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Author Topic:   The "Digital Code" of DNA
Fosdick 
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Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 39 of 143 (401374)
05-19-2007 1:30 PM
Reply to: Message 38 by ringo
05-19-2007 12:24 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
How is that information anything other than the structure of the molecule?
Because it comprises the encoded gene. Are you really denying that genes are encoded on DNA? Are you also saying that Watson and Crick should give back their Nobel Prize in chemistry?
”HM
Edited by Hoot Mon, : No reason given.

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 Message 38 by ringo, posted 05-19-2007 12:24 PM ringo has replied

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 41 of 143 (401386)
05-19-2007 3:22 PM
Reply to: Message 40 by ringo
05-19-2007 1:40 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Ringo, you wrote:
We're talking about how the genes are "encoded". I'm saying that the "code" is simply the structure of the DNA molecule.
Here's a simple schematic of a molecule:

O - G - D

It can carry different "information" just by the arrangement of the components:

G - O - D D - O - G

What's the problem?
Thank you demonstrating my point about SNPs. I guess you agree then that a codon is a genetic "word" that expresses any one of 20 amino acids. Case closed.
”HM

This message is a reply to:
 Message 40 by ringo, posted 05-19-2007 1:40 PM ringo has replied

Replies to this message:
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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 44 of 143 (401417)
05-19-2007 7:37 PM
Reply to: Message 42 by ringo
05-19-2007 3:31 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Ringo, you wrote:
There is no "code" other than the structure of the molecule.
I do see what you are saying here: If there were no structural DNA molecules there would be no genetic code. Of course that's true. And if there were no musical instruments there would be no music either. Yet music and genes have meaning beyond their respective tools of performance. Remember, a gene does not die when its chromosome is destroyed; there are many copies of it in the gene pool”redundantly digital information. Neither does a song die when a player and his paino and sheet music are lost in a fire. I don't mean to say there is anything necessarily ethereal about genes or music, only that their meanings can be intrepreted digitally in a digital context (which is ethereal enough for me, btw).
”HM

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 Message 42 by ringo, posted 05-19-2007 3:31 PM ringo has replied

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 45 of 143 (401419)
05-19-2007 7:49 PM
Reply to: Message 43 by Wounded King
05-19-2007 7:15 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
WK wrote:
A lot of things given the high level of polymorphism which can be present without having any structural effect at all on the produced protein. Do you think you could change every third note of a Piano concerto and get away with it?
No. That's the beauty of the genetic alphabet; it has evolved redundancy in its code definitions as a means to defend against third-order SNPs.
”HM

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 48 of 143 (409169)
07-07-2007 7:48 PM
Reply to: Message 47 by happy_atheist
06-23-2007 8:57 AM


Re: Back to digital codes
HM wrote:
Music is carried by the molecular structure of a CD too, but that doesn’t mean that music is only a condition of structured plastic molecules. The same thing is true for genes.
happy_atheist replied:
That isn't true, the music is not in any way imprinted onto the molecular structure of the CD. All that is on the CD is a collection of metaphorical 1's and 0's.
I don't understand what is "metaphoriocal" about 1's and 0's. What is a digital code a metaphor of? ...another digital code?
So the question is, can exactly the same sequence of DNA produce different proteins? Does CAG represent on (and only one) protein.
CAG does not "represent" a protein. CAG is a codon of three digital nucleotides, which codes for the amino acid glutamine. It takes many codons to hold the digital instructions of an entire protein.
I'd argue that all catalysts carry the same type of information as DNA (because from my limited understanding DNA appears to catylyse protein production). So yes, if a rock has a catalytic property then it would carry the same type of information as DNA.
I don't understand what you are saying. DNA certainly does not catalyze a protein. DNA is remote to the chemical production of proteins. (I threw in "chemical for Ringo's sake, who believes molecules are only chemicals and have no way to store digital codes.) DNA is linked to proteins only by way of code translation, which is performed by messenger RNA.
”HM

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 Message 47 by happy_atheist, posted 06-23-2007 8:57 AM happy_atheist has replied

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 Message 49 by happy_atheist, posted 07-08-2007 5:02 AM Fosdick has replied
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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 50 of 143 (409260)
07-08-2007 10:57 AM
Reply to: Message 49 by happy_atheist
07-08-2007 5:02 AM


Re: Back to digital codes
Noted, but it doesn't change my point. Can CAG code form anything other than glutamine?
No.
Does the physical structure of DNA directly determine the chemicals produced via deterministic physical (or chemical if you prefer) processes, or is there something arbitary in there imposed on top?...I think you missed the actual point of my post. I know that DNA produces RNA, which then is involved in producing proteins. That still is not in any way an analogy of the production of sound from a CD. It is an analogy of the production of sound from an LP though as far as I can see....However on the CD all you have is a bit pattern of 1's and 0's.
What you don't seem to understand is that A,G,T, and C are the "bits" of the digital genetic code. I suspect that you are fixed on the idea that digital coding must involve 1's and 0's. If this is true then you need to rexamine your position.
That is why the sounds you hear are not directly imprinted onto the CD in the same way as they are on an LP.
An LP recording is not digital, but instead analog, and therefore it is not in any way equivalent to to the genetic code. A CD recording is digital is every respect, and so are the genes on DNA. Perhaps you should take a closer look at how genes operate and how mutations occur.
”HM

