On 4-8-2011 17:18, Invisible wrote:
> On 04/08/2011 03:48 PM, andrel wrote:
>> That is sort of the software engineer's view. You can describe DNA as if
>> it is a program, but that misses most of the details.
>
> If you read most books about it, they will tell you that "hey, DNA has
> these 4 letters, and they go in groups of 3, and this table here shows
> you for every 3-letter word which animo acid it selects, and that's how
> you make proteins!"
>
> Which is basically true. But this isn't something some engineer
> designed. This is a crazy-ass thing that happened by accident! Suffice
> to say, it's way more complicated than that.

You need for instance the proteins of a living cell to do the 
transcription.

>
> You know the bit I said about compiled code being modified at runtime?
> It turns out that by attaching (or not attaching) various molecules to a
> DNA chain, you can activate or deactivate various genes. So DNA isn't
> just the program. In some sense it's also part of the cell state or
> "memory". Sometimes I wonder whether a "naked" copy of a given animal's
> genome would actually function at all; even at conception, there are
> probably markers turning genes on or off, to set the program in motion
> from the correct start point.

You can not boot a cell from scratch. 
http://www.ted.com/talks/lang/eng/craig_venter_unveils_synthetic_life.html

> Then there are the knots and tangles in DNA or RNA that affect the way
> it is processed. For example, human mRNA with a certain type of knot in
> it causes certain amino acids to have selenium added to them after
> transcription. So the whole "codons code amino acids" is a vast
> simplification.
>
> Let us not even get into the fact that many proteins are modified after
> being constructed, some fold up as they are transcribed (so trying to
> simulate folding of the complete, finished protein is a doomed
> endeavour), one require "chaperone" proteins to guide their folding in
> the correct direction, many proteins are synthesized inactive and have
> to be "activated" before they will do anything. Recent research even
> suggests that "cellular crowding" may be important for some protein
> activities.
>
> http://en.wikipedia.org/wiki/Cellular_crowding
>
> On top of all that, it turns out that RNA itself can be both a data
> carrier like DNA *and* a catalyst like proteins. Wrap your head around
> that one!

The mechanism that reads the code is a set of RNA molecules

>> Sometimes I wish I was 18 again today, so I could absorb enough facts
>> about how cells and organisms work to help advance the field. I am now
>> too old to understand a large enough portion to have any significant
>> contribution :(
>>
>> Yet, I still try to keep up with the field as much as I can, if only to
>> be able to understand the guys and gals further up the corridor.
>
> The more I find out, the more fascinating it all becomes. And the more
> frustrating that you can't see this stuff in action for yourself.
> (Unless your a subject area expert.)

I seem to remember you turned down an opportunity to work in my lab.

>> I do know that if I had to create life I would have done it more logical
>> and maintainable. But, that would probably not have survived for more
>> than a few generations.
>
> Computer programs generally have the property that any tiny alteration
> to them or any tiny fault in the hardware running them causes
> catastrophic failure. Living organisms are remarkably devoid of such a
> problem...
>
>
>
> Did you hear the one about the guy who tried to "evolve" an oscillator
> circuit in his lab? Used some kind of genetic algorithm to take randomly
> generated circuits and gradually modify them and keep the ones that
> acted most like an oscillator.
>
> When the guy analysed the "winning" design, it looked absolutely nothing
> like an oscillator. And yet it worked perfectly. Baffled, the guy took
> it to a friend's lab, whereupon it utterly stopped working. Now both of
> them are *really* puzzled.
>
> Long story short, it turns out it wasn't an oscillator at all. It was a
> radio receiver. It was picking up some kind of radio interference from
> some equipment in the guy's lab, which wasn't present in the other lab.
> So much for adapting to your environment, eh?

I know similar stories, yes.

-- 
Apparently you can afford your own dictator for less than 10 cents per 
citizen per day.

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