
Lab-made primordial soup yields RNA bases - headalgorithm
https://www.nature.com/articles/d41586-019-02622-4
======
aazaa
> Carell, an organic chemist, and his collaborators have now demonstrated a
> chemical pathway that — in principle — could have made A, U, C and G
> (adenine, uracil, cytosine and guanine, respectively) from basic ingredients
> such as water and nitrogen under conditions that would have been plausible
> on the early Earth. The reactions produce so much of these nucleobases that,
> millennium after millennium, they could have accumulated in thick crusts,
> Carell says. His team describes the results in Science on 3 October.

> The results add credence to the ‘RNA world’ hypothesis, says Carell, who is
> at the Ludwig Maximilian University of Munich in Germany. ...

It's worth noting that what was made were nucleobases - flat very low
molecular weight molecules - that when attached to ribose yield nucleotides.

It is nucleotides, not nucleobases, that form RNA.

The "RNA world hypothesis" still needs to explain where the ribose came from,
how it was joined with the bases that were supposedly littering the Earth's
surface, and how the resulting nucleotides started spontaneously assembling
themselves through combination with phosphate into polymers.

That's a very, very tall order in chemistry.

~~~
bduerst
I agree, but keep in mind abiogenesis is probably one of the tallest orders
for chemistry. I'm glad scientists are at least exploring possible
explanations, even if it means possibly disproving the mechanisms.

~~~
SomeOldThrow
What are the alternatives? Even with panspermia life would have had to begin
elsewhere. The universe would have been too hot at the Big Bang to support
organic molecules if that theory is true. Even with “intelligent design” the
intelligence would have its own heritage and origin. The implications of an
alternative to abiogenesis seem outside the realm of scientific inquiry
entirely. Is the desire here a coherent, detailed narrative for how we went
from hot plasma to RNA?

~~~
Smithalicious
>Even with “intelligent design” the intelligence would have its own heritage
and origin

Is this really a given? Certainly there must be _something_ in the universe
that "started it all" and has no origin of itself. Or, alternatively,
everything in the universe has a history stretching back infinitely far, but
that's equally incomprehensible and still allows you to perform the same
"trick" (in this case: life has always existed).

Not saying that I believe in intelligent design, but in this case it seems to
me that it _does_ answer a question without creating any new ones.

~~~
dTal
Without creating any new ones? I have _quite_ a lot of questions for our
erstwhile intelligent designer...

If you're happy to entertain a causeless cause to explain life, why make it an
intelligent designer, a very complicated object? Why couldn't life itself be
the causeless cause? A cell is much simpler than anything capable of inventing
the universe. All 'intelligent design' does is move the problem (and amplify
it).

I think an intelligent designer _feels_ simpler to a human because "conscious
entity" is implemented as a conceptual primitive in our minds, for obvious
evolutionary reasons. The idea of a non-corporeal mind spontaneously arising
feels more plausible than a single-celled organism spontaneously assembling,
because we need many more symbols to represent the latter. But it's a
misleading perception.

~~~
ibra77
> Why couldn't life itself be the causeless cause?

Because everything we know about this universe _needs_ a cause, nothing in
this universe is causeless, so you can't simply say that "something" inside
that universe is causeless.

And everything we know about life screams causality, from the need to eat and
drink to generate energy, to sex for reproduction. If life can actually be
causeless why is it so fragile and dependent on so many things to keep itself
from death?

> A cell is much simpler than anything capable of inventing the universe.

A cell is also not capable of creating itself out of nothing.

Your lack of knowledge/understanding about how can something create the
universe is not a justification for assuming that it created itself.

You need a causeless cause (otherwise we wouldn't exist), so you either choose
it to be the universe itself (which is a wild guess with zero evidence and
hence not even scientific as you claim), or it is God (and yes you can't and
will never understand how it is the first cause)

I'd rather believe in God and his messages to us that brought actual evidence,
than believe in an unconscious universe creating itself with no evidence.

~~~
dTal
To be clear, I think that both cells and gods are far too complex to be
satisfyingly acausal. I'm not willing to entertain more than a few bits (in
the information-theory sense) of acausality.

