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Let's discuss, not debate, RNA to DNA

SNP1
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4/8/2014 1:14:40 PM
Posted: 2 years ago
One of the things we have not yet discovered is how RNA actually became DNA or how DNA could form in the early Earth environment. I, personally, subscribe to the RNA world hypothesis since there is so much evidence that supports it.

In this thread I would like to have some intellectual discussions about how DNA could have originally formed.

_______________________________________________________________________________________________

First, I am not a biologist. I might be misinformed in a couple areas, if I am then please point it out.

I, like many scientists, believe that RNA could have become DNA under the right conditions. This is plausible because there exists self-replicating RNA and there also exists double-stranded RNA. If there was a double-stranded RNA that could self-replicate (I do not know if there is/was one or not) then the only difference between that and DNA would be the existence of a hydroxyl group attached to the pentose ring in RNA.

Since that type of RNA might be possible we need to find out how the hydroxyl group attached to the pentose ring might have detached from the RNA, thus forming primitive DNA.

So, what are your thoughts? I would like this to remain a thread about science, not science vs religion. Thank you.
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Sswdwm
Posts: 1,398
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4/8/2014 1:42:11 PM
Posted: 2 years ago
At 4/8/2014 1:14:40 PM, SNP1 wrote:
One of the things we have not yet discovered is how RNA actually became DNA or how DNA could form in the early Earth environment. I, personally, subscribe to the RNA world hypothesis since there is so much evidence that supports it.

I actually subscribe for the metabolism-first hypothesis, but I'm a chemist and I like kinetics and energy gradients :-p. RNA world on the face of it looks more versatile, we don't know yet though.

First, I am not a biologist. I might be misinformed in a couple areas, if I am then please point it out.

I, like many scientists, believe that RNA could have become DNA under the right conditions. This is plausible because there exists self-replicating RNA and there also exists double-stranded RNA. If there was a double-stranded RNA that could self-replicate (I do not know if there is/was one or not) then the only difference between that and DNA would be the existence of a hydroxyl group attached to the pentose ring in RNA.

DNA is just reduced RNA, and the biosynthesis of DNA as far as I understand is done via reduction of RNA, or it's precursors. There are other pathways, but this is a big flag in terms of evolution, as it seems the synthesis of DNA is a post-hoc step in the synthesis of RNA, and therefore would have had to evolve after RNA was already present.

I'm no biochemist either so I'm sure I got something wrong there :-p

Since that type of RNA might be possible we need to find out how the hydroxyl group attached to the pentose ring might have detached from the RNA, thus forming primitive DNA.

Well DNA has the advantages of being more stable over long term, which is inherant because the hydroxyl group allows for intramolecular base-catalyzed hydrolysis of the attached phosphate group.

http://www.rsc.org...

So anything that favors the formation of even a small% of reduced RNA for storage will confer an evolutionary advantage over previous generations with less reductive capability.

I think the more interesting question is why does RNA still exist if DNA is more stable? The answer to that is..... because DNA is too stable. mRNA (which codes for peptides/proteins) has a relatively short lifetime in the body (on the order of minutes). Which means the body can more rapidly and finely adapt the level of expression of any particular protein than if messages were purely done via DNA.

http://en.wikipedia.org...
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SNP1
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4/8/2014 2:04:33 PM
Posted: 2 years ago
At 4/8/2014 1:42:11 PM, Sswdwm wrote:
At 4/8/2014 1:14:40 PM, SNP1 wrote:
One of the things we have not yet discovered is how RNA actually became DNA or how DNA could form in the early Earth environment. I, personally, subscribe to the RNA world hypothesis since there is so much evidence that supports it.

I actually subscribe for the metabolism-first hypothesis, but I'm a chemist and I like kinetics and energy gradients :-p. RNA world on the face of it looks more versatile, we don't know yet though.

Correct. Best to keep an open mind, though I see the RNA world being closer to being confirmed than metabolism-first.

First, I am not a biologist. I might be misinformed in a couple areas, if I am then please point it out.

I, like many scientists, believe that RNA could have become DNA under the right conditions. This is plausible because there exists self-replicating RNA and there also exists double-stranded RNA. If there was a double-stranded RNA that could self-replicate (I do not know if there is/was one or not) then the only difference between that and DNA would be the existence of a hydroxyl group attached to the pentose ring in RNA.

DNA is just reduced RNA, and the biosynthesis of DNA as far as I understand is done via reduction of RNA, or it's precursors. There are other pathways, but this is a big flag in terms of evolution, as it seems the synthesis of DNA is a post-hoc step in the synthesis of RNA, and therefore would have had to evolve after RNA was already present.

