Life’s First Spark Re-Created in the Laboratory

[wautd]

Add another one for Abiogenesis

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.”

[Darth Wong]

Excellent news! Not that this will change the mind of any creationist of course (these people still think the 2nd Law of Thermodynamics prohibits natural formation of complex molecules of any kind), but very exciting news nonetheless.

[Themightytom]

Wait all they had to do was replicate a hot spring? What did they do that wasn't tried before?

[Darth Wong]

Wait all they had to do was replicate a hot spring? What did they do that wasn't tried before?

They threw in different ingredients: more basic ones. Previous researchers had taken more complex ingredients formed by other processes and hoped to get this result, but it actually works better when you use simpler ingredients. I suppose previous researchers had been working on the assumption that if you're going for a complex molecule, you need to start as high up on the ladder as possible. But that was clearly a flawed assumption. If you start with simpler precursors, there is more flexibility for more random combinations. Starting with complex precursors creates a lot of "lock-in", in terms of combinations.

[Themightytom]

Excellent news! Not that this will change the mind of any creationist of course (these people still think the 2nd Law of Thermodynamics prohibits natural formation of complex molecules of any kind), but very exciting news nonetheless.

Could you elaborate on that argument, out of curiosity? Not that it matters because as stated in the article "Simple molecules" were used to create the RNA. if anything this experiment shows that less complex molecules are neccesary.

[Stuart]

Excellent news indeed. What I particularly like is that the mechanism described could be applied in many places other than an earth-specific environment. In fact, it seems to me that the basic system is so simple that it implies that the evolution of life from a primordial mix is a necessary outcome rather than a rare chance. That implies that life should be widespread.

But, of course, basic chemistry is just a theory isn't it?

[Darth Wong]

Excellent news! Not that this will change the mind of any creationist of course (these people still think the 2nd Law of Thermodynamics prohibits natural formation of complex molecules of any kind), but very exciting news nonetheless.

Could you elaborate on that argument, out of curiosity? Not that it matters because as stated in the article "Simple molecules" were used to create the RNA. if anything this experiment shows that less complex molecules are neccesary.

You've never heard it before? You can Google it if you like. To wit, the idiot creationist believes that the Second Law of Thermodynamics says that all objects must naturally go from structural order to structural chaos (this is his hopelessly ignorant misinterpretation of the concepts of entropy and closed vs open systems). Therefore, he believes that it is impossible to naturally form a complex molecule or object. However, the idiot creationist also believes that intelligence can overcome the Second Law of Thermodynamics, so if you have an intelligent designer, then it becomes possible to create complex things. That's why the creationist believes humans can make complex structures: because we are intelligent. That is also how the creationist believes that all natural complex structures formed: from the Will of God, who is also intelligent. No word on how they interpret beehives or crystallization.

There are so many things wrong with that argument that it's hard to know where to begin, I know.

[Themightytom]

Excellent news! Not that this will change the mind of any creationist of course (these people still think the 2nd Law of Thermodynamics prohibits natural formation of complex molecules of any kind), but very exciting news nonetheless.

Could you elaborate on that argument, out of curiosity? Not that it matters because as stated in the article "Simple molecules" were used to create the RNA. if anything this experiment shows that less complex molecules are neccesary.

You've never heard it before? You can Google it if you like. To wit, the idiot creationist believes that the Second Law of Thermodynamics says that all objects must naturally go from structural order to structural chaos (this is his hopelessly ignorant misinterpretation of the concepts of entropy and closed vs open systems). Therefore, he believes that it is impossible to naturally form a complex molecule or object. However, the idiot creationist also believes that intelligence can overcome the Second Law of Thermodynamics, so if you have an intelligent designer, then it becomes possible to create complex things. That's why the creationist believes humans can make complex structures: because we are intelligent. That is also how the creationist believes that all natural complex structures formed: from the Will of God, who is also intelligent. No word on how they interpret beehives or crystallization.

There are so many things wrong with that argument that it's hard to know where to begin, I know.

