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vid
Verbosity in development


Joined: 05 Sep 2003
Posts: 7108
Location: Slovakia
vid
ever wondered how DNA works? You can see this excellent tutorial.

http://www.dnai.org

i tried many articles on this, but this one is by far best i've seen.
Post 16 May 2007, 16:40
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vid
Verbosity in development


Joined: 05 Sep 2003
Posts: 7108
Location: Slovakia
vid
note: click the "code" and other is main menu, on the top of page
Post 16 May 2007, 17:26
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DustWolf



Joined: 26 Jan 2006
Posts: 373
Location: Ljubljana, Slovenia
DustWolf
How unfortunate it's not interactive.

I've been pondering for some time if to make a page or article explaining the relationship between computer code and DNA... er... 'execution'. To explain one concept to those fammiliar with the other that is. Smile
Post 17 May 2007, 18:18
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vid
Verbosity in development


Joined: 05 Sep 2003
Posts: 7108
Location: Slovakia
vid
DustWold: there are some interactive parts. I understood everything i have read from there, without much effort.

"execution" (eg. translation) is explained there. Basically, various bits of DNA (genes) get translated to polypeptides... that's all Smile (oversimplified)
Post 17 May 2007, 21:08
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kohlrak



Joined: 21 Jul 2006
Posts: 1421
Location: Uncle Sam's Pad
kohlrak
DustWolf wrote:
How unfortunate it's not interactive.

I've been pondering for some time if to make a page or article explaining the relationship between computer code and DNA... er... 'execution'. To explain one concept to those fammiliar with the other that is. Smile


Amen, a video or something.
Post 17 May 2007, 22:22
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DustWolf



Joined: 26 Jan 2006
Posts: 373
Location: Ljubljana, Slovenia
DustWolf
vid wrote:
DustWold: there are some interactive parts. I understood everything i have read from there, without much effort.


I... kinda typoed (and so did you BTW Smile ). I wanted to say something allong the lines of "animated" instead of "interactive"... oh well.

vid wrote:
"execution" (eg. translation) is explained there. Basically, various bits of DNA (genes) get translated to polypeptides... that's all Smile (oversimplified)


Thing is tho... DNA doesn't simply translate itself to the polypeptides ( = protein), much the same way you can't always say binary code translates itself into a GUI... DNA factually processes itself, executes, much like program code, with combinational and environment-sensing logic inside to rearange the sequence of it's execution. The only difference is that DNA, utilizing a chemical process, does things very much at the same time (except where it uses semaphores), whereas binary computer code executes in distinct threads, which are no more than one, two or four (depending on number of computer cores) at a time.

Which is the main reason why it is so exciting to be explaining DNA processing to ASM coders and ASM coding to scientists aware of the function of DNA. Very Happy
Post 18 May 2007, 09:13
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Madis731



Joined: 25 Sep 2003
Posts: 2145
Location: Estonia
Madis731
"Me like very much!" Very Happy

Always been interested in chemistry/astro/phys/blah things and DNA is definitely one of them.
Post 11 Jun 2007, 17:32
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tom tobias



Joined: 09 Sep 2003
Posts: 1320
Location: usa
tom tobias
With the exception of our gametes, every other cell in our bodies contains precisely the same DNA. So, the real question is this: How does an embryonic cell "know" to activate only those components of the DNA which will cause the cell to become a big toe cell, or a tongue cell, or a retinal cell, or a stomach cell, or whatever? That is where the analogy with assembly language programming disappears. We have self modifying code, and self assembly code, but, we don't have code that "knows" when to execute only certain procedures, but not others, WITHOUT OUR EXPLICIT instructions, to do so. Yet, that is precisely the situation with a developing embryo. The DNA is there, alright, but how is regulated? Why doesn't every cell manufacture every protein? How does a cell "understand" that it must make hair, not fingernails, or teeth, or stomach acid, on the scalp? Aye. There's a thorny question....
Smile
Post 11 Jun 2007, 20:25
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vid
Verbosity in development


Joined: 05 Sep 2003
Posts: 7108
Location: Slovakia
vid
In assembly we have jumps for that Wink

AFAIK, in DNA, there are special places where DNA decoding can start, and before them are set of bases that must match set of bases in "decoder", otherwise decoder won't attach itself to DNA.

So to create cell that does something else, you must also create different "decoder".

But i am absolutely unsure about this, it would be very interesting to hear from some profesional on this.
Post 11 Jun 2007, 21:01
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tom tobias



Joined: 09 Sep 2003
Posts: 1320
Location: usa
tom tobias
vid wrote:
So to create cell that does something else, you must also create different "decoder".
The "decoder" is another nucleic acid, called "messenger RNA", mRNA. mRNA attaches in the nucleus of the cell, to one strand of the DNA (which strand???there are two, one maternal, one paternal!!), then, having "transcribed" the DNA, mRNA leaves the nucleus for the cytoplasm where it hooks up with "ribosomal RNA", a large molecule. Transfer RNA, tRNA has on one end, a specific amino acid (there are about 20 amino acids, and therefore about 20 different tRNA's, and on the other end, an "anticodon". The codon is a three nucleotide sequence on the mRNA. The anticodon has the opposite nucleotide sequence from the codon, i.e. from the mRNA. Thus if the mRNA was CGU, where C = cytosine, G = guanidine, U = uracil (thymidine in DNA), then the anticodon would have GCA, A = Adenine, because AU and CG exhibit favorable hydrogen bonding capability.
http://nucleotideresearch.com/chptr01.html
The amino acid on the opposite end of the tRNA forms a peptide bond with the growing protein, and thereafter is replaced by the succeeding tRNA, with its new amino acid. The "gene" of Gregor Mendel, 19th century (Czech? German?) monk who first demonstrated independent assortment of genes, represents a single protein. Thus, mRNA is one gene. In essence, the problem then is this: here is a huge DNA molecule. Gigantic. In our terms, it is an array of proteins, coded with triplets of nucleotides.
HOW DOES THE CELL "know" WHICH, among the thousands and thousands of genes available, to encode with the mRNA? Yet, it does, for we have fingers and toes and so on, and hair, not toenails, growing on top of our heads, yet, all those cells have precisely the same DNA, the same data base if you will. What is the selection mechanism???? That is the question.
Post 11 Jun 2007, 21:53
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Madis731



Joined: 25 Sep 2003
Posts: 2145
Location: Estonia
Madis731
Let me try to explain - we studied it long ago in school:
The cells interact with light-signals and they know who their neighbors are. This means that its built like a grid system. They "KNOW" because they can see their neighbors and act accordingly. Why we have scars is that sometimes we wreck our cells so much that they don't have sufficient info on their neighboring cells. If there's a small cut, then our bodies can heal themselves without seeming modification.
Post 14 Jun 2007, 14:16
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