Maybe junk DNA is not junk?
Not directly neuroscience-related but this is a pretty cool paper nonetheless. Basically, the authors use automated pattern recognition to pick out small strings in the “non-coding” regions of the human genome. They show that these pyknons are found at regular distances within coding regions and UTRs. Even more intriguing is that
approx. 40% of the known microRNAs are similar to 689 pyknons and that the pyknons subsume 56 of the 72 recently reported 3′ UTR motifs, lending further support to the possibility of a connection between the pyknons and RNAi/PTGS.
Both RNAi (RNA interference) and PTGS (post-transcriptional gene silencing) have recently been found to be major regulatory mechanisms for endogenous gene silencing and regulation. Here’s a link to a primer on PTGS and RNAi.
July 4th, 2006 at 12:33 pm
Rigoutsos’ “pyknon”-s are a major breakthrough towards PostGenetics. While the traditional dogma antagonizes the “nucleic acid coding” parts (”Genes”) and “non-coding” DNA (”Junk”), the short, repetitive sequences that are absolutely and definitely occur in the DNA appear both in non-coding, as well is coding parts. This finding will do away with the “old axiom” of seeing the DNA “through the looking glass of genes” - ignoring all 98.7% (in human) that are *not genes*.
While Dr. Rigoutsos sticks to his guns and does not really embark in functional interpretation of “pyknon”-s, there is at least one demonstrated connection of “pyknon”-s to algorithmic approaches to DNA; see “Rigoutsos’ pyknons and fractals” at http://www.pyknon.com
The latest development along these lines is the identification of FractoSet-s and FractoGem-s; see
at http://www.fractoset.com and http://www.fractogem.com
A “news column” riports on daily developments of the field (now also called PostGenetics, http://www.postgenetics.org) at http://www.junkdna.com/new_citations.html
Regards,
Dr. Pellionisz
July 31st, 2006 at 8:56 pm
BRAVO !!!
I spent 40 years designing computer software. I deal in Theoretical/Logical analysis. This has
been my position for more than 25 years: Every cell in the human body is a small computer; but a
computer more powerful than any we have built. Sure, it makes my eyes brown. It, however, also
controls the total development, operation, maintenance and finally aging and destruction of the body. In addition, some of it seems to be ancestrial, survival data, skills, etc.. A turtle
crawls from the ocean, lays eggs, covers with sand and returns to the sea. weeks later the eggs hatch and the young make a dash for the water. Some do not make it and are food. Survival is encoded in the DNA. A boy age four sits at a piano for the first time and plays Mozart. Where
is the coding……….
November 21st, 2006 at 12:49 am
A good question, where “Mozart” is coded… Time Magazine published about six weeks ago the “difference of apes and human”; in the 4% of non-coding (”junk”) DNA.
But the very article asked: “Where is the chimp Mozart” (with 0.1% difference in the genes)? “Where is the chimp Shakespeare”??
Now, the November 13 issue of Time Magazine features a “debate” (full of name-calling); two scientists arguing for and against God in the DNA. (see http://www.junkdna.com/new_citations.html)
Should we rather look into the real science issue, how the 4% “non-coding” actually codes the difference between chimp and man?