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Author Topic:   The "Digital Code" of DNA
Fosdick 
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From: Upper Slobovia
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Message 4 of 143 (397722)
04-27-2007 12:23 PM
Reply to: Message 3 by AZPaul3
04-26-2007 4:43 PM


Crick's seminal paper
AZPaul3 asks:

Cannot a simple chain of, say 5 aminos, or maybe even 50 aminos, not be considered a protein? The incredulity certainly lessens at this level. And if we take the reasonable assumption of many millions of trials daily over many millions of years, does this not lessen it even more?

Maybe they can, or did. Maybe the question has more to do with the first heritable protein. Anyway, your assumptions are not far fetched.

I finally got hold a copy of F.H.C. Crick's 1968 paper "The Origin of the Genetic Code" (J. Mol. Biol., 38, 367-379) through my public library (couldn't find a copy of it on web). I've read it once, and I will try to summarize it later when I feel I have my arms around all of his very well-considered points and principles. They must be given careful consideration. Another scientific cohort of Crick's, Leslie Orgel, came up with similiar arguments for the evolution of the genetic code, and his paper was co-published along with Crick's.

One thing I might say is that Crick, and apparently Orgel, too, give considerable credit to the possibility that proto-genes were indeed stereochemical with the proteins that produced, which is to say a nucleic acid could contain various "cavities" for various proteins and build them stereochemically without the need for a digital code. And this may have even been the predecessor of digitally coded genes. Crick also considers "the frozen accident theory," requiring a universal code.

Needless to say, there is a lot here to be digested. Crick's reasoning, and that of Orgel, must have sparked many studies and papers on this aspect of abiogenesis. If there are known mechanical links between primitive stereochemical processes for building proteins to the digital-encryption processes of genes that do not require stereochemistry, then I'm open for learning about them.

—HM

Edited by Hoot Mon, : No reason given.


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 5 of 143 (397723)
04-27-2007 12:28 PM
Reply to: Message 1 by kuresu
04-26-2007 2:17 PM


kureswu wrote:

I argue, as do many others:

DNA/RNA are just chemicals. Not something more thanks to this "digital code". This is not a hinderance to any hypothesis of abiogenesis.


kuresu, any chance you could get hold of a copy of Crick's paper "The Origin of the Genetic Code" (see Message 4)?

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 7 of 143 (397804)
04-27-2007 7:22 PM
Reply to: Message 6 by Modulous
04-27-2007 2:55 PM


I wasn't the first person to think of this by a long shot. Darwin said it a looong time ago.

Mod, did he? Do you happen to recall where? I think it deserves principle status.

—HM


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 Message 10 by Rob, posted 04-29-2007 10:23 AM Fosdick has responded

  
Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 12 of 143 (398129)
04-29-2007 12:10 PM
Reply to: Message 10 by Rob
04-29-2007 10:23 AM


rob, you wrote:

'I wonder how much entropy exists in the information processing of the two systems? And is that relevant to this discussion in your opinion'?...Is a pre-bio ecosystem really even an ecosystem?...It is not as though a universe could have just any combination of laws and componenets, and allow for life. And the same goes with the 'pre-bio ecosystem'. Is a pre-bio ecosystem really even an ecosystem? Now, I am a layman. So I am more than wiling to be corrected on any of this. But I will respond only to Hoot, and perhpas Modulus.

I'm not sure how to respond to you, except to say that mechanical systems, informational systems, genetic systems, biosystems, ecosystems, etc., all show evidence or appearance of entropy production, regardless of their material and/or informational content and structure.

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 13 of 143 (398137)
04-29-2007 12:19 PM
Reply to: Message 11 by ringo
04-29-2007 11:12 AM


It's a question of survival
Ringo wrote:

DNA isn't a blueprint, it's a machine.

I agree. But does this adequately account for the gene? Remember, the genes survives those DNA hangouts by some immense measure of time—much longer than those frilly and ephemeral molecules can endure.

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 16 of 143 (398217)
04-29-2007 8:02 PM
Reply to: Message 15 by NosyNed
04-29-2007 12:46 PM


Re: It's a question of survival
Nosy wrote:

Actually only very highly conserved genes survive long periods of time. The genes as patterns in the chemistry are constantly undergoing change and don't survive so very long in geologic time (some millions of years) (though the time is long compared to the lifetime of any molecule).

The fact that genes outlive their molecules is remarkable enough. They can outlive their species, too, often by a large margin. Your chemicals have long memories.

Even the conserved patterns don't survive because they are "special" in any mystical way. They are reproduced in astronomical numbers and almost astronomical numbers of them don't survive but "surcumb" to a mutation but "highly conserved" means any such changed ones are destroyed very quickly. So genes "survive" only by having most near copies of them thrown away. Yes, this mechanism does account for the conserved patterns we call genes.

Makes you wonder how there are any species at all, with so much change going on. What is the integrating factor that accounts for continuity in a species or a genome? (Darwinian bait for the students of molecules.)

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 18 of 143 (398322)
04-30-2007 10:46 AM
Reply to: Message 17 by NosyNed
04-29-2007 9:36 PM


Re: Selection is the "integrating" factor
Nosy wrote:

What accounts for the continuity is selection...It is awesome that these chemicals do have long memories indeed. As Dawkins has pointed out they are a history book recording the environments that our ancestors have had to survive in. It's just a bit of a cluttered recording now since the orginals have been used as sort of a palimpsest.

Why couldn't those molecular memories be the integrating factor? Selection doesn't remember anything. But a population does.

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 20 of 143 (398344)
04-30-2007 11:55 AM
Reply to: Message 19 by NosyNed
04-30-2007 11:10 AM


Re: Selection is the "integrating" factor
Nosy wrote:

Since you haven't defined "integrating factor" I can only guess at what the h. you are talking about.

