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Author Topic:   The "Digital Code" of DNA
ringo
Member (Idle past 437 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 46 of 143 (401421)
05-19-2007 8:47 PM
Reply to: Message 44 by Fosdick
05-19-2007 7:37 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Hoot Mon writes:
And if there were no musical instruments there would be no music either.
That's a poor analogy. Music is separate from the instrument that produces it. The instrument is the machine that moves the air.
Genetic information is not separate from the molecule that carries it.
... a gene does not die when its chromosome is destroyed....
Again, so what?
A gene is just a particular arrangement of atoms. Of course the arrangement doesn't "die". It can be reproduced in the same way it was produced the first time.
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....
The topic is about whether there is a "digital code", not whther or not genetic information "can be interpreted" as a digital code. Genetic information could be interpreted as poetry too.
My point is that it isn't necessary to interpret it as a "code". As I have said, the chemistry is enough to explain its behaviour.

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happy_atheist
Member (Idle past 4939 days)
Posts: 326
Joined: 08-21-2004


Message 47 of 143 (406988)
06-23-2007 8:57 AM
Reply to: Message 32 by Fosdick
05-16-2007 1:13 PM


Re: Back to digital codes
Hi Hoot, I know this thread has been innactive for a while but I read something that I want to comment on that might make clear what Ringo's objections are.
Hoot Mon writes:
Well, of course. 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.
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. There is absolutely no deterministic way to extract any music from that whatsoever. In PC's there is nothing special about any bit pattern at all. You can't take a bit pattern and extract meaning from it.
To illustrate this, delete all the codecs from your PC and then try and play something in Media Player (assuming you use Windows). You'll find that it won't work. The CD is not sufficient to reproduce the music. The music is contained in the codec more than in the bit pattern itself. It's the interpretation of the bit pattern that gets passed to the speakers and turned into acoustic vibrations. Change the codec and exactly the same bit pattern could produce a different piece of music, or it could turn out to be Shakespears Macbeth, or it could be a picture.
A more accurate representation of DNA would be an LP. An LP does have (deterministically) music 'imprinted' on it. The pitts and troughs in an LP are direct representations of the vibrations in music. There is no interpretation required. There is no codec involved at all. There is a one-to-one relationship between the LP and the produced music. A physical relationship, rather than an arbitrary relationship imposed by a codec.
So the question is, can exactly the same sequence of DNA produce different proteins? Does CAG represent on (and only one) protein. If so it fits the record player analogy. Or alternatively, can CAG produce many different proteins depending on some external 'codec', in which case it fits the CD analogy.
And if you still assert that DNA fits the CD analogy, I believe Ringo's question is what is acting as the 'codec' in DNA to interpret which protein CAG should produce.
But do they all carry digital information?
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.

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 Message 32 by Fosdick, posted 05-16-2007 1:13 PM Fosdick has replied

Replies to this message:
 Message 48 by Fosdick, posted 07-07-2007 7:48 PM happy_atheist has replied

  
Fosdick 
Suspended Member (Idle past 5525 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

This message is a reply to:
 Message 47 by happy_atheist, posted 06-23-2007 8:57 AM happy_atheist has replied

Replies to this message:
 Message 49 by happy_atheist, posted 07-08-2007 5:02 AM Fosdick has replied
 Message 51 by ringo, posted 07-08-2007 11:03 AM Fosdick has replied

  
happy_atheist
Member (Idle past 4939 days)
Posts: 326
Joined: 08-21-2004


Message 49 of 143 (409240)
07-08-2007 5:02 AM
Reply to: Message 48 by Fosdick
07-07-2007 7:48 PM


Re: Back to digital codes
Hoot Mon writes:
I don't understand what is "metaphoriocal" about 1's and 0's.
Erm, well unless you can show me some 1's and 0's on a CD then I'd say they're metaphorical....used to represent the patterns the laser made when burning the CD. We could have used A and B to represent the two states if we'd wanted. This doesn't really affect my point though so I'd be happy to ignore the word metaphorical completely.
Hoot Mon writes:
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.
Noted, but it doesn't change my point. Can CAG code form anything other than glutamine? 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?
Hoot Mon writes:
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.
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.
DNA is the pattern of ridges on the LP, RNA is the vibrations of the need/arm structure (which are deterministically produced by the ridges) and the protein is the sound. There is a direct physical link between each step, nothing at all arbitrary. The needle/arm structure can only interpret the ridges etc on the LP in one way, governed by physics.
However on the CD all you have is a bit pattern of 1's and 0's. In a PC every single bit pattern can and does mean different things in different circumstances. When the CD is played it requires something in place on the PC to decide what the bit pattern means, and if you don't get the right codex you'll get the wrong sound (or no sound at all). There is something completely arbitrary about what the bit pattern means, something that is not grounded in the physical world. That is why the sounds you hear are not directly imprinted onto the CD in the same way as they are on an LP.
Now I may be wrong and there may be something about DNA and how it works that is arbitrary. But I haven't seen that presented yet.
Edited by happy_atheist, : Corrected typo

This message is a reply to:
 Message 48 by Fosdick, posted 07-07-2007 7:48 PM Fosdick has replied

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Fosdick 
Suspended Member (Idle past 5525 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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Replies to this message:
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ringo
Member (Idle past 437 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 51 of 143 (409261)
07-08-2007 11:03 AM
Reply to: Message 48 by Fosdick
07-07-2007 7:48 PM


Re: Back to digital codes
Hoot Mon writes:
I threw in "chemical for Ringo's sake, who believes molecules are only chemicals and have no way to store digital codes.
I don't think I said that molecules "have no way to store digital codes". I said that molecules do what molecules do, with no need of a fictitious "code".
The only "code" involved is the molecule.
DNA certainly does not catalyze a protein. DNA is remote to the chemical production of proteins.
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".

