Total Posts:35|Showing Posts:1-30|Last Page
Jump to topic:

Prebiotic Deoxyribose Synthesis?

SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 4:51:54 PM
Posted: 4 years ago
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 5:35:07 PM
Posted: 4 years ago
I've never heard of an abiogenesis hypothesis that proposes the synthesis of DNA from scratch.

Instead, think about a cluster of molecules, a macro-molecule, which is chemically oriented such that, when it comes into contact with other molecules, a "copy" is made and the macro-molecule replicates.

The big argument is over what the original macromolecule was that eventually become DNA. A major competitor is pRNA World, since we know of RNA-like structures that exhibit everything needed in a macromolecule (can reproduce and mutate by itself).

Check out this link: http://thelivingcosmos.com...

Getting from pRNA to DNA is another story. One of the most interested hypothesis I've heard on that is that viruses and other single-strand organisms actually came much earlier in the evolutionary tree than we previously realized, and that the movement from single-strand to double-strand is related to the co-evolution of viruses and other organisms.

Here's a rather techy article on that: http://www.biology-direct.com...
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 6:09:58 PM
Posted: 4 years ago
Also, try to remember that the first prokaryotic cells weren't much more than a sack of DNA enclosed in a phospholipid (sp) bilayer. Cells didn't even a nucleus until quite far into evolution (in single cellular terms).
darkkermit
Posts: 11,204
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 8:43:55 PM
Posted: 4 years ago
Well DNA can theoretically though be synthesized though If it were created. It might take multiple steps, but it should be theoretically possible to synthesize anything that exists.
Open borders debate:
http://www.debate.org...
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 10:38:25 PM
Posted: 4 years ago
At 5/25/2012 8:43:55 PM, darkkermit wrote:
Well DNA can theoretically though be synthesized though If it were created. It might take multiple steps, but it should be theoretically possible to synthesize anything that exists.

Sure, in a lab, but he was talking about abiogenesis in pre-atmospheric earth.

Odd though, that a teacher would assign a project like "write a report on abiogenesis which leads directly to DNA." Maybe if its a grad class and you're supposed to spell out evolution from the macromolecule all the way up to eukaryotes.

Almost makes me think this OP is a subtle way of challenging abiogenesis without actually making an affirmative claim. But that's just a prima facie response.
darkkermit
Posts: 11,204
Add as Friend
Challenge to a Debate
Send a Message
5/25/2012 10:56:06 PM
Posted: 4 years ago
At 5/25/2012 10:38:25 PM, Wnope wrote:
At 5/25/2012 8:43:55 PM, darkkermit wrote:
Well DNA can theoretically though be synthesized though If it were created. It might take multiple steps, but it should be theoretically possible to synthesize anything that exists.

Sure, in a lab, but he was talking about abiogenesis in pre-atmospheric earth.

If it can be created in a lab, it could theoretically be created naturally, provided that the conditions are the same. How likely nature can simulate lab conditions, who knows.

Odd though, that a teacher would assign a project like "write a report on abiogenesis which leads directly to DNA." Maybe if its a grad class and you're supposed to spell out evolution from the macromolecule all the way up to eukaryotes.

I remember learning about abiogenesis in high school. It doesn't seem that difficult. Of course, abiogenesis is largely speculative due to it being impossible to know what actually took place. Hell, in abiogenesis, its one of the few times the argument "I don't know, therefore aliens" is actually considered a legit argument. Even if the process of life can be simulated, there's no way to know that's what actually happened, just its a possibility of what happened.

Almost makes me think this OP is a subtle way of challenging abiogenesis without actually making an affirmative claim. But that's just a prima facie response.
Open borders debate:
http://www.debate.org...
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 12:53:17 AM
Posted: 4 years ago
At 5/25/2012 5:35:07 PM, Wnope wrote:
I've never heard of an abiogenesis hypothesis that proposes the synthesis of DNA from scratch.

Instead, think about a cluster of molecules, a macro-molecule, which is chemically oriented such that, when it comes into contact with other molecules, a "copy" is made and the macro-molecule replicates.

Self-replicating molecules, I know.

The big argument is over what the original macromolecule was that eventually become DNA. A major competitor is pRNA World, since we know of RNA-like structures that exhibit everything needed in a macromolecule (can reproduce and mutate by itself).

Check out this link: http://thelivingcosmos.com...

