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Selfsim
2013-Dec-25, 08:31 PM
Here's an interesting study (Dec 14) which demonstrates self-assembly of nucleoside bases of RNA without the involvement of modern-day enzymes ..

New Study Brings Scientists Closer to the Origin of RNA (http://phys.org/news/2013-12-scientists-closer-rna.html)


In the study, Hud's team investigated bases that are chemically related to the bases of modern RNA, but that might be able to spontaneously bond with ribose and assemble with other bases through the same interactions that enable DNA and RNA to store information. They homed in on a molecule called triaminopyrimidine (TAP).

The researchers mixed TAP with ribose under conditions meant to mimic a drying pond on early Earth. TAP and ribose reacted together in high yield, with up to 80 percent of TAP being converted into nucleosides, which is the name for the ribose-base unit of RNA. Previous attempts to form a ribose-base bond with the current RNA bases in similar reactions had either failed or produced nucleosides in very in very low yields.

"This study is important in showing a feasible step for how we get the start of an RNA-like molecule, but also how the building blocks of the first RNA-like polymers could have found each other and self-assembled in what would have been a very complex mixture of chemicals," Hud said.

The researchers demonstrated this property of the TAP nucleosides by adding another molecule to their reaction mixture, called cyanuric acid, which is known to interact with TAP. Even in the unpurified reaction mixture, noncovalent polymers formed with thousands of paired nucleosides.
But what would we have all this mean?

Jens
2013-Dec-25, 11:23 PM
I'm far from an expert, but I think the significance is this. If there are bases that under certain conditions bond spontaneously to form RNA, then I guess you can speculate that RNA started that way and then evolved to incorporate other bases, like the current ones, that require enzymes to bond, thus allowing the RNA to carry information.

Colin Robinson
2013-Dec-27, 10:37 PM
Here's an interesting study (Dec 14) which demonstrates self-assembly of nucleoside bases of RNA without the involvement of modern-day enzymes ..

New Study Brings Scientists Closer to the Origin of RNA (http://phys.org/news/2013-12-scientists-closer-rna.html)


But what would we have all this mean?

Well, it doesn't mean Hud's team has found the answer to the big question about life, the universe and everything. :) It doesn't even mean that they've found the answer to the big question of how life got started on Earth.

What it does mean, becomes apparent if we consider that the latter big question (how life got started on Earth) can be broken into smaller questions, e.g.:

* How did the first protein-like molecules form?
* How did the first RNA-like molecules form?
* How did the first lipid membranes form?
* How did early proteins and/or RNA-like molecules first get concentrated within lipid membranes to form proto-cells?

The study you've linked to is a promising partial answer to one of these questions.

Selfsim
2013-Dec-28, 01:03 AM
Well howdy Colin .. where ya been lately?
Well, it doesn't mean Hud's team has found the answer to the big question about life, the universe and everything. :) It doesn't even mean that they've found the answer to the big question of how life got started on Earth.

What it does mean, becomes apparent if we consider that the latter big question (how life got started on Earth) can be broken into smaller questions, e.g.:Hmm so meaning appears when one breaks down a big question into a bunch of smaller questions, eh? Interesting.


* How did the first protein-like molecules form?
* How did the first RNA-like molecules form?
* How did the first lipid membranes form?
* How did early proteins and/or RNA-like molecules first get concentrated within lipid membranes to form proto-cells?

The study you've linked to is a promising partial answer to one of these questions.I'm not so sure it provides any answers to any "how" questions about origins, myself.

Demonstrating a feasible formation pathway, only tells us what we already know, no?
Ie: that it happened once upon a time ...

Oh well, just change the question to:
"How do I go about making (high yield) nucleosides from TAP and ribose?"
… There .. that now makes it a useful scientific exercise, I suppose.

Colin Robinson
2013-Dec-28, 04:20 AM
Well howdy Colin .. where ya been lately?

I recently had some issues with my home internet access. Which seem to be resolved, at least for the moment.


