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Lab-made primordial soup yields RNA bases (nature.com)
398 points by headalgorithm 11 days ago | hide | past | web | favorite | 127 comments





> 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.


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.

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?

>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.


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.


> 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.


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".


How does shortening "The Thing That Made The Things For Which There Is No Known Maker And Causes And Directs Events We Can't Otherwise Explain" to "God" actually brings any knowledge whatsoever? You didn't discover anything new.

It's much more honest to say "we don't know yet".


I agree completely with your points on complexity, but I also don't see why the causeless cause would more plausibly be simple rather than complex. In fact, I think a simple origin creates more problems than a complex origin; if the origin is simple, you need to explain why the universe is complex.

We should seek to minimize incidental complexity; this is what an "explanation" is. "Explaining" the complexity of the universe by moving that complexity wholesale into an entity you're not allowed to ask questions about, doesn't actually "explain" anything at all.

Fortunately, there's an abundance of evidence that complex phenomena can (and do, more often than not) arise from simple rules. Apart from this being the goal of all physics, at which it has been wildly successful, we can find examples all over mathematics. The cellular automaton "Rule 90" is a nice visual example of this: the rules are only a few bits and the initial state is a single cell, but the behavior is a tantalizing mix of ordered structures on the micro scale and chaos on the macro scale - a suggestive metaphor for our own universe.

If you saw a picture of a section of Rule 90 without knowing what it was, and tried to explain it, which explanation feels more satisfying? A mathematical rule + initial conditions that fit into a few bits? Or "someone drew it in an image editor because they thought it looked pretty"? Which has more predictive power?


> Certainly there must be something in the universe that "started it all" and has no origin of itself.

Why not have the creator exist inside of time, or around it, or beside it? Maybe all existence was just out to tea right then with its creator, because the creator’s very attached to a particular tea flavor only found on earth, but will later be the creator, and will one day be in between two dozen creators? These are valid phrases that do not refer to literal relations, like “I am beside myself”, or “snapped back to reality”—the spatial foundations of these linguistic concepts refer to distance and spatial/time relations but don’t describe anything testable or reliably true. Intelligent design as a concept exploits language to imply absurd things, like that an omniscient omnipresent, omnipowerful, undetectable force is somehow also analogous to a mortal, finite, fallible, conscious human.

FWIW all this applies to holographic universe theories as well. The narrative makes 100% sense, but it doesn’t refer to empirically meaningful concepts.


Intelligent design is a misnomer which has many forms, but at it's core it challenges naturalistic causation for abiogenesis on prebiotic Earth.

It doesn't posit anything about other intelligence or life, just that the biological information necessary to kick off a self-replicating cell that undergoes evolution is too complex and too specific to happen randomly on Earth.

Even naturalistic panspermia theories are compatible with intelligent design, because it shifts the frame of abiogenesis to different conditions where cellular formation may actually become probable.


You’ve just run into the classical “Prime Mover” paradox of infinite regression.

If nothing else Panspermia allows for more time assuming a similar chemical process but over a much longer time horizon than ancient Earth.

Of course! Disproving known stuff is the best thing about science.

Well said. I feel that documentaries, etc. hand-wave away abiogenesis as it's just obvious that it happened, but there's this elephant in the room regarding the question of "why?" Great, you're a puddle of RNA compounds, all 4 in fact. Just sitting there. A puddle.

Another way that nucleobases could have formed were in ice [1].

1. http://discovermagazine.com/2008/feb/did-life-evolve-in-ice


There's a multiverse theory that there are many possible or existing universes with different physical constants, affecting everything from chemistry to orbital mechanics, and the reason we are having this conversation is because this universe was conducive to the formation of highly organized lifeforms capable of abstract thought.

In this line of reasoning "Why this set of constants" doesn't matter, because only the universes that could have observers would be observed.


The anthropic principle doesn't depend on a multiverse.

Not on a multiverse directly, but I think there is merit to @hinkley's claim. Say there's a one trillionth chance that life forms on an earth-like planet. There are likely trillions of earth-like planets, so chances are good (given the assumptions) that life forms on (at least) one of those planets. People on that planet (Earth) will marvel that life was created and search for reasons that seem plausible and likely for life to have been created given the initial conditions, but the initial assumption that the chances were minuscule still remains.

