not so junk DNA

May 12, 2004 11:04 PM

not so junk DNA the idea has always made me uncomfortable. now scientists are taking a closer look at base-pair sequences that have been generally overlooked till now.
posted by jessica (9 comments total)

jessica, this is interesting, but it appears that another poster posted about the same thing yesterday.
posted by vacapinta at 11:32 PM on May 12, 2004

The most interesting thing that I've ever seen written about “junk” DNA was research by Professor John Mattick at the Institute of Molecular Bioscience within the University of Queensland. I sat in on a lecture he gave to a combined group of complex systems theorists and computer scientists with an interest in networking. Basically he thinks that what people now think of as “junk” DNA is interaction or networking code that is responsible for for the emergence of various characteristics in the organism.
posted by snarfodox at 11:55 PM on May 12, 2004

I find it hard to believe that 'junk' DNA exists. RNA isn't sentient. It doesn't know what base-pairs to "pass over". It's all physics at the core level. These DNA pairs must form something, which hangs arounds and interacts with everything else in the body.
posted by Gyan at 1:10 AM on May 13, 2004

It doesn't know what base-pairs to "pass over

It might if the DNA doesn't have the necessary start sequences (promoters) such as "TATA" sequences in eukaryotes. Junk DNA certainly does have a biological impact though, for instance, in creating space between genes and therefore influencing cross-over frequencies.

In addition, the existance of junk DNA seems to be logical - what happens to a gene once it has mutated beyond usefulness? It is, by definition, junk, even if the base-pairs are still there.

This is very interesting research, though.
posted by Jimbob at 2:01 AM on May 13, 2004

well, RNA isn't sentient, but there are rules which determine which bits of DNA code for RNA & proteins. if specialized promoter sequences [like the TATA box or CAAT box in eukaryotes] are absent, the RNA polymerase will not bind to the DNA strand and that bit of DNA will not be transcribed. there are two short 6-10 bp sequences which are nearly identical in almost all promoters. RNA polymerase isn't sentient, but its chemical structure requires certain shapes and charges in the DNA being transcribed; if the promoters aren't there... well, the base-pairs _do_ get "passed over." furthermore, when introns occur within gene regions [as they frequently do], various enzymes actively excise the intron RNA from the mRNA strand _before_ that strand is translated. what's left is swiftly degraded untranslatable RNA.

really, only 3% of the human genome actively codes for genes and regulatory stuff. over half of the genome is thought to be duplications of parts of the active protein-producing genome, ranging from a few basepairs to hundreds of kbp and multiple genes. people have hypothesized uses for introns before. one suggestion is that introns and non-coding regions provide a place where mutations can accumulate without harming the organism. this provides organisms with a sort of "bank" of different proto-genes, created by transposition, non-homologous unequal crossing-over, or simple mutation. occasionally this random mutation produces a new functional gene. sometimes these genes are deleterious to the organism, or simply neutral. but occasionally they provide a selective advantage, and persist. the myoglobin gene, for example, evolved from an extra copy of the human beta-globin gene.

so we already knew that the non-coding DNA wasn't simply "junk". but it's interesting to hear that such large and highly conserved regions exist. the fact that a quarter of these regions are actually introns in genes for embryonic development does seem to support professor hassler's suggestion, although i wouldn't necessarily assume that "all of the non-coding DNA" is actively doing something "more important than coding for proteins."
posted by ubersturm at 4:46 AM on May 13, 2004

i swear i did a search for dna and nothing that looked relevant came up. i'm sorry about the double post. poo.
posted by jessica at 5:45 AM on May 13, 2004

> I find it hard to believe that 'junk' DNA exists.

Do you find your appendix, tailbone, and second kidney hard to believe also?

Organisms aren't like designed machines, evolution is a blind process and leads to, on the surface, "odd" things. Junk DNA is just part of the game.
posted by skallas at 10:10 AM on May 13, 2004

I can't wait for Norton SpeedGene, the genetic optimizer that edits out junk DNA! There'll be genetically-complete humans with perhaps only one or two chromosomes.
posted by kindall at 11:40 AM on May 13, 2004

I'm glad you mentioned John Mattick's research, snarfodox -- his team was co-author of the Science paper referred to in the BBC story.
posted by blue at 4:52 PM on May 13, 2004