Well, there have been experiments where RNA formed in an early Earth environment. With DNA being more stable I do not see a problem in terms of evolution (but it appears you might be more well versed in this than I)

I'm no biochemist either so I'm sure I got something wrong there :-p

Well, better to try and fail.

Since that type of RNA might be possible we need to find out how the hydroxyl group attached to the pentose ring might have detached from the RNA, thus forming primitive DNA.

Well DNA has the advantages of being more stable over long term, which is inherant because the hydroxyl group allows for intramolecular base-catalyzed hydrolysis of the attached phosphate group.

http://www.rsc.org...

So anything that favors the formation of even a small% of reduced RNA for storage will confer an evolutionary advantage over previous generations with less reductive capability.

I think the more interesting question is why does RNA still exist if DNA is more stable? The answer to that is..... because DNA is too stable. mRNA (which codes for peptides/proteins) has a relatively short lifetime in the body (on the order of minutes). Which means the body can more rapidly and finely adapt the level of expression of any particular protein than if messages were purely done via DNA.

http://en.wikipedia.org...

Interesting. I will read through it when I have more time.
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Sswdwm
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4/8/2014 2:18:13 PM
Posted: 2 years ago
At 4/8/2014 2:04:33 PM, SNP1 wrote:
At 4/8/2014 1:42:11 PM, Sswdwm wrote:
At 4/8/2014 1:14:40 PM, SNP1 wrote:
One of the things we have not yet discovered is how RNA actually became DNA or how DNA could form in the early Earth environment. I, personally, subscribe to the RNA world hypothesis since there is so much evidence that supports it.

I actually subscribe for the metabolism-first hypothesis, but I'm a chemist and I like kinetics and energy gradients :-p. RNA world on the face of it looks more versatile, we don't know yet though.

Correct. Best to keep an open mind, though I see the RNA world being closer to being confirmed than metabolism-first.

First, I am not a biologist. I might be misinformed in a couple areas, if I am then please point it out.

I, like many scientists, believe that RNA could have become DNA under the right conditions. This is plausible because there exists self-replicating RNA and there also exists double-stranded RNA. If there was a double-stranded RNA that could self-replicate (I do not know if there is/was one or not) then the only difference between that and DNA would be the existence of a hydroxyl group attached to the pentose ring in RNA.

DNA is just reduced RNA, and the biosynthesis of DNA as far as I understand is done via reduction of RNA, or it's precursors. There are other pathways, but this is a big flag in terms of evolution, as it seems the synthesis of DNA is a post-hoc step in the synthesis of RNA, and therefore would have had to evolve after RNA was already present.

Well, there have been experiments where RNA formed in an early Earth environment. With DNA being more stable I do not see a problem in terms of evolution (but it appears you might be more well versed in this than I)

As far as I understand single strand RNA alone very unstable (as in impossible to do anything for OOL with), this stability improves when RNA is bound to itself in more complex structures, such as double stranded RNA, antibodies, tRNA etc.

Which is convenient as they form interesting structures when self-bound, aptamers are a real life application of RNA structures which effectively act as a pseudo-antibody, capable of binding to various surfaces and acting as catalysts. So the move to DNA seems to be an incremental change.

In RNA World one of the key proposed steps is compartmentalisation of RNA followed by replication. Without compartmentalisation any RNA structures that auto-catalyze will also catalyze the replication of non-'catalyst' strands of RNA. In a rudementary lipid membrane, you don't have that problem as only smaller molecules (nucleotides, etc) can access the inside of the membrane.

Has this got experimental backing?
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SNP1
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4/8/2014 3:17:55 PM
Posted: 2 years ago
At 4/8/2014 2:18:13 PM, Sswdwm wrote:
As far as I understand single strand RNA alone very unstable (as in impossible to do anything for OOL with), this stability improves when RNA is bound to itself in more complex structures, such as double stranded RNA, antibodies, tRNA etc.

Which is convenient as they form interesting structures when self-bound, aptamers are a real life application of RNA structures which effectively act as a pseudo-antibody, capable of binding to various surfaces and acting as catalysts. So the move to DNA seems to be an incremental change.

In RNA World one of the key proposed steps is compartmentalisation of RNA followed by replication. Without compartmentalisation any RNA structures that auto-catalyze will also catalyze the replication of non-'catalyst' strands of RNA. In a rudementary lipid membrane, you don't have that problem as only smaller molecules (nucleotides, etc) can access the inside of the membrane.

Has this got experimental backing?