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This message is a reply to:
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Replies to this message:
 Message 52 by Fosdick, posted 07-08-2007 11:37 AM ringo has replied

  
Fosdick 
Suspended Member (Idle past 5525 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

This message is a reply to:
 Message 51 by ringo, posted 07-08-2007 11:03 AM ringo has replied

Replies to this message:
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Rob 
Suspended Member (Idle past 5874 days)
Posts: 2297
Joined: 06-01-2006


Message 53 of 143 (409268)
07-08-2007 11:54 AM
Reply to: Message 50 by Fosdick
07-08-2007 10:57 AM


Re: Back to digital codes
I had to make a quick stop to give you a link.
Abiogenesis
After clicking on the link, scroll down to the animated sequence of the man writing on the chalkboard.
Click the play button if the YouTube link is displayed on the website. If it does not display, then click your refresh button.
The man on the chalkboard is clip 5. After watching it, other videos will pop up in the YouTube window. Find clip 6 and 7. Watch them consecutively.
After initially clinking the play button, you can also skip around through all 7 clips by clicking the menu button in the lower right hand corner of the YouTube window.
I recommend watching the entire 7 clips. They build their argument very systematically, but the meat of the matter for this topic... is found in clips 5,6, and 7.
There is also some fascinating animation from Harvard Biovisions at this site. It is the first animated link you will see while scrolling down.
Psalm 139:14 I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
Carry on...

This message is a reply to:
 Message 50 by Fosdick, posted 07-08-2007 10:57 AM Fosdick has replied

Replies to this message:
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ringo
Member (Idle past 437 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 54 of 143 (409270)
07-08-2007 12:00 PM
Reply to: Message 52 by Fosdick
07-08-2007 11:37 AM


Re: Back to digital codes
Hoot Mon writes:
"Fictitious" only if it offends your chemical religion.
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.
Belief in fictitious entities without evidence is religion. Understanding that molecules behave according to their chemical properties is not.
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....
Yeah, blah blah blah....
Show us where Crick and Watson talk about a genetic code that is separate from the chemical properties of the molecule.

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This message is a reply to:
 Message 52 by Fosdick, posted 07-08-2007 11:37 AM Fosdick has replied

Replies to this message:
 Message 55 by Fosdick, posted 07-08-2007 12:20 PM ringo has replied

  
Fosdick 
Suspended Member (Idle past 5525 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 5525 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

This message is a reply to:
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ringo
Member (Idle past 437 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 57 of 143 (409279)
07-08-2007 12:29 PM
Reply to: Message 55 by Fosdick
07-08-2007 12:20 PM


Re: Back to digital codes
Hoot Mon writes:
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?
If that's not what you're saying, please be more clear in what you are saying.
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.

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This message is a reply to:
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Replies to this message:
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Chiroptera
Inactive Member


Message 58 of 143 (409281)
07-08-2007 12:36 PM
Reply to: Message 57 by ringo
07-08-2007 12:29 PM


Re: Back to digital codes
The physical arrangement of the atoms on the molecule can be interpreted as a "code"....
Actually, the "genetic code" is a code for a very trivial reason: the word "code" is defined in such a way so as to include the genetic code.
The definition of "code" was so extended to include DNA because of the obvious analogy with pre-W&C uses of the word "code".
The problem is not with calling the genetic code a code; the problem is when people try to draw incorrect inferences based on mixing the different possible meanings of the word; like when IDists compare the genetic code to computer codes or to the use of symbols in language.

Q: If science doesn't know where this comes from, then couldn't it be God's doing?
A: The only difference between that kind of thinking and the stereotype of the savage who thinks the Great White Hunter is a God because he doesn't know how the hunter's cigarette lighter works is that the savage has an excuse for his ignorance. -- jhuger

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Fosdick 
Suspended Member (Idle past 5525 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

This message is a reply to:
 Message 57 by ringo, posted 07-08-2007 12:29 PM ringo has replied

Replies to this message:
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ringo
Member (Idle past 437 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 60 of 143 (409284)
07-08-2007 12:47 PM
Reply to: Message 59 by Fosdick
07-08-2007 12:42 PM


Re: Back to digital codes
Hoot Mon writes:
I fail to grasp the importance of your point. Of course it's all about physical arrangements of nucleotides.
Then why do you keep arguing with me?
... are you suggesting that I am referring to a metaphysical code?
I repeat: for @#$% sake, please tell us what you are referring to.

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This message is a reply to:
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