If you are willing to ascribe to selection the attribute of "force," as in "evolutionary force," then what is that "force" acting against? Answser: It is acting against some other "force," if the metaphor holds, and most people think it does. That "force" must be some measure of a popuation's "integrity" or "continuity." It makes no sense to use "force" as an evolutionary metaphor without referring its "anti-force." That "anti-force" woud be the population's memory of its operational structure. In such cases, then, a population's genes may act "forcefully" to resist the "forces" of selection. Yes or no?

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 22 of 143 (398450)
04-30-2007 7:11 PM
Reply to: Message 21 by NosyNed
04-30-2007 4:25 PM


Re: Crazy Conflation
Nosy said:

However, if selection is a 'force' 'pushing' against something then the something it 'pushes' against is mutation...Selection and mutation are the two major counter balancing "forces" that act upon the gene pool.

But mutation is a "force" that acts to change the gene pool. Does this mean that selection is what holds it together? Could be. This would mean then that internal "forces" act to corrupt the genome, while external "force" act to hold it together. Curious, but probably true, since selection is well known to shape genomes.

Somehow I need to see a ghost in the machine. Gotta do something about that!

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 26 of 143 (400592)
05-15-2007 12:16 PM
Reply to: Message 25 by ringo
05-01-2007 1:56 AM


Back to digital codes
Rob asks:

... aren't cookie cutters designed? And aren't cookies made (cutter or no cutter)?

Ringo responds:

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


Ringo, no matter how much you insist that DNA is only a machine, you continue to evade to point that this machine operates on the principles of digital codfication.

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:

I this case, the machine needs a digital "brain" (processor) to interpret the code. Change one digit and the result will be different. But the DNA "machine" has evolved a digital code that uses optimized redundancy as a hedge against mutation. Thus, changing one digit may not always mean a change in the machine's product—a protein.

My point, again, is that your DNA "machine" is more than just a chemical operation; it requires a digital code and a way to read it. 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? Obviously, that's what happened to form the genetic "machinery" of biological life. Any intelligent person would have to be quite impressed by this clever feat of natural evolution.

I believe nature invented her own digital code for biological applications. Indeed life may be nothing more than squishy versions of the Jaquard loom. The question bugging rob is whether or not life needed a special Jaquard equilavent to get going. He thinks it did. I think nature did it her own. And you, Ringo, believe it never happened to any level of importance anyway so why bother with it.

Some machine, this pooch sitting next to me, who is a Labrador-retriever/Irish-setter mix of digital information.

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 28 of 143 (400625)
05-15-2007 7:09 PM
Reply to: Message 27 by ringo
05-15-2007 1:58 PM


Re: Back to digital codes
Ringo, you wrote:

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.


Your insistence on "separate" is a bit arbitrary. Is the pilot really "separate" from his/her airplane? 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 don't think it was a "Magnificent" installment, as rob might prefer, but why didn't rocks get to have digital codes? They are chemical too.

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

Well then could you show me the principles that account for the iinstallation of a digital code into chemical machines? Do you know of any chemical machines that have this code that are not part of biological machines?

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 30 of 143 (400640)
05-15-2007 8:15 PM
Reply to: Message 29 by ringo
05-15-2007 7:45 PM


Re: Back to digital codes
Ringo, you said:

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.

Ringo, I think it ALL can be explained by chemistry to satisfy the context of your desire. But how can you disagree that DNA is different from other molecules when molecular biologists have adequately confirmed that DNA (and RNA) is the only carrier of genetic information, and that other big molecules are not.

Sure, it's ALL chemistry to a chemist. But try looking at it as an evolutionary biologist. Those genes are hard to ignore (especially living south of Canuckistan here in the 21st century!).

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 32 of 143 (400729)
05-16-2007 1:13 PM
Reply to: Message 31 by ringo
05-15-2007 8:27 PM


Re: Back to digital codes
Ringo, you wrote:

I'm saying that the information is carried in the structure of the molecule itself.

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.

The structure is the "information".

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

All molecules carry structural information -

But do they all carry digital information?

- it just isn't used as genetic information by other molecules.

True enough. The shifting sands of the Sahara Desert have no need for genetic information to shape its dunes.

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

Ah, yes, the imperious “us.” I doubt if I can show you anything that will correct your chronic myopia. If genetic codes are too much for you then what am I suppose to say.

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 34 of 143 (400754)
05-16-2007 3:04 PM
Reply to: Message 33 by ringo
05-16-2007 2:16 PM


Ringo's digitophobia
Ringo wrote:

The order is the structure.

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

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

…You haven't shown anything yet, except your personal incredulity.


And I suppose your personal credulity is sufficient to trump that of Richard Dawkins, who says in River Out Of Eden (1995, p. 19):

quote:
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.
Why are you so affraid of these biological digits? Aren't they chemical enough for you?

—HM


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Fosdick 
Suspended Member (Idle past 4491 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 37 of 143 (401365)
05-19-2007 12:12 PM
Reply to: Message 35 by ringo
05-16-2007 3:12 PM


Digital info: "single nucleotide polymorphisms" (SNPs)
Ringo, I still don't know why you object to viewing nucleotides as digits. You wrote:

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

Perhaps you have heard of "single nucleotide polymorphisms" (SNPs). Wouldn't you agree that SNPs are clear evidence of digital information located on the DNA moloecule? Obviously, digital SNPs are manifest in the DNA's structure, and in that of a gene, just like digital notes are manifest in a CD's structure. An entire gene can be affected by a SNP (and you wouldn't want to hear someone miss a single note of Mozart's "Piano Sonata in C "). What can be more digital than that, especially when it is encoded as a linear message on the DNA "structure" (nature's "sheet music," ay?)?

—HM


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