Of course, belief in God is an emotionally charged topic. Many people rely on
their belief for many things, and trying to argue against it is seldom
productive - I'm hesitant to engage for that reason. You're free to believe
what you'd like. But, since you've brought up "evidence"

I don't agree that there is more evidence for God creating the universe than
there is for some kind of spontaneous event. For a start, the existence of the
universe is extremely verifiable, much more so than God - no matter how much
you believe in the "messages". For another, the universe appears to governed
by very simple rules of physics (although not quite simple enough for my
"several bits" threshold of acausality, just yet). Attempting to explain a
fairly simple phenomenon that definitely exists with a very complex phenomenon
of uncertain existence doesn't seem to add any explanatory power, and in fact
just multiplies entities unnecessarily. All you've done there is take the
mystery, put it in a box labeled "God" (along with a bunch of other things),
and then said we're not supposed to look inside the box.

Addendum - I don't think the universe needs a "cause", per se - causality is
related to the arrow of time, and that is a property internal to the universe.
That's not to say that nothing needs explaining, but I think we should focus
on "simplicity" rather than "causality".

------
jonmc12
> Carell’s team has shown how all nucleobases could form under one set of
> conditions: two separate ponds that cycle through the seasons, going from
> wet to dry, from hot to cold, and from acidic to basic, and with chemicals
> occasionally flowing from one pond to the other.

I've enjoyed Bruce Damer's explanation of related theory, "The Hot Spring
Hypothesis for the Origin of Life". Search "goldilocks chemistry" for some
helpful background and visualizations on this page -
[https://extendedevolutionarysynthesis.com/the-hot-spring-
hyp...](https://extendedevolutionarysynthesis.com/the-hot-spring-hypothesis-
for-the-origin-of-life-and-the-extended-evolutionary-synthesis/)

~~~
salgernon
Is that the Brice Damer of “DigiBarn” fame (vintage computer restoration and
archiving)? An illustration shows a MITS Altair reading a paper tape,
presumably to illustrate interpreting dna instructions.

~~~
jamesakirk
Yes, it is the same Bruce Damer! Here is a clip of Bruce giving Wozniack a
tour of the DigiBarn:
[https://www.youtube.com/watch?v=OsHM3MXnrNM](https://www.youtube.com/watch?v=OsHM3MXnrNM)

He's a fascinating individual who wears many hats. He's done a ton of
interviews on podcasts (his own, Duncan Trussel Family Hour, Erik Davis's
Expanding Mind, Future Fossils, and Rogan come to mind).

------
JorgeGT
The actual paper:
[http://doi.org/10.1126/science.aax2747](http://doi.org/10.1126/science.aax2747)

------
pkrein
It may not be necessary for complex organic molecules to assemble out of
nothing in a finely tuned primordial soup. Two recent studies to illustrate
this:

1\. Simple chemical droplets can divide and multiply in the right conditions:
[https://arxiv.org/pdf/1603.01571v1.pdf](https://arxiv.org/pdf/1603.01571v1.pdf)

2\. “Evolution” from that simple beginning may be enough according to the
theory of dynamic kinetic stability:
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843823/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843823/)

------
pmiller2
Reminds me of the Miller-Urey experiment, except Miller and Urey didn’t find
amino acids that could form DNA or RNA.

[https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment](https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment)

~~~
gmoot
Miller-Urey found amino acids (not nucleotides as in the current experiment),
the building blocks of proteins. It's at the other end of the chicken/egg
"which came first" between proteins (which catalyze cellular reactions) and
DNA (information storage).

------
Roritharr
A while ago I read somewhere that the odds of life creating itself via basic
chemical pathways are so miniscule, that there must be quite a few instances
of mechanical clocks creating itself by rocks beating together over the aeons
in the universe before the first dna based organism appeared.

Might be very wrong but still a beautiful picture.

~~~
gus_massa
Do you have a link? It's easier to refute the specific claim, instead of using
a generic claim that they are wrong.

In particular, note that one of the current guess is that the first barely
living thing was based in RNA instead of DNA, so if they use DNA in the
calculation it is probably wrong. (But nobody is sure. More info
[https://en.wikipedia.org/wiki/RNA_world](https://en.wikipedia.org/wiki/RNA_world)
)

The first problem is that we don't know the exact chemical pathway, so it's
difficult to estimate how hard they are.

This article in particular is about that, in some conditions (that are similar
to a small pond that get desecated from time to time) it is posible to get the
four bases of RNA. The probability of the reactions change with the
concentration, metallic contamination, and with other molecules that are
around, so this article gives a new calculation of one of the pathways.

