Only tangentially related, but because they are so amazing here are a few videos that illustrate the process of transcription (creating mRNA from DNA) and translation (creating a protein from mRNA).
The common complaint with these videos is that everything is more complex. One thing that isn't evident is that these specific videos (built mostly by Drew Barry) actually model a lot of other molecules to create a more realistic physical environment with brownian motion and whatnot. Then the irrelevant molecules are simply made transparent in the rendering.
Obviously it's still much much more complex (eg the constant stream of ATP used to drive many of these operations is not illustrated).
There are these and many more great illustrations/explanations at WEHImovies on youtube
these videos are better than most, but are still bad in one sense, they really fail to capture just how random walk the movements are. For example, in the first video the script says "a mediator protein complex arrives" as if it is directed there by some sort of orchestration agent. It's not. It's more like "a mediator protein complex drunkenly stumbles in and connects after a few thousand misses". Of course it's hard to make that into a captivating video.
As I said, the WEHI movies are pretty good in that at least they add some random walk into the motions. There was a harvard artist-professor (can't remember who) who literally made videos with exact parabolic and helical trajectories and then was crowing about how beautiful the biological system is.
mongol 14 hours ago [-]
Thank you for clarifying what I have wondered. In most of these videos it appears as if the molecules have an intent and act on a plan. It makes me think "how do they know to do that".
throwawaymaths 10 hours ago [-]
OK to extra clarify there are techniques to make the drunken walk more efficient. You might compartmentalize interacting bits into a smaller compartment which scales with the cube of the compartment ratio. You might anchor the participants in an interaction to a membrane, which turns a ~>6 dof search into a ~>3 dof (x, y, rotation) search. You might anchor the participants to a filament or DNA which makes the search a ~> 1 dof search.
jcims 10 hours ago [-]
If you just listen to the narrative of most of these videos, there is all sorts of agency referenced in the vocabulary. When in reality it's like a bunch of tiny magnets of indescribably complex geometry bashed around in a box until an eyeball pops out.
divbzero 1 days ago [-]
> “The findings suggest that life’s eventual homochirality might not be a result of chemical determinism but could have emerged through later evolutionary pressures.”
Homochirality resulting from chemical determinism would be the more surprising result to me.
The straightforward explanation is that random perturbations early in the evolution of life broke symmetry and led to homochirality of all descendent life, similar to how random perturbations early in the life of the universe broke symmetry and led to our world being made of particles instead of antiparticles.
JackFr 19 hours ago [-]
>The straightforward explanation is that random perturbations early in the evolution of life broke symmetry and led to homochirality of all descendent life, similar to how random perturbations early in the life of the universe broke symmetry and led to our world being made of particles instead of antiparticles.
Straightforward (and plausible) are not the same as true. Random perturbations are a parsimonious explanation, but a deeply unsatisfying one. With respect to matter vs antimatter, my understanding is that this remains an open research question in physics.
throwawaymaths 10 hours ago [-]
The universe has no obligation to be satisfying to you or me. Seeking explanations that feel good at the expense of parsimony is veiled numerology, not science.
roughly 10 hours ago [-]
Given how much of the rest of the chemical processes of life seem to proceed fairly straightforwardly from the rules of chemical structure and energy requirements for various reactions, I’d almost expect the opposite - that there’s some structure or reaction core to life that’s marginally cheaper or easier with left chirality that caused the divide, and the rest is history.
andrewflnr 1 days ago [-]
It's still not obvious how they could be separated at all by pre-biotic processes. You need to go from (in principle anyway) a pretty well-mixed 50-50 mixture to basically only lefties. I believe this is still one of the bigger problems for abiogenesis, and frankly I think you're being too glib about the antimatter problem too. I expect we're eventually going to find out about specific mechanisms that cause those.
anlsh 1 days ago [-]
A very plausible explanation is that the separation was biotic
andrewflnr 18 hours ago [-]
There's a bootstrapping problem, though.
andrewflnr 2 days ago [-]
While all right-handed amino acids would presumably be fine, do we have any idea whether mixed chirality would work? I suspect no, since they presumably have different folding behavior but might be tricky to distinguish chemically during the protein synthesis process, making e.g. different codons for left and right-handed amino acids infeasible to implement. I'd love to hear from a biologist whether any of that is correct.
gilleain 2 days ago [-]
So a couple of things i remember from back in the old structural bioinformatics days...