Getting from pRNA to DNA is another story. One of the most interested hypothesis I've heard on that is that viruses and other single-strand organisms actually came much earlier in the evolutionary tree than we previously realized, and that the movement from single-strand to double-strand is related to the co-evolution of viruses and other organisms.

Here's a rather techy article on that: http://www.biology-direct.com...

Are you arguing that deoxyribose was created by enzymes created by RNA?

Anyway, in regards to pRNA:

"Consequently, pRNAs and RNAs are not able to form duplexes with each other, which would preclude exchange of information between these two molecules, suggesting that pRNAs are unlikely to have been the genetic material that preceded RNA." Leslie Orgel, 2000

Similar issues surround TNA, GNA, etc.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 12:56:39 AM
Posted: 4 years ago
At 5/25/2012 10:38:25 PM, Wnope wrote:
At 5/25/2012 8:43:55 PM, darkkermit wrote:
Well DNA can theoretically though be synthesized though If it were created. It might take multiple steps, but it should be theoretically possible to synthesize anything that exists.

Sure, in a lab, but he was talking about abiogenesis in pre-atmospheric earth.

Odd though, that a teacher would assign a project like "write a report on abiogenesis which leads directly to DNA." Maybe if its a grad class and you're supposed to spell out evolution from the macromolecule all the way up to eukaryotes.

Almost makes me think this OP is a subtle way of challenging abiogenesis without actually making an affirmative claim. But that's just a prima facie response.

It's a project I chose myself. Think of it as extra-credit. And yes, somewhat. I'm curious about theories for the origin of deoxyribose. There are mechanisms for the synthesis of ribose (though problematic), but I have yet to find any on the synthesis of deoxyribose.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
Thaumaturgy
Posts: 166
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 1:04:19 AM
Posted: 4 years ago
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

This is not my area but it seems as if some of the current discussion is around the "RNA World" in which RNA was the primary precursors to life. I found this abstract on PubMed: http://www.ncbi.nlm.nih.gov...
that discusses the RNA-->RNA+Protein-->DNA transition. Might be worth digging into.
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 1:43:53 AM
Posted: 4 years ago
At 5/26/2012 12:53:17 AM, SuburbiaSurvivor wrote:
At 5/25/2012 5:35:07 PM, Wnope wrote:
I've never heard of an abiogenesis hypothesis that proposes the synthesis of DNA from scratch.

Instead, think about a cluster of molecules, a macro-molecule, which is chemically oriented such that, when it comes into contact with other molecules, a "copy" is made and the macro-molecule replicates.

Self-replicating molecules, I know.

The big argument is over what the original macromolecule was that eventually become DNA. A major competitor is pRNA World, since we know of RNA-like structures that exhibit everything needed in a macromolecule (can reproduce and mutate by itself).

Check out this link: http://thelivingcosmos.com...

Getting from pRNA to DNA is another story. One of the most interested hypothesis I've heard on that is that viruses and other single-strand organisms actually came much earlier in the evolutionary tree than we previously realized, and that the movement from single-strand to double-strand is related to the co-evolution of viruses and other organisms.

Here's a rather techy article on that: http://www.biology-direct.com...

Are you arguing that deoxyribose was created by enzymes created by RNA?

Anyway, in regards to pRNA:

"Consequently, pRNAs and RNAs are not able to form duplexes with each other, which would preclude exchange of information between these two molecules, suggesting that pRNAs are unlikely to have been the genetic material that preceded RNA." Leslie Orgel, 2000

Similar issues surround TNA, GNA, etc.

You do realize that the article you just quoted, Orgel, 2000, is devoted to the argument that TNA is simpler than RNA, resembles RNA more closely than peptide nucleic acids, and forms stable heteroduplexes, right?

There are two steps we can talk about:

1. molecules -> self-replicating macromolecule A

2. self replicating macromolecule A -> self replicating macromolecule B -> RNA/DNA

The first step, pRNA, TNA, peptide nucleic acids, all of that, those refer only to "self replicating macromolecule A." In the second, Consider the hundred of thousands, if not millions, of years needed to get between macromolecule A to B and then from B to RNA/DNA.

The fact that self-replicating macromolecule A may not be directly compatible with RNA/DNA would only be surprising if you assume RNA/DNA arose almost immediately.