It's only a small steps, it only creates the bases of the RNA but this method
doesn't create the sugar part of the RNA or doesn't explain how they bind with
the phosphate ions. There are known pathways, for this, but we probably don't
know the scenario where these reactions are easiest. There are a lot of unknow
steps, a lot of unknow unknow steps and perhaps unknow unknow unknow steps.
I'm optimistic that this can be solved in 200 or 300 years, but it may be more
difficult.

The main point is that you don't need a full functional bacteria as the first
barely living thing. You need some crappy thing that can almost reproduce
itself a little.

(Some guess is that the initial version was a family of similar things with a
crappy copy system that produced a similar things instead of the same thing.
But nobody is sure.)

I'm more skeptical of the claim of the clocks. If the clock is made of metal,
most metal get oxidized very fast. We know this process very well so it's easy
to calculate how long it will survive. One of the exceptions is gold, but it
is too soft so it's easy to calculate how long it will survive. I can't
imagine how the mainspring gets winded, but it's difficult to calculate the
probability of such a device. Also it's difficult to calculate the probability
to get the shape and interconnections. But the easy part is that it will get
rusty and worn out in a short geological time.

The main problem is that a almost (or fully functional) watch doesn't create
more almost (or fully functional) watches. So if a lucky watch is created by
chance, you must wait approximately the same amount of time to get a second
one.

Instead, a short RNA piece may have some enzymatic properties to make the
production of copies easier, and may have some properties to be good as a mold
for copying. The details are far from clear, but some RNA have enzymatic
properties and RNA is good for getting copied. So RNA is a good candidate, but
again, nobody is sure.

(DNA is good for getting copied, but it doesn't have enzymatic properties.
Many proteins have enzymatic properties, but they are very difficult to copy.)

~~~
ec109685
This is a supremely good comment.

------
Gatsky
These abiogenesis experiments are a little strange... they aim to show that
something could have happened. Whether that is what actually happened is
considered less relevant and in fact can probably never be determined. Does
anyone really believe that it is impossible to get spontaneous nucleotide
generation under certain conditions (the conditions also being speculative)?

The really interesting thing would be finding nucleotides or nitrogenous bases
where there isn’t life, eg on Mars or an asteroid.

~~~
ecoled_ame
Meteorites contain nitrogenous bases
[https://www.pnas.org/content/108/34/13995](https://www.pnas.org/content/108/34/13995)

~~~
Gatsky
Fascinating thanks, sorry I should have searched it up.

------
GistNoesis
>The chemistry is also a “strong indication” that the appearance of RNA-based
life was not an exceedingly lucky event, but one that is likely to happen on
many other planets, he adds.

Does this mean a new lower bound for the fl factor for the drake equation ?

~~~
The_rationalist
Than why all earth living beings come from one common ancestry rather than
many different ones?

~~~
TheRealPomax
Mostly: because billions of years have passed. Even if it turns out there we
millions of different self-replication mechanisms that were complex enough to
give rise to (an abstract form of) competition, early Earth has a period of
hundreds of millions of years in which each and everyone one of those had
plenty of time to run their course to extinction.

Remember that that single common ancestor was _not_ alone on the planet. They
might have been millions or even hundreds of millions of other potential
ancestors, but if there were, all of them died out before the start of the
fossil record.

~~~
Grue3
At any point in time there was likely a great variety of ecological niches on
Earth. It seems weird that one kind of organism would achieve total global
domination. For example Bacteria and Archaea have diverged relatively early on
the scale of evolution, and both of these domains have survived until the
modern times without one dominating the other.

------
surfsvammel
I got extremely excited when I read the headline. Finally!, I thought. Then I
read the first part:

> Carell, an organic chemist, and his collaborators have now demonstrated a
> chemical pathway that — in principle — could have made A, U, C and G

 _in principle_ , what? No! The headline implies that actual RNA had formed,
spontaneously. Not _in principal_.

Going back to arguing with Creationists.

~~~
mannykannot
It says RNA _bases_ right in the title, though one has to know something about
RNA's structure to appreciate its limited relevance - see aazaa's comment.

The article claims the synthesis has been demonstrated, so I think that _in
principle_ is there because we do not actually know if this particular process
occurred in nature.