RNA moving to DNA does not. Biologists seem to do nothing involving abiogenesis, for some reason it is the Chemists that do (so we only really have RNA forming in an early Earth environment). I wish there were biologists researching this.
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Defro
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4/8/2014 3:47:09 PM
Posted: 2 years ago
At 4/8/2014 3:17:55 PM, SNP1 wrote:

RNA moving to DNA does not. Biologists seem to do nothing involving abiogenesis, for some reason it is the Chemists that do (so we only really have RNA forming in an early Earth environment). I wish there were biologists researching this.

That's because the theory of abiogenesis is mostly chemistry.

The one major flaw I find in the RNA world hypothesis is that it is too complex to have arisen prebiotically.
Sswdwm
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4/8/2014 4:57:32 PM
Posted: 2 years ago
At 4/8/2014 3:47:09 PM, Defro wrote:
At 4/8/2014 3:17:55 PM, SNP1 wrote:

RNA moving to DNA does not. Biologists seem to do nothing involving abiogenesis, for some reason it is the Chemists that do (so we only really have RNA forming in an early Earth environment). I wish there were biologists researching this.

That's because the theory of abiogenesis is mostly chemistry.

The one major flaw I find in the RNA world hypothesis is that it is too complex to have arisen prebiotically.

Why is that? That doesnt sound like a very objective... Objection

And the whole point of the RNA World hypothesis is that you can achieve complex features purely from very simple origins (RNA, Natural Catalysts, Heat, Lipids).
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whiteflame
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4/8/2014 10:47:41 PM
Posted: 2 years ago
I've had an extensive debate to this effect, one of the first I had on this site:

http://www.debate.org...

But as this is a discussion, I'll put in my two cents.

I'm a microbiologist, and I work mainly with a group of subviral pathogens called satellite RNAs. These are naked RNAs that survive, replicate, and act on their own, though admittedly they, along with their more complicated counterparts viroids, require certain proteins for replication and stability.

I tend to agree with RNA world theory. It's certainly not perfect, but it has a good plausibility to it. RNA is a highly versatile structure capable of forming many different catalytic structures necessary for basic cellular actions. It's not as effective as protein, but it has its benefits, and the fact that it can associate with amino acids as cofactors for its activity lends some credence to the claim that they could function by providing direction to the evolution of proteins.

Of course, this is all rather simplistic. The amount of evidence we have for how RNA was initially created and how it could form complex structures capable of increasingly complex actions is still up for debate. It's certainly not fully proven, but we're getting closer.
Sswdwm
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4/9/2014 5:04:30 AM
Posted: 2 years ago
At 4/8/2014 10:47:41 PM, whiteflame wrote:
I've had an extensive debate to this effect, one of the first I had on this site:

http://www.debate.org...

But as this is a discussion, I'll put in my two cents.

I'm a microbiologist, and I work mainly with a group of subviral pathogens called satellite RNAs. These are naked RNAs that survive, replicate, and act on their own, though admittedly they, along with their more complicated counterparts viroids, require certain proteins for replication and stability.

I tend to agree with RNA world theory. It's certainly not perfect, but it has a good plausibility to it. RNA is a highly versatile structure capable of forming many different catalytic structures necessary for basic cellular actions. It's not as effective as protein, but it has its benefits, and the fact that it can associate with amino acids as cofactors for its activity lends some credence to the claim that they could function by providing direction to the evolution of proteins.

Of course, this is all rather simplistic. The amount of evidence we have for how RNA was initially created and how it could form complex structures capable of increasingly complex actions is still up for debate. It's certainly not fully proven, but we're getting closer.

Loved the debate WF :-D
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whiteflame
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4/9/2014 2:17:56 PM
Posted: 2 years ago
At 4/9/2014 5:04:30 AM, Sswdwm wrote:
At 4/8/2014 10:47:41 PM, whiteflame wrote:
I've had an extensive debate to this effect, one of the first I had on this site:

http://www.debate.org...

But as this is a discussion, I'll put in my two cents.

I'm a microbiologist, and I work mainly with a group of subviral pathogens called satellite RNAs. These are naked RNAs that survive, replicate, and act on their own, though admittedly they, along with their more complicated counterparts viroids, require certain proteins for replication and stability.

I tend to agree with RNA world theory. It's certainly not perfect, but it has a good plausibility to it. RNA is a highly versatile structure capable of forming many different catalytic structures necessary for basic cellular actions. It's not as effective as protein, but it has its benefits, and the fact that it can associate with amino acids as cofactors for its activity lends some credence to the claim that they could function by providing direction to the evolution of proteins.

Of course, this is all rather simplistic. The amount of evidence we have for how RNA was initially created and how it could form complex structures capable of increasingly complex actions is still up for debate. It's certainly not fully proven, but we're getting closer.

Loved the debate WF :-D

I appreciate that. It was pretty intensive, even taught me a thing or two with regards to what research is out there on the subject.