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Author Topic:   Is Abiogenesis a fact?
ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 286 of 303 (369550)
12-13-2006 2:41 PM
Reply to: Message 285 by Fosdick
12-13-2006 2:17 PM


Re: Digital Origins of Life?
Hoot Mon writes:
This involve silicon crystals acting as sticky templates for nucleotide construction, and thus for building RNA. But he has nothing to say about the origin of the coded genetic language.
I'm wondering why you don't just use the "template" idea instead of getting tangled up in ideas about "genetic language". Each template produces what it produces. Why does a collection of templates have to form a "language"?

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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 287 of 303 (369561)
12-13-2006 3:40 PM
Reply to: Message 286 by ringo
12-13-2006 2:41 PM


Re: Digital Origins of Life?
Ringo, you ask:
I'm wondering why you don't just use the "template" idea instead of getting tangled up in ideas about "genetic language". Each template produces what it produces. Why does a collection of templates have to form a "language"?
I'm unclear as to why you reject the notion of "language." Perhaps I should use "code" instead, but I doubt if you'll like that any better. If you reject the fact that genes are digital codes with a clearly decipherable "language" for building proteins, then you need to explain why tRNA is necessary to translate those coded messages into the proper selection of amino acids. Bear in mind that the codons on DNA are not stereochemical with the amino acids they select or the proteins they buiild. This lifts genes out of the mechanical role of being "blueprints" for proteins and places them in a role of codified prescriptions. To me, and to a lot of geneticists (e.g. Hartl) and evolutionary biologists (e.g., Dawkin), genes are "pure digital information."
”Hoot Mon

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ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 288 of 303 (369568)
12-13-2006 4:35 PM
Reply to: Message 287 by Fosdick
12-13-2006 3:40 PM


Re: Digital Origins of Life?
Hoot Mon writes:
I'm unclear as to why you reject the notion of "language."
I don't "reject" the notion of language. I'm saying that, if the notion of language confuses you, why not let go of that notion? Why not focus on the individual components of the "language" - i.e. the "templates"?
This lifts genes out of the mechanical role of being "blueprints" for proteins and places them in a role of codified prescriptions.
Are you saying that there is not a one-to-one correspondence between the "templates" and what they produce?
Edited by Ringo, : Various.

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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 289 of 303 (369627)
12-13-2006 7:32 PM
Reply to: Message 288 by ringo
12-13-2006 4:35 PM


Re: Digital Origins of Life?
Ringo, you ask:
Are you saying that there is not a one-to-one correspondence between the "templates" and what they produce?
What I'm saying is that the molecular bonding sites of codons (triplets of digital nucleotides) on coded DNA are not stereochemical with the proteins they specify, meaning that they don't line up in any mechanical way that allows a protein to be built directly from its gene. Instead, messenger RNA (mRNA) must translate the genetic code and deliver it to transfer RNA (tRNA) to inform it on how to make a stereochemical configuration that will capture the right amino acids and put them in the right order. Ribosomes host of this process in eukaryotes.
”Hoot Mon

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ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 290 of 303 (369640)
12-13-2006 7:54 PM
Reply to: Message 289 by Fosdick
12-13-2006 7:32 PM


Re: Digital Origins of Life?
Hoot Mon writes:
... they don't line up in any mechanical way that allows a protein to be built directly from its gene.
What difference does it make whether the protein is built directly or indirectly from it's template/pattern/blueprint? You're describing a multi-step process where a tool builds a tool which builds a tool. A "language" might help to describe the process, but I don't think it's correct - or useful - to think of the process itself as a "language".

