the question "Is it time to retire provocative descriptors such as "junk DNA"?" His answer is negative, and he proceeds to justify the term on the grounds that: "junk DNA works as a catchy moniker that helps frame the debate for the general public while evoking passionate debate among scientists". This blog has drawn attention previously to the way evolutionary biologists like to frame the debate for the general public: instead of equipping the public with the concepts and resources to make informed judgments, the objective appears to be to safeguard Darwinism to ensure the public do not revolt!  

Tyler recalls the history:

There is no doubt that "Junk DNA" has been a controversial term within the scientific community. However, for many years, the sceptics were in a minority. The general public were presented with overwhelming evidence that our genomes are "filled with the remains of extinct genes" that are of marginal interest until advantageous mutations bring them back again into centre stage. The Framers made sure the public got the message: "...the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process . . ." (Kenneth Miller, 1994) and "DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed" (Richard Dawkins, 2004).

One consequence of growing efforts to "frame" science is that readers of reports on new research must be skilled at seeing past elaborate frames, in order to discern findings.

Citation, abstract, and other resources

Citation: Chaolin Zhang, Wen-Hsiung Li, Adrian R. Krainer, and Michael Q. Zhang Proc. Natl. Acad. Sci. USA, April 15 2008, 105(15, 5797-5802 | doi 10.1073/pnas.0801692105

Abstract: Accurate pre-mRNA splicing requires primary splicing signals, including the splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs). The SREs include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs), which are typically located near the splice sites. However, it is unclear to what extent splicing-driven selective pressure constrains exonic and intronic sequences, especially those distant from the splice sites. Here, we studied the distribution of SREs in human genes in terms of DNA strand-asymmetry patterns. Under a neutral evolution model, each mononucleotide or oligonucleotide should have a symmetric (Chargaff's second parity rule), or weakly asymmetric yet uniform, distribution throughout a pre-mRNA transcript. However, we found that large sets of unbiased, experimentally determined SREs show a distinct strand-asymmetry pattern that is inconsistent with the neutral evolution model, and reflects their functional roles in splicing. ESEs are selected in exons and depleted in introns and vice versa for ESSs. Surprisingly, this trend extends into deep intronic sequences, accounting for one third of the genome. Selection is detectable even at the mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of ESEs and ESSs. We developed a method that effectively predicts SREs based on strand asymmetry, expanding the current catalog of SREs. Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution. (A subscription is required to view the article.)

Other resources:

"Scientists find a fingerprint of evolution across the human genome"

"Raising the bar on the evolution debate" by Cornelius Hunter