In the wake of the publishing of the ENCODE project papers, researchers are discussing just what the investigators meant by reporting that 80 percent of the human genome is functional, and whether or not the idea of 'junk DNA' still stands.
At the Nature News blog, Brendan Maher writes that, in their papers, the ENCODE investigators do get more specific about what they mean by 'functional.' He writes that they found that 8 percent of the genome can be bound by a regulatory protein, in addition to the 1 percent that is protein coding itself. Then based on the completion of their sampling methods, the investigators estimate that there is another 11 percent of the genome with regulatory activity, bringing the total to 20 percent. "Perhaps the main conclusion should have been that 20% of the genome in some situation can directly influence gene expression and phenotype of at least one human cell type," Maher writes. "It's a far cry from 80%, but a substantial increase from 1%."
Michael Eisen at the University of California, Berkeley, says at his blog that the idea of 'junk DNA' has long been out of favor. "Nobody actually thinks that non-coding DNA is 'junk' any more," he says. "It's an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it."
But Larry Moran from the University of Toronto says that the ENCODE project does not show that most of the genome isn't 'junk DNA.' He writes that "Eisen is wrong, junk DNA is alive and well. In fact almost 90% of our genome is junk."
In a separate post, Moran notes that "creationists are going to love this," referring to the ENCODE project's findings. Indeed, a post at Uncommon Descent, an intelligent design blog, says that the ENCODE papers are a "spectacular vindication" of intelligent design's theory that all DNA must have a purpose.
"This is going to make my life very complicated," Moran adds.
What's the buzz? Do we really
What's the buzz? Do we really know whether protein synthesis and control is the only function of the genome? To keep 98%, 90% or 80% of the DNA as junk would be costly and not tolerated by evolution. So let's just think and work to discover its function. Michael Lerman, Ph.D., M.D.
The findings certainly
The findings certainly vindicate the hypothesis that much, most, or maybe all DNA has (or had) a purpose. I don't see how that validates the notion of intelligent design. It does, however, fit just fine with evolutionary theory.
One possible function of some of the extra-coding DNA might have to do with something as simple as proximity of structural features to genes or regulatory sequences. These could play a role in fine control of gene expression. Think closer to analog control than digital control.
Sheldon Engelhon
Dr. Lerman here is incorrect.
Dr. Lerman here is incorrect. Even casual observation shows that genome size is many times greater in some organisms than in others (e.g., 100 million nucleotides in thale cress, 2,500 million nucleotides in corn, 25,000 million nucleotides in some pine trees) and that the overwhelming majority of the inflated portion is not, and never has been functional in the sense of contributing to the phenotype of the organism. Evolution tolerates very well an enormous inflation of non-functional DNA sequences.