OT on DNA (or maybe not so OT) (Re: Meeting with a political person)

[kim2 at bruning.demon.nl]

On Sat, 19 Jan 2002, Alexandre Dulaunoy wrote:

> If I remember correctly my courses of biology, all the genome uses a
> representation with some proteine. (like ABCDBCDACBD...)
>

Yes well almost. Sort of. DNA is mixed source and executable code. It
stores information in quadrinary, and in eukaryotes (all multicellular
life is eukaryotic) it has double redundancy, both due to a mirror image
copy and a second total copy of {code+mirror image of code}. (the latter
is not *entirely* redundant, but let's keep it simple)

DNA is quadrinary. It has 4 "states" called bases: A T G C  .
3 bases together form a codon.

A string of codons can code for a protein, they can also code for other
things...


DNA together with its execution mechanism can probably be proved to be
able to form a turing machine. I am not aware of such a proof existing at
this time, but from where I'm sitting it seems pretty safe to at
least speculate that the system is turing complete.

[1st: All proteines are made according to DNA transcripts,
Enzyms are usually proteins. Enzyms have been shown to be able to perform
AND, OR and NOT operations, and from there you can form a turing machine,
right?]

[2nd: It's a tape, we have a tape reader, the reader can read
forward and backward, the reader has a state. The reader can alter the
tape (at "switch points" where proteines can bind). The state of the
reader can be altered when it reads the tape.]

If anyone knows a good and complete proof, I'd love to hear it. :-)

> So, is there a compiler for that (an interpreter in the cells?) ? Is it
> expression ? speech ? speech of nature ?

You could certainly recode anything currently written in binary to dna.
Try DCB (DNA coded Binary ;-)) or DCD (DNA coded Decimal ;-)), that would
always work. You might say you could express the content of a dna string
"naturally" as a sequence of base 64 (4^3) numbers.


In biological systems several values are mapped to the same meaning (as
far as proteine definition goes anyway), this makes for some extra
redundancy.

In case you hadn't noticed: In biology redundancy is a Good Thing(tm).

With or without redundancy you could store the GNU archive in DNA without
too much trouble if you like. It's a very compact and efficient data
storage medium. :-) (The only trouble is that people seem to have trouble
synthesizing really really long strands of it. But that's a different
story.)


I'm pretty much against people patenting genes. It makes it technically
illegal to do things like grow certain plants or to have sex. ^^;;;;;

Another reason it's a bad idea to patent genes is because well, it's
source code!

Maybe the biology world needs something like the FSF too. ^^;;


in the hope that this is useful,
	read you soon,
	K. Bruning