For that matter what is their take on Coral?

Well I was hesitant to google on my own because if I found the argument in the creationist's words I would be eating up misinterpretations and misleading statements like they were candy and never knowing the difference. now that I have context I found this amusing Link
http://www.christiananswers.net/q-eden/ ... amics.html

Note the yellow square where it clarifies that the argument is contingent on the lack of experimental evidence to disprove the argument.
oops

[Gil Hamilton]

Could you elaborate on that argument, out of curiosity? Not that it matters because as stated in the article "Simple molecules" were used to create the RNA. if anything this experiment shows that less complex molecules are neccesary.

Basically, there argument comes from a simplified statement of the 2nd Law of Thermodynamics and then misquoting it via the Telephone game until they think that at no point does entropy for a system ever decrease and it must always proceed from order to disorder. The problem is that entropy for a system decreases all the time, as they can find out by freezing water in an ice cube tray (defining the system to be the water and the surroundings to be the rest of the universe).

I got into argument with a creationist at school when I explained how thermodynamics works, where she accused me of being dishonest because I kept "defining" the systems I used as examples and that somehow that made my argument invalid because she reasoned that my logic was only panning out because I was rigging the arguments with definitions. Of course, the problem comes with how exactly you talk about thermodynamics AT ALL without defining what your system is and what your surroundings are, but I was losing interest in talking to her by this point.

[[R_H]]

Wasn't there a similar experiment that synthesized amino acids?

[Darth Wong]

Basically, there argument comes from a simplified statement of the 2nd Law of Thermodynamics and then misquoting it via the Telephone game until they think that at no point does entropy for a system ever decrease and it must always proceed from order to disorder. The problem is that entropy for a system decreases all the time, as they can find out by freezing water in an ice cube tray (defining the system to be the water and the surroundings to be the rest of the universe).

Even if you disregard the open system vs closed system problem, they are also misinterpreting the whole concept of entropy. Entropy is disordered energy, not physical structures. The "messy bedroom" analogy is an analogy, not an actual description of entropy. It is entirely possible for the neat and clean bedroom to have higher entropy than the messy one.

I got into argument with a creationist at school when I explained how thermodynamics works, where she accused me of being dishonest because I kept "defining" the systems I used as examples and that somehow that made my argument invalid because she reasoned that my logic was only panning out because I was rigging the arguments with definitions. Of course, the problem comes with how exactly you talk about thermodynamics AT ALL without defining what your system is and what your surroundings are, but I was losing interest in talking to her by this point.

Creationists often think that the models used to illustrate scientific principles are invalid because they are not accurate to complex real-life situations, totally disregarding the point of them. It's like people who dismiss analogies because the analogy is not perfectly identical to the situation under discussion in every conceivable way: what do they think the purpose of an analogy is?

I routinely get the same stupid shit attacks on my creationist page, where people point out that my "rolling dice" example is not an accurate representation of early primeval Earth conditions. No shit Sherlock, but the whole point of it was to illustrate how creationists are incorrectly describing the concept of probability, not to accurately model primeval Earth with dice. I've said it before and I'll say it again: it's actually easier to argue with a smart person than a moron. A smart person knows when he got nailed and will try to respond, whereas a dumb person has no idea what you're saying so it's impossible to make headway.

Arguing with a hard-line creationist about actual science is like arguing with my dog about physics. What would be the point? He doesn't understand what you're saying. In both cases, you might as well just pat him on the head and tell him to go lick his own balls. It's what he's planning to do anyway.

[Gil Hamilton]

Even if you disregard the open system vs closed system problem, they are also misinterpreting the whole concept of entropy. Entropy is disordered energy, not physical structures. The "messy bedroom" analogy is an analogy, not an actual description of entropy. It is entirely possible for the neat and clean bedroom to have higher entropy than the messy one.

Part of me is going "Of course its possible. Just turn on the air conditioning unit in the messy room."

