Missing links brewed in primordial puddles?

April 25, 2016
Nearly twins and possibly keys to a unlocking the mystery of the evolution of life-coding molecules. Nicholas Hud holds up Uracil, on the right, a nucleobase of RNA. Barbituric acid, on the left, looks very much like it and could have been part of a proto-RNA that preceded RNA. Credit: Fitrah Hamid, Georgia Tech

The crucibles that bore out early building blocks of life may have been, in many cases, modest puddles.

Now, researchers working with that hypothesis have achieved a significant advancement toward understanding an evolutionary mystery—how components of RNA and DNA formed from chemicals present on early Earth before life existed.

In surprisingly simple laboratory reactions in water, under everyday conditions, they have produced what could be good candidates for missing links on the pathway to the code of life.

And when those components joined up, the result even looked like RNA.

As the researchers' work progresses, it could reveal that much of the original chemistry that led to life arose not in fiery cataclysms and in scarce quantities, but abundantly and gradually on quiet, rain-swept dirt flats or lakeshore rocks lapped by waves.

In turn, their work could increase our understanding of the probability of life's existence elsewhere in the universe.

The research from the NSF/NASA Center for Chemical Evolution, headquartered at the Georgia Institute of Technology, is generously funded through a grant from the National Science Foundation and NASA. The recent results were published on April 25, 2016 in Nature Communications.

Pursuing the origins specifically of RNA, the close chemical relative of DNA, a research team led by Nicholas Hud, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology and director of the CCE, worked with a pair of potential chemical ancestors of the nucleobases of RNA.

For roughly half a century, scientists have hypothesized that life, which uses DNA to store genetic information, was preceded by life forms that used RNA very broadly. And RNA may have had a precursor, proto-RNA, with different but similar (the "N" in RNA).

"Early Earth was a messy laboratory where probably many molecules like those needed for life were produced. Some survived and prospered, while others eventually vanished," Hud said. "That goes for the ancestors of RNA, too."

Using two molecules known as barbituric acid and melamine, the researchers formed proto-nucleotides so strongly resembling two of RNA's nucleotides that it is tempting to speculate that they are indeed their ancestors.

The two ingredients would have been readily abundant for reactions on a prebiotic Earth, Hud said. "And they would have been well suited for primitive information coding," he added.

Because of the resemblances and properties, some scientists already have speculated on an ancestral role for melamine and barbituric acid.

But the CCE scientists are careful not to jump to that conclusion just yet.

"To claim ancestry, we would have to show a mechanism by which these nucleotides we made in the lab could turn into the existing nucleotides in RNA," said Ram Krishnamurthy, Hud's collaborator from the Scripps Research Institute in La Jolla, California. "It's a complex path that we'd have to at least design on paper, and we're not there."

Nicholas Hud holds up a sample of the gooey gel that forms when the nucleotides based on barbituric acid and melamine pair up into spiraled supramolecular assemblages. Under the microscope, the large molecule strings even look like RNA. Credit: Fitrah Hamid, Georgia Tech

Nonetheless, he's exited about the results. "There are umpteen possibilities of how that mechanism could have happened. Barbituric acid and melamine may have been place holders that dropped out and allowed adenine and uracil to come together with ribose."

Figuring out how adenine and uracil (nucleobases found in RNA today) combined with the sugar ribose (corresponding to the "R" in RNA) could answer one of the great questions of chemical evolution.

The formation of nucleotides from possible proto-nucleobases and ribose marks a significant advancement in research on the origin of life.

Nucleobases have been combined with other sugars in past studies, but the efficiency of the reactions discovered in this study is much greater than those of that past.

"We're getting close to molecules that look the way life may have looked in early stages," Krishnamurthy said.

A series of surprises added to the reactions' scientific significance.

First, they occurred quickly and the resulting nucleotides spontaneously paired with each other in water, forming hydrogen bonds like the Watson-Crick base pairs that create the "ladder-rung" pattern inside RNA and DNA helixes.

Then the monomers formed long, supramolecular assemblages that look like strands of RNA when viewed with a high resolution microscope.

Nearly twins and possibly keys to a unlocking the mystery of the evolution of life-coding molecules. Nicholas Hud holds up Uracil, on the right, a nucleobase of RNA. Barbituric acid, on the left, looks very much like it and could have been part of a proto-RNA that preceded RNA. Credit: Fitrah Hamid, Georgia Tech

There has been no reported chemical reaction so far that has produced existing components of RNA under commonplace circumstances that spontaneously form Crick-Watson pairs in water.