The second step is more controversial. One new hypothesis that I believe holds promise relates to how viruses and archea have variant ways of producing DNA and RNA. Namely, viruses were able to act as an co-evolutionary force with other prokaryotes.

A good explanation:
http://carlzimmer.com...;

"For viruses, DNA might have offered a very powerful, immediate benefit. It would have allowed them to ward off attacks from their hosts. Cells today use a number of weapons against RNA viruses. They can silence the viral RNA with special RNA molecules of their own. Or they can cut the genome of the virus into fragments.

"RNA viruses have to find a way to avoid these defenses," says Forterre. They do so by making it difficult for their hosts to grab their RNA. Living RNA viruses chemically modify their genes to thwart their hosts. Forterre proposes that some early RNA viruses altered their genes in a particularly effective way: They combined pairs of single-stranded RNA into double-stranded DNA. The vulnerable nucleotides carrying the virus's genetic information were now nestled on the inside of the double helix, while a strong backbone faced outward.

"The idea is that an older RNA virus could use this as a trick to modify the structure of its RNA. DNA is simply modified RNA," says Forterre.

If they were anything like viruses today, some of the viruses found a way to coexist inside the host's cells, surviving from one generation of host to the next. Forterre suggests that in the RNA world, some DNA viruses became domesticated and lost the genes they used for escaping their hosts and for making protein shells. They became nothing more than naked DNA, encoding genes for their own replication."
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 1:46:04 AM
Posted: 4 years ago
In a way, the thread title is almost nonsensical. DNA could only evolve after abiogenesis and the first self-replicating macromolecule. So there's no such thing as "prebiotic DNA synthesis" without a lab.
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 7:44:16 AM
Posted: 4 years ago
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 7:45:58 AM
Posted: 4 years ago
At 5/26/2012 1:46:04 AM, Wnope wrote:
In a way, the thread title is almost nonsensical. DNA could only evolve after abiogenesis and the first self-replicating macromolecule. So there's no such thing as "prebiotic DNA synthesis" without a lab.

I think he's talking about activation, rather than synthesis.

You can't synthesize DNA before it's formed. :P
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 8:08:52 AM
Posted: 4 years ago
At 5/25/2012 10:56:06 PM, darkkermit wrote:
At 5/25/2012 10:38:25 PM, Wnope wrote:
At 5/25/2012 8:43:55 PM, darkkermit wrote:
Well DNA can theoretically though be synthesized though If it were created. It might take multiple steps, but it should be theoretically possible to synthesize anything that exists.

Sure, in a lab, but he was talking about abiogenesis in pre-atmospheric earth.

If it can be created in a lab, it could theoretically be created naturally, provided that the conditions are the same. How likely nature can simulate lab conditions, who knows.

Odd though, that a teacher would assign a project like "write a report on abiogenesis which leads directly to DNA." Maybe if its a grad class and you're supposed to spell out evolution from the macromolecule all the way up to eukaryotes.

I remember learning about abiogenesis in high school. It doesn't seem that difficult. Of course, abiogenesis is largely speculative due to it being impossible to know what actually took place. Hell, in abiogenesis, its one of the few times the argument "I don't know, therefore aliens" is actually considered a legit argument. Even if the process of life can be simulated, there's no way to know that's what actually happened, just its a possibility of what happened.

Almost makes me think this OP is a subtle way of challenging abiogenesis without actually making an affirmative claim. But that's just a prima facie response.

Ambiogenesis is essentially the theory of circumstantially favorable conditions for producing life. It teeters between an indeterminate Universe and one that inevitably produces life when things are "just so."

In the science world, ambiogenesis is kind of starting midway through the story. Sure, there was a soup of popypeptides that may have produced nucleotides when exposed to heat. But, doesn't that seem to leave out a lot of the story?

How did those polypeptides get there, and was it inevitable that they were? I think it's rather relevant that deoxyribose is specifically an oxyribose -- a sugar molecule derived from the chemical structure of an oxygen molecule. Therefore, before there were polypeptides, there was RNA, and before there was RNA, there was oxygen.

For there to be oxygen, there had to be water.

Now, we're following the train of thought of those scientists that claim there's likely life on Io or Europa.