I don't think the "messy bedroom" analogy was ever meant to be anything more than an over-simplistic analogy. The issue with entropy is that even for people who've studied thermodynamics, it's fine to work with on paper. No issue. However, when you start to trying to explain what, exactly, that S actually means in practical terms, you end up falling into suspect analogies, whether its the "messy room" or the "poker hand" analogy (which is somewhat better).

Because very few diehard creationists have actually mucked about in thermodynamics in Physics/Engineering or have taken a Physical Chemistry class, they've got nothing but suspect analogies to work from.

[Darth Wong]

Creationists are not just ignorant of thermodynamics; they don't get the whole idea of science. They think it's just cool buzzwords and technology. And they really have no idea how complicated it is; that's why they think a class full of high-school kids is a qualified scientific peer review panel, fully capable of reviewing and judging scientific theories for their validity.

In a way, all of those efforts scientists make at "plain English explanations" just backfires with people like this: they read a super-simplified coffee-table version of a theory and then they think they totally understand it.

[wautd]

A blog post with a good laypersons explanation of the chemistry behind it, including some diagrams

[Tolya]

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

I hate to be jumping to conclusions, but doesn't that basically give the idea of extraterrestial life a huge green light? I mean, all you would need now is a suitable planet in the green zone? Like Gliese 581d.

[Ryan Thunder]

Wait all they had to do was replicate a hot spring? What did they do that wasn't tried before?

They threw in different ingredients: more basic ones. Previous researchers had taken more complex ingredients formed by other processes and hoped to get this result, but it actually works better when you use simpler ingredients. I suppose previous researchers had been working on the assumption that if you're going for a complex molecule, you need to start as high up on the ladder as possible. But that was clearly a flawed assumption. If you start with simpler precursors, there is more flexibility for more random combinations. Starting with complex precursors creates a lot of "lock-in", in terms of combinations.

Perhaps the assumption was that if they tried more basic chemicals it would take longer for the proper reaction to occur.

So they started with complex molecules and gradually moved to simpler ones, in hopes that they wouldn't have to wait millions of years for the reaction to occur.

Perhaps I'm just ignorant of how it works beyond the highschool level, but I'm surprised that this happened in our lifetimes. When did they start the experiment?

[RedImperator]

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

I hate to be jumping to conclusions, but doesn't that basically give the idea of extraterrestial life a huge green light? I mean, all you would need now is a suitable planet in the green zone? Like Gliese 581d.

I don't know if "tidally locked to a flare star" is anyone's idea of "suitable". But yeah, assuming Earth-like conditions, this seems to almost guarantee self-replicating molecules. The question is, how many planets have Earth-like conditions?

[GrandMasterTerwynn]

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

I hate to be jumping to conclusions, but doesn't that basically give the idea of extraterrestial life a huge green light? I mean, all you would need now is a suitable planet in the green zone? Like Gliese 581d.

I don't know if "tidally locked to a flare star" is anyone's idea of "suitable".

Worlds tidally-locked to flare stars will eventually be the only habitable real-estate in the universe. Also, with a thick enough atmosphere, you'll have substantial upper-level winds moving heat from the daylit-side to the night-side. With enough ocean, such worlds should be ideal locations for life. A red dwarf's propensity to flare will decrease with age, and such stars have lifespans of hundreds of billions of years.

But yeah, assuming Earth-like conditions, this seems to almost guarantee self-replicating molecules. The question is, how many planets have Earth-like conditions?

This ought to work on worlds that aren't anywhere near Earth-like. It looks like what you need are cycles of concentration and dilution, and enough energy to drive the reaction. Rocks deep underground with periodic exposure to water may be enough to do the job. And a lot of the basic ingredients are synthesized in cold molecular clouds, in space. So this ought to work for internally-heated rock-and-ice moons of gas giants.

Barring that, our simulations of planetary system formation tend to produce small rocky planets at habitable distances from their parent stars. Granted, you'll lose the first few iterations of terrestrial planet formation to gas giants spiraling into the parent star, but eventually the density of gas and dust in the system drops to the point where the giants stop falling into the star. Yes, we have detected a lot of oddball systems, but this was due to the selection bias imposed by our detection methods at the time. As we've gathered more data and refined our techniques, the number of 'normal' looking systems have grown.