Hmm so meaning appears when one breaks down a big question into a bunch of smaller questions, eh?

Yes, I think breaking down a big question into smaller questions is often the way science finds answers.


Demonstrating a feasible formation pathway, only tells us what we already know, no?
Ie: that it happened once upon a time ...

I think two key phrases in the passage in your OP are "conditions meant to mimic a drying pond on early Earth", and "high yield".

The idea that warm ponds had something to do with the origin of life, goes back to Darwin at least, but has recently been challenged by the black smoker theory. It is also possible that both environments played a part.

The point about high yield implies that on a planet with the sort of evaporating ponds being mimicked, containing TAP, ribose and cyanuric acid, formation of nucleoside polymers is not just a possible outcome, but a probable one.

This interesting because TAP, ribose and cyanuric acid are all quite simple organic molecules, each with just three to five carbon atoms. Cyanuric acid is C3H3N3O3.TAP is C4H7N5. Ribose is C5H10O5.

Selfsim
2013-Dec-28, 06:03 AM
I recently had some issues with my home internet access. Which seem to be resolved, at least for the moment.Ok .. thought you'd run away ... :)
... The point about high yield implies that on a planet with the sort of evaporating ponds being mimicked, containing TAP, ribose and cyanuric acid, formation of nucleoside polymers is not just a possible outcome, but a probable one.Then why isn't this 'probable' on Earth today? Why has this also 'baffled scientists for decades'?

I think the real purpose of the research is more along the lines of what Hud himself suggests (http://www.sciencedaily.com/releases/2013/02/130220123332.htm): "the self-assembly process could be used in the future to create new materials, such as nanowires".


This interesting because TAP, ribose and cyanuric acid are all quite simple organic molecules, each with just three to five carbon atoms. Cyanuric acid is C3H3N3O3.TAP is C4H7N5. Ribose is C5H10O5... Then he should show us the pond with this stuff in it!

Colin Robinson
2013-Dec-28, 07:54 AM
Ok .. thought you'd run away ... :)Then why isn't this 'probable' on Earth today?

In the first place, because conditions on Earth today are not conducive to simple organic molecules forming spontaneously.

As Miller and Urey demonstrated back in the fifties, it is easy to form a very big range of simple organics by applying an energy source to a mixture of even simpler gases, like ammonia, methane and/or carbon dioxide, and water vapor. BUT (as variations of the experiment demonstrated around the same time) this only happens if the mixture of gases is chemically reducing rather than oxidizing. If you start with the mixture of gases found in Earth's atmosphere today, (consisting mainly of N2 and O2, plus a little CO2 and H2O), and apply an energy source to that, you don't get a similar result.

In the second place, the probable fate of any of these simple organic molecules which did happen to appear in a pond on Earth today, is that they'd be eaten up by living organisms. Ribose is a sugar, after all. Cyanuric acid is a good source of fixed nitrogen, an element essential to growth of plants...


Why has this also 'baffled scientists for decades'?

I expect because there are so many different organic molecules, even smallish ones with just three, four or five carbon atoms plus nitrogen, hydrogen and oxygen. It did take decades of experimentation to find the combination of three molecules (TAP, ribose and cyanuric acid) which forms the RNA-like polymer spontaneously and with high yield.


I think the real purpose of the research is more along the lines of what Hud himself suggests (http://www.sciencedaily.com/releases/2013/02/130220123332.htm): "the self-assembly process could be used in the future to create new materials, such as nanowires".

One of the good things about scientific research is that it can lead both to new useful technologies and to new approaches to big questions like the origin of life on Earth and the probability of life on other planets.

Selfsim
2013-Dec-28, 09:58 PM
In the first place, because conditions on Earth today are not conducive to simple organics forming spontaneously.