That is to say, we may not be able to easily predict and rationalize the beginning of life based on the initial conditions of the earth, because it is likely that it was an improbable fluke. It feels like a lottery winner trying to explain how they won the lottery.


One of the things we're trying to figure out is how likely life is to form on an Earth-like planet. Of course it happened here, but we have no idea how common it is.

If we do the chemistry and figure out the mechanism and it looks like it happens all the time, then that tells us one more term in the Drake equation and gives us a reason to go check out the exoplanets.


I don’t disagree that having tighter bounds for the Drake equation is worth investing time and energy into.

I think we are going to find that the preconditions for life are quite common. The way solar fusion and supernovas work, what atoms are produced, The distribution of material and of those atoms within an accretion ring... if a planet forms at the right distance, then it will have the mix of chemical precursors.

Honestly I suspect the only thing that makes Earth rare is our freakishly large moon. If we can ever prove that life is viable on a timescale of eons on a planet without such huge tidal forces pumping the biosphere, that will be a revelation.


So the moon stirred the biosoup in a way only an earthmoon sized moon could? And then life formed?

None of what you said remotely answers their question.

Wow. You just found a reason for you not to get into science.

Now most of the rest of us are still curious to find out how stuff works around here.


And I just found a reason you should adjust your chemical intakes. Too much caffeine or not enough? You don’t know me, or how I work.

Indeed, the author does recognize it:

> The next major problem Carell wants to tackle is what reactions could have formed the sugar ribose, which needs to link to nucleobases before RNA can form.

Possibly something resembling the Calvin cycle could be the start you talk of. [1]

[1] https://link.springer.com/article/10.1007/s00239-018-9840-1


What are the alternative theories that are more plausible, in your opinion?

DNA teleportation.., the recent discussion on HN about the hydrophobic effect of DNA basically proves it is true... naysayers be damned!

https://en.m.wikipedia.org/wiki/DNA_teleportation

https://news.ycombinator.com/item?id=21051949

https://en.m.wikipedia.org/wiki/Water_cluster

http://www1.lsbu.ac.uk/water/magnetic_electric_effects.html


First you have some shell script, then you have static code (dna)?

> 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...


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.

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

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).


Yes, one and the same guy

I was going to reply with "now do it accidentally", but that actually seems like it could be a tidally guided experiment that would occur coincidentally with a relatively high frequency.

Another nice thing here is that we are left with a fairly low complexity - perhaps even high accuracy super-computer simulable - mechanism by which we can draw out viable candidates for probable forms of life across a wide variety of initial environments.

Which seems cool to me.


Just came here to say, I found this book pretty informative and persuasive: The Vital Question: Energy, Evolution, and the Origins of Complex Life https://www.amazon.com/dp/0393352978/ref=cm_sw_em_r_mt_dp_U_...

The book contains some counter arguments against the primordial soup theory

I am not really qualified to comment though.


Bruce gave a good summary presentation on his research (if you prefer this format):

https://www.youtube.com/watch?v=SsfCIR_6K0Y



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

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/


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


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).

I remember that one from school.

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.


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 )

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.)


This is a supremely good comment.

I tend to think statements like that say more about the knowledge and passions of the writer than about the laws of the universe.

The fundamental point underlying the Nature article is that we don't actually know "the odds of life creating itself via basic chemical pathways". What we do know is that life appeared on Earth quite soon after liquid water.


Indeed, the law of large numbers applied to quadrillions and quadrillions of atoms and essentially uncountable numbers of interactions between them yields a large likelihood for even very unlikely independent events. The important thing to remember is that bootstrapping means it only has to happen purely by chance a relatively small number of times - perhaps only once. It turns out that the number of rock clock trials are far, far fewer and they don't bootstrap and so it is much less likely for one to exist even if the independent probability may be much higher. Statistics is often paradoxical, but then again, that's why we have logical systems for dealing with it. We'd be much better off, as a species, if a better understanding of statistics and statistical analysis were more widely spread and valued. Dawkins's explaination in "climbing mount improbable" is a good one.

> the law of large numbers applied to quadrillions and quadrillions of atoms and essentially uncountable numbers of interactions between them yields a large likelihood for even very unlikely independent events

It’s not so simple. If something is extremely unlikely but also has many chances to occur, the probability of the thing occurring is a very large number divided by another very large number. In these cases, it’s not always clear if the resulting probability will be high or low.

