Well, actually very damned little junk DNA in the human genome. Back in the 20th century as the human genome was being sequenced researchers were betting that it must take around 100,000 genes to make something as complicated as a homo sapiens. The official Genesweep bet eventually settled on around a mere 21,000. That's less than half the number it takes to make a corn plant. So most of the genome was thought to be filled up with "junk DNA" that kind of sat around cluttering up the place.
Since 2003, the Encyclopedia of DNA Elements or ENCODE project has been sifting through all those apparently useless base-pairs and it turns out that many of them are regulatory sequences that are largely devoted to telling genes what to do. From the press release:
…researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions (emphasis added) where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.
"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. "ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms." …
"We were surprised that disease-linked genetic variants are not in protein-coding regions," said Mike Pazin, Ph.D., an NHGRI program director working on ENCODE. "We expect to find that many genetic changes causing a disorder are within regulatory regions, or switches, that affect how much protein is produced or when the protein is produced, rather than affecting the structure of the protein itself. The medical condition will occur because the gene is aberrantly turned on or turned off or abnormal amounts of the protein are made. Far from being junk DNA, this regulatory DNA clearly makes important contributions to human health and disease."
Ain't science grand!?