~~~
surfsvammel
Ok. My RNA/DNA knowledge is quite limited. But I still don’t get it. Did they
come up with a way it could happen, or did they actually make it happen out of
the “soup”. To me—as someone who knows little about it, except for the fact
that having RNA/DNA spontaneously form under these conditions would be be
awesome for our understanding of our origins, and would make a killer argument
when talking to creationists—the difference between the two is very
significant.

~~~
mannykannot
The article shows that RNA bases were actually created in the lab.
Furthermore, this is not the first time, but it is the first time they have
all been produced by one process:

 _Now, Carell’s team has shown how all nucleobases could form under one set of
conditions: two separate ponds that cycle through the seasons, going from wet
to dry, from hot to cold, and from acidic to basic, and with chemicals
occasionally flowing from one pond to the other. The researchers first let
simple molecules react in hot water and then allowed the resulting mix to cool
down and dry up, forming a residue at the bottom that contained crystals of
two organic compounds.

They then added water back, and one of the compounds dissolved and was washed
away into another reservoir. The absence of that water-soluble molecule
allowed the other compound to undergo further reactions. The researchers then
mixed the products again, and their reactions formed the nucleobases._

This is progress (especially as the yield is apparently quite high), but as
both azaa and the last paragraph of the article point out, we are still
lacking the ribose backbone of the RNA molecule.

I don't think it is possible to have a killer argument against determined
creationists, as they do not regard evidence in the same way as you and I do.
Any discusion with them will take the form of a whack-a-mole game.

------
unexaminedlife
Has anyone proven that the "soup" has to be liquid?

I'm no chemist, but I was curious one day so I looked through the chemical
composition of humans, and was surprised to see that almost all of the base
elements from the periodic table that we are composed of are lighter than air.
Just ran the numbers again for this post: ~96.2%
oxygen,hydrogen,nitrogen,carbon ~ 3.8% calcium,phosphorus,
potassium,sulfur,sodium, chlorine,magnesium

The highest atomic number for any of these elements is 20 (calcium), while
krypton is listed on wikipedia as a "major constituent in earth's atmosphere"
with an atomic number of 36.

EDIT: And in fact it gets more interesting when you analyze the chemical
composition of DNA / RNA.

~~~
naniwaduni
> almost all of the base elements from the periodic table that we are composed
> of are lighter than air

This is almost completely gibberish since you don't find atoms in isolation.

~~~
outworlder
> This is almost completely gibberish since you don't find atoms in isolation.

No you don't. You find them in molecules. Nowadays it is a bit tough to find
the pure gases in our planet, but they are readily available in high
quantities in our universe. In gaseous form, even.

~~~
unexaminedlife
Very interesting. That's probably another assumption that may be worth
attention. Is it necessary that DNA / RNA molecules were originally formed on
earth?

This may not be directly relevant to this idea, but first thing that came to
mind when I read your comment was this:

[https://en.wikipedia.org/wiki/Panspermia](https://en.wikipedia.org/wiki/Panspermia)

------
roland00
How is this different from the Miller-Urey experiments from the 1950s ? I am
asking this for someone who is more knowledgeable and technical than me.

"To my understanding" ? Those 1952 experiments yielded 20 amino acids, and
this experiment in 2016 to 2019 experiments merely are demonstrating RNA can
be made with a similar experiment? Our cells naturally use RNA, specifically
mRNA in a "translation" process at the Ribosomes part of our cells where the
Amino Acids are used to create longer protein chains.

Am I remembering my AP Biology correctly or did I get something wrong?

------
microcolonel
I was just having a conversation about the probabilistic craziness of
abiogenesis this morning with a young christian who was out proselytizing,
this is a step toward the real deal (though I think the title goes further
than the research here).

Glad to see chemists are still trying to answer this beautiful, burning
question. To those in this thread wondering: yes, there are people so
flabbergasted by abiogenesis that they turn to alternative answers.

------
joyjoyjoy
I came across an article about DNA but did not had time to read it and lost
it. It was about some ideas why DNA has 4 bases (and not 6 or 8). They also
mention why 20 (?) amino acids. It was something similar to degrees of
freedom.

Not sure where I saw it. hackernews? Might have been Scientific American.

I anyone remembers I would appreciate a link.

~~~
david-gpu
Was it an article about how there are 64 possible encodings of 3 bases
(codons), but some of them are synonymous and only 20 unique amino acids are
synthetized? And how this redundant encoding appears to be unusually resistant
to mutations, as replacing one base with another would often encode a
chemically similar amino acid? I remember reading something like that, but I
couldn't find it either.

