Lab-made primordial soup yields RNA bases • Hacker News Board

Re: Lab-made primordial soup yields RNA bases

#101

Post by username90 » Sat, Oct 05, 2019, 7:00 AM UTC

gmoot wrote: post #68

tlb wrote: post #37

Earlier quoted context omitted.

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 mak…

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").

Re: Lab-made primordial soup yields RNA bases

#102

Post by justinjlynn » Sat, Oct 05, 2019, 7:56 AM UTC

marshray wrote: post #96

Roritharr wrote: post #85

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.

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.

Re: Lab-made primordial soup yields RNA bases

#103

Post by speedplane » Sat, Oct 05, 2019, 8:06 AM UTC

justinjlynn wrote: post #102

marshray wrote: post #96

Earlier quoted context omitted.

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 trial…

> 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.

Re: Lab-made primordial soup yields RNA bases

#104

Post by Grue3 » Sat, Oct 05, 2019, 8:26 AM UTC

TheRealPomax wrote: post #55

The_rationalist wrote: post #49

Earlier quoted context omitted.

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

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…

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.

Re: Lab-made primordial soup yields RNA bases

#105

Post by surfsvammel » Sat, Oct 05, 2019, 9:09 AM UTC

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.

Re: Lab-made primordial soup yields RNA bases

#106

Post by joyjoyjoy » Sat, Oct 05, 2019, 9:26 AM UTC

david-gpu wrote: post #82

joyjoyjoy wrote: post #65

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.

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.

Re: Lab-made primordial soup yields RNA bases

#107

Post by novalis78 » Sat, Oct 05, 2019, 10:38 AM UTC

SomeOldThrow wrote: post #99

bduerst wrote: post #28

Earlier quoted context omitted.

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, de…

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

Re: Lab-made primordial soup yields RNA bases

#108

Post by benogorek » Sat, Oct 05, 2019, 10:59 AM UTC

bduerst wrote: post #28

aazaa wrote: post #17

> 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 a…

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.

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.

Re: Lab-made primordial soup yields RNA bases

#109

Post by Smithalicious » Sat, Oct 05, 2019, 11:02 AM UTC

SomeOldThrow wrote: post #99

bduerst wrote: post #28

Earlier quoted context omitted.

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, de…

>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.

Re: Lab-made primordial soup yields RNA bases

#110

Post by dmpanch » Sat, Oct 05, 2019, 11:19 AM UTC

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.