No Junk DNA vs. Rarity of Function

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@T_aquaticus
I like what you have written and it would be my position with a little modification.

  1. Functional sequence in the sense of ENCODE is sequence with any biochemical activity at all. Transcription, methylation, a site for DNA binding etc Even ENCODE workers admit they don’t know how much of that “function” will be meaningful.
    2.In the ENCODE sense, most genomic sequence is functional, thus functional sequence is common (20-80% was the original range offered). Just remember what function means here.
  2. When we say functional sequence is rare in sequence space, we mean a different sort of function. We mean the ability to carry out an enzymatic reaction. It is our claim that proteins made from random sequence will rarely have any sort of enzymatic activity. Mung was right when he said in one case we were talking about DNA function, and in the other, protein.
  3. That is why experimental tests are important. Can random DNA sequence produce functional proteins with enzymatic activity.
    Our prediction is that such experiments will fail, because of the inability to test enough sequence to detect such a small signal. YET if you look at the actual number of orphans, that suggests design.
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