It seems obvious that if replication of elementary particles appears that everything else will be an emerging property given enough time. And if you look at atoms and math there're definite parallels that once atoms can interconnect stronger than everything else (considering the 3d world) and something like Penrose's tiles where you get repeating interconnecting structures that more higher level structures would be possible. And with energy connected to the particles momentum and Heisenberg's uncertainty principle you get fluctuations in the structures that allow for both new structures and enforcing of the construction rules. You also have clear levels between forces that work on different levels that create boundaries to the structures. 3 spacial dimensions give additional directions of interactions between structures. And voila, given conditions, there's a place for emerging properties. Whether it was RNA who knows. It does seem that the search becomes way murkier toward going into the actual mechanism but the ingredients seem to be in place
The big problem I have with the RNA world idea, and its experimental implementation, is that it runs in a soup that doesn't seem plausible.
RNA gets made from pure, energy-rich molecules that themselves are quite complex. This soup of pure monomers isn't something that just arises naturally in the absence of life. Prebiotic chemistry produces a random soup of a wide variety of chemical species, with the abundance of each declining exponentially in its size and complexity.
You see this issue all the time in origin of life claims. For example, that recent result of "all the bases of RNA and DNA were found on this asteroid by the Japanese" tended to slide over the fact that they were there at extremely low levels, mixed with huge numbers of other non-biological organic molecules.
Trying to replicate RNA in a mix of random crap will just give you polymers of crap, if it gave you anything at all.
OoL needs an idea that will work in a soup of junk, not in massively artificial pure soup on a lab bench.
f6v 16 hours ago [-]
Well we don’t know what is and what’s not possible on a planetary scale (i.e. trillions of interactions daily). At least not yet.
pfdietz 16 hours ago [-]
Robert Shapiro's 1986 book "Origins" had a rather snarky takedown of that kind of OoL research.
The research does something like this. You run an experiment and show some chemicals are present in low concentration. You say "ah ha, we've shown one step". Those chemicals are now taken off the shelf in high concentration and used in the next experiment, which makes slightly more complex chemicals in low concentration. Repeat this multiple times until done.
Lampooning this, the fictional OoL researcher in the book also demonstrates that monkeys can type out "To be or not to be, that is the question" on a typewriter. He arranges the typewriter with an automatic right margin and lets them type away until he gets a line starting with "T". First letter demonstrated! Now he rereun the experiment, but now with paper the "T" in the first column and margins set to the second column. Repeat this with subsequent letters until the entire sentence is produced. Of course, the monkeys didn't type the sentence, the researcher did.
Getting around the exponential complexity barrier is the whole goddamn point, it's not something to just wave away with a "we don't know" comment.
IMO some fundamentally new idea is needed for OoL.
ceejayoz 15 hours ago [-]
> Of course, the monkeys didn't type the sentence, the researcher did.
But the researcher is performing the selection process for the purposes of the experiment, to speed things up. Evolution functions via natural selection. That's what makes it different from the pure random chance processes.
pfdietz 15 hours ago [-]
The researcher speeds up the process from exponential time to linear time. It's not just a little speedup, it's a huge change in algorithmic complexity.
ceejayoz 15 hours ago [-]
Yes, that accounts for the fact that one researcher can't possibly do as many experiments over a billion years or so as an entire planet worth of muck can.
pfdietz 14 hours ago [-]
Say you don't understand exponentials without explicitly saying you don't understand exponentials.
ceejayoz 14 hours ago [-]
More chances to start an exponential process doesn't impact the likelihood of that process starting?
pfdietz 14 hours ago [-]
Exponentials quickly outgrow the number of particles in the universe, never mind the number of molecules on Earth. Pointing to Earth, waving your hands, and saying it's big is no argument.
ceejayoz 14 hours ago [-]
> Pointing to Earth, waving your hands, and saying it's big is no argument.
And "it's not exponential, therefore it's not possible" is?
pfdietz 14 hours ago [-]
Comparing numbers is hard, I see.
The general problem here is that handwaving ignores the issue I raised, and those making OoL theories have to address these issues, not require skeptics to disprove their handwaving. Requiring the skeptical to disprove such things is classic crank behavior.
ceejayoz 14 hours ago [-]
> those making OoL theories have to address these issues
They certainly warrant discussion and investigation.
Handwaving away the possibly infinite nature of the available experimentation space and the anthropic principle is the same failing you're widely accusing others of.
pfdietz 13 hours ago [-]
It's not infinite. This is the kind of handwavy bullshit I was criticizing. Just stop.
ceejayoz 13 hours ago [-]
> It's not infinite.
You, elsewhere in the thread: "I expect people to not make declarations about things we don't know."