Firstly, there are naturally occurring mixed-chirality (alternating) peptides. They are usually circular iirc.
Secondly, no you can't really have larger proteins with both left and right (ignoring glycine). They would not fold into nice helix/sheet strucures and likely just be random coil.
For cells to have mixed populations of all-L and all-R proteins would mean doubling up all the machinery for creating them.
One theory that I thought was reasonable for why there's a monochiral world is that once the arbitrary choice is made (L or R) then that gets 'locked in' by all the machinery around that choice. As in, L 'won'.
phkahler 20 hours ago [-]
>> One theory that I thought was reasonable for why there's a monochiral world is that once the arbitrary choice is made (L or R) then that gets 'locked in' by all the machinery around that choice. As in, L 'won'.
This seems obviously true to me. Mixed doesn't work, so as molecules and systems of molecules started replicating one chirality won out. It's just chance and there's nothing magical about the chirality "chosen" by the process.
brnaftr361 18 hours ago [-]
My initial hypothesis is that there's something present in the early stages of life that has a higher energy state making it unsustainable for use in a certain conformation and so it was nearly immediately selected out.
E.g. a ring structure whose substituents are affected by steric hindrance in the left-handed scheme.
And the path of least resistance was just to adapt and build around it. Once that precedence was set everything became as such. I expect in the earliest stages of life this would have been an immense factor as metabolism was not nearly as sophisticated as we know it today.
And this selective process may have ocurred well before anything we have observed/modeled, and may well be erased. Which is to say I agree, but with the caveat that it was a substrate-dependent mechanism which selected the downstream components rather than random chance.
gilleain 18 hours ago [-]
Seems quite possible, but the difficulty would be why one enantiomer is less favourable than the other.
Totally agree that it is hard to test these things experimentally, or through historical analysis of structural remnants. I understand there have been efforts to model at a system level these ancient metabolic networks but ... then how do you experimentally validate these models?
gus_massa 1 days ago [-]
It's a good question, but:
> might be tricky to distinguish chemically during the protein synthesis process
No, amino acids are bind to tRNA by special proteins that have handiness and can easily distinguish the L and R version. Most proteins can only operate on one handiness of the target molecule.
> making e.g. different codons for left and right-handed amino acids infeasible to implement
No, there are 64 codons and we are using them to map only 20 amino acids and a stop signal. So there is a lot of duplication. Some bacterias have one or two more amino acids or a small tweak in one or two of the conversion table, so it's possible to add more stuff there if necessary.
My guess is that mixing L and R amino acid would break ribosomes. The ribosomes read the mRNA and pick the correct tRNA and connect the amino acid that the tRNA has. I guess that the part that makes the connection assumes the correct handiness of the amino acids.
Going down the rabbit hole I found https://en.wikipedia.org/wiki/Nonribosomal_peptide that explains that some peptides (that are like small proteins) are formed by special enzymes instead of ribosomes, and some of them have D-amino acids or other weirs stuff.
andrewflnr 1 days ago [-]
> No, amino acids are bind to tRNA by special proteins that have handiness and can easily distinguish the L and R version. Most proteins can only operate on one handiness of the target molecule.
