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I would appreciate help in understanding the meaning, logic, and, in particular, how to interpret the phrase:

The fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%

I could ask numerous question regarding the biology (including what happens to the rest of the genome, and positive selection) and formal logic of this statement, but maybe I could impose, and just leave it to whomever kindly replies.

This remark comes from the abstract of Grauer & al. "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE"

And the Abstract itself:

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.

Thanks

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  • $\begingroup$ Fine. I’ve deleted. $\endgroup$ – David Jul 19 at 21:51
  • $\begingroup$ So basically you want someone to explain the ENCODE position that DNA can be functional without it being subject to purifying selection, carefully defining functional conservation and purifying selection and the level (base or greater) that they apply. With examples. I think this is a good question and hope you will get a good answer. Methinks Grauer et al. protest a little too much. One doesn’t imagine they have made a great effort to understand the other point of view. But I may be doing them an injustice. $\endgroup$ – David Jul 19 at 22:05
  • $\begingroup$ @David On the most basic level, I'm stuck trying to understand their verbiage. Conserved = kept, through purifying selection = discarded. So I don't understand how they line up. Then, less than 10%, so what about the other 90+% and positive selection; or is that irrelevant to their assertion? $\endgroup$ – user663837 Jul 19 at 23:12
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I will try to tackle the terminology first

  • Conserved: That remains identical (or at least very similar) across species.

  • Purifying selection: Is one of the possible forces that lead to conservation of important sequences of DNA, by removing deleterious alleles.

So, the phrase simply means that the proportion of the genome that is very similar in sequence with the genome of other species (i.e. evolutionarily conserved) is less than 10%.

This is the answer to you question. Then, I just want to add that I share David's view on the abstract.

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