For RNA to predate DNA or even the polypeptides that it becomes is not outrageous. It's just a collection of electrolytes -- a base, a sugar, and a phosphate -- that construct in such a way that make it favorable that nucleotides develop.
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 12:27:21 PM
Posted: 4 years ago
At 5/26/2012 1:43:53 AM, Wnope wrote:
At 5/26/2012 12:53:17 AM, SuburbiaSurvivor wrote:
At 5/25/2012 5:35:07 PM, Wnope wrote:
I've never heard of an abiogenesis hypothesis that proposes the synthesis of DNA from scratch.

Instead, think about a cluster of molecules, a macro-molecule, which is chemically oriented such that, when it comes into contact with other molecules, a "copy" is made and the macro-molecule replicates.

Self-replicating molecules, I know.

The big argument is over what the original macromolecule was that eventually become DNA. A major competitor is pRNA World, since we know of RNA-like structures that exhibit everything needed in a macromolecule (can reproduce and mutate by itself).

Check out this link: http://thelivingcosmos.com...

Getting from pRNA to DNA is another story. One of the most interested hypothesis I've heard on that is that viruses and other single-strand organisms actually came much earlier in the evolutionary tree than we previously realized, and that the movement from single-strand to double-strand is related to the co-evolution of viruses and other organisms.

Here's a rather techy article on that: http://www.biology-direct.com...

Are you arguing that deoxyribose was created by enzymes created by RNA?

Anyway, in regards to pRNA:

"Consequently, pRNAs and RNAs are not able to form duplexes with each other, which would preclude exchange of information between these two molecules, suggesting that pRNAs are unlikely to have been the genetic material that preceded RNA." Leslie Orgel, 2000

Similar issues surround TNA, GNA, etc.

You do realize that the article you just quoted, Orgel, 2000, is devoted to the argument that TNA is simpler than RNA, resembles RNA more closely than peptide nucleic acids, and forms stable heteroduplexes, right?

Yes. The problems with TNA do not involve the ability of the polymer to form double helixes, but in how the TNA replication system could have been replaced by an RNA system. Do you support the idea that an RNA system developed alongside TNA and then eventually replaced it, or that TNA bases were gradually substituted by RNA bases until the TNA replication system turned into RNA?

There are two steps we can talk about:

1. molecules -> self-replicating macromolecule A

Ah yes, the synthesis of the amino acids, nucleic acids, and sugars required for life. Let's talk about that.

2. self replicating macromolecule A -> self replicating macromolecule B -> RNA/DNA

The first step, pRNA, TNA, peptide nucleic acids, all of that, those refer only to "self replicating macromolecule A." In the second, Consider the hundred of thousands, if not millions, of years needed to get between macromolecule A to B and then from B to RNA/DNA.

The fact that self-replicating macromolecule A may not be directly compatible with RNA/DNA would only be surprising if you assume RNA/DNA arose almost immediately.

I do not see how this can be remedied by time unless there are mechanisms through which TNA/PNA/GNA can be replaced by RNA.

The second step is more controversial. One new hypothesis that I believe holds promise relates to how viruses and archea have variant ways of producing DNA and RNA. Namely, viruses were able to act as an co-evolutionary force with other prokaryotes.

A good explanation:
http://carlzimmer.com...;

"For viruses, DNA might have offered a very powerful, immediate benefit. It would have allowed them to ward off attacks from their hosts. Cells today use a number of weapons against RNA viruses. They can silence the viral RNA with special RNA molecules of their own. Or they can cut the genome of the virus into fragments.

"RNA viruses have to find a way to avoid these defenses," says Forterre. They do so by making it difficult for their hosts to grab their RNA. Living RNA viruses chemically modify their genes to thwart their hosts. Forterre proposes that some early RNA viruses altered their genes in a particularly effective way: They combined pairs of single-stranded RNA into double-stranded DNA. The vulnerable nucleotides carrying the virus's genetic information were now nestled on the inside of the double helix, while a strong backbone faced outward.

Are there any proposed mechanisms that actually demonstrate this as being possible?

Anyway, it seems that this system already requires the existence of an RNA replication system in a working organism. By that point it would appear that abiogenesis has already taken place.

"The idea is that an older RNA virus could use this as a trick to modify the structure of its RNA. DNA is simply modified RNA," says Forterre.

How was this done? Unsupported hypotheses are pretty much useless to me.

If they were anything like viruses today, some of the viruses found a way to coexist inside the host's cells, surviving from one generation of host to the next. Forterre suggests that in the RNA world, some DNA viruses became domesticated and lost the genes they used for escaping their hosts and for making protein shells. They became nothing more than naked DNA, encoding genes for their own replication."