Ah, neat. That was the step where I worried about coding being infeasible, too, coding for R amino acids wouldn't do any good if you couldn't distinguish them. I did know there was plenty of room in the encoding scheme.
fredgrott 2 days ago [-]
fun fact some left handed amino acids are poisonous to most mammals
ngneer 6 hours ago [-]
Can someone please explain the big mystery in simple terms? The article sure doesn't. Why does RNA being ambi-valent deepen the mystery? As others have noted, it could have been a toss up early on that persisted. If a coin comes up heads, no one is looking to explain why the coin "favors" heads or is "predisposed" to come out heads. Neither is true. The coin just came up heads. Is the mystery why homochirality persisted?
throwawaymaths 2 days ago [-]
What is the mystery? Perhaps one handedness was just first by chance and won because it self replicated the other handedness away by consuming it as food.
griffzhowl 2 days ago [-]
Well, that's the question isn't it? Is it just a frozen accident, or is there some nonarbitrary reason for the left-handed molecules to be favoured?
throwawaymaths 1 days ago [-]
Sure but that might be an unknowable problem. What if the difference in likelihood were 60/40.
You could go down all sorts of rabbit holes and none of them would truly be falsifiable unless you observed an enantiomeric lifeform on some distant planet.
madaxe_again 2 days ago [-]
Perhaps aliens eat right handed life, but left handed life is poison to them.
Seriously. It would be a pretty good selector, and said “alien” need be no more than a snippet of RNA - and it would be entirely gone from earth now, eliminated by us sinister life forms.
The only evidence would be the ubiquitous absence of R-entantiomers in life.
I think I might be lifting from Asimov - The Left Hand of the Electron.
Terr_ 1 days ago [-]
That kinda kicks the can down the road though, because we are faced with almost the same set of questions except about the hypothetical alien life.
throwawaymaths 1 days ago [-]
(Comsuming enantiomers and pooping out metabolic fragments in its native chirality)
alganet 1 days ago [-]
That assumption is even more mysterious.
Why one specific handedness "won"? What caused the other one to be food? How can we be sure it was by chance?
Lots of questions.
throwawaymaths 15 hours ago [-]
> Why one specific handedness "won"?
Place two competitors at the origin on the number line. On any given turn they walk either to the left or to the right, with exactly 50% odds of each. First competitor to +100 wins.
> What caused the other one to be food?
Basic chemistry.
> How can we be sure it was by chance?
We can't. If the odds are sufficiently close, we probably can't be sure it wasn't chance, either. If we go to space and find a planet with life with the other handedness, it was probably chance.
alganet 14 hours ago [-]
I have so many questions.
How do you know the evolutionary model of these early organisms? How do you know that a competition had taken place?
If you can't know if it is by chance of not, why hypothesize it?
throwawaymaths 7 hours ago [-]
Well we don't truly know. A full analysis of the best prebiotic chemistry hypotheses can't fit in an HN thread so if you want your questions answered you should consider studying organic chemistry, biochemistry, and then going to chemistry grad school.
Suffice it to say all of the best models are reasonably plausible, and like everything in chemistry operates on the principle of chance molecular motions.
alganet 7 hours ago [-]
You said there was no mystery. I was under the impression that you knew and had a very simple explanation that could be referenced to.
When I think of "chance molecular motions", I don't immediatelly jump to "well, that leads to biological evolution". I don't understand how you connected the two ideas. I mean, there's a path there, but a whole theory is missing. I searched for it but couldn't find it.
I really don't know organic chemistry, but I'm fascinated by the mystery. You don't need to write here, just give me some good links or references I can read that support your case.
So if more than one amino acid chirality could have emerged, why did we get the one we got and not several?
From the paper in the parent comment:
> Achiral linearly polarized light interacts with chiral objects and their enantiomers differently. An interesting example is a light-driven motor. Linearly polarized light can rotate a gammadion-shaped gold structure embedded in a silica block as a motor.
Imagine you were using some kind of optical tweezers to manipulate chiral molecules. I wonder if there's a reason that such a device would work better if you had a sample which had the same chirality. Suppose so...
