Read any introductory text on the subject of DNA/RNA and a simple 
picture emerges:

RNA has one strand, while DNA has two strands which are inverses of each 
other. Either way, each strand consists of four kinds of molecule 
chained together, representing four possible "letters". Three "letters" 
make a codon, which selects an animo acid. A gene describes how to make 
a protien; just read the codons and they tell you what animo acids to 
chain together, and there's your protien.

If you're lucky, you'll even get a little table listing all 4^3 possible 
codons and which of the 20 possible amino acids each one represents. 
(And you'll notice that the 3rd letter often makes no difference!) More 
to the point, there are a couple of "stop" codons which mark the end of 
the protien sequence.

That all sounds pretty simple, but back up a sec: This table can exist 
because EVERY ORGANISM KNOWN TO SCIENCE uses exactly the same 20 amino 
acids, *and* the same DNA/RNA molecules with the same four letters, 
*and* encodes animo acids in exactly the same way. (If this weren't so, 
you'd have to have a different table for each kind of organism.)

This is of course why you can take the gene for spider silk and insert 
it into a goat and have it synthesize the protien; both spiders and 
goats use DNA molecules in exactly the same way.

So all living organisms, from bacteria and fungi to mammals and birds 
(and, hell, even viruses) have this "DNA computer" that reads "programs" 
written in DNA and uses it to produce protiens. The only difference is 
that each organism is running a different program - it has different 
DNA. The machine that "runs" it is the same. Which isn't that 
surprising, given that all life presumably evoled from a single common 
ancester.



Now, dig a little deeper and you'll find that all is not quite so simple 
and straight-forward. If a *human being* had designed the system, they 
would have designed something simple like this. But life was not 
designed, it happened by accident. And the more you study it, the more 
you realise that it often goes about things in the most over-complicated 
way possible! ;-)

Firstly, the books tell you that a protien is just a chain of amino 
acids, but that's not strictly true. Some protiens are actually several 
"seperate", unattached chains, which are knitted together as they're 
synthesized in such a way that you can't easily pull them apart. 
Strictly they're seperate molecules (they aren't chemically bonded), but 
in reality they function as a single chemical entity.

Not only that, but some protiens are "modified" after being built. You 
read off the DNA and chain the designated animo acids together, but then 
you take the resulting molecule and add extra bonds or glue bits onto it 
or otherwise modify it. So the final result is no longer a simple chain 
of 20 animo acids; it has become a bit more complex than that.

(For example... hemoglobin contains iron. That's not an animo acid!)



It gets slightly weirder than that, though:

http://en.wikipedia.org/wiki/Selenocysteine

This is a standard amino acid, but there's no codon for it. Instead, the 
RNA strand has a kind of a kink in it, and that turns the UGA (uracil, 
guanine, adenine) codon from being a stop codon into being a 
selenocysteine codon. (Over a certain range of bases, anyway.)

So the "standard genetic code" is modified by a loop in the RNA. Weird!



OK, so it's not quite as simple as it looks. But stick this in your pipe 
and smoke it:

http://en.wikipedia.org/wiki/Pyrrolysine

Pyrrolysine is an animo acid similar to lysine. But here's the 
interesting thing: The RNA code for pyrrolysine is "UAG" (uracil, 
adenine, guanine). The thing is, in *most* living organisms, that's a 
stop codon. But in certain archaea species, instead of being a stop 
signal, it selects pyrrolysine.

Read that again: The *same* genetic code has a *different* meaning in 
different organisms.

In these obscure organisms, there are 22 available amino acids, not 21. 
And that means that the genetic code itself can change over time. That 
least the question: Did the original genetic code have more than 21 
amino acids? Did these organisms evolve a new amino acid, or did all 
life originally have it and subsequently lost it? And when did all this 
happen??

