
Hidden Treasures in Junk DNA [2012] - MichaelAO
http://www.scientificamerican.com/article/hidden-treasures-in-junk-dna/
======
throwanem
Results from the ENCODE consortium, and this result in particular, must not be
considered in a vacuum. In particular, review Graur et al.'s comprehensive
analysis and rebuttal: "On the immortality of television sets: "function" in
the human genome according to the evolution-free gospel of ENCODE." [1]

The abstract: > A recent slew of ENCyclopedia Of DNA Elements (ENCODE)
Consortium publications, specifically the article signed by all Consortium
members, put forward the idea that more than 80% of the human genome is
functional. This claim flies in the face of current estimates according to
which the fraction of the genome that is evolutionarily conserved through
purifying selection is less than 10%. Thus, according to the ENCODE
Consortium, a biological function can be maintained indefinitely without
selection, which implies that at least 80 - 10 = 70% of the genome is
perfectly invulnerable to deleterious mutations, either because no mutation
can ever occur in these "functional" regions or because no mutation in these
regions can ever be deleterious. This absurd conclusion was reached through
various means, chiefly by employing the seldom used "causal role" definition
of biological function and then applying it inconsistently to different
biochemical properties, by committing a logical fallacy known as "affirming
the consequent," by failing to appreciate the crucial difference between "junk
DNA" and "garbage DNA," by using analytical methods that yield biased errors
and inflate estimates of functionality, by favoring statistical sensitivity
over specificity, and by emphasizing statistical significance rather than the
magnitude of the effect. Here, we detail the many logical and methodological
transgressions involved in assigning functionality to almost every nucleotide
in the human genome. The ENCODE results were predicted by one of its authors
to necessitate the rewriting of textbooks. We agree, many textbooks dealing
with marketing, mass-media hype, and public relations may well have to be
rewritten.

[1]
[http://www.ncbi.nlm.nih.gov/pubmed/23431001](http://www.ncbi.nlm.nih.gov/pubmed/23431001)