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This message is a reply to:
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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 291 of 303 (369734)
12-14-2006 1:07 PM
Reply to: Message 290 by ringo
12-13-2006 7:54 PM


Re: Digital Origins of Life?
Ringo, you asked:
What difference does it make whether the protein is built directly or indirectly from it's template/pattern/blueprint? You're describing a multi-step process where a tool builds a tool which builds a tool. A "language" might help to describe the process, but I don't think it's correct - or useful - to think of the process itself as a "language".
No, it's not a case of a tool building a tool building a tool. There actually are genetic instructions coded on DNA that specify the sequence of amino acids needed to make a specific protein. A language is involved beyond the tools you prefer. That seems clear enough to me.
Suppose, if you will, that genes were never discovered because they simply didn't exist and play no part in expaining biological life. Suppose instead that the proteins of life are made entirely by mechanical processes”"a tool building a tool building a tool." Life and its evolution, under this scenario, would have been an enterprise of macromolecules building more macromolecules, all neatly contained inside cells like a Tinker Toy set replicating itself somehow using unknown laws self-organization.
Well, life didn't happen that way. Life needs a non-mechanical code with a highly specific language. Obviously, genes exist in nature to inform, not to machine, the proteins of life. Proteins are very difficult to build without genes, No webpage found at provided URL: but it was done recently in the lab, proving that proteins can be built mechanically. Now that's a case of a tool building a tool building a tool. Add to that the prions, which are proteins that can produce more proteins without the need for genes. It is usually quite a destructive process, though”Mad Cow disease demonstrates that. So there are at least two examples of how proteins can be made mechanically.
Let the living cell have all the proetins it needs to stay alive, but take away its genes and see how long it lives. Life is more than a box of tools. It comes with an instruction manual that is as easy to read as a comic strip. That's because there are only 64 words in its language.
”Hoot Mon

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ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 292 of 303 (369741)
12-14-2006 1:28 PM
Reply to: Message 291 by Fosdick
12-14-2006 1:07 PM


Re: Digital Origins of Life?
Hoot Mon writes:
Life needs a non-mechanical code with a highly specific language.
So you keep saying. But the building of proteins, etc. does happen - i.e. this molecule gets built on that template and it gets carried to a new location by a specially-shaped receptacle, where it's held in the proper position to be joined to that other molecule....
There is a mechanical process. You haven't explained (sufficiently for my understanding ) why there needs to be another level of magic (language) superimposed on that mechanical process.
The very idea of language suggests communication. Communication between what and what? What is the transmitter, what is the receiver and what is the channel/medium? You need a mechanical explanation of that, too.

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This message is a reply to:
 Message 291 by Fosdick, posted 12-14-2006 1:07 PM Fosdick has replied

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Chiroptera
Inactive Member


Message 293 of 303 (369742)
12-14-2006 1:34 PM
Reply to: Message 292 by ringo
12-14-2006 1:28 PM


Yuck!
quote:
The very idea of language suggests communication. Communication between what and what? What is the transmitter, what is the receiver and what is the channel/medium? You need a mechanical explanation of that, too.
And now we start moving into the junk that Werner Gitt writes. Gitt does exactly this: he extends the meanings of words like this not because they provide useful analogies to help in remembering how the process works, but because the words already have semantic meaning to the readers, and so, by equivocation, he can lead the reader to his desired conclusion.
It only takes a little bit of training in critical thinking to read Gitt's, er, "work" and see that he really doesn't say anything, despite how impressive sounding it is when one just listens to it without thinking too hard.

Never believe anything in politics until it has been officially denied. -- Otto von Bismarck

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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 294 of 303 (369753)
12-14-2006 2:51 PM
Reply to: Message 292 by ringo
12-14-2006 1:28 PM


Re: Digital Origins of Life?
Ringo, you wrote:
The very idea of language suggests communication. Communication between what and what? What is the transmitter, what is the receiver and what is the channel/medium? You need a mechanical explanation of that, too.
Communication between the gene on the chromosome and tRNA in the ribosome. And I can make it even more troubling for you. Francis Crick coined the term "central dogma" to insist that a genetic message is communicated only from DNA/RNA to the protein and never in the opposite direction. Yes, this nature of genetic communication does rely on a language. If you care to look at it this way, you could even say that those genetic instructions are "channeled" by messenger RNA.
”Hoot Mon

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Replies to this message:
 Message 295 by ringo, posted 12-14-2006 2:59 PM Fosdick has replied
 Message 296 by Chiroptera, posted 12-14-2006 3:30 PM Fosdick has replied

  
ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 295 of 303 (369757)
12-14-2006 2:59 PM
Reply to: Message 294 by Fosdick
12-14-2006 2:51 PM


Re: Digital Origins of Life?
Hoot Mon writes:
... you could even say that those genetic instructions are "channeled" by messenger RNA.
And how is that not a mechanical process?