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On 6/4/2010 4:08 AM, Invisible wrote:
> Read any introductory text on the subject of DNA/RNA and a simple
> picture emerges:
>
> RNA has one strand, while DNA has two strands which are inverses of each
> other. Either way, each strand consists of four kinds of molecule
> chained together, representing four possible "letters". Three "letters"
> make a codon, which selects an animo acid. A gene describes how to make
> a protien; just read the codons and they tell you what animo acids to
> chain together, and there's your protien.
>
> If you're lucky, you'll even get a little table listing all 4^3 possible
> codons and which of the 20 possible amino acids each one represents.
> (And you'll notice that the 3rd letter often makes no difference!) More
> to the point, there are a couple of "stop" codons which mark the end of
> the protien sequence.
>
> That all sounds pretty simple, but back up a sec: This table can exist
> because EVERY ORGANISM KNOWN TO SCIENCE uses exactly the same 20 amino
> acids, *and* the same DNA/RNA molecules with the same four letters,
> *and* encodes animo acids in exactly the same way. (If this weren't so,
> you'd have to have a different table for each kind of organism.)
>
> This is of course why you can take the gene for spider silk and insert
> it into a goat and have it synthesize the protien; both spiders and
> goats use DNA molecules in exactly the same way.
>
> So all living organisms, from bacteria and fungi to mammals and birds
> (and, hell, even viruses) have this "DNA computer" that reads "programs"
> written in DNA and uses it to produce protiens. The only difference is
> that each organism is running a different program - it has different
> DNA. The machine that "runs" it is the same. Which isn't that
> surprising, given that all life presumably evoled from a single common
> ancester.
>
>
>
> Now, dig a little deeper and you'll find that all is not quite so simple
> and straight-forward. If a *human being* had designed the system, they
> would have designed something simple like this. But life was not
> designed, it happened by accident. And the more you study it, the more
> you realise that it often goes about things in the most over-complicated
> way possible! ;-)
>
> Firstly, the books tell you that a protien is just a chain of amino
> acids, but that's not strictly true. Some protiens are actually several
> "seperate", unattached chains, which are knitted together as they're
> synthesized in such a way that you can't easily pull them apart.
> Strictly they're seperate molecules (they aren't chemically bonded), but
> in reality they function as a single chemical entity.
>
> Not only that, but some protiens are "modified" after being built. You
> read off the DNA and chain the designated animo acids together, but then
> you take the resulting molecule and add extra bonds or glue bits onto it
> or otherwise modify it. So the final result is no longer a simple chain
> of 20 animo acids; it has become a bit more complex than that.
>
> (For example... hemoglobin contains iron. That's not an animo acid!)
>
>
>
> It gets slightly weirder than that, though:
>
> http://en.wikipedia.org/wiki/Selenocysteine
>
> This is a standard amino acid, but there's no codon for it. Instead, the
> RNA strand has a kind of a kink in it, and that turns the UGA (uracil,
> guanine, adenine) codon from being a stop codon into being a
> selenocysteine codon. (Over a certain range of bases, anyway.)
>
> So the "standard genetic code" is modified by a loop in the RNA. Weird!
>
>
>
> OK, so it's not quite as simple as it looks. But stick this in your pipe
> and smoke it:
>
> http://en.wikipedia.org/wiki/Pyrrolysine
>
> Pyrrolysine is an animo acid similar to lysine. But here's the
> interesting thing: The RNA code for pyrrolysine is "UAG" (uracil,
> adenine, guanine). The thing is, in *most* living organisms, that's a
> stop codon. But in certain archaea species, instead of being a stop
> signal, it selects pyrrolysine.
>
> Read that again: The *same* genetic code has a *different* meaning in
> different organisms.
>
> In these obscure organisms, there are 22 available amino acids, not 21.
> And that means that the genetic code itself can change over time. That
> least the question: Did the original genetic code have more than 21
> amino acids? Did these organisms evolve a new amino acid, or did all
> life originally have it and subsequently lost it? And when did all this
> happen??
Even crazier, the whole thing is massively parallel, so unlike a CPU, 
**everything** tries to happen all at once, with the only limitation 
being the room available to run the code. Sort of what Microshaft tries 
to do when booting Windows, but which doesn't work, causing your 
computer to slow to a nightmare crawl for 3-4 minutes, when loading 
things with delays would only take 3 seconds. lol

But, in general, its figured that things started with a very "small" 
number. And, more interestingly, there is a guy working on seeing if he 
can make other patterns, and have them code things too, which don't 
exist at all in any organism.

