Was the secret spice in primal gene soup a thickener?

Was the secret spice in primal gene soup a thickener?
Gene puddle primeval, a drawing by first author Christine He illustrates her discovery that viscosity moves spontaneous gene strand copying forward. Credit: Georgia Tech / Christine He

The original recipe for gene soup may have been simple—rain, a jumble of common molecules, warm sunshine, and nighttime cooling. Then add a pinch of thickener.

The last ingredient may have helped gene-like strands to copy themselves in puddles for the first time ever, billions of years ago when Earth was devoid of life, researchers at the Georgia Institute of Technology have found. Their novel discoveries add to a growing body of evidence that suggests first life may have evolved with relative ease, here and possibly elsewhere in the universe.

And they offer a straightforward answer to a gnawing 50-year-old question: How did precursors to the present-day genetic code first duplicate themselves before the existence of enzymes that are indispensable to that process today?

The spice of life?

For generations, scientists pursuing an answer performed experiments in water but hit a wall.

Georgia Tech researchers Christine He and Isaac Gállego overcame it by adding an off-the-shelf viscous solvent (the thickener). In separate experiments with DNA then RNA, the copying process proceeded.

"I think it's very, very different from anything that's been done before," said researcher He. "We can change the physical environment in an easy way, and promote these processes that wouldn't happen in conditions ordinarily being used."

Easy recipe

Easy is crucial, said Martha Grover, a professor who oversaw the research at Georgia Tech's School of Chemical and Biomolecular Engineering. Easy reactions are likely to be more productive and more prevalent.

"A simple and robust process like this one could have operated in a variety of environments and concentrations making it more realistic in moving evolution forward," she said.

Grover's lab and that of Nick Hud at Georgia Tech's School of Chemistry and Biochemistry published the results on Monday, October 10, 2016 in the journal Nature Chemistry. Their research has been funded by the National Science Foundation and the NASA Astrobiology Program under the NASA/NSF Center for Chemical Evolution.

Nucleotide noodles

Earliest life was based on RNA, or a similar polymer, according to a hypothesis called the RNA World. In that scenario, on the evolutionary timeline, the self-replication of RNA strands long enough to be potential genes would roughly mark the doorstep to life.

Those long nucleotide chains may have been mixed together in puddles with shorter nucleotide chains. Heat from the sun would have made long strands detach from their helix structures, giving short ones a chance to match up with them, and become their copies.

But there's a problem.

In water alone, when cooling sets in, the long chains snap back into their helix structure so rapidly that there's no time for the matching process with the shorter chains. That snapping shut, which happens in both RNA and DNA, is called "strand inhibition," and in living cells, enzymes solve the problem of keeping the long chains apart while gene strands duplicate.

More like a stew

"The problem is a problem in water, which everybody sort of looks at in prebiotic (pre-life) chemistry," said graduate research assistant He. She felt it was time to rethink that, and her expertise in chemical engineering helped.

Was the secret spice in primal gene soup a thickener?
Image "a" shows that water alone will not allow copying to go forward. Image "b" shows that viscosity allows gene strands to pair up with components of potential copies. Credit: Georgia Tech / Christine He

High viscosity has been known to slow down the movement of long strands of DNA, RNA and other polymers.

"It's a little like making them swim in honey," Grover said. Applying that to origin-of-life chemistry seemed obvious, because in prebiotic times, there probably were quite a few sticky puddles.

"In that solution, it gives the short nucleotides, which move faster, time to jump onto the long strand and piece together a duplicate of the long strand," researcher He said. In her experiments, it worked.

Hairpins in the soup

And it produced an encouraging surprise. The DNA and RNA strands folded onto themselves forming shapes called hairpins.

"In the beginning, we didn't realize the importance of the internal structure," Christine He said. Then they noticed that the shape was helping keep RNA and DNA available for the pairing process. "Hairpin formation is integral to keeping them open," Grover said.

But it also could have accelerated chemical evolution in another way. "The solution is selecting here for sequences that fold, and that would have more potential for functional activity - like a ribozyme," said researcher He.

Ribozymes are enzymes made of RNA, and enzymes catalyze biochemical processes. To have them evolve in the same solution that promotes replication could have shortened the path to first life.

"You really need to amplify functional sequences for evolution to move forward," Grover said. The folds were an unexpected side-effect, and finding them paves the way for future research.

Next ingredient?

The Georgia Tech scientists used real gene strands in their experiments, which may sound mundane, but in the past, some researchers have specially engineered DNA and RNA sequences in attempts to arrive at similar results.

He and Gállego's use of a naturally occurring gene, rather than a specifically engineered sequence, shows that viscosity could have been a very general solution to promote copying of nucleic acids with mixed length and sequences.

