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Old 4th January 2008, 09:37 AM   #1
Mister Agenda
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Got Sucked into an Abiogenesis Debate

I'm in a debate over at FrostCloud about abiogenesis. My resources (and time) at work are limited and I'm in the process of replacing my PC. So I need help. My opponent has a question:

"Can you show me even a possible, simple RNA sequence that can reproduce itself with fidelity of mutation?"

Does anyone know of an example (or proposed example) I can refer to? I believe my opponent is seeking to prove that no likely RNA sequence that arose spontaneously would be capable of both reproducing itself and preserving mutations (that is, in such a simple strand of RNA, any mutation would prevent replication). Thanks in advance for any assistance.
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Old 4th January 2008, 09:39 AM   #2
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Originally Posted by Mister Agenda View Post
I'm in a debate over at FrostCloud about abiogenesis. My resources (and time) at work are limited and I'm in the process of replacing my PC. So I need help. My opponent has a question:

"Can you show me even a possible, simple RNA sequence that can reproduce itself with fidelity of mutation?"

Does anyone know of an example (or proposed example) I can refer to? I believe my opponent is seeking to prove that no likely RNA sequence that arose spontaneously would be capable of both reproducing itself and preserving mutations (that is, in such a simple strand of RNA, any mutation would prevent replication). Thanks in advance for any assistance.
I wonder what he means by "fidelity of mutation".
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Old 4th January 2008, 10:00 AM   #3
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I'm taking it as a replicator that preserves any mutations. Logically it would have to have high "fidelity" for replicating itself to avoid too many errors/mutations while being able to successfully replicate while retaining any mutations that do arise.
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Old 4th January 2008, 10:06 AM   #4
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This isn't my area of expertise, but don't viruses do that? I think this applies to SARS, Influenza and Hepatitis C.
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Old 4th January 2008, 10:09 AM   #5
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I would clarify what he means by "fidelity of mutation" before going further...
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Old 4th January 2008, 10:10 AM   #6
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That's definitely true (at least for DNA) KSBluesfan, but we're going back to RNA world where the RNA strand would have had to form abiotically, sans DNA or proteins.

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Old 4th January 2008, 10:11 AM   #7
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Originally Posted by JoeEllison View Post
I would clarify what he means by "fidelity of mutation" before going further...
Good advice, I will.
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Old 4th January 2008, 10:20 AM   #8
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Originally Posted by Mister Agenda View Post
{snip} "Can you show me even a possible, simple RNA sequence that can reproduce itself with fidelity of mutation?"

{snip}
This sounds like a case of "lack of evidence is not evidence of lack."

Did you encumber yourself with the need to provide such an example? Without experimental evidence, any proposal you make is mere argument, and will likely be met with such.
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Old 4th January 2008, 10:27 AM   #9
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Is this perhaps what he's after?
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Old 4th January 2008, 11:20 AM   #10
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Originally Posted by JJM View Post
This sounds like a case of "lack of evidence is not evidence of lack."

Did you encumber yourself with the need to provide such an example? Without experimental evidence, any proposal you make is mere argument, and will likely be met with such.
No, all I have to do is provide a POSSIBLE candidate. We're also sparring over the amount of evidence required for a plausible hypthesis vs. a scientific theory.
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Old 4th January 2008, 11:40 AM   #11
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Originally Posted by Ocelot View Post
Is this perhaps what he's after?
I registered so I could see the abstract, and it looks like it fits the bill. Thanks! I'll post how it turns out.
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Old 4th January 2008, 12:46 PM   #12
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Originally Posted by Mister Agenda View Post
That's definitely true (at least for DNA) KSBluesfan, but we're going back to RNA world where the RNA strand would have had to form abiotically, sans DNA or proteins.

But the lack of protiens would be a silly hypothesis. :?:
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Old 16th January 2008, 02:24 PM   #13
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How so? RNA is made of nucleotides, at least short strands should be able to form without the assistance of proteins.
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Old 16th January 2008, 02:46 PM   #14
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Originally Posted by Mister Agenda View Post
I registered so I could see the abstract, and it looks like it fits the bill. Thanks! I'll post how it turns out.
Their closing statements gave some grist for my opponent, who takes it as saying that an RNA first replicator could not have formed given our present understanding of prebiotic chemistry. Hopefully I made a good case against that interpretation.
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Old 16th January 2008, 02:49 PM   #15
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People who think a POORLY reproducing system cannot evolve into a robust system have no concept whatsoever of Deep Time.