I fully expect that this galaxy is absolutely lousy with planets with the right conditions to spawn life.

[Patrick Degan]

The idiot brigade's rankers on the Wired comment board attached with the article have, of course, come out with the usual suspect "rebuttals":

Posted by: theMage | 05/13/09 | 11:19 pm

Nobeliefrequired: check the bible, God specifically said 120 years max.

Everyone is missing a very big detail: this experiment created a COMPONENT of RNA, not even a single molecule of RNA. You evolutionists need to realize you have your own religion: Evolution. How else you explain how this reaction would have to be repeated hundreds of times, creating hundreds of different proteins, and then they have to assemble themselves in perfect order (violating the law of entropy). All this has to happen JUST TO CREATE DNA, then of course you also have to form the DOZENS of other structures REQUIRED for a SINGLE CELL ORGANISM. Your have to throw your brains in the trash to believe that was plausible.

Posted by: exparrow | 05/14/09 | 2:41 am

I find it funny that the so-called primordial soup, that were supposedly formed through chance and time only, were created, key word created, in a lab. Science with all its logic seems to miss that fact. It took us how long to replicate it? We consider ourselves thinking beings, I’m sure, yet we couldn’t do for quite some time (and it’s debateable if we’ve done it now) what nature did byitself? Right…

Posted by: theMage | 05/14/09 | 11:52 am

Kradlum, you obviously have “peer reviewed” this experiment. A similar experiment was done decades ago. Unfortunately, anyone with a brain saw that the conditions in the experiment could not have possibly existed. As far as the 2nd Law of Thermodynamics (law of entropy), you might want to perform a few lab experiments and not just imagine the exceptions to a rule. By your theory, a tornado could blow through a junkyard and assemble a perfectly functional 747. Pull up an electron microscope photo of the simplest form of life (ANY single cell organism). Perhaps if that was just a piece of RNA in a bag of protein jelly, this could be plausible. I’m not forcing any belief on anyone (alien origins are more likely than this evolution theory, but then again, where did THEY come from?), I’m just calling BS on bad science.

Posted by: seektruth | 05/14/09 | 9:10 pm

timequake said
“To those who say “it was done in a lab, nature couldn’t have done it”: The conditions created in the experiment were intended to mimic probable conditions on early earth.”

Exactly…the conditions created…Follow the logic. How do we know what the exact conditions were millions of years ago? What conditions are being left out? Are all the variables being taken into account? How would they know? The burden of proof lies with the creators of the experiment to show that they are not cooking the mix with the end result already in mind. It seems that they need to justify why such a pure mixture would exist in nature and not just in the lab. They took out a number of compounds to get to the end result.

Posted by: jlo0312 | 05/15/09 | 10:14 am

I usually enjoy Wired…interesting content and all. However, the “spark of evolution article” is the most ridiculous piece of crap that I ever read. If the Earth was in a state of primordial ooze, where did the boiling water come from? It takes more faith and less brains to believe in this crap than it does to believe in an intelligent God. The deal is this: EVOLUTION HAS BEEN PROVEN FALSE by numerous outstanding scientists. Why we base our theories on Darwin, whose work “evolved” BEFORE BIOCHEMISTRY is beyond me. It is ridiculous. Look up irreducible complexity.

[Patrick Degan]

Oh, almost forgot about this one. Comedy gold:

Posted by: joniscream | 05/13/09 | 2:30 pm
Mr Keim,
Let me ask you this. Were these “scientists” (from the University of Obama) able to reproduce their
results? Were ANY of their conclusions verified by a credible independent source? Leave science to the
scientists. Keep publishing this voodoo, just don’t delude yourself that it is science.

This one got shredded almost immediately.

