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

Re: Lab-made primordial soup yields RNA bases

#111

Post by qubex » Sat, Oct 05, 2019, 11:23 AM UTC

Smithalicious wrote: post #109

SomeOldThrow wrote: post #99

Earlier quoted context omitted.

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…

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

Re: Lab-made primordial soup yields RNA bases

#112

Post by gus_massa » Sat, Oct 05, 2019, 11:38 AM UTC

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.

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.)

Re: Lab-made primordial soup yields RNA bases

#113

Post by justinjlynn » Sat, Oct 05, 2019, 12:00 PM UTC

speedplane wrote: post #103

justinjlynn wrote: post #102

Earlier quoted context omitted.

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’…

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.

Re: Lab-made primordial soup yields RNA bases

#114

Post by mannykannot » Sat, Oct 05, 2019, 1:13 PM UTC

surfsvammel wrote: post #105

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.

Re: Lab-made primordial soup yields RNA bases

#115

Post by memling » Sat, Oct 05, 2019, 2:32 PM UTC

h9n wrote: post #98

memling wrote: post #84

Earlier quoted context omitted.

> 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…

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…

What I mean is that how one feels 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.

Re: Lab-made primordial soup yields RNA bases

#116

Post by ec109685 » Sat, Oct 05, 2019, 3:59 PM UTC

gus_massa wrote: post #112

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.

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…

This is a supremely good comment.

Re: Lab-made primordial soup yields RNA bases

#117

Post by lurquer » Sat, Oct 05, 2019, 4:07 PM UTC

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.)

Re: Lab-made primordial soup yields RNA bases

#118

Post by hinkley » Sat, Oct 05, 2019, 4:24 PM UTC

tapland wrote: post #54

hinkley wrote: post #42

Earlier quoted context omitted.

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…

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.

Re: Lab-made primordial soup yields RNA bases

#119

Post by hinkley » Sat, Oct 05, 2019, 4:33 PM UTC

ramshorns wrote: post #94

chrisshroba wrote: post #64

Earlier quoted context omitted.

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 f…

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.

Re: Lab-made primordial soup yields RNA bases

#120

Post by SomeOldThrow » Sat, Oct 05, 2019, 5:27 PM UTC

Smithalicious wrote: post #109

SomeOldThrow wrote: post #99

Earlier quoted context omitted.

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…

> 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.