Given a few hundred million years of semi-stable conditions it is probably not only possible but nearly inevitable.
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Old 16th January 2008, 03:31 PM   #16
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Originally Posted by BenBurch View Post
People who think a POORLY reproducing system cannot evolve into a robust system have no concept whatsoever of Deep Time.

Given a few hundred million years of semi-stable conditions it is probably not only possible but nearly inevitable.
I agree. It seems to me that a maelstrom of variation is the most likely source of an interacting group of RNA strands that reproduce rigidly enough, but not too rigidly, to produce life as we know it.

I tend towards the view that metabolism is the way to tackle the issue rather than reproduction per se. Without metabolism you've got squat. Without fuel the most efficient engine in the world is essentially indistinguishable from geology.
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Old 16th January 2008, 06:07 PM   #17
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Also, the success ratio is fairly irrelevant to survival if there are enough copies.

How many hatchling sea turtles make it all the way down that beach to the sea? Not bloody many.
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Old 16th January 2008, 07:14 PM   #18
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Originally Posted by BenBurch
People who think a POORLY reproducing system cannot evolve into a robust system have no concept whatsoever of Deep Time.
These are the same people who are looking forward to sitting at the right hand of God forever.

~~ Paul
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Old 17th January 2008, 12:01 AM   #19
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Spiegelman's Monster?
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Old 17th January 2008, 09:36 AM   #20
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Originally Posted by Paul C. Anagnostopoulos View Post
These are the same people who are looking forward to sitting at the right hand of God forever.

~~ Paul
Of course they also believe the universe is less than 8000 years old.
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Old 17th January 2008, 01:04 PM   #21
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Originally Posted by arthwollipot View Post
That's worth throwing in for the name alone.
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Old 17th January 2008, 01:33 PM   #22
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If anyone is interested, the debate is in the Biology & Genetics subforum at FrostCloud. I use the same handle there. If anyone has criticisms I'll try to take them in the spirit of self-improvement.
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Old 17th January 2008, 02:06 PM   #23
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I would suggest going to pubmed, searching "self replicating" AND ribozyme, and reading the reviews that you can obtain free online, especially Minimal self-replicating systems.
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Old 18th January 2008, 05:49 AM   #24
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Originally Posted by Mister Agenda View Post
How so? RNA is made of nucleotides, at least short strands should be able to form without the assistance of proteins.
Because they are proteins? Or the precursors to proteins.

That is like saying something about assembling cars without screwdrivers?
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Old 18th January 2008, 05:51 AM   #25
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Originally Posted by CapelDodger View Post
I agree. It seems to me that a maelstrom of variation is the most likely source of an interacting group of RNA strands that reproduce rigidly enough, but not too rigidly, to produce life as we know it.

I tend towards the view that metabolism is the way to tackle the issue rather than reproduction per se. Without metabolism you've got squat. Without fuel the most efficient engine in the world is essentially indistinguishable from geology.

Thanks you!

People are always showing bias in even thinking about evolution. You start with what you have and go on from there. Tasok leading questions, often done by both sides is very misleading.
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Old 18th January 2008, 06:19 AM   #26
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Originally Posted by Paul C. Anagnostopoulos View Post
These are the same people who are looking forward to sitting at the right hand of God forever.

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Old 18th January 2008, 11:57 AM   #27
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Originally Posted by mijopaalmc View Post
I would suggest going to pubmed, searching "self replicating" AND ribozyme, and reading the reviews that you can obtain free online, especially Minimal self-replicating systems.
Thanks, that is very educational, especially as it goes over reasons why it is so difficult to parse out how to form such a molecule, which my opponent seems to think should be as easy as designing next year's car.
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Old 18th January 2008, 12:01 PM   #28
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Originally Posted by Dancing David View Post
Because they are proteins? Or the precursors to proteins.

That is like saying something about assembling cars without screwdrivers?
I hope not. My case is stronger if a relatively short RNA strand can replicate itself without the assistance of proteins. As far as I know, proteins aren't something you find floating around in the prebiotic soup.
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Old 18th January 2008, 12:15 PM   #29
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Originally Posted by Mister Agenda View Post
I hope not. My case is stronger if a relatively short RNA strand can replicate itself without the assistance of proteins. As far as I know, proteins aren't something you find floating around in the prebiotic soup.