I'm mainly attacking the synthesis of RNA ingredients and the subsequent polymerization of those ingredients. As of yet, I've yet to hear of any mechanisms that demonstrate A) how TNA/GNA/PNA can be polymerized in a prebiotic world and subsequently replaced by RNA.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 12:29:11 PM
Posted: 4 years ago
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 1:20:45 PM
Posted: 4 years ago
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/26/2012 1:22:56 PM
Posted: 4 years ago
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Well, when I said that it doesn't construct on its own, I meant in the form of a double-helix.

Sorry.

It does occur in nature quite frequently, obviously, as all sugars do. As I indicated, it forms in rings within aqueous solutions out of strings of carbon molecules.

In DNA, it transposes one of the carbon groups for a hydroxide or something, I think.
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 12:49:42 AM
Posted: 4 years ago
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
Ren
Posts: 7,102
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 1:32:41 AM
Posted: 4 years ago
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

???

...????

Errr...

...naw, man, I wasn't being condescending. I was just trying to help.

The first line of the introduction I linked you to is:

"How proteins and nucleic acids originated under prebiotic conditions is still under investigation."

In other words, obviously, you didn't even read it. In any case, my point was that deoxyribose forms separate of the construction of nucelotides or polypeptides. All I was saying is that, to determine how ribose forms, simply refer to how a saccharide forms. In this case, out of strings of carbon molecules.

I thought that answered your question quite effectively, but somehow, even though I didn't even directly address you, it offended you.

For that, I guess I'm sorry, but not really, because I really didn't do anything but answer your question.

I would also figured you wanted all of the information about the study, since you clearly have university access and can find it on JSTOR or something. I could have just linked you this: http://resources.metapress.com... if it would have made you happier.

Well, whatever. I don't really focus on biology much, anyway. I'm more a physics kind of guy.

I'll let someone else answer your question.
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 2:32:50 AM
Posted: 4 years ago
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

Are you still not seeing the problem with your terminology?

There is no such thing as prebiotic DNA synthesis outside of the lab.

It's like saying "prebiotic mammalian birth."

You can talk about "prebiotic synthesis of self-replicating macromolecules" in which case it's TNA, pRNA World, etc. That's when abiogenesis has occurred and thus the "pre" and "post biotic" stages pass.

Similarly, you can talk about what the direct evolutionary prescursor of DNA is.

But the direct evolutionary precursor of DNA is NOT whatever self-replicating macromolecule passed the pre to postbiotic stage.
tarkovsky
Posts: 212
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 2:43:57 AM
Posted: 4 years ago
Don't know whether or not it's relevant, not going to read this whole thread.

The popular theory is that, rather than DNA, RNA was the first genetic material. The genetic material of the very first forms of life was RNA, so the question of prebiotic deoxyribose synthesis is moot.
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 1:41:29 PM
Posted: 4 years ago
At 5/27/2012 1:32:41 AM, Ren wrote:
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

???

...????

Errr...

...naw, man, I wasn't being condescending. I was just trying to help.

The first line of the introduction I linked you to is:

"How proteins and nucleic acids originated under prebiotic conditions is still under investigation."

In other words, obviously, you didn't even read it. In any case, my point was that deoxyribose forms separate of the construction of nucelotides or polypeptides. All I was saying is that, to determine how ribose forms, simply refer to how a saccharide forms. In this case, out of strings of carbon molecules.

That may have been the first sentence, but in the second paragraph it discusses prebiotic nucleotide and polypeptide synthesis. Also, the abstract and title talks about nucleotide and polypeptide synthesis from N-(O,O-diisopropyl)phosphothreonine. Anyway, ribose is formed either via enzymes or the formose reaction. But the formose reaction doesn't synthesize deoxyribose.

I thought that answered your question quite effectively, but somehow, even though I didn't even directly address you, it offended you.

In hindsight, I'd say I overreacted. But since you were replying to my post it does seem that you were directly addressing me.

I would also figured you wanted all of the information about the study, since you clearly have university access and can find it on JSTOR or something. I could have just linked you this: http://resources.metapress.com... if it would have made you happier.

Well, that particular page doesn't address ribose or deoxyribose synthesis. Though it would have been useful if we were discussing prebiotic nucleotide and protein synthesis.

