Just like in our DNA...

[Martijn Faassen]

Guido van Rossum <guido at cnri.reston.va.us> wrote:
> wtanksle at dolphin.openprojects.net (William Tanksley) writes:

>> I thought that had been determined a while ago -- it's the explanation I'm
>> familiar with, in my non-specialist position.  In fact, one source I saw
>> (I have no recollection at all where) claimed that most of our coding DNA
>> is similar to most other species, and only the noncoding DNA is really
>> different.
>> 
>> Seems kinda far-fetched, but there you have it.

> The idea that most DNA is the same seems plausible to me -- like a
> "subroutine library".  It could explain how certain variations
> (e.g. different skin coloring patterns) can show up through
> "mutations" very quickly if the environment changes.

> It would also explain in part what viruses (the biological kind!) do:
> they make calls into the subroutine library!

Actually viruses in Tierra evolve that do exactly that. At least, they
call the main copying subroutine of the host's sequence. Tierra is 
mentioned earlier in this thread. My own non-released Tierra-like
system, Cielo, does not evolve such viruses, however; probably because
I didn't code a 'call' and 'ret' opcode. I do see weird code reuse
and bizarre assembler language trickery; I need to study these critters
that evolved in this program I wrote to figure out why the heck they
do whatever they do. Evolved doubly nested loops (with exit conditions, of
course!) from scratch. Little or no junk 'DNA' appears, because 
construction materials are a scarce resource. If it's not, lots of junk
does appear and I tend to get mass extinctions due to overcrowding and
gluttony. :)

> Of course there's also the matter that a large fraction of the genetic 
> code encodes the basic cell metabolism (which is extremely complicated 
> and totally essential to everything else) rather than outward
> appearance and specializations like fang size or tail length.

> I don't know that the difference would be in the non-coding DNA, though.

I don't think so, as the cell metabolism is still ran by proteins,
which DNA codes for. It's been found that DNA and especially RNA
can have quite significant enzymatic effects, however (like proteins). It's
though that this was important in early pre-protein evolution. It's 
conceivable some non coding DNA still has this effect, though since it's
not transcribed to RNA (which would be the real enzyme) this is unlikely..

Okay, looking this all up a bit:

There are introns, which can apparently can be spliced or even be self
splicing, so these can be there due to self replication on the genetic
level. Such a viral intron could replicate quite a bit until the cell
started to suffer from it significantly, though there's a limit of course.
This limit is far smaller for bacteria which rely on replication speed, so
that there is strong pressure against such introns there, and you see
far less of them as a result.

The big mystery is the stuff that doesn't seem to be translated into RNA
at all and thus doesn't seem to code for any protein (or has enzymatic
RNA). One theory I heard about is the following; often these junk regions
look very much like genes that are active, but mutated somewhat. They may
become accidentally activated through mutation. Thus this junk DNA could
form an evolutionary reservoir for interesting genes. It's unclear how 
such a setup could evolve, though, I think.

Anyway, way off topic. I probably got it all wrong anyway. :)

Regards,

Martijn
-- 
History of the 20th Century: WW1, WW2, WW3?
No, WWW -- Could we be going in the right direction?