Really, oh, I don't see why. Prions and all that protein folding is cool stuff. But I think that it would be backended to look at replication without life.

Take a self catalyzing aggregate, put it in a lipid bilayer, wait a million years.
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Old 18th January 2008, 12:21 PM   #30
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Originally Posted by Dancing David View Post
Really, oh, I don't see why. Prions and all that protein folding is cool stuff. But I think that it would be backended to look at replication without life.

Take a self catalyzing aggregate, put it in a lipid bilayer, wait a million years.
I am in agreement, sir. I had to supply a few linkys to convince my esteemed opponent prions are real. I think I may be dealing with an engineer, since he seems educated enough but unable to imagine design without a conscious designer. Essentially he thinks science is barking up the wrong tree with this abiogenesis thing, they should admit they can't explain it and move on to something more productive, as when it abandoned the steady state theory of the universe.

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Old 18th January 2008, 01:21 PM   #31
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Originally Posted by Mister Agenda View Post
Thanks, that is very educational, especially as it goes over reasons why it is so difficult to parse out how to form such a molecule, which my opponent seems to think should be as easy as designing next year's car.
Which some consumers think is easy because they only see the finished product.
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Old 18th January 2008, 02:26 PM   #32
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Oooh oooh, I know this one.

I find this topic fascinating and notice as usual, people arguing, "God did it", are so unaware of the vast amount of current research. They only argue what they learned in church or what they learned in grade school without making any effort to see if anyone has done any work in the field. As I looked for information on the most recent work to come from Stanley Miller's research, which I just read about very recently, I found the AIG sites all arguing against Miller's 1953 graduate student work.

Stanley Miller

Miller put some chemicals that were likely representative of conditions which life originated in into containers 25 years ago and froze them. Recently, some of the specimens were analyzed and it was discovered that organic chemicals actually formed much longer chains and more rapidly than they would have in liquid water. Who'd have thought?

What is believed to occur is as the water forms ice, the crystalline structure excludes everything that isn't H & O. That leaves high concentrations of everything else in minute layers between the ice crystals.

Did Life Begin in Ice? [1]

This may be the answer to the problem the RNA-as-original-life-molecule theorists have had, mainly, how do you get to those 200 and something nucleic acid size molecules which appear to be the minimum required having been trimmed down as far as possible while still remaining functional from actual reproducing organisms.

The idea replicating molecules began in ice rather than water is also presented in this paper from 2005.

Did life begin in ice? [2]

This research might also add to the hypothesis these chemicals were originally synthesized in comets or other very cold regions of space and were brought here on those traveling bodies.

Organic Molecules in Comets and Meteorites and life on Earth Interstellar medium

Unfortunately Miller died last year and many of his 25 year old frozen specimens were ignorantly tossed out. The article on Miller I recently read was in Discover Magazine, (Feb, 2008). Unfortunately, you can't get to the article online without a subscription.

Credit for the original RNA hypothesis and work has been attributed to Orgel.

The Origin of Life on Earth, by Leslie E. Orgel

Orgel and another researcher, Joyce, have both done extensive research in this field. Orgel also died a few years ago but leaves behind his interesting web site (linked above).

There are other hypotheses out there and before he died, Orgel was working on replicating RNA precursors rather than thinking the RNA was the first molecule in the origin of life.

ORIGIN OF LIFE: Enhanced: A Simpler Nucleic Acid, Leslie Orgel
Quote:
What was the genetic material of the earliest life forms on Earth if it was not RNA? As Orgel explains in his Perspective, the answer may be simpler nucleic acid polymers perhaps like the RNA analogs called (L)-a-threofuranosyl oligonucleotides or TNAs (Schöning et al.). These molecules have threose rather than ribose in their sugar-phosphate backbones and yet retain many of the properties of RNA including the ability to pair up in double helices.
And others are looking in this direction.

Nucleotide synthetase ribozymes may have emerged first in the RNA world

Peptide nucleic acids rather than RNA may have been the first genetic molecule (Miller contributed to this paper.)

The message all this should get across to those wishful thinking God believers is, the work is simply not done. Have they not learned that lesson yet? The fact we don't have an answer to something is not a reason to throw up your hands and fill in the gap with god magic.



(BTW, you have my permission to just copy & paste this whole post into the thread on the other forum.)

