The term “Junk DNA” refers to regions of DNA that are noncoding—or, in other words, they do not code for a protein. Scientists note that evolution is messy, incomplete, and inefficient and, consequently, it results in DNA sequences with varying degrees of function or no function at all. In the human genome, almost all (98%) of DNA is noncoding.
The challenge for those who think most non-coding DNA is vital is to explain why an onion needs five times as much of it as we do, says Gregory. “I would like to think that most knowledgeable biologists who properly appreciate evolutionary theory and genomic diversity are well aware of the many problems with ENCODE’s claim,” he says.
But most people and even some scientists are uncomfortable with the idea that most of their DNA is junk, says Ponting. Even worse for such people, other genomic studies are now revealing that we all carry plenty of mutations that affect both our coding DNA and non-coding DNA. While evolution weeds out some of the worst ones, this doesn’t stop plenty of mutations collecting in our genome.
“We are walking around as individuals with relatively large numbers of our genes not working properly,” he says. “These are ideas some find shocking.”
Journal reference: Genome Biology and Evolution, DOI: 10.1093/gbe/evx121
http://www.genomicron.evolverzone.com/2007/04/onion-test/
Researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.
It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.
A May 30 news article on Science Daily observes that “tandem repeats” are now thought to have function, even though we used to think they were “useless trash”:
http://www.genomicron.evolverzone.com/2007/04/onion-test/
“A geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in 1972.He used the term to refer to pseudogenes (commonly thought of as defunct relatives of known genes that do not code for proteins), but with time its meaning broadened to include all non-coding DNA (DNA that does not contain genes and does not produce proteins).1 Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”1 Due to his evolutionary presupposition, he assumed that non-coding DNA was merely a “genetic fossil” that may have been useful somewhere in our evolutionary past but had been discarded as we evolved into more complex, higher organisms. Since this “junk” DNA was no longer needed, it would not be under selective pressure, and mutations could accumulate without any harm to the organism.