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Author Topic:   The "Digital Code" of DNA
kuresu
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From: boulder, colorado
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Message 1 of 143 (397547)
04-26-2007 2:17 PM


Okay, so this is going to be a continuation off of the Abiogenesis thread. And, it's one I get to start! (yes, there's some humor there--there are already like 3 or so threads that got started thanks to the Abiogenesis thread, one I started. Not sure if a single one made it out of here [the PNT])

Anywho, in the previous thread, unless I'm grossly misrepresenting Hoot Mon's argument, he argues that:

DNA/RNA is a "digital" code. And, while this code is an intrinsic property of DNA, it is not the result of any chemical properties that we know of today. This, he argues, is an argument against any hypothesis of abiogenesis, because he just can't see how this "code" arose. Nevermind the argument of incredulity present.

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.

Keep in mind, these two arguments are just rough approximations of what is like the last 50ish posts in the linked thread (Abiogenesis). That thread has hit the 300 mark, and the discussion still continues. Let it continue here.


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AdminNosy
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Message 2 of 143 (397549)
04-26-2007 2:26 PM


Thread moved here from the Proposed New Topics forum.
  
AZPaul3
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Message 3 of 143 (397578)
04-26-2007 4:43 PM


From Abiogenesis - the closed thread.

Hoot Mon:

I believe its was Hoyle and Wickramasinghe who calculated the probability of the first protein molecule to be on the order 1 in 10^120.

I don’t know about those two and I’m being lazy in not looking them up, but, seems to me the first question is “What first protein?” Proteins are chains of amino acids. Reasonable speculations indicate a whole slog of aminos in a pre-biotic Earth environment. Doesn’t seem to me to be so far fetched that two such thingies glom on to each other and viola…first protein. Probably doesn’t do much except float around looking for more candidates to join with.

10 to some big number seems a bit linear in thinking, doesn’t it? If we’re talking some large mega-protein like hemoglobin then I can understand the incredulity of its spontaneous generation, but, I hope this is not what is being offered here.

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?


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Fosdick 
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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 
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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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Modulous
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Message 6 of 143 (397732)
04-27-2007 2:55 PM
Reply to: Message 5 by Fosdick
04-27-2007 12:28 PM


In the previous thread, Hoot, you said:

If you are right, Mod, then you have discovered an important biological principle. I'll call it the "abiogenic truncation principle"—once abiogenesis is successfuly established it cannot happen again, because existing biotic will truncate its late appearance by having it for lunch.

Modesty forbids me from leaving it there. I wasn't the first person to think of this by a long shot. Darwin said it a looong time ago.


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Fosdick 
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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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Modulous
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Message 8 of 143 (397873)
04-28-2007 5:44 AM
Reply to: Message 7 by Fosdick
04-27-2007 7:22 PM


It is mostly referenced to a letter he wrote to JD Hooker:

quote:
It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.

The date given for this is often February 1, 1871. I am unfortunately unable to find the full letter online.


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Dr Adequate
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Message 9 of 143 (397928)
04-28-2007 11:24 AM
Reply to: Message 8 by Modulous
04-28-2007 5:44 AM


To be precise, Darwin's son added this quotation from Darwin as a note in parentheses to a letter Darwin wrote to Hooker. See Life and Letters of Charles Darwin, Vol. II. He doesn't say where Darwin wrote this.

Edited by Dr Adequate, : No reason given.


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Rob 
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(1)
Message 10 of 143 (398091)
04-29-2007 10:23 AM
Reply to: Message 7 by Fosdick
04-27-2007 7:22 PM


I have a question for Hoot.

Kuresusaid:

DNA/RNA are just chemicals. Not something more thanks to this "digital code".

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

But then I thought to myself, 'I wonder how much entropy exists in the information processing of the two systems? And is that relevant to this discussion in your opinion'?

Btw, I first saw that 'Darwin?' quote Mod is reffering on a DVD produced by the discovery institute. They had brought it up for a different reason and also did not give it with full conviction. They did attribute it to Darwin, but if my memory serves, it was offered as conjecture on the part of Darwin. Yet subsequent biologists have remained in that arena which we affectionately call abiogenesis.

My own thoughts are that the ecosystem is greatly interdependant. We have many cases of symbiosis. We are reminded constantly (in the political arena) that the environment is 'so sensitive'. Remove one domino and the whole system collapses. And though I believe those in the 'environmetalist camp' dramatize the issue, it is obviously partially correct and stands to reason.

So the question is more than how the first life could have found food 'unproduced by a biological ecosystem' (a relatively simple problem on it's own) but also that the first ecosystem would have had to form in one locale without the tendancy (that present life has) to eat itself out of house and home. I don't hink I said that very well, but I think Hoot understands.

There is so much that would have to go right, that a one time event would almost assuredly fail. And to counter this, we must believe that abiogenesis was (in a sense) being attempted many times over, and that everything (and everything adds up to a lot) just fell into place, with the failures forgotten and the sucesses moving on. And this latter deduction is the hook upon which natural selection (and evolutionary biology)is hung.

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.


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ringo
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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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Fosdick 
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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 
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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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ringo
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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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NosyNed
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Message 15 of 143 (398148)
04-29-2007 12:46 PM
Reply to: Message 13 by Fosdick
04-29-2007 12:19 PM


Re: It's a question of survival
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.

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).

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.


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