And up until now, there had also been no report of a similar pair of nucleotides, like those produced with barbituric acid and melamine, behaving in a like manner, making this another first.

"It works even better then we thought," Hud said. "It's almost too easy."

There was one small caveat.

"The reaction does not work as well if barbituric acid and melamine are present in the same solution before reacting with ribose because their strong attraction for each other can cause them to precipitate," Hud said. So, the scientists completed the reaction involving barbituric acid separately from the one involving melamine.

But that should not have proven prohibitive on prebiotic Earth. Barbituric acid and melamine nucleotides could have been formed in separate locations, even in the same pond. And they could have very well been plentiful.

"These reactions are exceptionally productive, especially if you compare them to analogous reactions with existing RNA components, which do not produce any nucleotides under the same conditions," Hud said.

If melamine and barbituric acid formed their respective nucleotides (C-BMP for barbituric acid and MMP for melamine) in separate puddles on the early Earth, then rain could have easily washed the components together, where they would have rapidly assembled into what could have been a precursor to proto-RNA.

"The question is: Can these self-assemblies make the transition into what makes up life today," Krishnamurthy said.

The researchers hope their work will help expand the scientific community's approach to chemical evolution.

"If you want to look at what brought about these properties of life you have to go back and consider all the other molecules that would have been present and see how they would have facilitated the molecules that are present in life today," Krishnamurthy said.

Their work also could serve as a basis for important practical applications, such as the creation of DNA or RNA-like polymers that could spawn production of advanced materials and therapeutic agents.

The chemical reactions that produce the barbituric acid and melamine nucleotides don't require the use of enzymes and extreme parameters like high heat and pressure. Reminiscent of click chemistry, they could contribute to safe, cost-effective and abundant industrial production.

Explore further: New Study Brings Scientists Closer to the Origin of RNA

More information: Nature Communications, DOI: 10.1038/NCOMMS11328

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torbjorn_b_g_larsson
5 / 5 (3) Apr 25, 2016
Ha, I knew it was Hud's research already from the title.

The evidence is that there were no proto-RNA, it shows up at the root of phylogenetic trees (core of genetic machinery), and it is sufficient in geologist's vent theories. Also, vents naturally concentrate biomolecules while they react, while soup theory has to rely on drying up of puddles.

I know that Benner has made the many pot soup theory of chemists popular. "Many pot" meaning there had to be a complicated series of successive chemical reactors (pots) that emerging life systems transported between, among them tidal pools that could go dry every tide.

But it is complicated!

[tbctd]
FredJose
1.4 / 5 (20) Apr 25, 2016
understanding an evolutionary mystery—how components of RNA and DNA formed from chemicals present on early Earth before life existed.

It's an evolutionary mystery because if you assume there is no creator then you are left with the in-your-face problem of having to explain how biological life can arise from DEAD materials all by itself. So much for all hose raging on about abiogenesis and evolution being separate domains. It's two sides of the same coin.

Good luck to the researchers showing how the conditions they've conjured up in the lab can exist in the wild. Plus how to retain the results of the experiment without the highly reactive RNA being split apart by the very water it "finds" itself in. Look carefully at the experiment and show just how the products are spontaneously preserved from disassociation.....if you can find it.
torbjorn_b_g_larsson
5 / 5 (4) Apr 25, 2016
[cdt]

"There has been no reported chemical reaction so far that has produced existing components of RNA under commonplace circumstances that spontaneously form Crick-Watson pairs in water."

They have not kept up with the start of the art. On vent pores making RNA complementary, sorted and long strands (neither of which soups aren't known to do yet - "look like" isn't objectively quantified and confirmed science): "The separation is so effective that certain types of fragments actually condense into gels when they hybridize with complementary partner molecules." [ http://www.astrob...t-chaff/ ]

That said, anything that elaborates on early Hadean chemistry is exciting and useful for emergence theories!
FredJose
1.4 / 5 (19) Apr 25, 2016
"The question is: Can these self-assemblies make the transition into what makes up life today," Krishnamurthy said.

Excellent question. The pursuit of which will definitely bankroll multiple careers no doubt since there is no naturalistic answer to how that can happen. First one requires all the components in the right place and order, then the exacting functionality of each needs to be commissioned in exactly the right way, ie. fully working life processes needs to be kick- started without any outside help whatsoever. How many chances does one get before the proto "life" resumes its dead state?
antialias_physorg
4.1 / 5 (15) Apr 25, 2016
of having to explain how biological life can arise from DEAD materials all by itself

Only if you cling to the alive/not-alive distinction. Which is a quantitative one - not a qualitative one (read: not really a distinction at all but just a strawman argument)

So much for all hose raging on about abiogenesis and evolution being separate domains. It's two sides of the same coin.