Well, whatever. I don't really focus on biology much, anyway. I'm more a physics kind of guy.

I'll let someone else answer your question.

Sorry, I apologize. I read that at like, midnight and for some reason it seemed really condescending to me. I don't think my negative response was really warranted.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 1:48:05 PM
Posted: 4 years ago
At 5/27/2012 2:32:50 AM, Wnope wrote:
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

Are you still not seeing the problem with your terminology?

There is no such thing as prebiotic DNA synthesis outside of the lab.

It's like saying "prebiotic mammalian birth."

I was curious about hypotheses regarding the origin of the components of DNA and subsequent polymerization of said componennts. Though the ingredients for life certainly would have had to be synthesized prebiotically at some point. Unless you're arguing that an RNA replicating system could have created the enzymes required to catalyze it all. If that's what you're arguing, I'm curious as to how you propose this could have happened.

You can talk about "prebiotic synthesis of self-replicating macromolecules" in which case it's TNA, pRNA World, etc. That's when abiogenesis has occurred and thus the "pre" and "post biotic" stages pass.

Similarly, you can talk about what the direct evolutionary prescursor of DNA is.

But the direct evolutionary precursor of DNA is NOT whatever self-replicating macromolecule passed the pre to postbiotic stage.


I don't see how this last sentence doesn't contradict the rest of what you just said. If the direct evolutionary precursor of DNA isn't whatever self-replicating macromolecule passed pre to postbiotic stage, then in essence you're saying that DNA didn't have a precursor such as RNA, TNA, or pRNA.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 1:48:53 PM
Posted: 4 years ago
At 5/27/2012 2:43:57 AM, tarkovsky wrote:
Don't know whether or not it's relevant, not going to read this whole thread.

The popular theory is that, rather than DNA, RNA was the first genetic material. The genetic material of the very first forms of life was RNA, so the question of prebiotic deoxyribose synthesis is moot.

You still need an origin for the components of DNA.
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
tarkovsky
Posts: 212
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 4:51:24 PM
Posted: 4 years ago
At 5/27/2012 1:48:53 PM, SuburbiaSurvivor wrote:
At 5/27/2012 2:43:57 AM, tarkovsky wrote:
Don't know whether or not it's relevant, not going to read this whole thread.

The popular theory is that, rather than DNA, RNA was the first genetic material. The genetic material of the very first forms of life was RNA, so the question of prebiotic deoxyribose synthesis is moot.

You still need an origin for the components of DNA.

Yeah, but that origin need not be prebiotic. If an organism can synethisize deoxyribose sugars ex post facto then why go looking for the origin in the wrong place? If the theory is true the question is moot.
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 6:54:11 PM
Posted: 4 years ago
At 5/27/2012 4:51:24 PM, tarkovsky wrote:
At 5/27/2012 1:48:53 PM, SuburbiaSurvivor wrote:
At 5/27/2012 2:43:57 AM, tarkovsky wrote:
Don't know whether or not it's relevant, not going to read this whole thread.

The popular theory is that, rather than DNA, RNA was the first genetic material. The genetic material of the very first forms of life was RNA, so the question of prebiotic deoxyribose synthesis is moot.

You still need an origin for the components of DNA.

Yeah, but that origin need not be prebiotic. If an organism can synethisize deoxyribose sugars ex post facto then why go looking for the origin in the wrong place? If the theory is true the question is moot.

*Sigh*, and how do you propose an organism consisting of only an RNA strand inside of a lipid could synthsize deoxyribose?
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"
Wnope
Posts: 6,924
Add as Friend
Challenge to a Debate
Send a Message
5/27/2012 9:17:22 PM
Posted: 4 years ago
At 5/27/2012 1:48:05 PM, SuburbiaSurvivor wrote:
At 5/27/2012 2:32:50 AM, Wnope wrote:
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

Are you still not seeing the problem with your terminology?

There is no such thing as prebiotic DNA synthesis outside of the lab.

It's like saying "prebiotic mammalian birth."

I was curious about hypotheses regarding the origin of the components of DNA and subsequent polymerization of said componennts. Though the ingredients for life certainly would have had to be synthesized prebiotically at some point. Unless you're arguing that an RNA replicating system could have created the enzymes required to catalyze it all. If that's what you're arguing, I'm curious as to how you propose this could have happened.