How do we know that? When did we confirm what came before the Big Bang? How do we know this isn't the sixty trillionth iteration of a 15 billion year process that only just now resulted in life on one of untold trillions of planets to pay notice to it?
mrkstu 13 hours ago [-]
Natural selection can’t start working until life is present- you’re eliding the whole point…
nh23423fefe 13 hours ago [-]
No, selection requires a population, inheritance, variation, and death. It doesn't require life. Selection creates life and acts on it. It doesn't depend on it. Selection alters the population of entities.
Please don't say death implies life. By death you should infer removal from category a la RNA depolymerization, or lipid membrane lysis.
Of course I don't know what the pre-life entities are. But they were surely selected for.
pfdietz 12 hours ago [-]
Selection requires accurate replication, and there's no plausible way proposed that can occur without life already existing. Getting the point where selection can take over is the central problem of OoL.
nh23423fefe 11 hours ago [-]
> requires accurate
what does accurate mean
> there's no plausible way proposed that can occur without life already existing
Why do you say that. RNA can replicate by templating. obviously replicators came to exist from non replicators. and life from nonlife. what claim are you making? that that isn't selection because you have a definition of selection that excludes that process?
pfdietz 7 hours ago [-]
Accurate means with low information loss. Selection can counter this loss only very slowly, so the larger the genome, the more accurate replication must be or the genome degrades to nonfunctional noise faster than selection can purify it.
Life has very complicated mechanisms for ensuring very accurate replication of DNA, but of course these mechanisms would not have been available at OoL.
hackeraccount 10 hours ago [-]
Is that a true statement? Self reinforcing processes happen without life all the time.
sandworm101 15 hours ago [-]
Except evolution does really exist without life. Evolution through natural selection requires some sort of data that is passed from one generation to the next. Without that data passing you cannot have inherited traits building towards increased complexity. If you have data passing, you have life.
patcon 15 hours ago [-]
> Except evolution does really exist without life.
Biochemist and OoL enthusiast here. This is very not true. Evolution happens in even the simplest complex systems. It's very likely a process of matter.
Look up the work of Dr Michael Levin. He shares on YouTube many of his convos with leading thinkers. He's quite prolific lately.
pfdietz 15 hours ago [-]
Unless you have highly accurate replication, selection is limited in the amount of information it can accumulate. 90% accurate replication gives you ~10 bits of information. Much beyond that and information is erased faster than selection can create it.
So I strongly dispute your assertion there.
mrkstu 13 hours ago [-]
Does he point to abundant examples of this happening in nature? I can’t think of any following an evolutionary pattern outside of life.
sandworm101 13 hours ago [-]
I have heard arguments that some forms of crystal growth display patterns similar to life. If a substance has two different crystal options, an early selection of one over the other yields a growing crystal that continues to match that pattern. If two crystals are growing beside each other, they will compete for space/resources, with the better-growing pattern thriving over the less-adapted pattern.
Similarly, when creating single-crystal metal parts (turbine blades) a handful of growing crystals is put through a maze, with only one surviving to continue out into the bulk of the part. One is selected and thrives, the others stop growing after being out-competed for resources/space. It looks and sounds like life but... crystals are a special case imho.
sandworm101 15 hours ago [-]
Evolution as in change from one state to another, but is that change from natural selection? I suspect it is change based on chemistry without inherited traits. A mountain can evolve through natural processes from a lump of fresh rock to a complex structure of peaks and valleys, but a mountain does not pass those traits along to offspring. So there is no natural selection driving the evolution of mountains.
FrustratedMonky 11 hours ago [-]
"The research does something like this. You run an experiment and show some chemicals are present in low concentration. You say "ah ha, we've shown one step". Those chemicals are now taken off the shelf in high concentration and used in the next experiment, which makes slightly more complex chemicals in low concentration. Repeat this multiple times until done."
Not the best analogy.
Lets say you are looking for 'any sentence'. What if you never get the T, you get a G. The sentence is what your looking for, not a specific one. It could be another sentence, but a sentence none the less. Then you can ask, how many typewriters did it take to get the first letter, then how many for the next, (not infinite). Now how likely would this sentence appear in nature if a bunch of chimps were let loose in a typewriter store.
Its funny you are using this as an argument against. When it is actually is the process in Assembly Theory.
"Life As No One Knows It: The Physics of Life's Emergence ". Assembly Theory: A centerpiece of the book is Assembly Theory, which Walker co-developed (with Lee Cronin and collaborators). Assembly theory measures the "assembly index" of an object—quantifying the minimum number of steps and building blocks required to construct it.
kakacik 15 hours ago [-]
Well, what do you expect. We don't have direct evidence, apart from the fact that we evolved from single cells to a man typing response to a clueless comment which wants to see everything laid out nicely and every part covered 100% because thats how it should be.