If you think that then you haven't understood what abiogenesis means. Or evolution. Or both.

Good luck to the researchers showing how the conditions they've conjured up in the lab can exist in the wild.

No luck needed. That part is already done.

how the products are spontaneously preserved from disassociation

As with any production: There is an equilibrium concentration between production and dissociation depending on availability of raw materials and energy source. Where's the problem?
FredJose
1.5 / 5 (16) Apr 25, 2016
Where's the problem?

The problem lies in getting ALL the required items required for life in working order at the same time. Piecemeal is unfortunately not going to cut it, no matter how much you dream it's going to happen that way.
People like to think that by some luck, one piece will assemble then drift around whilst the other pieces gets assembled by luck somewhere else with it all followed by some gargantuan miraculous coming together to click into life. Or else that by some even greater miracle, the one piece starts to gather together all the others as it drifts along on its merry way.
Perhaps some review of principles of probability, physics and chemistry is required?

We've had about 6000 years of documented, repeated, verifiable evidence that once something dies it stays DEAD. There is no verified case of ANYTHING ever coming back to life from the dead state all by itself. Playing with words as to what is dead and or alive is not going to help one little bit.

FredJose
1.5 / 5 (16) Apr 25, 2016
If you think that then you haven't understood what abiogenesis means. Or evolution. Or both.

On the contrary, it is quite clear that you need to have life before you have any kind of biological evolution. So, since abiogenesis is the only way to get life started if you have no creator, it follows that you need to have abiogenesis as the basis for your biological evolution. There is no chemical evolution to talk about [even though the authors refer to such a non-entity] since it does not conform to the accepted idea of evolution.
So there you have it - you cannot separate abiogenesis from your evolutionary paradigm - not unless you subscribe to the idea of a creator kick starting life and then leaving it to "evolve". But that won't square with atheistic thought.
torbjorn_b_g_larsson
4.1 / 5 (9) Apr 25, 2016
Nice, I needed some interruption!

"explain how biological life can arise from DEAD materials".

Same as how dead material arise from biological life when we die, it is a gradual transition. Creationism can't explain that, because of their magic of life which simply is there and can't go away.

"abiogenesis and evolution being separate domains".

They aren't. What is observed is that evolution is a fact regardless of existence of abiogenesis of the first population, in the same way that gravity is a fact regardless of how mass comes into existence.

"without the highly reactive RNA".

You may need to check your facts, the half life of an RNA strand is 4 years, the half life of a cell is hours. Plenty of time, and indeed we know that RNA cells preceded DNA cells (due to evolution and its phylogenetic tree).

We cross posted, my link goes to an observation of how the products are sorted and preserved in gels. This result is key, it solves abiogenesis for vents.

[tbctd]
torbjorn_b_g_larsson
4.1 / 5 (9) Apr 25, 2016
[ctd]

"Excellent question. The pursuit of which".

It is a good question which has already been around seriously for 2 centuries, with little bank rolling.

I have already mentioned the two top theories (vents, soups), and one of the observed transitions from non-genetic monomers to genetic polymers that constitutes the transition between production vs replication of biomolecules, non-life vs life according to evolution. It happens in geological systems which are our ancestors by heredity, if you will.

[tbctd]
torbjorn_b_g_larsson
4 / 5 (9) Apr 25, 2016
[ctd]

"How many chances does one get".

Well, vents have been seen (or are implied) for 4.5 billion years, and the vent hypothesis puts a top time window for emergence at 10 kyrs. (Feasible with the number of chemical events that needs to take place; vents become 30 kyrs or so at most.)

Say that vents were at least as numerous as today. With the current 500+ found [ http://www.southe...-mining/ ], let's estimate ~ 1000 alkaline ones globally for convenience. That means ~ 6*10^9/10^4*1000 ~ 10^9 chances during our planets lifetime before the oceans evaporate.

More interesting, how many do we need? 1.

The likelihood for failure is ~ 10^-9, while the likelihood for creationism failure = 1 (didn't happen, since evolution is a fact).

[tbctd]
torbjorn_b_g_larsson
4.5 / 5 (8) Apr 25, 2016
[ctd]

"The problem lies in getting ALL the required items required for life in working order at the same time."

No, it doesn't. Besides being the generally rejected idea of Paley since it clashes with evolution, vent theory observations show it is erroneous.