Just stating that there are quadrillions of potential interactions is meaningless if the chances of any one forming something useful can range from one in a billion to one in a quadrillion quadrillion quadrillion. Much like zero divided by zero (or in this case infinity divided by infinity) the overall probability is pretty much undefined.


True, there's no known analytical solution to the statistical likelyhood of abiogenesis. How one defines likelihood is rather important when discussing a statistical analysis.

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.


It is the law of large numbers. It goes with the theory that if you buy 100 billion lottery tickets you asymptotically approach 100% chance of winning. In the case of abiogenesis, if you can show that the conditions for this effect were possible, and that those conditions could persist for millions of years, the probability that the "special" one occurs, approaches 100%.

It doesn't explain everything, it is just a link in the chain of things that increases our understanding of our world.


Meteorites contain nitrogenous bases https://www.pnas.org/content/108/34/13995

Fascinating thanks, sorry I should have searched it up.

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.


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.


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.

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.


>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 ?


No. The problem is that one would expect the "easy" steps to be resolved first, so uncovering them says very little about how unlikely the hard steps are.

That "strong indication" comment is BS.


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

First mover advantage probably. If abiogenesis is common but not too common, whatever starts reproducing first might have a few billion years to spread everywhere and take over all possible niches.

The 'common ancestor' dates back to about the same time as the late heavy bombardment. It's been theorised that earth may have been suitable for life earlier than originally hypothesised, but the bombardment wiped the record.

If this is true, then there may have been many independently evolved microorganisms pre-bombardment, but only a few colonies survived because they happened to live deep underwater near volcanic vents. Perhaps also, in this era of reduced genetic diversity, one colony was especially capable of adapting to the new environment and quickly outcompeted all the other surviving colonies.

Or maybe aliens did it. Who knows.


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.


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.

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.


> 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.


> 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.


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


Reluctantly I have to admit my knowledge here is minimal, though I find it extremely interesting. And from another comment I recognized that though I was questioning whether the "soup" was liquid, I was still assuming that this reaction occurred on earth. If I remember correctly I believe all (or probably at least "most") of the basic elements do start out in their elemental form as the result of supernovae. I think this would be a relevant wikipedia article:

https://en.wikipedia.org/wiki/Supernova_nucleosynthesis


Of those elements you list, only hydrogen and nitrogen are "lighter than air" (in the sense that they are commonly found in gaseous form with molecular weight below that of the air average).

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?


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.


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.)


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.


This Stack Exchange thread has some fascinating answers and links to sources: https://biology.stackexchange.com/questions/2874/why-are-the...

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.

No, it argued on a mathematical basis for this.

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.

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

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.

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

Plus carbon, of course.

> 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)


GUAC is always extra

darn you chipotle!

Primordial guac

The avocado industry didnt see this one coming or they probably would have paid for that change.

Your comment made my day :)

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

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.

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.


> 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.


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.


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.


> it can't really be just survival of the fittest can it?

Why not?


Ockham's Razor might be helpful here.

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.


To get from the basic building blocks to a fully functioning working cell, you need steps A, B, C, D, ...

This article shows that C could have spontaneously happened. It's not at all meaningless. Is it the whole story? Of course not. But it's an interesting part of the chain. Science is slow. Don't throw out the transistor because it's not an iphone.


The Neo-Darwinians don't have an origin of life model. Neo-Darwinism was a synthesis of Darwin's theory of evolution by natural selection with genetics. It was about fleshing out an actual mechanism behind heritability and variation (two of the three necessary ingredients for evolution by natural selection; the other being selection). It was not about explaining how life started.

The origin of life is very much a speculative area of science. I thought Nick Lane's The Vital Question was an interesting take on how life could have gotten started. I'm not qualified to comment on the validity of the chemistry behind it, though.


Aren't alkaline hydrothermal vents[0] a pretty good candidate for that? AFAIK they provide almost everything necessary for the creation of cellular life. Once you have cells and RNA everything else is just time + evolution.

[0] https://schaechter.asmblog.org/schaechter/2014/03/from-geolo...


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.


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.

See my response above. Neo-Darwinianism has nothing to do with explaining the origin of life. It was strictly concerned with explaining the mechanism (genetics) underpinning Darwin's theory of evolution by natural selection. And the fact that the OP has engaged in name calling that isn't even correct kind of implies that their objection is ideological rather than merely logical.