You cannot point out exact steps how we evolved till now yet here we are. "We don't know" is a perfectly fine answer even if it somehow triggers you. Universe is not arranged around such folks, universe doesn't care about some tantrums, universe just is, in ways we still don't fully understand and thats fine.
pfdietz 15 hours ago [-]
I expect people to not make declarations about things we don't know. But OoL conversations are filled with bullshit that our knowledge can't support. We see that here in the comments.
ceejayoz 14 hours ago [-]
> I expect people to not make declarations about things we don't know.
Who, specifically, is doing this in this thread? People are very clearly discussing hypotheses, possibilities/probabilities, and outstanding questions. No one's claiming "here's the answer".
alphasm 22 hours ago [-]
Is there a reason why the alternative idea of closed autocatalytic sets from Stuart Kauffman doesn't get nearly as much attention or discussion as the RNA origin hypothesis?
Ever since I first learned about it, it seems to me a much more likely origin of life hypothesis, as it doesn't require something to catalyze itself, which causes inevitable problems with mutation causing loss of catalytic efficiency.
Also, it is not incompatible with RNA being one of the early building blocks. It just doesn't require RNA to be where everything started.
Selkirk 9 hours ago [-]
To me the Closure of Constraints theory sounds the most promising, which is based partly from Kauffman. Life is very complex and interconnected. So any "this was first" theory has issues explaining complexity. Was it replication (RNA?) or cell walls or metabolism? Closure of constraints gives a path forward where everything evolves together and nothing complicated has to be first (except "closure"). What was first? All of the key functions were equally "first", but in simpler forms and provided by the environment not the organism. So we don't need a complicated self replicating molecule, replication is provided by the environment, not the closure being replicated. Slowly over time, more and more functionality shifts from environment to the closure.
Neb_OoL 10 hours ago [-]
Autocatalysis is essentially the goal of an RNA world right - we want an RNA that can make more RNA using RNA - autocatalysis. The problem with vague autocatalytic sets is they are very hard to find and if not also coupled to information storage their utility is limited. An innovation in a catalytic set is lost when conditions change - which coded information (RNA) does not suffer from!
cowlevel 20 hours ago [-]
You need evolution to have life. Why is mutation a deal-breaker?
jacquesm 20 hours ago [-]
> You need evolution to have life.
I don't think you can say this with certainty. It is assumed that life and evolution go hand-in-hand from the beginning but it is not proven to be the case.
cowlevel 7 hours ago [-]
If life didn't evolve it would have to have been intelligently designed...
usrnm 18 hours ago [-]
How exactly can it be proven? Even if we create life from scratch and see it evolve, it won't be a definitive proof
jacquesm 17 hours ago [-]
It could be proven if there was a record found of something that predated the currently known fossilized bits from really long ago that would give a hint about how life at that stage was put together. This is highly unlikely to happen.
cwmoore 16 hours ago [-]
“ Holliger’s team looked for catalytic activity in small RNAs (between 20 and 40 nucleotides in length), allowing for small changes in length in each cycle of mutation. They found a 45-nucleotide molecule that they christened QT45 (“quite tiny”) that could seize another RNA strand and copy it. “In principle it can copy any sequence,” Holliger said.”
MarceliusK 18 hours ago [-]
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torcete 18 hours ago [-]
> There’s scarcely any corner of Earth in which life hasn’t gained a foothold[..]
About that, not that long ago I was entertaining the idea of what environments can be completely devoid of life. I was thinking about examples like a volcano Cauldron, a nuclear reactor or the insides of a particle accelerator.
joshuahedlund 15 hours ago [-]
If you expand the bounds beyond Earth there are a lot of environments completely devoid of life…
The hardest part of the transition from prebiotic chemistry (assembling the building blocks) to an 'RNA World' is doing so in a way that can support RNA copying. As others have shown the chance of finding one replicator is low - so you need supporting RNA copying chemistry at a pretty substantial level to help that happen.
This is where the hard part of the field is currently: finding chemistry that can support accurate RNA copying that is also both sufficiently high yielding and also compatible with these reactions being inside protocells (fatty acids for example). An RNA genome only really has value when it can be selfish and keep any innovations it makes to itself inside a protocell!
I work in Origins Research - if you have questions please ask and ill try to answer with the current opinions of the field!
durianizok 22 hours ago [-]
For a long time, since I learned about how evolution works at the gene level, I’ve been bedazzled by sharks. Here is a configuration of genes which has reached such a sweet spot in the eyes of evolution that it has cruised mostly uncharged (modulo the shrinking due to change in oxygen composition) for hundreds of millions of years. Then I learned about the code of RNA (credit to Deutsch I think in his treatment of evolution in Fabric or maybe it was Beginning, I don’t recall) and my mind was blown! The actual knowledge encoded in the RNA sequence—†not the physical stuff; but the precise coded sequence—required for replication is actually quite ubiquitous across species and unchanged on timescales vastly larger than I had previously fathomed, mountains look like sand castles and sharks are brand new in the eyes of the code of RNA. This is only an analogy; but it felt like how Unix works: RNA is like the tiny kernel which has spread everywhere due to being tiny and good enough to solve the problem and therefore difficult to replace. Anyways, this is only a day dream since I’m not really in the weeds; but I wonder if you can correct any of my misconceptions. Like: RNA is like code for DNA replication, is it sort of like low-level machinery for life? Has the precise RNA code survived a really long time and it’s sort of like an old operating system which just keeps humming in the background? And it is older than sharks right? Any other cool stuff to recommend pursuing for someone like me who really loves evolution; but is just a layperson?