"We've had about 6000 years of documented".

No. Science is 400 years old, written texts are perhaps 8-10 000 years old (an open question). Everyone knows that.

"it is quite clear that you need to have life before you have any kind of biological evolution."

You need cellular populations to have full blown evolution with all its mechanisms.

Abiogenesis comprises but two evolutionary mechanisms, the rise of genetics and of selection. The former mechanism is what locks in Hadean geological traits, the 20+ of which shows that we are descendants of Hadean geology.

[tbctd]
torbjorn_b_g_larsson
4.5 / 5 (8) Apr 25, 2016
[ctd]

"6000 year", "atheistic thought".

You have twice mentioned magic thought, three times really with the stupid clock argument.

If science, which started out agnostic as in every question, is now effectively atheist it is only because religious magic didn't work and didn't exist.

Whose fault is that? On whose shoulders lie the cause of magic's failure?

Take you non-existent religious magic elsewhere, and comment on the science.
warmonger
4.6 / 5 (10) Apr 25, 2016
FredJose, clearly, you don't know what you're talking about. Life doesn't arrive from "DEAD" materials. Inorganic is probably the word you were looking for.

This claim that there is no naturalistic explanation for life is a bit like saying there is no naturalistic explanation for disease. Only God can cause disease, based on when he is angry or feeling vengeful. Now, that might seem reasonable to a believer, but once bacteria and viruses are discovered, they're going to be left looking pretty freaking stupid.

The reality is that virtually any conditions produced in a lab will exist at some point in the billion year history of the earth prior to the emergence of life. So questioning whether these conditions happen in the 'wild' is just more foolery.

Furthermore, if scientists can create 'living' matter from organic chemicals, it wouldn't make any different how plausible the conditions were. It would mean your God theory for the origin of life is without merit.
torbjorn_b_g_larsson
4.4 / 5 (7) Apr 25, 2016
"The likelihood for failure is ~ 10^-9".

Oops, That is the maximum likelihood assuming abiogenesis works at all (which it did, or we wouldn't be here)but as sloppy as it could possibly have worked.

In reality the failure likelihood must have been much lower, seeing how we can recreate all the main steps in the laboratory easy as baking cake now that we know what to study.
torbjorn_b_g_larsson
4.3 / 5 (6) Apr 25, 2016
warmonger, good points.

We can take that further, we know that cells take organic materials and create 'living' matter (grow, multiply).

But we can mimic that in the lab, the Keller pathway does sugar (ribose, pentose) metabolism, and we can multiply lipid vesicles.

By the stated criteria those lab experiments create 'living' matter from organic, doing what is claimed to be impossible,

All humdrum of course, it is emergence of life that is interesting. I consider the problem solved, but it will take time and more experiments to convince the consensus. [/roll up sleeves]
ogg_ogg
1 / 5 (11) Apr 25, 2016
Yeah, I'm with FH! I mean it's not like dead molecules like water, N2, or CO2 can be transformed into biological materials, or even organic chemicals - that's well established, just read the Bible! OTOH, fanboys who claim that abiogenesis is a fact are almost as pathetic. Panspermia hasn't (and may never be) ruled out. We can NOT prove the first steps towards cells & genes occurred on Earth (or Earth-like planet). Perhaps someday we'll have sufficient samples of the interstellar medium to (statistically) rule it out, but it'll be a long long long time from now. We can not say with certainty under what conditions life is able to develop, although it's obvious to me that we can build a living cell (given information, equipement & chemicals) in the lab. We should not imho use the term "evolution" with abiotic/pre-biotic processes. There are some tautological & existential problems broadening the term to include systems which aren't self-sustaining (alive). Plausibility isn't proof.
torbjorn_b_g_larsson
4.4 / 5 (7) Apr 25, 2016
"molecules like water, N2, or CO2 can be transformed into biological materials, or even organic chemicals".

Very true. We have known for 6 decades that organic material like amino acids can be made from water, N2 and CO2. [ https://en.wikipe...periment ]

And of course lipids are long known to be produced abiotically as well. [ http://www.ncbi.n...16642268 ]

The new thing is that vents are shown to be able to produce pyruvate, and the Keller pathway produces ribose/pentose from that as I already mentioned. A similar synthesis, or the pathways of Benner et al, produces nucleotides from that.

In sum, we now know that all cell components are abiotically produced in nature, at least the Hadean environment.

Moreover, we also know how to produce replicating cells from that, see my above comments.

