> According to billgr@cco.caltech.edu:
>
> Gene:
> > > Information loss for eucaryotic cells (for all I know about it) seems
> > > to not occur until the mRNA is generated. At this point the introns
> > > are removed and the 5' and 3' regions which govern the RNA polymerase
> > > action are cut off. How you could possibly reconstruct them is not known
> > > to me. I would say the lesser information loss occurs at mRNA
> > > translation to protein. You could, in theory, duplicate the codons since
> > > you have a limited number of selections. How you would replace the
> > > control regions and introns is harder. Codon usage is specific for
> > > individual creatures and the wrong codon choice could doom your coded
> > > protein in certain instances. I work on Entamoeba histolytica and it
> > > has never yet been seen to use 4 codons and another 6 are quite rare.
> > > E. histolytica is a very AT rich organsim. Certain thermophilic organisms
> > > are very GC rich.
>
> Sorry I was wrong here. Upon further discussion, there are three places
> that information seems to be lost. When the DNA goes to the initial RNA
> transcript, you lose the information contained in the 5' and 3' control
> regions--that is upstream and downstream of the DNA there are elements
> which tell RNA polymerase where to bind and (I think) how tenaciously.
> These are not included in the RNA transcript. I don't know how they
> could be retrieved.
OK, so these are like the 'start' and 'stop' codons? Or just catalysts
which mark off coding and non-coding regions of the genome? (By telling
the polymerase where to bind.)
> Next, the introns are lost when RNA goes to mRNA. HOw this could be
> reconstructed is also a mystery to me.
>
> Lastly, the information about the specific codons used is lost in the
> degeneracy of the genetic code when mRNA is translated to protein.
OK, this last sounds like what my idea of the coding process was. I'm
not very familiar with introns and why they'd be lost. Would my
molbio textbook talk about this? I understand introns are fairly new
on the scene (at least as far as textbooks might be concerned).
> > > thermophilic organisms would result in the DNA being denatured (AT-rich
> > > regions melt more readily than GC rich regions since ATs are held together
> > > by two hydrogen bonds while GC pairs have three) at the temperatures at
> > > which they exist.
> >
> > Fascinating. So there are 'higher-level' constraints on relative
> > abundances on the bases?
>
> Yes, certain molecules of the DNA or RNA duplicating machinery seem to
> have different tolerances for stretches of particular bases depending on
> the organism.
That is interesting. As you may know, in coding theory such codes sound
like NRZ codes (non-return-to-zero). That is, your code can't allow more
than a certain number of zeroes in a row, otherwise the timing will drift
on the readout device. For example, in a CD player, I think the max number
of zeroes in a row is like 4 or 5. This makes it necessary to pick an
ECC which doesn't have the possibility of concatenating more than the
critical number of zeroes. i.e. you can't have one codeword with 101000
and another of 000101110 because if the two come in order, you have 6
zeroes--too many.
-Greg