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Old 18th January 2008, 05:01 PM   #33
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Originally Posted by Dancing David View Post
Because they are proteins? Or the precursors to proteins.
RNA is neither. It's a chain of ribonucleotides. Proteins are chains of amino acids.

A ribonucleotide consists of a base group (Adenine, Guanine, Cytosine, or Uracil), a monosaccharide (ribose), and a phosphate group.

An amino acid is a carbon atom connected to an amino group (NH2), a carboxyl group (COOH), and a radical (there are 20 different amino acid radicals that occur in biological systems).

What makes both kinds of chains interesting is that nucleotide bases can bind to their complementary nucleotide bases, and amino-acid radicals can bind to other amino-acid radicals. Thus, each long-chain molecule can fold back on itself and have different parts of the chain stick together. If the shapes of these folds are just so, the folded chain can act as a catalyst, facilitating chemical reactions between other molecules.

An RNA molecule that can act as a catalyst in this fashion is called a ribozyme. A protein molecule that can act as a catalyst in this fashion is called an enzyme.

It is theoretically possible to construct an entire biological system exclusively out of RNA -- some RNA for carrying genetic information, and other RNA for catalytic activity. The possiblility that the first life on Earth was such a system is called the "RNA World Hypothesis."
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Old 19th January 2008, 05:33 AM   #34
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Originally Posted by Mister Agenda View Post
I am in agreement, sir. I had to supply a few linkys to convince my esteemed opponent prions are real. I think I may be dealing with an engineer, since he seems educated enough but unable to imagine design without a conscious designer. Essentially he thinks science is barking up the wrong tree with this abiogenesis thing, they should admit they can't explain it and move on to something more productive, as when it abandoned the steady state theory of the universe.
Well arguing with people about faith usualy just makes their faith stonger. There are many reasons abiogenesis is atheory. I doubt that his has any predictive power at all.


Is he trying some sort of time travelling panspermia or a goddidit?
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Old 19th January 2008, 05:39 AM   #35
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Originally Posted by tracer View Post
RNA is neither. It's a chain of ribonucleotides. Proteins are chains of amino acids.

A ribonucleotide consists of a base group (Adenine, Guanine, Cytosine, or Uracil), a monosaccharide (ribose), and a phosphate group.

An amino acid is a carbon atom connected to an amino group (NH2), a carboxyl group (COOH), and a radical (there are 20 different amino acid radicals that occur in biological systems).

What makes both kinds of chains interesting is that nucleotide bases can bind to their complementary nucleotide bases, and amino-acid radicals can bind to other amino-acid radicals. Thus, each long-chain molecule can fold back on itself and have different parts of the chain stick together. If the shapes of these folds are just so, the folded chain can act as a catalyst, facilitating chemical reactions between other molecules.

An RNA molecule that can act as a catalyst in this fashion is called a ribozyme. A protein molecule that can act as a catalyst in this fashion is called an enzyme.

It is theoretically possible to construct an entire biological system exclusively out of RNA -- some RNA for carrying genetic information, and other RNA for catalytic activity. The possiblility that the first life on Earth was such a system is called the "RNA World Hypothesis."
Cool, it has been thirty years since I took organic chem.


My point was that it would be silly for the opponet to ask that RNA be made in the abscense of proteins, while it may make Mr. Adequate's argument stronger. I am sure that the opponent is using what SJ Gould would label deterministic errors in discussing evolution and life.
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Old 19th January 2008, 01:35 PM   #36
Beerina
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Originally Posted by BenBurch View Post
Also, the success ratio is fairly irrelevant to survival if there are enough copies.

How many hatchling sea turtles make it all the way down that beach to the sea? Not bloody many.
And why is a god who enjoys baby turtles getting eaten somehow a preferred situation?

Are these believers psychotic, like their god is?

And when (not if) a full, reasonable path for this to occur is discovered, will the religious people re-evaluate their belief in God?

To sum up:

1. Desiring that your belief in a psychotic god is true, is itself psychotic.

2. Overturning the illogic of "Can't figure it out, therefore goddidit" will not occur once humanity does figure it out.

Yeah, that's about it.
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Last edited by Beerina; 19th January 2008 at 01:39 PM.
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Old 19th January 2008, 01:42 PM   #37
Mister Agenda
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Originally Posted by skeptigirl View Post
Oooh oooh, I know this one.