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Chiroptera
Inactive Member


Message 296 of 303 (369762)
12-14-2006 3:30 PM
Reply to: Message 294 by Fosdick
12-14-2006 2:51 PM


Re: Digital Origins of Life?
quote:
you could even say that those genetic instructions are "channeled" by messenger RNA.
Why would we say this? What insight do we get if we say this?

Never believe anything in politics until it has been officially denied. -- Otto von Bismarck

This message is a reply to:
 Message 294 by Fosdick, posted 12-14-2006 2:51 PM Fosdick has replied

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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 297 of 303 (369766)
12-14-2006 3:45 PM
Reply to: Message 295 by ringo
12-14-2006 2:59 PM


Re: Digital Origins of Life?
Ringo, re:
Hoot Mon writes:
... you could even say that those genetic instructions are "channeled" by messenger RNA.
And how is that not a mechanical process?
It certainly is a mechanical process, but it is still carrying genetic information forward.
”Hoot Mon

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 Message 295 by ringo, posted 12-14-2006 2:59 PM ringo has replied

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Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 298 of 303 (369769)
12-14-2006 3:49 PM
Reply to: Message 296 by Chiroptera
12-14-2006 3:30 PM


Re: Digital Origins of Life?
Chiropter, you wrote:
Hoot Mon wrote:
you could even say that those genetic instructions are "channeled" by messenger RNA.
Why would we say this? What insight do we get if we say this?
Absolutely none, only the exercising of a metaphor.
”Hoot Mon

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ringo
Member (Idle past 411 days)
Posts: 20940
From: frozen wasteland
Joined: 03-23-2005


Message 299 of 303 (369771)
12-14-2006 4:10 PM
Reply to: Message 297 by Fosdick
12-14-2006 3:45 PM


Re: Digital Origins of Life?
Hoot Mon writes:
It certainly is a mechanical process, but it is still carrying genetic information forward.
And that "information" is the equivalent to a stack of soup cans at the Kwik-E-Mart.
What I've been trying to get out of you is: why superimpose a "language" on that mechanical process if all the language does is make it more mysterious?

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 300 of 303 (369797)
12-14-2006 7:20 PM
Reply to: Message 299 by ringo
12-14-2006 4:10 PM


Re: Digital Origins of Life?
Ringo,
I don’t mean to put a hoot in an owl’s beak, but, Hoot is essentially correct in his “language” analogy. DNA is a code. There is no better way to describe the function of DNA than as a code. Keep in mind that Hoot (and he should correct me if I am wrong) is building a metaphor to describe what is happening. The DNA as a code is especially apt and describing the code as a language is not beyond reason.
We use symbols (A,G,C,T and sometime U) to represent the nucleic acids in the gene and the RNA. Every triplet of nucleotides is akin to a “word.” The word is a code for a specific amino acid and the “syntax” of this “language,” its sentence structure, codes for a specific protein to be built.
The science of “information theory” likes to treat such systems akin to computer codes and DNA fits information theory quite well as an analogous computer language.
I, as I suspect you, have been awaiting Hoot to drop the other shoe and expand the analogy to justify some metaphysical underpinnings to the “code,” “language,” “digital instruction” whatever. He hasn’t crossed that line, yet, and I am willing to agree with Hoot that the analogy of DNA as code, codon as language, is, as restricted to analogy, quite appropriate.
Let’s see where he goes with this.

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