You can talk about "prebiotic synthesis of self-replicating macromolecules" in which case it's TNA, pRNA World, etc. That's when abiogenesis has occurred and thus the "pre" and "post biotic" stages pass.

Similarly, you can talk about what the direct evolutionary prescursor of DNA is.

But the direct evolutionary precursor of DNA is NOT whatever self-replicating macromolecule passed the pre to postbiotic stage.


I don't see how this last sentence doesn't contradict the rest of what you just said. If the direct evolutionary precursor of DNA isn't whatever self-replicating macromolecule passed pre to postbiotic stage, then in essence you're saying that DNA didn't have a precursor such as RNA, TNA, or pRNA.

Let's take the example, for instance Cairns-Smith model of inorganic clay surfaces with different ion charges (I am not endorsing this hypothesis, just using it an as example).

Cairns-Smith would be an example of prebiotic synthesis of self-replicating macromolecules.

After a few hundred thousand years, "clay surfaces" evolve into an information system which would be directly more like precursors to DNA.

There are two questions with different answers:

1. What passed from prebiotic to postbiotic.
2. What inheritance system came directly before DNA.

You are conflating the two and saying that we should expect clay surfaces to be compatible with DNA, an information system which would have evolved for hundreds of thousands of years, if not millions.

That's why "prebiotic DNA synthesis" outside the lab is nonsensical and misleading terminology.

DNA in its present form cannot self-replicate without pawning the job off to enzymes. The previous inheritance system had to gain that division of labor instead of self-replicating.

No abiogenesis hypothesis expects the first inheritance system (self-replicating macromolecules) to express phenotypes through transcription. They didn't even have self-generated membranes.
tarkovsky
Posts: 212
Add as Friend
Challenge to a Debate
Send a Message
5/28/2012 3:14:24 AM
Posted: 4 years ago
At 5/27/2012 6:54:11 PM, SuburbiaSurvivor wrote:
At 5/27/2012 4:51:24 PM, tarkovsky wrote:
At 5/27/2012 1:48:53 PM, SuburbiaSurvivor wrote:
At 5/27/2012 2:43:57 AM, tarkovsky wrote:
Don't know whether or not it's relevant, not going to read this whole thread.

The popular theory is that, rather than DNA, RNA was the first genetic material. The genetic material of the very first forms of life was RNA, so the question of prebiotic deoxyribose synthesis is moot.

You still need an origin for the components of DNA.

Yeah, but that origin need not be prebiotic. If an organism can synethisize deoxyribose sugars ex post facto then why go looking for the origin in the wrong place? If the theory is true the question is moot.

*Sigh*, and how do you propose an organism consisting of only an RNA strand inside of a lipid could synthsize deoxyribose?

Really? Why couldn't have Deoxyribose synthesis occurred after organisms had taken a sufficient amount of complexity? You're bringing up a really weak point...

Again, if the theory is true the question is moot.
SuburbiaSurvivor
Posts: 872
Add as Friend
Challenge to a Debate
Send a Message
5/29/2012 12:52:16 AM
Posted: 4 years ago
At 5/27/2012 9:17:22 PM, Wnope wrote:
At 5/27/2012 1:48:05 PM, SuburbiaSurvivor wrote:
At 5/27/2012 2:32:50 AM, Wnope wrote:
At 5/27/2012 12:49:42 AM, SuburbiaSurvivor wrote:
At 5/26/2012 1:20:45 PM, Ren wrote:
At 5/26/2012 12:29:11 PM, SuburbiaSurvivor wrote:
At 5/26/2012 7:44:16 AM, Ren wrote:
At 5/25/2012 4:51:54 PM, SuburbiaSurvivor wrote:
I literally can't find ANY articles ANYWHERE illustrating any sort of mechanism for getting deoxyribose. There's the whole formose reaction that gets ribose (of course, there's the list of problems with that) but I can't find anything for ribose. I'm writing a paper on abiogenesis and it's going to be really hard to refute something if there aren't even any arguments for it >.<

It derives circumstantially from oxygen atoms during the formation of nucleotides.

http://www.springerlink.com...

I don't see where this article talks about deoxyribose synthesis. Can you cite the specific page this paper talks about deoxyribose synthesis?