†one note about my em dashes: I am a real person who thinks evolution AND em dashes are cool and for a total aside: it’s such a bummer people think I’m a bot just because I like tinkering w/ f* punctuation marks.
Neb_OoL 10 hours ago [-]
Yeah this is an interesting way to think about. In modern biology DNA still acts as long term data storage with RNA acting as a mostly transient species that while essential is slightly more disposable. However, we think that RNA probably satisfied both roles at the origin of life which simplifies many problems including the need for simultaneous synthesis of RNA and DNA building blocks, the segregated polymerization of RNA and DNA and any cross talk between them.
We have a lot of conserved RNA sequences because it has done a good enough job since LUCA (Last Universal Common Ancestor - 4.2 billion years ago!) and its been trapped epistatically ever since! Things like the ribosome (an RNA based machine that makes all our proteins) for example is very conserved across all domains of life from us to sharks and trees and bacteria!
I would recommend reading the primary literature and asking AI to help you fill in context that authors leave out!
> actual knowledge encoded in the RNA sequence—†not the physical stuff; but the precise coded sequence—required for replication is actually quite ubiquitous across species and unchanged on timescales
There is a chance that before 'LUCA' there were many dead ends and we ended up on the lucky branch by definition, and we don't actually know much about what happened before then so there is some possibility that what you are seeing there is the single largest example of 'survivorship bias'.
Neb_OoL 10 hours ago [-]
We have started to call the first life FUCA (First universal common ancestor)! There must have been much evolution before LUCA as we know that it had a complex metabolism and a sophisticated DNA genome - far more advanced than and RNA based life could probably achieve!
jacquesm 9 hours ago [-]
Yes, untold generations in between those two. What I'm wondering though: if we had a nice sample of 'FUCA' in a petri dish, would we even recognize it as life?
Teever 3 hours ago [-]
Yes, I often think about that scenario. It's interesting to think about it in a sort of like alternate history sort of way like 'what if Wang computer survived' or 'Xerox had commericalized Parc instead of giving the keys to the kingdom Apple'
It may just be that the life that ended up thriving on Earth isn't objectively the best for the environment but it just happens to be what won out by being at the right place at the right time and the better chemistry or body plan was at the wrong place at the wrong time and got hit by a meteor or some massive gas burst from the interior of the earth that wiped them out.
In that context it's neat to think about alternate biochemical systems that could be available to us provided that we can figure them out and that would have tremendous economic potential.
chistev 22 hours ago [-]
Dinosaurs were the same.
MarceliusK 18 hours ago [-]
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Taek 23 hours ago [-]
Does the current SOTA believe that it's most likely that life originated on Earth? I know there are some theories that at least one of the critical building blocks was delivered via asteroid or other extra-terrestrial process.
M95D 20 hours ago [-]
But that doesn't answer the origin of life. Even if it came from outer space, it must have an origin somewhere. Currently, the science is focusing on the possibility that life originated here because the problem does not become easier to solve by considering another planet's environment.
Most people think that is the case yes but we have n=1 data points right? We are mostly in the business of learning the physical processes that create life like phenomena and not perfectly recreating how life arose on this planet - which seems unsolvable to any degree of satisfaction!
PS most asteroids that hit earth hit with such an angle and speed that pretty much nothing survives! When you read articles about finding building blocks of life on steroids it doesn't matter as they wont survive impact with a planet - its mostly just interesting that the chemistry is general enough to work in space and on earth!
torcete 17 hours ago [-]
When I read about self-replicating RNA I always think about the equivalent in the protein world, the prions. One can make many parallelisms with these scary proteins, responsible of the Creutzfeldt-Jakob disease.
Of course, the are too many limitations for evolving into some more complex, but they can self-replicate and they can infect other organisms. If we could give them an oceanic soup of PrPC and enough time, who knows?
anonymous_sorry 17 hours ago [-]
Prion "replication" seems rather different from self-replicating RNA.
Isn't the building block that a prion requires to create a copy of itself essentially a chemically almost-identical protein that is just folded differently?