-- 
void main () {

     if version = "Vista" {
       call slow_by_half();
       call DRM_everything();
     }
     call functional_code();
   }
   else
     call crash_windows();
}

<A HREF='http://www.daz3d.com/index.php?refid=16130551'>Get 3D Models, 
3D Content, and 3D Software at DAZ3D!</A>

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Patrick Elliott wrote:

> But, in general, its figured that things started with a very "small" 
> number. And, more interestingly, there is a guy working on seeing if he 
> can make other patterns, and have them code things too, which don't 
> exist at all in any organism.

http://en.wikipedia.org/wiki/Expanded_genetic_code

-- 
http://blog.orphi.me.uk/
http://www.zazzle.com/MathematicalOrchid*

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Am 04.06.2010 13:08, schrieb Invisible:

> So all living organisms, from bacteria and fungi to mammals and birds
> (and, hell, even viruses) have this "DNA computer" that reads "programs"
> written in DNA and uses it to produce protiens.

(Not exactly - Viruses are just "programs", using the "DNA computer" - 
or the "RNA computer subsystem" - built into cells of other organisms.)

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clipka wrote:
> Am 04.06.2010 13:08, schrieb Invisible:
> 
>> So all living organisms, from bacteria and fungi to mammals and birds
>> (and, hell, even viruses) have this "DNA computer" that reads "programs"
>> written in DNA and uses it to produce protiens.
> 
> (Not exactly - Viruses are just "programs", using the "DNA computer" - 
> or the "RNA computer subsystem" - built into cells of other organisms.)

Viruses are also not "living organisms". (Depending on which definition 
you use...)

-- 
http://blog.orphi.me.uk/
http://www.zazzle.com/MathematicalOrchid*

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On 2010-06-04 07:08, Invisible wrote:
> If a *human being* had designed the system, they would have designed
> something simple like this. But life was not designed, it happened by
> accident.

"Prove it."

;)

(What if it turns out that life on earth was in fact deliberately 
designed by aliens, which in turn...unquestionably evolved?  *x-files 
and/or twilight zone music*)

--
Tim Cook
http://empyrean.freesitespace.net

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On 07/06/2010 10:50 AM, Tim Cook wrote:
> On 2010-06-04 07:08, Invisible wrote:
>> If a *human being* had designed the system, they would have designed
>> something simple like this. But life was not designed, it happened by
>> accident.
>
> "Prove it."
>
> ;)
>
> (What if it turns out that life on earth was in fact deliberately
> designed by aliens, which in turn...unquestionably evolved? *x-files
> and/or twilight zone music*)
>

Then sue them for gross neglect <Boston Legal theme music>

-- 

Best Regards,
	Stephen

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On 2010-06-07 06:06, Stephen wrote:
> On 07/06/2010 10:50 AM, Tim Cook wrote:
>> (What if it turns out that life on earth was in fact deliberately
>> designed by aliens, which in turn...unquestionably evolved? *x-files
>> and/or twilight zone music*)
> Then sue them for gross neglect <Boston Legal theme music>

Further entertainment:  what are the implications of human beings 
creating lifeforms that can evolve?  Will they dismiss our existence at 
a certain point because we would then have to have been created and so 
forth?  Will we then not have existed, in the first place?  Are we just 
a mechanism of evolution that will eventually result in supersentient 
grey goo?

--
Tim Cook
http://empyrean.freesitespace.net

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