To facilitate quick, clear outcomes, the Georgia Tech researchers used purified short nucleotide chains and applied them in ratios that favored productive reactions. But they had started out with messier, less pure ingredients, and the experience was worthwhile.

"Considering a pre-biotic soup, it's probably messy; it's got a lot of impurities," Christine He said. "When we first started out with more impure nucleotides, it still worked. Maybe the same reaction really could have happened in a messy puddle billions of years ago."

The viscous solvent was glycholine, a mixture of glycerol and choline chloride. It was not likely present on pre-biotic Earth, but other viscous solvents likely were.

Also, after the short strands matched up to each long one, the researchers did apply an enzyme to join the aligned short pieces into a long chain, in a biochemical process called ligation.

The enzymes would not have been present on a prebiotic Earth, and although there are chemical procedure for ligating RNA, "no one has developed a chemistry so robust yet that it could replace the enzyme," Grover said.

Finding one that could have worked on a prebiotic Earth would be a worthy aim for further research.


Explore further

Scientists find evidence for alternate theory of how life arose

More information: A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle, Nature Chemistry, nature.com/articles/doi:10.1038/nchem.2628
Journal information: Nature Chemistry

Citation: Was the secret spice in primal gene soup a thickener? (2016, October 10) retrieved 21 May 2019 from https://phys.org/news/2016-10-secret-spice-primal-gene-soup.html
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Oct 10, 2016
Are amines "life"?

Oct 11, 2016
This is just terrible "science". You need a lot more than rain, a jumble of molecules, sunshine, and chance. Life just doesn't form like that. Mathematics give it a 0% chance. Intuition gives it even less chance. Only scientists that are adamant that life can only come from non-life subscribe to such bizarre theories as this one.



We all know about the "science" you support. It's even more unclear and thick.

Oct 11, 2016
Life just doesn't form like that.

And how would you know? Read it in a book, have you?

Mathematics give it a 0% chance.

And how would you know? You know nothing about math or probability theory. If you do: here's your chance to pin your formulas and let them be examined how you arrive at "0% chance".
You continually throw around these patently absurd probabilities and never back them up with anything. That#s not smart. That just makes you look dumb.

Go away. Play with bible verses. That's all you're good for. Leave real life to grown-ups.

Oct 11, 2016
Their novel discoveries add to a growing body of evidence that suggests first life may have evolved with relative ease, here and possibly elsewhere in the universe.

Problem with this statement is that it ignores reality. If this statement was true we should be witnessing the birth and re-birth of life on an ongoing stream at present and that is certainly NOT the case. To turn around and now say that things were different in the past is disingenuous because then you're reasoning from absence of observation, i.e. pure speculation.
Either way, people who keep chasing the impossible dream willfully ignore all the established and fundamental principles of chemistry, physics, probability and information science we have at our disposal today. They also completely ignore the fact that the complexity inside the cell simply blows away even our most sophisticated computing, communications and ingenious scientific contrivances. The cell is irreducibly complex. Like it or not.

Oct 11, 2016
... The cell is irreducibly complex. Like it or not.

Fred,
A cell may APPEAR irreducibly complex, but the individual processes that make it look like that -
do not...

The only reality that's ignored is your willingness to stretch your mind around that paradigm...

Oct 11, 2016
This is just terrible "science". You need a lot more than rain, a jumble of molecules, sunshine, and chance.

Such as?
Life just doesn't form like that.

References?
Mathematics give it a 0% chance.

Math only suggests probabilities, not "chance"
Intuition gives it even less chance.

Intuition is subjective.
Only scientists that are adamant that life can only come from non-life subscribe to such bizarre theories as this one.

Only scientists who believe things work in causal steps, you mean...?
Even a god has to have non-life to work with, in the first place...
Doesn't the book say we were formed from clay? (non-life)
That would appear that you believe life only comes from non-life, as well...

Oct 11, 2016
A cell may APPEAR irreducibly complex, but the individual processes that make it look like that -
do not...

Truly naive Gyre, have you even looked at what happens inside the cell? Perhaps you'd like to trace the path of the signalling that occurs when neutrofil exrtavasation occurs? Or describe how the right ingredients are attracted to the site of protein synthesis in the right order, quantity and speed?
Once you've given us a full rundown of that then perhaps you qualify to say that individual processes are not irreducibly linked to their main event.

Oct 11, 2016
A cell may APPEAR irreducibly complex, but the individual processes that make it look like that -

This statement is not far from what Francis Crick recommends you do: Even though it looks like it was designed we must remember that all of this happened by accident: "Biologists must constantly keep in mind that what they see was not designed, but rather evolved." In other words keep on lying to yourselves, because sooner or later the lie will be fully accepted as truth. Looks like it has happened.