As Miller and Urey demonstrated back in the fifties, it is easy to form a very big range of simple organics by applying an energy source to a mixture of even simpler gases, like ammonia, methane and/or carbon dioxide, and water vapor. BUT (as variations of the experiment demonstrated around the same time) this only happens if the mixture of gases is chemically reducing rather than oxidizing. If you start with the mixture of gases found in Earth's atmosphere today, (consisting mainly of N2 and O2, plus a little CO2 and H2O), and apply an energy source to that, you don't get a similar result.Well that's strange .. given that (http://pubs.acs.org/doi/abs/10.1021/ja410124v?prevSearch=%255BContrib%253A%2BCafferty% 252C%2BBrian%2BJ.%255D&searchHistoryKey=):
A major product of the TAP+ribose reaction is a β-ribofuranoside of TAP, which we term TARC. This nucleoside is also shown to efficiently form supramolecular assemblies in water by pairing and stacking with CA.


In the second place, the probable fate of any of these simple organic molecules which did happen to appear in a pond on Earth today, is that they'd be eaten up by living organisms. Ribose is a sugar, after all. Cyanuric acid is a good source of fixed nitrogen, an element essential to growth of plants...Surely if its 'probable' ... not just 'possible', (your words), then one would think it'd be happening more often than not, and there'd be some evidence of it happening in a natural setting? ... Not everything is eaten by living organisms, y'know(?) ...
And, from an earlier article:
I expect because there are so many different organic molecules, even smallish ones with just three, four or five carbon atoms plus nitrogen, hydrogen and oxygen. It did take decades of experimentation to find the combination of three molecules (TAP, ribose and cyanuric acid) which forms the RNA-like polymer spontaneously and with high yield... and this doesn't suggest a deliberately designed experiment? From the earlier paper (http://pubs.acs.org/doi/abs/10.1021/ja312155v?prevSearch=%2528Hud%2529%2Band%2B%255BTi tle%253A%2BSelf%2BAssembly%255D%2Band%2B%255BContr ib%253A%2BHud%252CNicholas%2BV.%255D&searchHistoryKey=) (published in Feb)...
The results of our study have implications for the design of new self-assembling structures and hydrogel-forming molecules.. and the afterthought ...
... and may provide insights into the origin of the first RNA-like polymers.

One of the good things about scientific research is that it can lead both to new useful technologies and to new approaches to big questions like the origin of life on Earth and the probability of life on other planets.Methinks the 'big question' had little/nothing to do with the origin of life on Earth and the probability of life on other planets (IMO) ...

Colin Robinson
2013-Dec-29, 01:07 AM
In the first place, because conditions on Earth today are not conducive to simple organic molecules forming spontaneously.

As Miller and Urey demonstrated back in the fifties, it is easy to form a very big range of simple organics by applying an energy source to a mixture of even simpler gases, like ammonia, methane and/or carbon dioxide, and water vapor. BUT (as variations of the experiment demonstrated around the same time) this only happens if the mixture of gases is chemically reducing rather than oxidizing. If you start with the mixture of gases found in Earth's atmosphere today, (consisting mainly of N2 and O2, plus a little CO2 and H2O), and apply an energy source to that, you don't get a similar result.

Well that's strange .. given that (http://pubs.acs.org/doi/abs/10.1021/ja410124v?prevSearch=%255BContrib%253A%2BCafferty% 252C%2BBrian%2BJ.%255D&searchHistoryKey=):


A major product of the TAP+ribose reaction is a β-ribofuranoside of TAP, which we term TARC. This nucleoside is also shown to efficiently form supramolecular assemblies in water by pairing and stacking with CA.

I'm not quite sure what you find strange here...

The results of the Miller-Urey experiment (and similar experiments with different mixtures of gases) are about how simple organic compounds can be formed. It requires an energy source (such as a spark of electricity), and gases such as CH4 (or CO2), NH3 (or N2), and H2O. The overall mixture of gases also needs to be chemically reducing rather than oxidizing; in other words, hydrogen-rich rather than oxygen-rich.

Hud's experiment is about the next step: once simple organics are present, how can they form more complex molecules or supramolecular assemblies (polymers)? The finding: in the case of the simple organics TAP, ribose and cyanuric acid, polymerization can happen in a pool of evaporating water.