If one of your samples made its way to Earth and replicated... Well that would be a reason for earth proteins to be biased in one direction, despite the laws of physics not prescribing such a bias.
I suppose there’s no reason you couldn’t use circularly polarised light to achieve the effect you’re talking about.
nativeit 2 days ago [-]
> “We are analyzing OSIRIS-REx samples for the chirality (handedness) of individual amino acids, and in the future, samples from Mars will also be tested in laboratories for evidence of life including ribozymes and proteins,” said Dworkin.
I clicked the hyperlink for OSIRIS-REx samples, and it didn’t contain any information about what kinds of materials were found, but this statement suggests amino acids were collected from OSIRIS-REx—did I miss this news? Were there proteins found on an asteroid?
nativeit 2 days ago [-]
Indeed I did miss that, what an incredible find, I can’t believe this never broke through into my routine news feeds!
How suggestive is this of life elsewhere in the universe?
staplung 1 days ago [-]
On it's own, probably not that much. We know that amino acids can form in interstellar space and have in fact observed clouds of them in star-forming regions[1]. Finding them on a non-planetary object in our own solar system is certainly very cool but we already knew they existed in this neck of the woods. ;-)
>Oftentimes both the left- and right-handed versions of, for example, an amino acid, were found in equal amounts—exactly what might be expected. But in many cases, one or more organic molecule was found with an excess of one hand, sometimes a very large excess. In each of those cases, and in every meteorite studied so far by other researchers in the field, the molecule in excess was the left-handed amino acid that is found exclusively in life on Earth.
polishdude20 2 days ago [-]
Could these asteroids be from when the moon was created?
skykooler 1 days ago [-]
The moon was created far before life formed - the best estimates put its formation about 4.5 billion years ago, while life didn't form until 3.7 billion years ago. So any complex molecules from that process would not be present on asteroids of lunar origin.
nkrisc 20 hours ago [-]
A better way to put it might be that current lineages of life on Earth arose after the moon was created - the assumption being any life that arose before the moon was created would not have survived a fully molten Earth.
gcanyon 1 days ago [-]
For a really brilliant visualization of the time scale, I can't recommend this Kurzgesagt video highly enough. It's an animation of the condition of the entire history of the Earth, at 1.5 million years per second of video. https://www.youtube.com/watch?v=S7TUe5w6RHo
If there is locomotion due to a dynamic between handed molecules and, say, helically polarized fields; is such handedness a survival selector for life in deep space?
Are chiral molecules more likely to land on earth?
> Is there a way to get to get the molecular propeller effect and thereby molecular locomotion, with molecules that contain sugar and a rotating field or a rotating molecule within a field?
westurner 2 days ago [-]
Though, a new and plausible terrestrial origin of life hypothesis:
> A terrestrial life origin hypothesis: gamma radiation mutated methane (CH4) into Glycine (the G in ACGT) and then DNA and RNA.
mannyv 1 days ago [-]
Isn't it the same reason that the right hand rule works?
hydrolox 1 days ago [-]
Right hand rule is just an arbitrary decision defining counterclockwise to be positive, but I guess it's true that it could be "less arbitrary" if certain things are more counterclockwise than clockwise
hoc 1 days ago [-]
Waiting for the
Creator -> left-handed
conclusion...
theodorejb 1 days ago [-]
What evidence would it take for more scientists to recognize that perhaps life didn't evolve through some evolutionary process, but was intentionally created? It seems like few ever consider that their starting presupposition may be wrong.
IAmGraydon 1 days ago [-]
I know I really shouldn’t take this bait, but…no one has proof either way. That said, we have a massive amount of scientific evidence that shows it could have naturally evolved and zero evidence that something created us. Finding something that we don’t understand doesn’t mean we have evidence of creation. Ancient civilizations believed that rain came from the gods because they were unaware of how weather combines with the phases of matter and creates atmospheric condensation.