[Gil Hamilton]

Why do they insist on calling the 2nd Law of Thermodynamics the "Law of Entropy"? That entropy tends to always increase for an isolated system is more a consequence of traditional statements of the 2nd Law, not the law itself. In fact, the only statement of the 2nd Law that I learned in school came from Physical Chemistry, when we were doing the grand tour of state quantities. In Uni. Physics, the teacher approached it specifically about heat and work specifically, and tacked the entropy consequence on later (we arrived at it FROM the Clausius and Kelvin statements).

Don't get me wrong, its an important consequence, but its being horribly abused. By their own damn logic, we should all be dead, because small molecules are chucked into large molecules, as when proteins or fatty acids are made, there is a DECREASE IN ENTROPY for the system, if you take the system to be the molecules themselves (as well you should). The difference is that it is being made up elsewhere in heat dispersed to the surroundings.

I can't stand the tornado assembling a 747 analogy. There is a big fucking difference between the assemby of macromolecules and a tornado blowing together an airplane in that chemicals AREN'T RANDOM. What the hell do they think chemists study? If atoms randomly bonded and banged together and all that dross, then chemistry wouldn't be a science. Their analogy assumes that atoms arrange themselves totally randomly into molecules, which is completely and totally false.

[Themightytom]

A Nanoceph wrote:
Posted by: jlo0312 | 05/15/09 | 10:14 am

I usually enjoy Wired…interesting content and all. However, the “spark of evolution article” is the most ridiculous piece of crap that I ever read. If the Earth was in a state of primordial ooze, where did the boiling water come from? It takes more faith and less brains to believe in this crap than it does to believe in an intelligent God. The deal is this: EVOLUTION HAS BEEN PROVEN FALSE by numerous outstanding scientists. Why we base our theories on Darwin, whose work “evolved” BEFORE BIOCHEMISTRY is beyond me. It is ridiculous. Look up irreducible complexity.

um... as previously demonstrated I am not an advanced physicist,is there any particular reason there couldn't be boiling water in the "promordial ooze"? To my knowledge you jsut need water and heat (and I suppose air pressure? but I assume taht has something to do with heat transfer and getting water TO boil?)

So is nanoceph referring to "Primoridal ooze" in terms of the earth is moltne crap still forming into a planet, is he talking about muddy hot springs... is he talking out of his ass... How did his ass evolve in such a manner that he could talk out of it...

[Darth Wong]

I love the way they totally ignore the fact that these scientists just did something they called "impossible" for the last hundred years. They don't even modify their reasoning; they just declare that it doesn't count as legitimate abiogenesis for various bullshit reasons. Who said it had to be abiogenesis? The point is that according to the probability model they have been promoting, this should have been essentially impossible. Therefore, their model is obviously wrong.

Unfortunately, they don't think that way. That's the way a scientist would think. These imbeciles argue science the same way they argue politics: with verbal talking points, instead of the scientific method of establishing or disproving a theory.

[Zablorg]

I was kind of interested about the argument that said the same reaction would have to occur hundreds of times and that it was absurd. Surely if this is on an atomic scale, if this process were done to a "batch" of ingredients in a cubed-inch puddle there could be thousands of these RNA components floating around?

How would RNA behave without the presence of DNA? I've heard an argument that as one can't exist without the other it's an irreducibly complex thing.

[Academia Nut]

No, there are a lot of abiogenesis hypotheses that postulate that RNA came before DNA and DNA was stumbled upon later as a more effective long term storage element than RNA because uracil and cytosine only vary in their structure by one methyl group (-CH3) and thus damage can cause the conversion between the two. There are error checking enzymes that scan over DNA and look for such mutation. If both uracil and cytosine were present on the same strand then it would be fifty-fifty to get it right, but by using thymine instead of uracil it is much simpler to detect the change and the mutation rate would be much higher. This is one reason why retroviruses like HIV change so much, they are based off of RNA as their inheritable material, which is much less stable than DNA.

Incidentally, retroviruses right there shoot down the idea of it being impossible to have one without the other.