Just what do you find "strange" here, Selfsim? Are you supposing that the presence of water makes an environment oxidizing rather than reducing?


Surely if its 'probable' ... not just 'possible', (your words), then one would think it'd be happening more often than not, and there'd be some evidence of it happening in a natural setting?

Surely the likelihood of such a polymerization is going to be affected by factors like:

* Are simple organic molecules being formed, if so how abundantly?
* What else can happen to any simple organic molecules? Apart from them reacting with each other? Are there other processes that can break them down or incorporate them into something else?


… Not everything is eaten by living organisms, y'know(?) ..

Not everything… but sugars (of which ribose is one) are especially easy to metabolize…


and this doesn't suggest a deliberately designed experiment?

Isn't every scientific experiment "deliberately designed"?

Selfsim
2013-Dec-29, 05:53 AM
... Hud's experiment is about the next step: once simple organics are present, how can they form more complex molecules or supramolecular assemblies (polymers)? The finding: in the case of the simple organics TAP, ribose and cyanuric acid, polymerization can happen in a pool of evaporating water.What I'm happy to admit is a lack of detail about what kind of assumptions they made about the environment in which their hypothesised pond of evaporating water was in, and how does this compare with the experiment they conducted? Without this information, I don't see why we should accept that they created any queriable pre-biotic 'analogues' in a lab environment at all. Whether or not their experiment corresponds in detail, with the environment hypothesised to exist on early Earth, is left open to guesswork and assumption.


Surely the likelihood of such a polymerization is going to be affected by factors like:

* Are simple organic molecules being formed, if so how abundantly?
* What else can happen to any simple organic molecules? Apart from them reacting with each other? Are there other processes that can break them down or incorporate them into something else? .. or what are the effects of a reducing or oxidising atmosphere on the polymerisation reaction itself? What might be the inhibiting factors and what might be the sensitivity limits of the reaction to these?
Isn't every scientific experiment "deliberately designed"?Well, yes. Just what exactly was the primary purpose of this experiment and how did that influence the setup conditions?

Colin Robinson
2013-Dec-29, 02:49 PM
What I'm happy to admit is a lack of detail about what kind of assumptions they made about the environment in which their hypothesised pond of evaporating water was in, and how does this compare with the experiment they conducted? Without this information, I don't see why we should accept that they created any queriable pre-biotic 'analogues' in a lab environment at all. Whether or not their experiment corresponds in detail, with the environment hypothesised to exist on early Earth, is left open to guesswork and assumption.

.. or what are the effects of a reducing or oxidising atmosphere on the polymerisation reaction itself? What might be the inhibiting factors and what might be the sensitivity limits of the reaction to these?Well, yes. Just what exactly was the primary purpose of this experiment and how did that influence the setup conditions?

If you'd like more detail about how the experiment was designed and carried out, perhaps you should take the trouble to read the full journal article (http://pubs.acs.org/doi/abs/10.1021/ja410124v), instead of relying on popularizations and abstracts?

Accessing the full text will cost you 35 US dollars, if you're not already a subscriber to the journal.

MaDeR
2013-Dec-30, 02:48 PM
Then why isn't this 'probable' on Earth today?
This is standard-issue creationist silly question. Your cover up is failing there.

Answer: Earth before emergence of life had different environmental conditions. Life changed environment radically. What is so hard in understanding that, I do not know.

Selfsim
2013-Dec-30, 10:15 PM
This is standard-issue creationist silly question. Your cover up is failing there.Ha!
Keep trying MaDeR ... I'm sure if you try hard enough, you'll end up convincing someone.

Answer: Earth before emergence of life had different environmental conditions. Life changed environment radically. What is so hard in understanding that, I do not know.What's hard to understand, is your use of an hypothesis to explain the implications of a lab test for which you have not cited the designed conditions and method.

You really must try to improve the thoroughness of your research before jumping to conclusions deduced from the hypothesis, which itself, (you seem to have decided), was in fact, the primary objective of the test.