Dude. Deoxyribose is simply a sugar. It is the ribose saccharide from an oxygen molecule. It is essentially the material from which a helix is constructed. In a building, it would the wooden or metal infrastructure. It also contributes to communication and transcription, obviously, as it contributes to cellular metabolism. Accordingly, it's only part of the description of DNA, and it doesn't simply construct on its own. It merely needs to be present when nucleotides form from heating polypeptides or in the circumstantial presence of RNA. Ribose forms in rings out of chains of carbon molecules. This is why we consider life on this planet carbon-based.

A) Deoxyribose is a sugar? No sh!t, Sherlock. So is ribose. Immediately assuming it can be synthesized easily because it's a sugar is pretty intellectually naive. B) Thank you for describing the structure and function of deoxyribose while completely failing to describe how deoxyribose can be synthesized prebiotically. I can tell you're being condescending, but next time try and be condescending while remaining relevant. No offense.

When you go to the page, click on the preview link and it should open the first page, where they give you a historical overview of prebiotic DNA synthesis.

Ren, this is kind of sad. The introduction not only fails to discuss prebiotic DNA synthesis (as if the prebiotic synthesis of DNA could be summarized in an introduction), but merely cites the ability of RNA to cleave DNA strands. This implies that the DNA was already synthesized and polymerized.

The title claims that nucleotides and polypeptides can be formed simultaneously from n-phosphoreonine, but I really can't critique the article as I have no access to it... Though I can already tell there are problems with it since it involves reactions with nucleosides (where'd we get those) and N-(O,O-diisopropyl)phosphothreonine in anhydrous pyridine. Quite frankly, I've never heard of this chemical in any RNA World paper and I'm curious as to how it would have synthesized in prebiotic earth.

Are you still not seeing the problem with your terminology?

There is no such thing as prebiotic DNA synthesis outside of the lab.

It's like saying "prebiotic mammalian birth."

I was curious about hypotheses regarding the origin of the components of DNA and subsequent polymerization of said componennts. Though the ingredients for life certainly would have had to be synthesized prebiotically at some point. Unless you're arguing that an RNA replicating system could have created the enzymes required to catalyze it all. If that's what you're arguing, I'm curious as to how you propose this could have happened.

You can talk about "prebiotic synthesis of self-replicating macromolecules" in which case it's TNA, pRNA World, etc. That's when abiogenesis has occurred and thus the "pre" and "post biotic" stages pass.

Similarly, you can talk about what the direct evolutionary prescursor of DNA is.

But the direct evolutionary precursor of DNA is NOT whatever self-replicating macromolecule passed the pre to postbiotic stage.


I don't see how this last sentence doesn't contradict the rest of what you just said. If the direct evolutionary precursor of DNA isn't whatever self-replicating macromolecule passed pre to postbiotic stage, then in essence you're saying that DNA didn't have a precursor such as RNA, TNA, or pRNA.

Let's take the example, for instance Cairns-Smith model of inorganic clay surfaces with different ion charges (I am not endorsing this hypothesis, just using it an as example).

Cairns-Smith would be an example of prebiotic synthesis of self-replicating macromolecules.

After a few hundred thousand years, "clay surfaces" evolve into an information system which would be directly more like precursors to DNA.

There are two questions with different answers:

1. What passed from prebiotic to postbiotic.
2. What inheritance system came directly before DNA.

You are conflating the two and saying that we should expect clay surfaces to be compatible with DNA, an information system which would have evolved for hundreds of thousands of years, if not millions.

That's why "prebiotic DNA synthesis" outside the lab is nonsensical and misleading terminology.

DNA in its present form cannot self-replicate without pawning the job off to enzymes. The previous inheritance system had to gain that division of labor instead of self-replicating.

No abiogenesis hypothesis expects the first inheritance system (self-replicating macromolecules) to express phenotypes through transcription. They didn't even have self-generated membranes.

Ugh, Wnope, everyone from Orgel to Shapiro has criticized clay theory. How on earth do you propose that crystal could carry the kind of information required by RNA? As Massimo Pigluicci explains [1]:

"An argument can be made that crystals are not actually capable of incorporating new information in their inherited "code," unlike what happens with mutations in living beings. True, they can assimilate impurities from the environment and "transmit" such "information" to their "descendants" for some time; but these impurities do not get replicated, they need continually to be imported from the outside, and they do not become a permanent and heritable part of the crystal."

http://web.archive.org...
"I'm going to tell you something that you're never going to forget, SuburbiaSurvivor. Women... Are just human beings"