How about an alternative analogy of the prion folding pattern spreading through chemically-similar molecules like a meme through a population of similarly conditioned brains?
torcete 15 hours ago [-]
Yes, I agree and that is why I mentioned that there are limitations. It really depends how one interprets "replication" and that the ingredients needed to self-propagate are to be considered valid building blocks for the beginning of life or not. As far as I know, RNA would use nucleotides and prions similar already existing complex proteins. It seems that the RNA hypothesis is more plausible. However, I just found out that there's some that actually believe that life started with prions and not RNA since proteins are more stable. Although
I like your analogy memes and prions need an already existing condition and then twist them into something else. If we are allowed to enter the philosophical domain, it's like the devil's work twisting the mind of the righteous or the Sith turning the force-sensitive beings :-)
Sorry, I went off the rails.
MarceliusK 18 hours ago [-]
I think the biggest unresolved question isn't whether RNA can replicate itself, but how you get from occasional replication to a self-sustaining system
zmgsabst 1 days ago [-]
I don’t understand the objections:
Most mutations are negative dead-ends, not unlikely DNA now where most pregnancies spontaneously abort due to errors. But life has many, many chances — especially at the molecular scale. So what’s the actual problem?
Similarly, if you have a soup of 10-15 nucleotide sequences, what are the odds actually that they’d link into larger segments?
Let’s suppose that density is a million times lower than blood, so you have one picogram per gram of water. There are 10^24 grams of water on Earth’s surface and 10 base pairs weighs 10^-20 grams, giving us approximately 10^32 segments of that length.
Feel free to play with my numbers, but I’m supposed to believe that with ~10^30 pieces, we can’t have ten of them form the right sequence?
red75prime 1 days ago [-]
> what’s the actual problem?
A combinatorial explosion. To have mutations you need to have replication first. If a smallest viable self-replicator is, say, 100 nucleotides long, and there's not many other such replicators of the same length, the improbability of its spontaneous formation (~4^-100) dwarfs any amount of material available on Earth.
The researchers have found QT45 replicator. But it replicates other RNA strands, that is it needs another replicator nearby to replicate itself, which brings the probability down to 4^-90 range.
And it's not clear from the article whether QT45 is a viable replicator. That is whether it is stable enough and replicates other RNA strands correctly enough to sustain exponential growth instead of petering out due to filling its surroundings with broken copies that don't perform replication before decaying itself.
xyzzy_plugh 24 hours ago [-]
I doubt a replicator came out of thin air. It seems more likely, at least to me, that we started with constructors, that created primitive sequences.
Imagine you have molecules that can form spontaneously, like gliders in Conway's Game of Life. You may have several different molecules that are capable of helping to create one another -- an autocatalytic set.
Eventually this could result in more complex chains, and eventually a self replicating molecule can arise.
Imagine slamming a bunch of gliders together to make a machine that replicates more gliders. It's possible! Not likely, but there are so many variables that can influence the environment substantially. It's not like there was a giant homogeneous soup. Parts from over here and over there would form differently and when they meet, amazing things can happen.
In the Game of Life, this spontaneous event is extremely unlikely, astronomically unlikely.
Unlike Game of Life, the real world has a few advantages that improve performance. For one, it's less fragile. Bonds are much stronger and collisions don't cause everything to break. Another advantage is that bonds are attractive: molecules can rotate and turn to snap together strongly. Gliders just explode violently. And finally, the real world is very dense. We're talking trillions of molecules mixing around millions of times per second per microdroplet. Compound that with a few hundred million years... it certainly doesn't feel as surprising as you might expect.
If there were a highly advanced alien race watching earth over a long period of time, it might be interesting, but not unexpected, that suddenly an Eiffel tower springs forth from the surface of the planet, erected by intelligent organisms.
kannanvijayan 24 hours ago [-]
The simple combinatorial explosion criticism feels reductive to me. It's exceedingly unlikely that a single "self-replicating RNA molecule" formed independently by chance and then propagated.
Let's say that you have some RNA soup with some ribozymes some of which weakly encourage some reaction involving other RNA molecules. The occurrence of a cycle of reinforcing reactions might be sufficient to build a crude evolutionary ratchet.
In fact the "cycle of reactions" perspective feels a bit more robust to me since it allows for the proto-replication process to take place over a longer period of time and over larger areas.
red75prime 23 hours ago [-]
Yeah, it's more probable a priory, but it still can be false. For example, such reaction chains might not lead to a sufficiently probable increase in complexity.
Core wars (1984) strongly favored short replicators, so at least in some possible universes complexity growth is not a given.
9991 1 days ago [-]
Life didn't have to start on Earth. It could have started on any one of an unbounded number of worlds. It's only in retrospect that this world seems special.
What's the probability of spontaneous formation across an infinite universe?
red75prime 1 days ago [-]
In an infinite universe even events with probability 0 can happen[1], but it's hard to find this explanation satisfactory. Any hypothesis that raises probability of abiogenesis to make it likely to happen at least in the observable universe looks more satisfactory than "but it could have happened anyway in an infinite universe despite being totally improbable."
