Comments on: Hey junk people, I accept your challenge (part II)

By: Hammering nails in the “junk-DNA” coffin « The Sciphu Weblog

Hammering nails in the “junk-DNA” coffin « The Sciphu Weblog — Tue, 28 Oct 2008 14:12:50 +0000

[...] talk (see this previous post and links within), on to the peer-reviewed science. Below you will find a list of references that I [...]

By: It’s not all about the genes, well it’s not all about the environment either « The Sciphu Weblog

Thu, 16 Oct 2008 20:35:29 +0000

[...] noise as they do so. Examples I have been involved in lately are debates on race, IVF, abortion, junk-DNA and open access publishing. Arguably, this mechanism is present for almost any discussion. So [...]

By: Hitting three peeves with one stone « The Sciphu Weblog

Hitting three peeves with one stone « The Sciphu Weblog — Mon, 13 Oct 2008 18:14:27 +0000

[...] This is good…..if it means what I mean: that labeling DNA of unknown function as “junk” by default is wrong. Which it most certainly is. For more on this topic, see my 6 post discussion with Larry Moran (1,2,3,4,5,6). [...]

By: Dunbar

Dunbar — Sun, 28 Sep 2008 19:31:48 +0000

I believe Larry would characterise the transcription of junk DNA as sloppy binding by RNAP, which I think he goes into length in some of his posts on the ENCODE project. Also, you’re assuming that selection would yield a perfect RNAP based on an energetic argument which I think is wrong. Firstly, there may be evolutionary contraints to evolving a perfect RNAP that only transcribes non-junk DNA. Similarly, there may be biochemical contraints in the sense that it may be impossible to evolve an RNAP that only recognises genuine promotors all the time. Thirdly, a sloppy RNAP may be tolerable to most cells in spite of its energetic cost. This is not inconceivable, since one only need to compare with the energetic cost of translation, especially since not all protein is translated perfectly. Finally, it may be more energetically costly for a cell to have regulatory machinery to ensure perfect RNAP efficiency than it would be to have a somewhat inefficient RNAP.

that’s just my two cents