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Author Topic:   The "Digital Code" of DNA
Fosdick 
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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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NosyNed
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Posts: 8933
From: Canada
Joined: 04-04-2003
Member Rating: 4.5


Message 17 of 143 (398228)
04-29-2007 9:36 PM
Reply to: Message 16 by Fosdick
04-29-2007 8:02 PM


Selection is the "integrating" factor
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.)

Why do my make up things like "integrating factor">? Would you now supply your definition for this term?

What accounts for the continuity is selection. If a gene is changed too much or too fast it is selected out. Some genes have more room to move and allow for speciation. Some genes that appeared a long time ago and upon which subsequent organisms are built (things that control basic biochemical processes) are too basic and are selected for over and over. There is no mystery here at all.

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.


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Fosdick 
Suspended Member (Idle past 4045 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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NosyNed
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Posts: 8933
From: Canada
Joined: 04-04-2003
Member Rating: 4.5


Message 19 of 143 (398331)
04-30-2007 11:10 AM
Reply to: Message 18 by Fosdick
04-30-2007 10:46 AM


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

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

I never said selection remembers anything. I did, in effect, say that a population does (as recorded in it's genes) so I agree with you on that.


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Fosdick 
Suspended Member (Idle past 4045 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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NosyNed
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Posts: 8933
From: Canada
Joined: 04-04-2003
Member Rating: 4.5


Message 21 of 143 (398411)
04-30-2007 4:25 PM
Reply to: Message 20 by Fosdick
04-30-2007 11:55 AM


Crazy Conflation
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?

You are actually conflating the word force in something like F= MA with a metaphorical expression like "evolutionary force"??? !! That isn't going to enable you to make sense of things or be understood.

However, if selection is a 'force' 'pushing' against something then the something it 'pushes' against is mutation. Without selection mutation would slowly randomize the genome up to the point where there was no viable organisms.

It is acting against some other "force," if the metaphor holds, and most people think it does.

What "most" people? Metaphors are an aid to understanding they are not otherwise meaningful.

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?

To the degree that this makes any sense at all you have it backwards. The populations "memory" (whatever you might think that is) is the current state of the genome. This, in a twisted sort of way, acts as a "selective" agent too. That is you can't make up just any old genome whatever you're going to get has to come from what you had in the previous generation. And the size of change from that can't be so great as to be utterly destructive. This winnows down the vast number of possible genetic patterns that could be imagined to a terribly, eensy, teensy tiny fraction that will actually appear in the next generation.

Selection and mutation are the two major counter balancing "forces" that act upon the gene pool.


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Fosdick 
Suspended Member (Idle past 4045 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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Rob 
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Posts: 2297
Joined: 06-01-2006


Message 23 of 143 (398493)
05-01-2007 1:15 AM
Reply to: Message 11 by ringo
04-29-2007 11:12 AM


Ringo:
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.

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


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Rob 
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Posts: 2297
Joined: 06-01-2006


Message 24 of 143 (398494)
05-01-2007 1:21 AM
Reply to: Message 12 by Fosdick
04-29-2007 12:10 PM


I 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'?...

HM

I'm not sure how to respond to you,...

I was asking if you there is a tremendous difference in the amount of entropy between the two systems, and if (in you opinion) that was a clue to whether or not intelligence was involved because of the difference in efficiency?

I am not knowledgeable as to the basis of the question, but thought you might be. IOW, I do not know the difference (if any) between them, in terms of entropy, or if entropy is necessarily equivilant to efficiency. But I am hoping my gut is right, that's all...


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ringo
Member
Posts: 18286
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 1.9


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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Fosdick 
Suspended Member (Idle past 4045 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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ringo
Member
Posts: 18286
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 1.9


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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Fosdick 
Suspended Member (Idle past 4045 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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ringo
Member
Posts: 18286
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 1.9


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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Fosdick 
Suspended Member (Idle past 4045 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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