If you mean panspermia specifically in respect to earth it's a lot more bounded in space and time to the parts that were close enough to interact with earth, but if not then yes there is probably anything that can be represented by atoms out there somewhere or other.
13 hours ago [-]
Neb_OoL 23 hours ago [-]
Your numbers are fine - but RNA is fragile; making one copy of something really rare will not be able to do anything as it will not last long enough to meaningfully contribute.
Interestingly we now are thinking about ways to use mutations in other ways, youve spent a lot of energy making these polymers, so it would be a shame to waste that right? We think that they can be used to assemble larger functional pieces as mutations are mostly deterministic meaning you'll get the same kinds of errors - so why not put them to use!
jacquesm 20 hours ago [-]
> but RNA is fragile
Early on that may have been a feature though, isn't it?
What strikes me as the most interesting thing about life is that almost immediately (on geological time scales) after Earth had developed an environment where life in theory could exist it came to be. That suggests strongly that the mechanism to do so was relatively simple. Then again, the Earth was a vast laboratory and it only has to happen once.
aside: you have the most interesting job!
Neb_OoL 10 hours ago [-]
Fragility may indeed have been a feature as separating 2 RNA strands when they get even quite long (69 nt -> melting temp ~100 C) is almost impossible on the Early Earth and perhaps you just have to fragment long RNA to be able to reuse it. What we havent figured out yet is how to do that recyling - the 2,3cyclic phosphate that RNA terminates with when hydrolyzing is very stable!
Yes it is remarkable how seemingly quickly life started however most productive chemical reactions occurr on the order of hours and days so a couple of million years is still a long time to explore chemical space!
jeef_berky 23 hours ago [-]
I also don't understand. Adding billions of years to your numbers probably makes it an even better point.
"Life's first molecule." Take your favorite quantum field theory and consider how it draws a line between a molecule and not a molecule. Consider how it draws a line between life or not. That'd be cool. Consider that it doesn't give a shit who did what first.
"given any word, there's no such thing"
lakt42t 1 days ago [-]
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singularity2001 19 hours ago [-]
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metchio 19 hours ago [-]
this kind of speculation only moves the needle forward, the main question remains: even if life on earth is part of an intelligent design experiment, how does life in this intelligent entity world began in a first place?
ceejayoz 14 hours ago [-]
Short version: "Who designs the designer?"
Rendered at 04:22:06 GMT+0000 (Coordinated Universal Time) with Vercel.
RNA gets made from pure, energy-rich molecules that themselves are quite complex. This soup of pure monomers isn't something that just arises naturally in the absence of life. Prebiotic chemistry produces a random soup of a wide variety of chemical species, with the abundance of each declining exponentially in its size and complexity.
You see this issue all the time in origin of life claims. For example, that recent result of "all the bases of RNA and DNA were found on this asteroid by the Japanese" tended to slide over the fact that they were there at extremely low levels, mixed with huge numbers of other non-biological organic molecules.
Trying to replicate RNA in a mix of random crap will just give you polymers of crap, if it gave you anything at all.
OoL needs an idea that will work in a soup of junk, not in massively artificial pure soup on a lab bench.
The research does something like this. You run an experiment and show some chemicals are present in low concentration. You say "ah ha, we've shown one step". Those chemicals are now taken off the shelf in high concentration and used in the next experiment, which makes slightly more complex chemicals in low concentration. Repeat this multiple times until done.
Lampooning this, the fictional OoL researcher in the book also demonstrates that monkeys can type out "To be or not to be, that is the question" on a typewriter. He arranges the typewriter with an automatic right margin and lets them type away until he gets a line starting with "T". First letter demonstrated! Now he rereun the experiment, but now with paper the "T" in the first column and margins set to the second column. Repeat this with subsequent letters until the entire sentence is produced. Of course, the monkeys didn't type the sentence, the researcher did.
Getting around the exponential complexity barrier is the whole goddamn point, it's not something to just wave away with a "we don't know" comment.
IMO some fundamentally new idea is needed for OoL.
But the researcher is performing the selection process for the purposes of the experiment, to speed things up. Evolution functions via natural selection. That's what makes it different from the pure random chance processes.
And "it's not exponential, therefore it's not possible" is?
The general problem here is that handwaving ignores the issue I raised, and those making OoL theories have to address these issues, not require skeptics to disprove their handwaving. Requiring the skeptical to disprove such things is classic crank behavior.
They certainly warrant discussion and investigation.
Handwaving away the possibly infinite nature of the available experimentation space and the anthropic principle is the same failing you're widely accusing others of.
You, elsewhere in the thread: "I expect people to not make declarations about things we don't know."