That being the state of things at the moment, I lean towards the evidence. Also, this is a scientific oriented discussion forum, so you must expect that many people here are going to disagree with you. Could you be correct? Sure, but we just don’t have reason to believe that at this point.
myflash13 14 hours ago [-]
> we have a massive amount of scientific evidence that shows it could have naturally evolved
Define “naturally”. However you define it, that is precisely what some people call “divinely”.
luqtas 18 hours ago [-]
yeah but what if the creators of life orchestrate the condensation? /s
the amount of text (considering this is a hardware/software community) i read here defending psychoanalys/acupuncture & the likes as well some opinions on ecology/nutrition makes me pretty agnostic of scientific orientation from users... we are (most of the times) just a bunch of laypersons often only reading titles & conclusions of most papers we read
andrewflnr 1 days ago [-]
Enough evidence to overcome the enormous pile of evidence that life evolved over billions of years. Often literal piles, in the case of geology, but there's a lot of different kinds of interlocking evidence that suggest a pretty clear picture, even if a few puzzle pieces are still missing.
Unless you're thinking of panspermia, in which case most any hard evidence would do. But that doesn't really sound like your thing.
- a former creationist
myflash13 14 hours ago [-]
It’s not just that a few puzzle pieces are missing. Abiogenesis is entirely unproven and nobody has a clue how it works and nobody can demonstrate experimentally any of the hypothetical mechanisms.
andrewflnr 12 hours ago [-]
No, that actually is still "a few puzzle" pieces compared to the entirety of the geologic record, relatively clear progressions of life forms over time that broadly line up with physical and genetic taxonomy. There are some gaps, yeah, but enough to clearly imply that the overall picture is correct.
By contrast, the epistemological picture for creationism is a trash fire. It requires an ever increasing amount of special pleading to explain all the other evidence. And you don't get to complain that "abiogenesis is entirely unproven", about an event that necessarily happened long before recorded history under entirely different conditions, unless your own theory can stand up to a higher standard of evidence. Which it can't. Speaking, again, as someone who grew up under creationism and had to lever myself out of it piece by piece of evidence.
(Oh, and if you think "nobody has a clue" how abiogenesis worked, you're out of date. Try reading about the work of Nick Lane and Jeremy England, IIRC.)
myflash13 12 hours ago [-]
You don’t get to claim that an “event happened long before recorded history under entirely different conditions”, because anyone can make that claim. That’s not science, not evidence. I can claim the same thing for intentional creation, for example.
If anybody has a clue how abiogenesis works, then they should prove it by doing it. Manufacture some bacteria out of sand. Claiming “it takes a trillion years of primordial soup” is an another wild unsubstantiated claim that anyone can make. That’s the same thing as saying: ”wait a few centuries and God will show you.”
By the way, evidence for natural evolution does not contradict creationism, because God could’ve created some things through a process of natural evolution — it’s a false dichotomy to assume that evidence for evolution is evidence against creationism; it’s not. Whether or not natural evolution happened is tangential to the claim of creationism.
The epistemological picture for creation is quite sound. Fermi’s paradox is clear evidence we’re special. Logically, we can define
God as existence itself, and the existence of “anything” is proof of Him. It simply can’t be any other way. The fact that we have intentionality is also proof that intentionality “exists” and that in turn is proof that Existence is intentional.
andrewflnr 11 hours ago [-]
Still ignoring geology, huh? The long timeline and different conditions at the start of life are clearly readable in the geology. For instance, the banded iron formations.
> If anybody has a clue how abiogenesis works, then they should prove it by doing it. Manufacture some bacteria out of sand.
Naturally the only way to demonstrate "having a clue" is to jump straight to accomplishing your favorite chemically implausible but snappily-phrased challenge, that requires full understanding of life itself as well as advanced experimental manufacturing facilities. This is definitely how science works, and there's no way you would turn around and claim that because it was an orchestrated experiment under controlled conditions, it doesn't actually prove anything about the early earth. Anyway, give them time, they're working on it.