I find this topic fascinating and notice as usual, people arguing, "God did it", are so unaware of the vast amount of current research. They only argue what they learned in church or what they learned in grade school without making any effort to see if anyone has done any work in the field. As I looked for information on the most recent work to come from Stanley Miller's research, which I just read about very recently, I found the AIG sites all arguing against Miller's 1953 graduate student work.

Stanley Miller

Miller put some chemicals that were likely representative of conditions which life originated in into containers 25 years ago and froze them. Recently, some of the specimens were analyzed and it was discovered that organic chemicals actually formed much longer chains and more rapidly than they would have in liquid water. Who'd have thought?

What is believed to occur is as the water forms ice, the crystalline structure excludes everything that isn't H & O. That leaves high concentrations of everything else in minute layers between the ice crystals.

Did Life Begin in Ice? [1]

This may be the answer to the problem the RNA-as-original-life-molecule theorists have had, mainly, how do you get to those 200 and something nucleic acid size molecules which appear to be the minimum required having been trimmed down as far as possible while still remaining functional from actual reproducing organisms.

The idea replicating molecules began in ice rather than water is also presented in this paper from 2005.

Did life begin in ice? [2]

This research might also add to the hypothesis these chemicals were originally synthesized in comets or other very cold regions of space and were brought here on those traveling bodies.

Organic Molecules in Comets and Meteorites and life on Earth Interstellar medium

Unfortunately Miller died last year and many of his 25 year old frozen specimens were ignorantly tossed out. The article on Miller I recently read was in Discover Magazine, (Feb, 2008). Unfortunately, you can't get to the article online without a subscription.

Credit for the original RNA hypothesis and work has been attributed to Orgel.

The Origin of Life on Earth, by Leslie E. Orgel

Orgel and another researcher, Joyce, have both done extensive research in this field. Orgel also died a few years ago but leaves behind his interesting web site (linked above).

There are other hypotheses out there and before he died, Orgel was working on replicating RNA precursors rather than thinking the RNA was the first molecule in the origin of life.

ORIGIN OF LIFE: Enhanced: A Simpler Nucleic Acid, Leslie Orgel

And others are looking in this direction.

Nucleotide synthetase ribozymes may have emerged first in the RNA world

Peptide nucleic acids rather than RNA may have been the first genetic molecule (Miller contributed to this paper.)

The message all this should get across to those wishful thinking God believers is, the work is simply not done. Have they not learned that lesson yet? The fact we don't have an answer to something is not a reason to throw up your hands and fill in the gap with god magic.



(BTW, you have my permission to just copy & paste this whole post into the thread on the other forum.)
Thanks! The debate is closed, as we were going around in circles, but I am going to drag your quote to the commentary thread, because it's too great not to share.
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Old 19th January 2008, 01:46 PM   #38
Mister Agenda
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Originally Posted by Dancing David View Post
Well arguing with people about faith usualy just makes their faith stonger. There are many reasons abiogenesis is atheory. I doubt that his has any predictive power at all.


Is he trying some sort of time travelling panspermia or a goddidit?
He's played his actual beliefs close to his chest, and I thought he might be leaning toward panspermia, but now I'm pretty sure he's backing some form of goddidit.
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Old 20th January 2008, 06:31 AM   #39
Dancing David
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Not that they will listen but you would have to wonder why if goddidit they would make diversity so high amongst the bacteria and so low amongst everything else, and why mitochondria have a seperate set of DnA.

You sound very patient.

Here is a panspermia thread from JREF:

http://www.internationalskeptics.com...ad.php?t=79256
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Old 20th January 2008, 11:01 AM   #40
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Panspermia still assumes abiogenesis at some time prior to the appearance of life on earth.

Moreover, when Earth was formed there likely had not been enough time yet since the formation of our galaxy and the beginning of nucleosynthesis for there to have been much opportunity for the formation of planets and life elsewhere in our solar neighborhood.

Panspermia is MUCH more likely in this era of the universe, and we are its agents; We have found bacteria on the moon that we sent there. (The Surveyor III parts returned by Apollo 12.) And we have likely contaminated Mars as there really is no way whatsoever to ensure absolute sterility of the vehicles we send there. And if there are other races who are spacefaring in a more serious fashion than we are, their microbes will spread far and wide in a much more certain fashion than any natural physical process could ever achieve.

So, resort to panspermia just pushed the argument back in time and to another locale, it does not invalidate the need to abiogenesis.
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