How do we know that? When did we confirm what came before the Big Bang? How do we know this isn't the sixty trillionth iteration of a 15 billion year process that only just now resulted in life on one of untold trillions of planets to pay notice to it?
Please don't say death implies life. By death you should infer removal from category a la RNA depolymerization, or lipid membrane lysis.
Of course I don't know what the pre-life entities are. But they were surely selected for.
what does accurate mean
> there's no plausible way proposed that can occur without life already existing
Why do you say that. RNA can replicate by templating. obviously replicators came to exist from non replicators. and life from nonlife. what claim are you making? that that isn't selection because you have a definition of selection that excludes that process?
Life has very complicated mechanisms for ensuring very accurate replication of DNA, but of course these mechanisms would not have been available at OoL.
Biochemist and OoL enthusiast here. This is very not true. Evolution happens in even the simplest complex systems. It's very likely a process of matter.
Look up the work of Dr Michael Levin. He shares on YouTube many of his convos with leading thinkers. He's quite prolific lately.
So I strongly dispute your assertion there.
Similarly, when creating single-crystal metal parts (turbine blades) a handful of growing crystals is put through a maze, with only one surviving to continue out into the bulk of the part. One is selected and thrives, the others stop growing after being out-competed for resources/space. It looks and sounds like life but... crystals are a special case imho.
Not the best analogy.
Lets say you are looking for 'any sentence'. What if you never get the T, you get a G. The sentence is what your looking for, not a specific one. It could be another sentence, but a sentence none the less. Then you can ask, how many typewriters did it take to get the first letter, then how many for the next, (not infinite). Now how likely would this sentence appear in nature if a bunch of chimps were let loose in a typewriter store.
Its funny you are using this as an argument against. When it is actually is the process in Assembly Theory.
"Life As No One Knows It: The Physics of Life's Emergence ". Assembly Theory: A centerpiece of the book is Assembly Theory, which Walker co-developed (with Lee Cronin and collaborators). Assembly theory measures the "assembly index" of an object—quantifying the minimum number of steps and building blocks required to construct it.
You cannot point out exact steps how we evolved till now yet here we are. "We don't know" is a perfectly fine answer even if it somehow triggers you. Universe is not arranged around such folks, universe doesn't care about some tantrums, universe just is, in ways we still don't fully understand and thats fine.
Who, specifically, is doing this in this thread? People are very clearly discussing hypotheses, possibilities/probabilities, and outstanding questions. No one's claiming "here's the answer".
Ever since I first learned about it, it seems to me a much more likely origin of life hypothesis, as it doesn't require something to catalyze itself, which causes inevitable problems with mutation causing loss of catalytic efficiency.
Also, it is not incompatible with RNA being one of the early building blocks. It just doesn't require RNA to be where everything started.
I don't think you can say this with certainty. It is assumed that life and evolution go hand-in-hand from the beginning but it is not proven to be the case.
About that, not that long ago I was entertaining the idea of what environments can be completely devoid of life. I was thinking about examples like a volcano Cauldron, a nuclear reactor or the insides of a particle accelerator.
This is where the hard part of the field is currently: finding chemistry that can support accurate RNA copying that is also both sufficiently high yielding and also compatible with these reactions being inside protocells (fatty acids for example). An RNA genome only really has value when it can be selfish and keep any innovations it makes to itself inside a protocell!
I work in Origins Research - if you have questions please ask and ill try to answer with the current opinions of the field!
†one note about my em dashes: I am a real person who thinks evolution AND em dashes are cool and for a total aside: it’s such a bummer people think I’m a bot just because I like tinkering w/ f* punctuation marks.
We have a lot of conserved RNA sequences because it has done a good enough job since LUCA (Last Universal Common Ancestor - 4.2 billion years ago!) and its been trapped epistatically ever since! Things like the ribosome (an RNA based machine that makes all our proteins) for example is very conserved across all domains of life from us to sharks and trees and bacteria!
I would recommend reading the primary literature and asking AI to help you fill in context that authors leave out!
Evolutionary theory: https://www.nature.com/articles/227520a0
Origins research: https://www.nature.com/articles/35053176 https://www.science.org/doi/abs/10.1126/sciadv.aax3419
Good source that develops on this?
https://en.wikipedia.org/wiki/Ribosomal_RNA#Sequence_conserv...
It may just be that the life that ended up thriving on Earth isn't objectively the best for the environment but it just happens to be what won out by being at the right place at the right time and the better chemistry or body plan was at the wrong place at the wrong time and got hit by a meteor or some massive gas burst from the interior of the earth that wiped them out.
In that context it's neat to think about alternate biochemical systems that could be available to us provided that we can figure them out and that would have tremendous economic potential.
PS most asteroids that hit earth hit with such an angle and speed that pretty much nothing survives! When you read articles about finding building blocks of life on steroids it doesn't matter as they wont survive impact with a planet - its mostly just interesting that the chemistry is general enough to work in space and on earth!
