Life’s First Spark Re-created In The Laboratory

[Reverend AtheiStar]

http://www.wired.com/wiredscience/2009/05/ribonucleotides/

 

Life’s First Spark Re-Created in the Laboratory

 

By Brandon Keim

 

May 13, 2009 |

 

1:40 pm |

 

 

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

 

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn’t explain how these ingredients might have formed.

 

“It’s like molecular choreography, where the molecules choreograph their own behavior,” said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

 

RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth’s history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

 

However, though researchers have been able to show how RNA’s component molecules, called ribonucleotides, could assemble into RNA, their many attempts to synthesize these ribonucleotides have failed. No matter how they combined the ingredients — a sugar, a phosphate, and one of four different nitrogenous molecules, or nucleobases — ribonucleotides just wouldn’t form.

 

Sutherland’s team took a different approach in what Harvard molecular biologist Jack Szostak called a “synthetic tour de force” in an accompanying commentary in Nature.

 

“By changing the way we mix the ingredients together, we managed to make ribonucleotides,” said Sutherland. “The chemistry works very effectively from simple precursors, and the conditions required are not distinct from what one might imagine took place on the early Earth.”

 

Like other would-be nucleotide synthesizers, Sutherland’s team included phosphate in their mix, but rather than adding it to sugars and nucleobases, they started with an array of even simpler molecules that were probably also in Earth’s primordial ooze.

 

They mixed the molecules in water, heated the solution, then allowed it to evaporate, leaving behind a residue of hybrid, half-sugar, half-nucleobase molecules. To this residue they again added water, heated it, allowed it evaporate, and then irradiated it.

 

At each stage of the cycle, the resulting molecules were more complex. At the final stage, Sutherland’s team added phosphate. “Remarkably, it transformed into the ribonucleotide!” said Sutherland.

 

According to Sutherland, these laboratory conditions resembled those of the life-originating “warm little pond” hypothesized by Charles Darwin if the pond “evaporated, got heated, and then it rained and the sun shone.”

 

Such conditions are plausible, and Szostak imagined the ongoing cycle of evaporation, heating and condensation providing “a kind of organic snow which could accumulate as a reservoir of material ready for the next step in RNA synthesis.”

 

Intriguingly, the precursor molecules used by Sutherland’s team have been identified in interstellar dust clouds and on meteorites.

 

“Ribonucleotides are simply an expression of the fundamental principles of organic chemistry,” said Sutherland. “They’re doing it unwittingly. The instructions for them to do it are inherent in the structure of the precursor materials. And if they can self-assemble so easily, perhaps they shouldn’t be viewed as complicated.”

 

Image: Universitat Pampeu Fabra

 

Tags: Astrobiology, Biology, Chemistry, Complexity, Evolution, origins of life, RNA

[Dagan]

Fascinating article, thanks for posting!

 

Pretty interesting how Darwin had the right idea, long before scientists really knew the importance of DNA.

[Jedah]

One less thing for theists to use God-of-the-Gaps on.

[Reverend AtheiStar]

Fascinating article, thanks for posting!

 

Pretty interesting how Darwin had the right idea, long before scientists really knew the importance of DNA.

 

You're welcome. I'm just passing it on from one of my friends on MySpace. It was sent to me marked "THE MOST IMPORTANT NEWS EVER!" lol...

 

I knew it was just a matter of time. How long, though, I didn't know. I'm glad it was sooner than later.

 

Darwin was a brilliant man in so many ways. If only he could still be alive to see how far his theory has come since his time! I'm sure he wouldn't be surprised, at all, about the current creationist opposition, though.

[Reverend AtheiStar]

One less thing for theists to use God-of-the-Gaps on.

 

It won't stop them, though, from saying that since this experiment took scientists to set it up and make it happen, so, too, did the original abiogenesis.

[Reverend AtheiStar]

One less thing for theists to use God-of-the-Gaps on.

 

LMAO! I LOVE your sig! That's too funny!

[Neon Genesis]

One less thing for theists to use God-of-the-Gaps on.

I love how the creationists in the comments on that article claim it wasn't peer reviewed and then they said God was the only scientist they trusted.

[Legion]

I think scientists are making a mistake if they’re looking for a particular kind of molecule that initiated life. I have no doubt that organisms emerged according to natural means, but I have serious doubts about this particular approach.

[Dhampir]

One less thing for theists to use God-of-the-Gaps on.

 

It won't stop them, though, from saying that since this experiment took scientists to set it up and make it happen, so, too, did the original abiogenesis.

True, but, if they acknowledge it at all, they'll also have to acknowledge that it doesn't take an all-knowing, perfect god to create life.