Oct 11, 2016
Let's all take a moment and read over the Fermi paradox, in particular the rare earth solution.
There are billions of stars in our milky way galaxy and billions of galaxies in the observable universe. The universe may be infinite or there could be an infinite number of unverises that have formed. On all those planets around all those stars earth may be the only place with intelligent life.
It doesn't matter what the odds of basic life forming by chance is because given enough chances eventually one will succeed.
We can't see all the countless planets that failed to produce life by chance. We only see the one planet that did, earth. The chances don't matter with infinite trials, eventually one will "win".

Oct 11, 2016
That is the whole point! Evolution just doesn't stack up to what is needed to bring about life as we know it
I know, you guys love just declaring things as if this alone will make them so. As in 'Let there be light!'

But thats not the way it works. You should be angry with the guys who wrote your book for giving you this misconception.

They were the same people who coined the terms 'abracadabra' and 'poof' did you know it?

Oct 11, 2016
Truly naive Gyre, have you even looked at what happens inside the cell?

As an artist, I don't have the memory retention or attention span for that. But I do know that it parses down in layers.
Perhaps you'd like to trace the path of the signalling that occurs when neutrofil exrtavasation occurs?

Since you can't spell it, I'm calling your bluff - you pulled that one out of your butt. However, it is essentially a series of chemical reactions. And billions of years of "practice"...
Or describe how the right ingredients are attracted to the site of protein synthesis in the right order, quantity and speed?

Once again, a series of chemical reactions. Oh- and billions of years of working out the bugs...
Once you've given us a full rundown of that then perhaps you qualify to say that individual processes are not irreducibly linked to their main event.

It would also take someone of equal qualification to state that they are...

Oct 11, 2016
You need a lot more than rain, a jumble of molecules, sunshine, and chance....

Such as?


That is the whole point! Evolution just doesn't stack up to what is needed to bring about life as we know it.
Then you don't understand evolution. Hell, even scientists have a tuff time with the growing mountain of evidence.
Life just doesn't form like that.....

References?

Again, that is the whole point! There are no references in the literature that can back up the preposterous claims of evolution.

evolution makes no "claims". It simply describes a process. "Science" is the observation and documentation of that process and ain't done by a long shot - yet. It appears you have not delved very deeply into that available documentation. Why does it scare you?
Just for kicks, show how YOUR literature backs up it's own preposterous claims.
(hint - The fact that someone stated it, way back when, is NOT acceptable evidence)

Oct 11, 2016
The cell is irreducibly complex.

Actually, no it's not. When you say the "cell" do you mean Eukaryotes, Prokaryotes, Archaea? There are clear cellular components in e.g. Eukaryotes that are "reducible" in the sense that they have been incorporated from the external environment or evolved over time from more primitive elements. There is a clear line of evolution from cells with relatively few and very simple components to those that are highly complex.

I suggest you learn something about cytology before you make such statements.

Your argument is, by the way, reminiscent of the old and disproved statement by creationists that the mammalian eye is irreducibly complex, or similarly the cellular flagella. It's an argument that is so unscientific, so disproved and so bad that it's not even wrong.

Oct 11, 2016
Your question to Gyre about
neutrofil exrtavasation [sic]
and signalling was rather disingenuous by the way.

If you know about this topic then you must also know that it is a tissue-based response to pathogen invasion or other tissue damage. While cellular movement and signalling of leucocytes, mediated by cytokine release at the point of the tissue insult, is part of the broader response, this overall process is not in and of-itself a cellular activity in the sense that you meant in your initial post because the cells involved cannot be considered in isolation from their surrounding tissue and the overarching life processes of the organism.

In addition, the metabolic signalling pathways and processes of a large-scale, highly evolved mechanism like this can be seen, when appropriately researched, to have built over evolutionary time from simpler components and processes in simpler and more primitive organisms.

Oct 11, 2016
Your argument is, by the way, reminiscent of the old and disproved statement by creationists that the mammalian eye is irreducibly complex, or similarly the cellular flagella. It's an argument that is so unscientific, so disproved and so bad that it's not even wrong.


Creationism = ID. ID = creationism. Heck, even the US courts could see that. It is just another supernatural explanation for things, which is useless. Oh, God did it! Brilliant. They can invoke intelligent aliens as the designers, for all I care. Somewhere, somehow, the very first designer came into existence. Was that by evolution? Not according to the ID brigade. Ergo, ID = creationism - which is unscientific b*llocks.


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