Of course, the are too many limitations for evolving into some more complex, but they can self-replicate and they can infect other organisms. If we could give them an oceanic soup of PrPC and enough time, who knows?
Isn't the building block that a prion requires to create a copy of itself essentially a chemically almost-identical protein that is just folded differently?
How about an alternative analogy of the prion folding pattern spreading through chemically-similar molecules like a meme through a population of similarly conditioned brains?
https://www.youtube.com/watch?v=K0K-pMPFzGY
I like your analogy memes and prions need an already existing condition and then twist them into something else. If we are allowed to enter the philosophical domain, it's like the devil's work twisting the mind of the righteous or the Sith turning the force-sensitive beings :-)
Sorry, I went off the rails.
Most mutations are negative dead-ends, not unlikely DNA now where most pregnancies spontaneously abort due to errors. But life has many, many chances — especially at the molecular scale. So what’s the actual problem?
Similarly, if you have a soup of 10-15 nucleotide sequences, what are the odds actually that they’d link into larger segments?
Let’s suppose that density is a million times lower than blood, so you have one picogram per gram of water. There are 10^24 grams of water on Earth’s surface and 10 base pairs weighs 10^-20 grams, giving us approximately 10^32 segments of that length.
Feel free to play with my numbers, but I’m supposed to believe that with ~10^30 pieces, we can’t have ten of them form the right sequence?
A combinatorial explosion. To have mutations you need to have replication first. If a smallest viable self-replicator is, say, 100 nucleotides long, and there's not many other such replicators of the same length, the improbability of its spontaneous formation (~4^-100) dwarfs any amount of material available on Earth.
The researchers have found QT45 replicator. But it replicates other RNA strands, that is it needs another replicator nearby to replicate itself, which brings the probability down to 4^-90 range.
And it's not clear from the article whether QT45 is a viable replicator. That is whether it is stable enough and replicates other RNA strands correctly enough to sustain exponential growth instead of petering out due to filling its surroundings with broken copies that don't perform replication before decaying itself.
Imagine you have molecules that can form spontaneously, like gliders in Conway's Game of Life. You may have several different molecules that are capable of helping to create one another -- an autocatalytic set.
Eventually this could result in more complex chains, and eventually a self replicating molecule can arise.
Imagine slamming a bunch of gliders together to make a machine that replicates more gliders. It's possible! Not likely, but there are so many variables that can influence the environment substantially. It's not like there was a giant homogeneous soup. Parts from over here and over there would form differently and when they meet, amazing things can happen.
In the Game of Life, this spontaneous event is extremely unlikely, astronomically unlikely.
Unlike Game of Life, the real world has a few advantages that improve performance. For one, it's less fragile. Bonds are much stronger and collisions don't cause everything to break. Another advantage is that bonds are attractive: molecules can rotate and turn to snap together strongly. Gliders just explode violently. And finally, the real world is very dense. We're talking trillions of molecules mixing around millions of times per second per microdroplet. Compound that with a few hundred million years... it certainly doesn't feel as surprising as you might expect.
If there were a highly advanced alien race watching earth over a long period of time, it might be interesting, but not unexpected, that suddenly an Eiffel tower springs forth from the surface of the planet, erected by intelligent organisms.
Let's say that you have some RNA soup with some ribozymes some of which weakly encourage some reaction involving other RNA molecules. The occurrence of a cycle of reinforcing reactions might be sufficient to build a crude evolutionary ratchet.
In fact the "cycle of reactions" perspective feels a bit more robust to me since it allows for the proto-replication process to take place over a longer period of time and over larger areas.
Core wars (1984) strongly favored short replicators, so at least in some possible universes complexity growth is not a given.
What's the probability of spontaneous formation across an infinite universe?
[1]https://en.wikipedia.org/wiki/Almost_surely
Interestingly we now are thinking about ways to use mutations in other ways, youve spent a lot of energy making these polymers, so it would be a shame to waste that right? We think that they can be used to assemble larger functional pieces as mutations are mostly deterministic meaning you'll get the same kinds of errors - so why not put them to use!
Early on that may have been a feature though, isn't it?
What strikes me as the most interesting thing about life is that almost immediately (on geological time scales) after Earth had developed an environment where life in theory could exist it came to be. That suggests strongly that the mechanism to do so was relatively simple. Then again, the Earth was a vast laboratory and it only has to happen once.
aside: you have the most interesting job!
Yes it is remarkable how seemingly quickly life started however most productive chemical reactions occurr on the order of hours and days so a couple of million years is still a long time to explore chemical space!
"Life's first molecule." Take your favorite quantum field theory and consider how it draws a line between a molecule and not a molecule. Consider how it draws a line between life or not. That'd be cool. Consider that it doesn't give a shit who did what first.
"given any word, there's no such thing"