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 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.

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!

> 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 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?

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