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Author Topic:   The "Digital Code" of DNA
ringo
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From: frozen wasteland
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Message 11 of 143 (398108)
04-29-2007 11:12 AM
Reply to: Message 10 by Rob
04-29-2007 10:23 AM


Rob writes:

I was thinking of responding with, "schematics and blueprints for the F22 Raptor are just pieces of paper".. or something like that.

Talk of "schematics and blueprints" seems to assume the conclusion that there is a "code".

DNA isn't a blueprint, it's a machine. And it isn't just a complex machine like an F-22, it's a machine that builds other machines.

It builds what it is capable of building, just like a cookie-cutter builds cookie-cutter-shaped cookies. No blueprint required.


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ringo
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Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 14 of 143 (398146)
04-29-2007 12:36 PM
Reply to: Message 13 by Fosdick
04-29-2007 12:19 PM


Re: It's a question of survival
Hoot Mon writes:

... the genes survives those DNA hangouts by some immense measure of time—much longer than those frilly and ephemeral molecules can endure.

Don't think in terms of individual molecules. Think in terms of "generations" of molecules.

The machines build the factories and the factories build more machines, which build more factories which build more machines.... The machines are tailor-made by the factories to tailor-make more factories.

There are no "genes" except the functions of the machines.


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ringo
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Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
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Message 25 of 143 (398503)
05-01-2007 1:56 AM
Reply to: Message 23 by Rob
05-01-2007 1:15 AM


Rob writes:

... aren't cookie cutters designed?

"Design" isn't the issue here. It doesn't matter where the cookie-cutter came from. Once it exists, it continues to turn out cookies with no need of a blueprint.

And aren't cookies made (cutter or no cutter)?

The point of the analogy is that DNA is made by a jig/template/cookie-cutter with no need of a blueprint.


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ringo
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Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
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Message 27 of 143 (400597)
05-15-2007 1:58 PM
Reply to: Message 26 by Fosdick
05-15-2007 12:16 PM


Re: Back to digital codes
Hoot Mon writes:

Let's look at the Jaquard loom for example; it's a machine for sure, but its operation is controlled by a digital code recorded on a sequence of perforated data cards:

Yes, and in the Jacquard loom, the code, cards, card-reader, etc. are separate from the machine that does the work. What you need to do (and what I have asked you to do in several other threads) is show us a separate code, separate code-carrier, separate code-reader, etc. All you've done so far is insist that they "must" be there.

Essentially, you're saying that an airplane has a pilot, so a bird must have a pilot too.

But the DNA "machine" has evolved a digital code that uses optimized redundancy as a hedge against mutation.

The DNA molecule is simply using the chemical principles built into each of its atoms and bonds. If a molecule has "evolved" to have a certain behaviour, that behaviour is still dependent on the structure of the molecule.

Don't you see why rob or any other curious person might wonder how a biological machine can evolve so as to invent it own digital code?

I haven't said anything about biological machines. I'm talking about chemical machines.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 29 of 143 (400632)
05-15-2007 7:45 PM
Reply to: Message 28 by Fosdick
05-15-2007 7:09 PM


Re: Back to digital codes
Hoot Mon writes:

Is the pilot really "separate" from his/her airplane?

He/she is certainly more "separate" from the plane than a bird's "pilot" is separate from the bird. Again, that is basically what you're claiming: that there is some spooky "pilot" which is not part of the bird's ordinary "birdness".

All I'm saying is that somewhere, somehow a digital code crept in from the side or over the top in the coruse of chemical abiogenesis.

I know, you're saying that and saying that and saying that and saying that.... I'm asking you to show us some indication that it's true. Show us something in the "behaviour" of DNA that can not be explained by chemistry.

... why didn't rocks get to have digital codes? They are chemical too.

Rocks do have "codes" - every bit as much as DNA does.

Well then could you show me the principles that account for the iinstallation of a digital code into chemical machines?

I'm saying there is no digital code. Therefore, there is no need for installation or principles to account for installation.

It's time for you to show some evidence that the "code" exists. Show us something in the nature of DNA that can not be explained by chemistry.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 31 of 143 (400642)
05-15-2007 8:27 PM
Reply to: Message 30 by Fosdick
05-15-2007 8:15 PM


Re: Back to digital codes
Hoot Mon writes:

... molecular biologists have adequately confirmed that DNA (and RNA) is the only carrier of genetic information, and that other big molecules are not.

So what?

Every molecule can do something that no other molecule can do.

The question here isn't whether or not DNA/RNA can carry genetic "information". It's how that information is carried.

I'm saying that the information is carried in the structure of the molecule itself. The structure is the "information". All molecules carry structural information - it just isn't used as genetic information by other molecules.

You have claimed that that is not a sufficient explantion. Show us the inadequacy.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 33 of 143 (400739)
05-16-2007 2:16 PM
Reply to: Message 32 by Fosdick
05-16-2007 1:13 PM


Hoot Mon writes:

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 assertion is getting old. Show us that "the same thing is true for genes".

The structure is the "information".

No. It is the order in the structure that is the information.

The order is the structure.

All molecules carry structural information -

But do they all carry digital information?

  1. You haven't shown that DNA carries "digital information".
  2. What difference does it make whether or not the information is "digital"?

I doubt if I can show you anything that will correct your chronic myopia.

That's just the point: You haven't shown anything yet, except your personal incredulity.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 35 of 143 (400756)
05-16-2007 3:12 PM
Reply to: Message 34 by Fosdick
05-16-2007 3:04 PM


Re: Ringo's digitophobia
Hoot Mon writes:

You mean to say that "Beethoven's 5th Symphony" and "O Canada" are only bunches of structural blips on a plastic disk?

I have asked you to show how DNA is analogous to a CD. Please do that.

Richard Dawkins writes:

Genes are pure information—information that can be encoded, recorded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense.

I'm not disagreeing with Dawkins at all.

Dawkins said that genes are "pure information". I'm saying that the information on a DNA molecule is based on its structure. The information is the "gene". The "gene" is the structure.

Why are you so affraid of these biological digits?

Why would I be afraid of something that doesn't exist?


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
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Message 38 of 143 (401366)
05-19-2007 12:24 PM
Reply to: Message 37 by Fosdick
05-19-2007 12:12 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Hoot Mon writes:

Wouldn't you agree that SNPs are clear evidence of digital information located on the DNA moloecule?

How is that information anything other than the structure of the molecule?


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 40 of 143 (401375)
05-19-2007 1:40 PM
Reply to: Message 39 by Fosdick
05-19-2007 1:30 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Hoot mon writes:

Are you really denying that genes are encoded on DNA?

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?

Edited by Ringo, : Added missing quotation mark.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


Message 42 of 143 (401390)
05-19-2007 3:31 PM
Reply to: Message 41 by Fosdick
05-19-2007 3:22 PM


Re: Digital info: "single nucleotide polymorphisms" (SNPs)
Hoot Mon writes:

I guess you agree then that a codon is a genetic "word" that expresses any one of 20 amino acids.

No. There are no "words" in DNA other than the structure of the molecule. The information is carried by the structure of the molecule. There is no "code" other than the structure of the molecule.

The structure of the molecule is sufficient to explain the reactions of the molecule.


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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


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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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


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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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


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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ringo
Member
Posts: 19233
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.6


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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