[Karhoof]

I think scientists are making a mistake if they’re looking for a particular kind of molecule that initiated life. I have no doubt that organisms emerged according to natural means, but I have serious doubts about this particular approach.

Why? What's your line of thinking here?

(I'm no scientist and won't even pretend to understand it all,

so maybe if you keep it on a fairly "common man" level... LOL)

[Legion]

I think scientists are making a mistake if they’re looking for a particular kind of molecule that initiated life. I have no doubt that organisms emerged according to natural means, but I have serious doubts about this particular approach.

Why? What's your line of thinking here?

(I'm no scientist and won't even pretend to understand it all,

so maybe if you keep it on a fairly "common man" level... LOL)

Well Karhoof I am no scientist either. But I have had a bit of interest in this subject. I’ll try to make a long story short and simple.

 

There was a time when I thought that an RNA like molecule might have been the progenitor of life on Earth. But then the biologist Stuart Kauffman introduced me to the idea of an autocatalytic set. One of the simplest is shown here.

Here a set of molecules (AB and BA) replicate themselves from a food set (A and B ) by reflexive catalysis. It’s kind of like an “I’ll scratch your back and you scratch mine” situation.

 

Once I understood the idea behind an autocatalytic set I could see that replication need not be based on a template (like RNA or DNA) at all. And Kauffman points this out in nearly as many words.

 

These days I tend to lean towards the ideas being espoused by Doron Lancet and his colleagues. They are working on an idea for the origins of life which they call composomes. And as I read more of the work of Robert Rosen I have a growing sense that he’s right. Life is not about any special properties of matter per se. I think life is the result of a certain type of organization.

[Karhoof]

But I have had a bit of interest in this subject.

Same here. I've been waiting for it ever since the early 70's, when they were zapping "soup" with extremely high voltage.

(The method was to try and replicate lightning strikes hitting available materials.)

I was pretty excited when they produced amino acids where there were none before.

 

May take a while to sift through their material and I've been crazy busy too,

but when I understand it better I may run it past you here to see if I have it right.

 

Thanks.

[Reverend AtheiStar]

One less thing for theists to use God-of-the-Gaps on.

I love how the creationists in the comments on that article claim it wasn't peer reviewed and then they said God was the only scientist they trusted.

 

Well, that would just prove the athropomorphic origin of their god that much more. He is whatever version of superhuman they need at the time. This context calls for their god program to don the lab coat. Guess who made a quick change?

[Reverend AtheiStar]

One less thing for theists to use God-of-the-Gaps on.

 

It won't stop them, though, from saying that since this experiment took scientists to set it up and make it happen, so, too, did the original abiogenesis.

True, but, if they acknowledge it at all, they'll also have to acknowledge that it doesn't take an all-knowing, perfect god to create life.

 

That's a lot to assume from a creationist, sir! Just because they should acknowledge that doesn't mean they actually will.

[Reverend AtheiStar]

I think scientists are making a mistake if they’re looking for a particular kind of molecule that initiated life. I have no doubt that organisms emerged according to natural means, but I have serious doubts about this particular approach.

Why? What's your line of thinking here?

(I'm no scientist and won't even pretend to understand it all,

so maybe if you keep it on a fairly "common man" level... LOL)

Well Karhoof I am no scientist either. But I have had a bit of interest in this subject. I’ll try to make a long story short and simple.

 

There was a time when I thought that an RNA like molecule might have been the progenitor of life on Earth. But then the biologist Stuart Kauffman introduced me to the idea of an autocatalytic set. One of the simplest is shown here.

Here a set of molecules (AB and BA) replicate themselves from a food set (A and B ) by reflexive catalysis. It’s kind of like an “I’ll scratch your back and you scratch mine” situation.

 

Once I understood the idea behind an autocatalytic set I could see that replication need not be based on a template (like RNA or DNA) at all. And Kauffman points this out in nearly as many words.

 

These days I tend to lean towards the ideas being espoused by Doron Lancet and his colleagues. They are working on an idea for the origins of life which they call composomes. And as I read more of the work of Robert Rosen I have a growing sense that he’s right. Life is not about any special properties of matter per se. I think life is the result of a certain type of organization.

 

Very interesting! I think all scientific avenues should be walked. It's the quickest route to the truth.

[Legion]

I think all scientific avenues should be walked. It's the quickest route to the truth.

I think this is a great attitude for spectators to have. But if someone is interested in actually discovering truths they usually have to pick a specific route that they believe will take them to these truths.

[RisingPhoenix]

Wow. Can't claim to know much about the subject, but...it sure does raise some interesting questions about just what natural processes it might have taken to create life in the first place. This is very fascinating to discover in its own right.