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 52 of 143 (409265)
07-08-2007 11:37 AM
Reply to: Message 51 by ringo
07-08-2007 11:03 AM


Re: Back to digital codes
Nevertheless, directly or indirectly, it's the "shape" of the DNA molecule that determines what proteins are produced, with no need of a fictitious "code".
"Fictitious" only if it offends your chemical religion.
Maybe then we should demand that Watson & Crick give back their Nobel Prize in chemistry, and that Crick should retract his pivotal paper on the origin of the genetic code (1968, J. Mol. Biol., 38:367-379). How can two such astute chemists wander so far off into the digital woo-woos of genetic encryption and get away with it?
”HM

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 55 of 143 (409275)
07-08-2007 12:20 PM
Reply to: Message 54 by ringo
07-08-2007 12:00 PM


Re: Back to digital codes
I use the word "fictitious" because you have still not produced one shred of evidence that the "digital code" of DNA is fact and not fiction
Well, Bill Hamilton was fond of referring to the "narrow roads of Gene Land.
Show us where Crick and Watson talk about a genetic code that is separate from the chemical properties of the molecule.
This is an absurd assertion. Of course there are no gene fairies who lift the codes gently off the DNA molecules and keep them safe in their digital hooches until they can be selected for or aganist by Mother Nature or Father Time. Is that what you think I am saying? Is this how people do their thinking up there in Canuckistan?
”HM

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 56 of 143 (409277)
07-08-2007 12:25 PM
Reply to: Message 53 by Rob
07-08-2007 11:54 AM


Re: Back to digital codes
Sorry, rob. Can't go there. Too busy picking my nose.
”HM

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 Message 53 by Rob, posted 07-08-2007 11:54 AM Rob has replied

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 59 of 143 (409282)
07-08-2007 12:42 PM
Reply to: Message 57 by ringo
07-08-2007 12:29 PM


Re: Back to digital codes
To recap, here's what I'm saying: DNA operates according to chemical principles. Period. The physical arrangement of the atoms on the molecule can be interpreted as a "code", but there is no code above and beyond the physical arrangement of the atoms in the molecule. Period.
Ringo, are you suggesting that I am referring to a metaphysical code? I fail to grasp the importance of your point. Of course it's all about physical arrangements of nucleotides. The literal equivalent to what you are saying would be something like ...'there can be no written language without words' or 'there are no oceans without water.' Ay?
”HM

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 70 of 143 (409932)
07-12-2007 10:29 AM
Reply to: Message 67 by ringo
07-12-2007 10:03 AM


Code above-and-beyond DNA
Ringo wrote:
The issue is whether or not genetic information is a "digital code" that is somehow above and beyond the structure of the DNA molecule.
No one ever said that genetic code is "somehow above and beyond the structure of the DNA molecule." That's just more tripe rolling off your finger tips. You need to get clear about what you are saying. And you have not yet shown us how or why genetic code is NOT digital. Still waiting for the revelation.
”HM

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 Message 67 by ringo, posted 07-12-2007 10:03 AM ringo has replied

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 72 of 143 (409936)
07-12-2007 10:47 AM
Reply to: Message 71 by ringo
07-12-2007 10:35 AM


Re: Code above-and-beyond DNA
Then why do you keep arguing?
Because you refuse to see that nucleic acids are capable of encoding, storing, translating, and transmitting digital genetic information. That's all.
”HM

This message is a reply to:
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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 74 of 143 (409943)
07-12-2007 11:09 AM
Reply to: Message 73 by ringo
07-12-2007 10:54 AM


Re: Code above-and-beyond DNA
Do you know of any other natural molecules besides nucleic acids that contain digital codes?

This message is a reply to:
 Message 73 by ringo, posted 07-12-2007 10:54 AM ringo has replied

Replies to this message:
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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 76 of 143 (409951)
07-12-2007 11:32 AM
Reply to: Message 75 by ringo
07-12-2007 11:20 AM


Re: Code above-and-beyond DNA
The "code" is simply a human construct used to help understand the structure. It's simpler to write a short code-word than to draw the whole structure of the molecule. That's all the "code" is. It isn't something inherent in the molecule itself.
Wrong! If DNA is not inherently capable of storing digital code, wherein the nucleotides A, C, T, and G serve as digits, then how do you explain genetic mutation by way of single nucleotide polymorphisms (SNPs)?
”HM

This message is a reply to:
 Message 75 by ringo, posted 07-12-2007 11:20 AM ringo has replied

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Fosdick 
Suspended Member (Idle past 5754 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 78 of 143 (409955)
07-12-2007 11:56 AM
Reply to: Message 77 by ringo
07-12-2007 11:43 AM


Re: Code above-and-beyond DNA?
I said that the "code" is the structure of the molecule.
Of course it is, physically, but your point is quite silly. The same thing could be said about a written language: 'Words are in the structure of the sentence, or letters are in the structure of the word.' What does that mean? Of course they are. And of course you have to have something physical to hold a code. No one's saying that genetic codes fly around on their own. Can we get past that now?
”HM

This message is a reply to:
 Message 77 by ringo, posted 07-12-2007 11:43 AM ringo has replied

Replies to this message:
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 Message 80 by ringo, posted 07-12-2007 12:05 PM Fosdick has replied

  
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