> Claiming “it takes a trillion years of primordial soup” is an another wild unsubstantiated claim that anyone can make. That’s the same thing as saying: ”wait a few centuries and God will show you.”
Good thing no one is actually claiming that then, huh? You should really catch up on the science. You sound like you stopped reading ICR tracts in the 90s.
Moving on, I notice you're already jumping into the classic "the creator could have created things in a way consistent with evolution" brand of special pleading. This is 3/4 of the way to admitting that the evidence clearly favors evolution.
Your last paragraph is too divorced from actual logic and evidence to be worth dissecting. Suffice to say, you fallacy is non sequitur.
scrapcode 1 days ago [-]
I certainly am trending that way as I grow older. As I've recently started to re-dive into Christian theology, the fine-tuning argument seems more and more interesting, and it's pretty difficult to find "good" secular arguments against it.
roncesvalles 15 hours ago [-]
Aside from the mountain of actual evidence, just to build a philosophical intuition against fine-tuning - you need to appreciate the enormous scale of trial and error at play.
- The Earth seems like the perfect planet but looking out into the sky there are trillions of planets that aren't perfect at all.
- Most likely the universe also appears "perfect" for the same reason - there must be a graveyard of universes where the parameters just didn't work out for life.
- Evolution is much the same - many mutations occur all the time, most are fixed by cellular machinery, most that aren't are deleterious, but once in a while a helpful mutation emerges. Take a moment to understand the timescale involved. Don't just handwave away 3.8 billion years as some number - feel it, starting at 1 year and stepping up each order of magnitude. You will realize that a million years is essentially "forever ago", and we had 3800 of those to get here. Consider how many species exist that aren't civilizational sentient intelligence.
beltsazar 13 hours ago [-]
Fine tuning for the earth might be able to be explained away most easily, like you said. Fine tuning for the universe, though...
Firstly, we have zero evidence for multiverse. Some scientists even argue that the idea is untestable and unfalsifiable.
When you said:
> there must be a graveyard of universes where the parameters just didn't work out for life
You just committed inverse gambler's fallacy. It's like:
> You wake up with amnesia, with no clue as to how you got where you are. In front of you is a monkey bashing away on a typewriter, writing perfect English. This clearly requires explanation. You might think: “Maybe I’m dreaming … maybe this is a trained monkey … maybe it’s a robot.” What you would not think is “There must be lots of other monkeys around here, mostly writing nonsense.” You wouldn’t think this because what needs explaining is why this monkey—the only one you’ve actually observed—is writing English, and postulating other monkeys doesn’t explain what this monkey is doing.
You’re misunderstanding the point about fine-tuning entirely. It doesn’t matter how many billions of years it took, if some of the parameters of fundamental physics were slightly different, even trillions of years would’ve resulted in nothing.
Terr_ 1 days ago [-]
I don't know, I think the arthropic principle is still going really strong: It's like this because if it wasn't we would be asking different questions or not around to ask at all.
It's hard to consider something "so improbable that it must have been God" when we look out at a universe so incomprehensibly bigger that the real question becomes why we haven't evidence of it happening more.
philsnow 14 hours ago [-]
I know it was just a typo but "arthropic principle" sounds like something from A Deepness in the Sky
As it's often used, the anthropic principle is fatally flawed.
It often starts with an argument between a creationist (could also be an advocate of intelligent design, but I'll just call them the creationist) and an evolutionist. The creationist says, look, the origin of life by purely naturalistic means is ridiculously improbable (and therefore it's reasonable to consider the possibility that God did it). They trot out some generally-accepted scientific principle, do a back-of-the-envelope calculation, and come up with a number that is, in fact, ridiculously improbable.
The evolutionist responds with the anthropic principle - if no life had arisen in this universe, we would not be here arguing about how life arose. This is clearly logically correct. It is also completely irrelevant.