[Karhoof]

Don’t mind me if I dumb this down to a level I can understand.

 

 

Okay, what I’ve got so far is…

On a molecular level, "friendly molecule" pairs join chemically to form a very base compound. These in turn (with its new chemical make-up) interact/attract with other molecules and other base compounds, forming larger sets.

Growing larger, they split or calf new sets that represent enough of the original to continue attracting more of these “friendly” molecules along with other new material.

(I’ll add my own two cents here - “unfriendly” material is either disregarded or destroys this compound molecular set)

 

A point is reached where these chemical sets will only gather particular materials and produce similarly particular sets.

This is the point where RNA is attained. (<- - or am I reaching too far?)

 

This is happening simultaneously along with many other completely different sets.

Kinda along the lines of the old “1,000 monkeys with 1,000 typewriters in 1,000 years would produce Dickens - A Tale of Two Cities” scenario.

On a chemical level... it was inevitable.

 

I know, I’m skipping an awful lot of steps in there, but I think you can get what I mean.

 

The model in the original post is already too far along to have simply sprung up “as is”. Lancet et al are backing the process up to a more base level and working on life occurring chemically first, rather than “viable life” in and of itself.

 

 

So… how far off am I?

[Legion]

Karhoof I am encouraged by your interest in this subject. I want to treat your last post in greater detail. But it is late here and I really must go to bed. I will try to post in here tomorrow.

[Legion]

Okay Karhoof, I have a bit of time today.

 

It seems to me that you might be in the general area. I believe that as we ask how organisms came into being simultaneously, by necessity, we have to ask ourselves what life is. (Though I’ve been informed that why organisms are alive and why they came into existence are two generally unrelated areas.)

 

I think an important thing to focus on at the moment is the catalytic actions (efficient causes) of things rather than the material aspect (material causes) of things. Kauffman asserts that organisms have achieved “catalytic closure”. And Rosen asserts that organisms are “closed to efficient causation.” In both instances when we ask where some component of an organism came from, we get an answer, in terms of efficient cause, from within the organism itself, and never external to it.

 

In other words, it seems to be a distinguishing aspect of organisms that they manufacture themselves. The specific chemistry of an organism may be far less important than the organization that provides for this self-manufacturing capability. And it might very well be that the organization that characterizes life can be realized in some very exotic materials.

 

If you’re still interested Karhoof then I highly recommend that you read some Kauffman and Rosen. They go into far greater detail than I can here.

[Karhoof]

It seems to me that you might be in the general area.

Ha!?! Who woulda' thunk it!

I have to tell you, I really am enjoying this. The sciences have always held my attention and trying to engage the locals in a conversation like this would likely result in a response of, "Wellll... ain't you just plumb full o' brains!"

 

I believe that as we ask how organisms came into being simultaneously, by necessity, we have to ask ourselves what life is. (Though I’ve been informed that why organisms are alive and why they came into existence are two generally unrelated areas.)

Agreed. The why is mostly irrelevant. The how may even answer the why.

 

I think an important thing to focus on at the moment is the catalytic actions (efficient causes) of things rather than the material aspect (material causes) of things.

Agreed again. The mechanics I described (or tried to) in my post above mostly brushed over that, but it's the reaction of those molecules joining that drive the process. I described it as chemical, but it really could be as simple as hydrogen and oxygen (2 + 1 = water). Vitally important that they join, but the catalytic reaction when they join is what's important... yet still chemistry.

 

Kauffman asserts that organisms have achieved “catalytic closure”. And Rosen asserts that organisms are “closed to efficient causation.” In both instances when we ask where some component of an organism came from, we get an answer, in terms of efficient cause, from within the organism itself, and never external to it.

 

In other words, it seems to be a distinguishing aspect of organisms that they manufacture themselves.

This is still a little gray, but I'm starting to get it.

 

The specific chemistry of an organism may be far less important than the organization that provides for this self-manufacturing capability.

Yes, I see that too. But again, that point of self replication is what's hanging for me.

 

And it might very well be that the organization that characterizes life can be realized in some very exotic materials.

Life as we know it could have been something completely different but for a few molecular changes?

Our microbial ancestors won out in a battle for survival?

 

If you’re still interested Karhoof then I highly recommend that you read some Kauffman and Rosen. They go into far greater detail than I can here.

I may need to start with a primer on microbiology, but I'll give them a shot.

Most of what I got, I got from here, section 3 (b ).

http://www.pubmedcentral.nih.gov/articlere...bmedid=17008217

The sections are seperated by bold blue headers. Should be easy to find.