Because the first two sentences in the GP comment are false and the third is a non-sequitur.

[flagged]

nurettin 11 days ago [flagged]

It is great that you've found a way to feel superior to others with your purpose narrative.

Please don't take HN threads further into flamewar, and please don't cross into personal attack.

https://news.ycombinator.com/newsguidelines.html


Fair enough

So... you flagged me because you think I'm making some supposed statement of superiority?

Also, what "purpose" narrative?

Is contradicting the Neo-Darwinist model of life somehow not allowed?

Does contradicting it make me a closet Christian, in your eyes?

Because I don't see an answer in Neo-Darwinism or any religion.

I'm happy not knowing, just as I'm happy to criticize people who claim to know.


I didn't flag you, dang flagged me for criticising your character instead of an idea. In any case, I think there is a case of false dichotomy going on here.

You should read "The Vital Question" by Nick Lane. He puts forward a theory for what the first life might look like, based on the shared common genes between bacteria and archea.

I'm giving you the benefit of the doubt that you're genuinely curious.


So? Don't you think it’s important to understand even this first basic step?

Sure, I guess.

But we've been down this road of chemical soups before ~ and gotten nothing out of it.

I'm just frustrated that they seem to keep chasing the same failed ideas.

It's time to look for other explanations... not a religious one, at that.

Some biologists look towards a meteoric explanation of life, but punting it off-planet isn't an explanation, either...


the same failed ideas

Saying that the idea of "a primordial soup produced the building blocks that eventually led to all life on earth" has failed because some extraordinarily limited experiments (spatially, chemically, temporally, and complexity limited) haven't produced cellular life is about like saying that the "fusion of hydrogen produces the heat of stars" theory has failed because we haven't been able to produce stable fusion here on earth. The scope of the effect that was likely produced in the primordial environment over billions of years is beyond basic human comprehension.


I don't think the idea is failed. Yes, attempts to replicate it in laboratory-scale tanks haven't succeeded yet. But that isn't evidence against the theory that it occurred sometime over millions of years in billions of cubic kilometers of water. It happens at some statistical rate, and lab experiments so far have put an upper bound on the rate.

This is interesting. If we can put an upper bound on the rate (what is it?) we could rule out abiogenesis if we could lower that upper bound sufficiently.

Most here seem to reason the other way around - it must have happened, so we'll just keep looking until we figure out how. I'd like to think that we could reach a point at which we could confidently say "this universe doesn't have the probabilistic resources to make it happen" instead of kicking the can down the road indefinitely.


Scientists will chase chemical soups as long as it is the most probable theory, it is that simple. The thing with chemical soups is that some of them form very complex structures, so it is pretty easy to imagine that the right kinds of soups was the origin of life. Everything else people have suggested are either much less probable (not sure how it could happen without chemical soup) or they are nonsense (intelligent design, ie "life was created by life that was already there, just don't ask me how that other life appeared").

I don't see how one could rule it out, since we don't know the number of planets on which the conditions required for abiogenesis could have occurred. It's not limited to the # of planets in the volume of the universe observable from Earth.

Right, given the Anthropic principle the probability has to be nontrivial when multiplied by all the oceans and the lifetime of the planet, but also by billions of planets and billions of galaxies. So there may be no way of ruling it out by any experiment.

All you can do is build bigger vats, just like physicists build bigger supercolliders, hoping for a result.


Here's a working theory. Warning: turn down the volume. https://youtu.be/U6QYDdgP9eg?t=227

How?: Time

Time cannot logically explain it.

Given such complex lifeforms, even a billion years wouldn't suffice to explain going from a RNA bases to a modern day human.

And no, I don't buy the Christian fairytale, either.

It's fine for me to accept that we humans have no answer as to life's origins.


Just because you can't explain it doesn't mean it cannot be explained. It could just be a reflection of you.

Be patient, this step is part of the process of discovering the part that you are focused on.

Fwiw I think the transition from single cellular life, or even non-callulqr life like viruses, is fairly easy to imagine.

[flagged]


Personal attacks will get you banned here, no matter how wrong or annoying another comment is. If you'd please review https://news.ycombinator.com/newsguidelines.html and stick to the rules when posting, we'd be grateful.

I dislike parties. Too much noise. Plus, I get bored easy. :P



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