The creationist didn't argue that life couldn't have arisen in this universe. They argued that it could not have arisen by purely naturalistic means. They're arguing about how, not about whether. The creationist might answer: "Yes, I agree that if life had not arisen in this universe, either by creation or by naturalistic processes, then we would not be here having this conversation. But the question is, which way did life begin?" The anthropic principle doesn't address that issue whatsoever.
It doesn't address that issue unless you add an assumption - that life had to begin by purely naturalistic means, that is, that the probability of creation is precisely zero. Then the anthropic principle is relevant, but then there's a new issue, that of begging the question.
I suspect that this assumption is present on the side of everyone on the evolution side that pulls out the anthropic principle in an argument with a creationist, but I have never heard it explicitly stated. I'm not even sure the evolutionist realizes they're making an assumption - it's so ingrained in their world view that they can't think that the alternative might be possible.
I grant you that the universe is huge and the evidence available is small. But that can turn into an "evolution of the gaps" argument quite easily, so I'm not sure you want to seriously use it.
beltsazar 12 hours ago [-]
The anthropic principle is ridiculous. Suppose that, against all odds, you survive the worst plane crash in history. Then you ask NTSB what caused the crash and why you survived. They answer:
"Nonsense! You wouldn’t have asked the questions if you hadn't survived."
Questions stand alone, regardless of whether someone or something exists to ask them.
cowl 18 hours ago [-]
Anthropic principle is the most useless of all and it's used to avoid explanation instead of trying to find one.
Imagine Newton answering to why objects fall with "because if they did not we would be asking different questions"... what a great advance for humanity /s
recursive 17 hours ago [-]
I don't think your fictional Newton is really invoking the anthropic principle.
In all the zillions of galaxies that exist, the ones where intelligent life developed are more likely to be observed by intelligent life. Therefore, intelligent life can't make any arguments based on probability that intelligent life developed, because our observation of the phenomenon is not independent.
And maybe some people have used it to avoid explanation, but it also doesn't really conflict with any effort to explain either.
cowl 16 hours ago [-]
more likely or less likely has nothing to do with observation indipendece.
I flip a weighted coin and it's tails 99% of the time, it's the coin that is weighted it has nothing to do with me.
The same thing with the parameters of the universe, the fact that life is present on Earth and not on Mercury (to take an exterme example) is not dependent on the observer being intelligent or even alive. even a non intelligent "aparatus" can detect it. it may not "know" to clasify it as life/not life but it can detect the difference.
Saying that we wouldn't be here to ask the question is not an answer to anything because we are here and we need to understand how and why.
recursive 13 hours ago [-]
I think we are vigorously agreeing with each other.
Terr_ 16 hours ago [-]
You're confusing two different kinds of question:
1. "What the mechanisms or rules that explain or seem to govern this observable phenomenon?"
2. "The rules behind our own existence seem unique or low-probability, can I use our N=1 sample to safely assume we are inherently special and/or the existence of a god?"
cowl 16 hours ago [-]
Those are the same kind of question. take god or the "special" out of the second one and you will see that is only that part that most react against. Noone reacts with the antropic principle to the Fermi's paradox, noone even reacted with it to the simulation hypotheses that in my view is for all intents and purposes the religious one. but only because it did not contain, by Name, the God, it is acceptable.
photonthug 1 days ago [-]
For better or worse the standard of evidence for almost everything is more like “smoking gun” than “I found a bullet”. In some cases this is bad, in others it is good. Just consider all the criminal matters where the crime is only a crime if you can additionally demonstrate intent, which is strange right, since it doesn’t change outcomes / injuries at all. Since sufficiently ancient guns won’t even be smoking anymore this will be problematic for creationists even if they are correct, so I think we’d need a new kind of burning bush.
bediger4000 13 hours ago [-]
If we decided that life had been deliberately created, we could get some insight into the god or gods who did it. What kind of a diety creates parasites, for example. What kind of pantheon creates a universe with Goedel's Incompleteness built in, or the difficulty of the Busy Beaver game?