~~~
joyjoyjoy
No, it argued on a mathematical basis for this.

------
lurquer
Before inquiring whether something can be made accidentally, perhaps one
should determine if it can be made intentionally.

That is, can organic chemists create functioning RNA from scratch? How about a
strand of DNA? (And, by scratch, I mean starting with components that were not
derived from living organisms.)

------
dmpanch
I recommend reading "Origin of life. From nebula to cell" of Michail Nikitin.
Not sure if it's translated from Russian, but the book is fresh and considers
many modern theories in terms of chemistry.

------
miles_matthias
If you’re looking for a good fiction read relating to this, I just finished
“Origin” by Dan Brown, would recommend.

~~~
aomega08
I am amazed by the timing. Literally finished reading the book this morning
and spent most of the day deep in Wikipedia researching primordial soups.

------
SomeOldThrow
The claim is that only hydrogen, oxygen, and nitrogen are necessary for the
base nucleotides, right?

~~~
mannykannot
Plus carbon, of course.

------
badloginagain
> could have made A, U, C and G (adenine, uracil, cytosine and guanine,
> respectively)

Im kind of upset that they don't refer to it going forward as GUAC (as in
guacamole)

~~~
overcast
GUAC is always extra

~~~
holler
darn you chipotle!

------
rpmisms
Whoa. I didn't know we could do that.

------
andy_ppp
I sometimes find the chances of us being here so remote, it can't really be
just survival of the fittest can it? There must be other means for evolution
to be more intelligently selective. I'm arguing that you'd see some kind of
evolved "invisible" hand rather than an actual maker behind all of this.

~~~
outworlder
No invisible hand is required.

Any life form that has reached the cognitive capability to reason about itself
will be amazed by the sheer "coincidence" of their habitat. "wow, isn't it
amazing that our planet's atmosphere is composed of the very ammonia we need
to survive in?"

No invisible hand required.

Also evolution is "intelligently selective". Surviving and reproducing is a
pretty intelligent mechanism. It will find local maxima pretty effectively.

~~~
memling
> Any life form that has reached the cognitive capability to reason about
> itself will be amazed by the sheer "coincidence" of their habitat. "wow,
> isn't it amazing that our planet's atmosphere is composed of the very
> ammonia we need to survive in?"

Isn't this a non sequitur? Whether any life form would wonder about its
existence (probable or otherwise) has no bearing whatever on whether it
evolved or was designed or specially created.

~~~
h9n
We should not be surprised that the environment we find ourselves in is so
seemingly well-suited to the flourishing of life. I believe the grandparent
post was saying this as a response to the idea that things are too improbably
perfectly-suited for us. Far from being a non-sequitur, it is almost stating a
tautology. The environment we find ourselves in is the one that has given rise
to us, with our ability to think about these things.

I'm sure there is a Douglas Adams passage that illustrates this but I can't
remember it.

~~~
memling
What I mean is that how one <i>feels</i> about his existence has no bearing on
how one came to exist. That is why it is a non-sequitur. (One is reminded that
the rose is not special because it is rare.)

Now the question of exactly how improbable is more relevant, and this is why
people care about making primordial soups more easily: everyone agrees that
abiogenesis is improbable.

Since chemistry is not selective (or at least no one has demonstrated a
parallel mechanism for natural selection that applies to chemistry), our tools
are to somehow find ways to change random chance to dependent probabilities
and to find enough time for the chemistry to happen. While we have a fairly
good grasp of the time limits, it's the probability that is harder to
quantify.

------
Valmar
For all of these lab soups, it means basically nothing.

None of this has advanced any understanding of the Neo-Darwinian origin of
life model.

There's still no working theory of how one gets from basic building blocks to
a fully-functioning working cell, nevermind the rest.

~~~
brink
To those downvoting this comment, can you please clarify why you're
downvoting?

This is also how I see it, and I'd like to know the counter-argument.

~~~
bediger4000
Dragging "Darwinism", which is a theory of evolution, into an argument about
abiogenesis, which is life coming from non-living stuff, is a hallmark of
Creationism. Creationist are known to argue in bad faith. Best just to rid the
space of Creationist arguments. Like Mark Twain once wrote, if you wrestle
with pigs, you'll get very dirty, and the pigs just might enjoy it.

