Encode discussion (Introduction)

by David Turell , Saturday, April 13, 2013, 20:11 (4243 days ago) @ David Turell

Another point of view re' Encode. How valid are the findings? How much is junk? Should we drop the phrase?-http://online.wsj.com/article/SB10001424127887323550604578410794018082244.html-"The first row concerns the phrase "junk DNA." Coined in 1972 by the geneticist Susumu Ohno, it is an attempt to explain why vast stretches of animal genomes, far more in some species than in others, seem to serve no purpose. Genes of all kinds and their control sequences make up maybe 9% of the human genome at the very most. The rest may be nonfunctional "junk," mainly there because it is good at getting itself duplicated. Yet the phrase has always caused a surprising amount of offense. Reports of the discrediting of junk-DNA theory have been frequent."
"Late last year, a huge team of scientists running a consortium called Encode published an analysis of the human genome that they said showed some kind of activity in 80% of the genome. They later conceded that perhaps 20% is actually functional, yet insisted the phrase "junk DNA" could now be "totally expunged from the lexicon."
"According to Dan Graur of the University of Houston and his colleagues, even this is a wild overestimate—not least because it uses a "causal role" definition of function that is all wrong, as if you were to describe among the heart's functions adding 10.5 ounces to the weight of the body, along with pumping blood. After a few exchanges, the Encode team leader Ewan Birney conceded that in hindsight, the team overstated its conclusions. But he added that whatever the interpretation, the Encode data are sound."
"Are they? Here's where the junk-DNA row meets the other conflagration in molecular biology. All the Encode data were derived from cancer-cell lines. To describe human cancer cells as having the human genome looks increasingly unwise. Most cancer cells have extra chromosomes, fragmented and rearranged DNA and unusual patterns of gene activity."-"Comment: "The supposed junk may be "functional" simply by virtue of its space-filling role."-The 3-D approach to DNA is right on. It is coiled around spools of histone and parts of the gene are then in contact with modifiers elsewhere, which would not be the case if the DNA were linear.