Evidence: "Junk" DNA

           The discovery that "junk" DNA is not junk but rather a vast context dependent set of controls is yet another embodiment of context dependence.

           The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. Large stretches of DNA that appeared to serve no functional purpose in fact contain about 400,000 regulators, known as enhancers, that help activate or silence genes, even though they sit far from the genes themselves.

           Researchers deciphered the intricate regulatory code that controls the human genome. They discovered that genetic changes linked to more than 400 common diseases all affect the genome's ability to control when, where and how genes behave—not the genes themselves.

           The human genome consists of about 3 billion nucleotides — the “letters” — strung one to another in chains. Specific stretches of those nucleotides carry the instructions for making specific proteins. The proteins, in turn, become the blocks of tissues and the enzymes, hormones and carrier molecules that do most of the cell’s work. The Human Genome Project identified the correct linear sequence of those letters. At its completion in 2003, only 21,000 genes had been identified — far fewer than most biologists predicted. Furthermore, the genes constituted only 3 percent of the cell’s DNA, leaving biologists to wonder about what function, if any, the remaining 97 percent had.

           The Encyclopedia of DNA Elements Project, nicknamed Encode, is the most comprehensive effort to make sense of the totality of the 3 billion nucleotides that are packed into our cells. The project’s chief discovery is the identification of about 4 million sites involved in regulating gene activity. Previously, only a few thousand such sites were known. In all, at least 80 percent of the genome appears to be active at least sometime in our lives. Further research may reveal that virtually all of the DNA passed down from generation to generation has been kept for a reason.

           The new research helps explain how so few genes can create an organism as complex as a human being. The answer is that regulation — turning genes on and off at different times in different types of cells, adjusting a gene’s output and coordinating its activities with other genes — is where most of the action is. By turning switches on and off, and varying the duration of their activity, a nearly infinite number of circuits can be formed. Similarly, by activating and modulating gene function, immensely complicated events such as the development of a brain cell or a liver cell from the same starting materials is possible.