By the way, referencing a magic myth isn't science. Haven't I asked you guys to stop inserting irrelevancies?
torbjorn_b_g_larsson
4.4 / 5 (7) Apr 25, 2016
Re panspermia, it isn't viable in a 14 billion year old universe for the same reason we know life emerged on Earth from organic material. The early universe/planet was sterile, then it wasn't.

But moreover, it is unlikely for other reasons.

a) Life appeared early. Transpermia between planets could happen at any time, so we - living 4.5 billion years after the planet formed - would then expect to see life emerged at 2 billion years,, not 4.

b) There are 20+ traits that we uniquely share with Hadean Earth, not say Mars. The pH differential across the cell membrane match to Hadean Earth ocean composition vs alkaline hydrothermal vents, the early enzymes use ocean Hadean Earth metal atoms (Fe, say), et cetera.

[tbctd]
torbjorn_b_g_larsson
4.3 / 5 (6) Apr 25, 2016
[ctd]

c) Chemiosmosis of all cells could only evolve on the surface of an alkaline hydrothermal vent situated in the slightly acidic Hadean ocean. Similar conditions are possible elsewhere, see the modern Enceladus, but rare, see the modern Enceladus vs the original one (that likely lacked the ocean according to current models).

If you argue, against the likelihood vs early timing above - that life was transported here in a less evolved form than the LUCA that had evolved chemiosmosis/non-permeable membranes (and DNA, et cetera), then you have a serious timing problem. Transpermia had to happen "just so".

I know that Benner has made the many pot soup theory of chemists popular. "Many pot" meaning there had to be a complicated series of successive chemical reactors (pots) that emerging life systems transported between, among them tidal pools that could go dry every tide.

[tbctd]
torbjorn_b_g_larsson
4.4 / 5 (7) Apr 25, 2016
[ctd]

But it is complicated even without the timing problem. And anyway, where do you find the largest tides for a terrestrial planet in the system anyway? That is right, the early (and even late) Earth, when the Moon was orbiting close. The geologists with their vent theory win over the chemists with their soup theory on this one, as far as I can see.

So possible yes, likely no.

I am sorry if the answer is the trivial and most down to Earth, near laying one. [Pun intended.]

http://orig15.dev...qsc9.png

Oops: I meant that (eternal) panspermia isn't a viable solution for creationists.
antialias_physorg
5 / 5 (3) Apr 26, 2016
So, since abiogenesis is the only way to get life started if you have no creator, it follows that you need to have abiogenesis as the basis for your biological evolution.

So? You need electriocity to run a light bulb. That doesn't mean the theory of how light bulbs are manufactured is validated or invalidated by the theory of how coal powerplants work.

Abiogenesis and evolution are separate theories. They state explain different things. One is the theory of how you can get self replicating systems started from sratch. The other is how self replicating systems can mutate over time to become very different systems. If you have a problem with one or the other then state an argument in that regrad. But stating that you have a problem with one and therefore this invalidates the other is just idiotic.

Simple proof: Abiogenesis can do very well without evolution. You could have a self replicating system start up that is so rigid that it cannot evolve.
torbjorn_b_g_larsson
5 / 5 (1) Apr 26, 2016
Good point, I'm so going to steal that! (I'm fairly sure I will forget the source down the years... :-/)
cgsperling
5 / 5 (1) Apr 29, 2016
@ fredjose said "We've had about 6000 years of documented, repeated, verifiable evidence that once something dies it stays DEAD. There is no verified case of ANYTHING ever coming back to life from the dead state all by itself."

So, you don't buy into that Jesus resurrection story either, huh?
Zorcon
not rated yet Apr 30, 2016
...if you assume there is no creator then you are left with the in-your-face problem of having to explain how biological life can arise from DEAD materials all by itself.


FredJose is left with the in-his-face problem of having to explain how a creator can arise from DEAD materials all by itself.

Good luck to the researchers showing how the conditions they've conjured up in the lab can exist in the wild...


Good luck to the theists showing how the magical sky daddies they've conjured up in their imaginations can exist in the wild...
Zorcon
not rated yet Apr 30, 2016
...since abiogenesis is the only way to get life started if you have no creator, it follows that you need to have abiogenesis as the basis for your biological evolution.


Since abiogenesis is the only way obtain your creator, it follows that you need to have abiogenesis as the basis for your religion.

So there you have it - you cannot separate abiogenesis from your evolutionary paradigm - not unless you subscribe to the idea of a creator kick starting life and then leaving it to "evolve". But that won't square with atheistic thought.


So there you have it - you cannot separate abiogenesis from your theistic paradigm. But that won't square with superstitious thought.

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