From: jdale@cats.ucsc.edu (Jonathan Dale)
Newsgroups: sci.bio
Subject: Re: Mutations: Mostly Harmful, or Not?
Date: 30 Jul 92 06:33:14 GMT
Organization: University of California; Santa Cruz
NNTP-Posting-Host: si.ucsc.edu


In article <1992Jul30.010858.13987@cs.mun.ca> paulk@garfield.cs.mun.ca (Paul E. King) writes:
>murph_kp@jhunix.hcf.jhu.edu (Kenneth Paul Murphy) writes:
>
>>In article <1992Jul22.152155.3619@HQ.Ileaf.COM> bcking@HQ.Ileaf.COM (Christine King) writes:
>>>On another thread ("Better Living through DNA Encryption"), Jonathan Dale
>>>(jdale@cats.ucsc.edu) writes:
>>>
>>>  ...You could probably simplify it a lot (at least the engineering
>>>  parts) by ripping out all the useless garbage in our DNA, which is
>>>  over 95% (?) useless....
>>>
>>>I keep reading and hearing statements like this.  Then there's the one
>>>that goes, "Most mutations are fatal."
>>I've often heard this too and I don't see how one determines the useless-
>>ness of the 95%.  It seems unlikely to me that an organism would waste so
>>much energy synthesizing something that's useless.  Maybe we just haven't
>>figured out what it's for yet.  This is certainly true of many proteins.
>
>DNA has four nucleotides. These are linked in sequence in no particular pattern.
>The ribosomes decode this DNA into RNA by reading these nucleotides in groups of
>three. Let's call the nucleotides C, G, A, and T to make this a little clearer.
>The three nucleotides may appear in almost any combination, eg: ATT, CAT, AAA,
>GGT, and so on. Only certain combinations will code for one of 20 amino acids
>which make up all of our proteins. Other combinations simply instruct the
>ribosome to start and stop transcribing. The rest has no known purpose, except
>to protect the "good" DNA from chance mutation, and are called "missense", or
>"nonsense" sequences.
>
>paulk :-)

Wait, are you saying that some combinations code for nothing?  ie, they don't
code for either amino acids or stop/start codes?  If so, that's wrong; while
there are 64 possible combinations and only 20 amino acids, most (all?) amino
acids are coded by 2-4 different (usually similar) combinations.  These
protect against mutations because many mutations result in the same amino
acid being used, but they aren't missense or nonsense.  Missense and nonsense
sequences are sequences that don't code for proteins, but each set of three
bases still codes an amino acid or start/stop code, it just doesn't get used.

Having 64 possible combinations is redundant, and useful for protection 
against mutation.  If you had other protections against mutations (such as
CRCs and encoding, as previously described), you might want to eliminate this
redundancy and gain higher density of information.  However, changing the
nature of DNA struck me as a bit too complex, so I didn't propose it.

In another message, you respond to my comment about "ripping out the useless
garbage" in our DNA, by pointing out that much of it is necessary to protect
against mutation.  Well, yes, but this is immaterial in the context of 
installing a failsafe mutation check, such as the proposed CRC.  Incidentally,
I wonder how true this is.  Certainly, redundant sections of the code provide
protection, by being back-up copies (and all of us computer users know about
the importance of making back-ups, right?).  But entirely non-coding sections
(which no one here has estimated the amount of) might provide little or none.
A mutation event doesn't just come to the cell and randomly decide where to
hit the DNA, thus providing safety in numbers.  A smaller DNA would be a
smaller target for an x-ray, or whatever mutagen, that comes along.  Comments?
Xref: sparky sci.bio:2719 sci.med:14286 sci.cryonics:435