Author Topic: Junk DNA  (Read 1176 times)

Offline shvarz

  • Moderator
  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Junk DNA
« on: June 09, 2005, 03:24:07 PM »
A good introduction into this topic can be found at wikipedia: http://en.wikipedia.org/wiki/Junk_DNA

As explained there, the term "junk DNA" is now considered to be not accurate.  What is missing from that article is a list of different kinds of junk DNA, so I'll try to make something up here.  It probably will not be complete, as I am just going to rely on my memory at this point:

1. Non-coding parts of gene.  These are regulatory sequences.  In essense, these are "cond" part of a gene.  This DNA is very well represented in DBs.
2. DNA maintenance sequences.  Centromeres and telomeres - these are needed to keep chromosomes from damage, to regulate their separation during division and other maintenance functions.  There is no need for these sequences in DBs, cause maintenance is automatic.
3. Repeatative sequences.  These are essentially viruses that got messed up, so that instead of killing the cell and coming out, they got stuck inside the cell.  They kept "re-infecting" the same cell over and over, inserting their DNA into DNA of the cell in many positions.  Many of these are non-functional.  DBs does not have this, but we have something similar with viruses - they can accumulate with time.  These sequences don't add much to evolution, they are really just parasites.
4. Pseudogenes.  These are genes that got messed up in some way and they just sit there, slowly (sic!) accumulating mutations.  They can come back to life, most likely through a recombination with an active copy of the gene.  The analog in DBs is a gene that has a messed-up condition, like "1 2 =".  The problem is that due to high mutation rate in DBs, these genes accumulate mutations much more rapidly than they do in real organisms.  Also, we don't have a workable recombination mechanism.  In this category would also go remnants of genes - not complete genes, but pieces large enough to code for something.  We don't have this kind in DBs and it would be nice to get it.
5. True junk.  Seqences that either never coded anything useful or mutated so much that there is no useful information left at all.  it is unreasonable to expect any useful thing to come out of these sequences, because they are absolutely random.  Even if you start to express them, you would not make a protein.  This is the kind of stuff that is analogous to "monkeys and War and Peace" idea.  DBs does not have this and I don't see why we would need this.  In fact, we may be better to actively avoid this.

Maybe I forgot something, but these are the major classes of junk DNA.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7716
    • View Profile
Junk DNA
« Reply #1 on: June 09, 2005, 04:04:35 PM »
Quote
2. DNA maintenance sequences.  Centromeres and telomeres - these are needed to keep chromosomes from damage, to regulate their separation during division and other maintenance functions.  There is no need for these sequences in DBs, cause maintenance is automatic.

I've been thinking of adding centromeres.  They would allow chromosomes bound together to ensure that they'll end up on opposite ends during mitosis (reproduction), and to allow crossing over to take place between them.  Obviously you need chromosomes first.

They would evolve (I imagined) from long strands of similar, repeating patterns (alpha-satellite DNA).  Like mult add mult add mult add mult add mult add mult add mult add mult add.  This would add a very functional aspect to DB junk DNA.  (Although once the centromere is formed, the DNA can change to be anything it wants, since the centromere becomes epigenetic.)

I wrote a thread on it in the suggestions forum not too long ago.

The new mutations I proposed, specifically copy, would be the main source of long repeats of the same patterns.  I'm hoping bots will eventually evolve their chromosomes to have long repeating patterns so crossing overe can occur.

Quote
4. Pseudogenes.  These are genes that got messed up in some way and they just sit there, slowly (sic!) accumulating mutations.  They can come back to life, most likely through a recombination with an active copy of the gene.  The analog in DBs is a gene that has a messed-up condition, like "1 2 =".  The problem is that due to high mutation rate in DBs, these genes accumulate mutations much more rapidly than they do in real organisms.  Also, we don't have a workable recombination mechanism.  In this category would also go remnants of genes - not complete genes, but pieces large enough to code for something.  We don't have this kind in DBs and it would be nice to get it.

This is my thinking for the primary push for DB junk DNA.  If I can get a Diploid system working, crossing over also becomes possible and allows organisms to reshuffle chromosomes every so often.

Quote
5. True junk.  Seqences that either never coded anything useful or mutated so much that there is no useful information left at all.  it is unreasonable to expect any useful thing to come out of these sequences, because they are absolutely random.  Even if you start to express them, you would not make a protein.  This is the kind of stuff that is analogous to "monkeys and War and Peace" idea.  DBs does not have this and I don't see why we would need this.  In fact, we may be better to actively avoid this.

I think this is sort of a buy 2 get 1 free.  I can't see how to have the program actively avoid something like this.  Simple deletions though, if we make organisms pay a bit of energy for every DNA instruction they copy, will keep a downward push on these kinds of sequences.

Offline Ulciscor

  • Bot Destroyer
  • ***
  • Posts: 401
    • View Profile
    • http://spaces.msn.com/members/shadowedjustice
Junk DNA
« Reply #2 on: June 09, 2005, 06:15:50 PM »
No. 3 is quite cool. I have heard of things like retrotransposons, minisatellites and stuff. Genetic parasites would be something quite cool to add because they can cause massive mutations by moving in the middle of key genes, so they have the same effect as viruses. But I'd guess the mutations they cause are probably apocalyptic for the organism, so they wouldn't be that good to have.
:D Ulciscor :D

I used to be indecisive, but now I'm not so sure.