Those are fun questions.
latentsea 9 hours ago [-]
The real question, according to HN, is why did god create Kubernetes and have every developer glom onto it when only a handful of companies in the universe truly need it?
Edit: the follow up question is "why isn't the universe just a shell script?"
Rendered at 10:25:45 GMT+0000 (UTC) with Wasmer Edge.
https://www.youtube.com/watch?v=SMtWvDbfHLo
https://www.youtube.com/watch?v=TfYf_rPWUdY
The common complaint with these videos is that everything is more complex. One thing that isn't evident is that these specific videos (built mostly by Drew Barry) actually model a lot of other molecules to create a more realistic physical environment with brownian motion and whatnot. Then the irrelevant molecules are simply made transparent in the rendering.
Obviously it's still much much more complex (eg the constant stream of ATP used to drive many of these operations is not illustrated).
There are these and many more great illustrations/explanations at WEHImovies on youtube
https://www.youtube.com/@WEHImovies
https://library.ucsd.edu/dc/object/bb90484996
As I said, the WEHI movies are pretty good in that at least they add some random walk into the motions. There was a harvard artist-professor (can't remember who) who literally made videos with exact parabolic and helical trajectories and then was crowing about how beautiful the biological system is.
Homochirality resulting from chemical determinism would be the more surprising result to me.
The straightforward explanation is that random perturbations early in the evolution of life broke symmetry and led to homochirality of all descendent life, similar to how random perturbations early in the life of the universe broke symmetry and led to our world being made of particles instead of antiparticles.
Straightforward (and plausible) are not the same as true. Random perturbations are a parsimonious explanation, but a deeply unsatisfying one. With respect to matter vs antimatter, my understanding is that this remains an open research question in physics.
Firstly, there are naturally occurring mixed-chirality (alternating) peptides. They are usually circular iirc.
Secondly, no you can't really have larger proteins with both left and right (ignoring glycine). They would not fold into nice helix/sheet strucures and likely just be random coil.
For cells to have mixed populations of all-L and all-R proteins would mean doubling up all the machinery for creating them.
One theory that I thought was reasonable for why there's a monochiral world is that once the arbitrary choice is made (L or R) then that gets 'locked in' by all the machinery around that choice. As in, L 'won'.
This seems obviously true to me. Mixed doesn't work, so as molecules and systems of molecules started replicating one chirality won out. It's just chance and there's nothing magical about the chirality "chosen" by the process.
E.g. a ring structure whose substituents are affected by steric hindrance in the left-handed scheme.
And the path of least resistance was just to adapt and build around it. Once that precedence was set everything became as such. I expect in the earliest stages of life this would have been an immense factor as metabolism was not nearly as sophisticated as we know it today.
And this selective process may have ocurred well before anything we have observed/modeled, and may well be erased. Which is to say I agree, but with the caveat that it was a substrate-dependent mechanism which selected the downstream components rather than random chance.
Totally agree that it is hard to test these things experimentally, or through historical analysis of structural remnants. I understand there have been efforts to model at a system level these ancient metabolic networks but ... then how do you experimentally validate these models?
> might be tricky to distinguish chemically during the protein synthesis process
No, amino acids are bind to tRNA by special proteins that have handiness and can easily distinguish the L and R version. Most proteins can only operate on one handiness of the target molecule.
> making e.g. different codons for left and right-handed amino acids infeasible to implement
No, there are 64 codons and we are using them to map only 20 amino acids and a stop signal. So there is a lot of duplication. Some bacterias have one or two more amino acids or a small tweak in one or two of the conversion table, so it's possible to add more stuff there if necessary.
My guess is that mixing L and R amino acid would break ribosomes. The ribosomes read the mRNA and pick the correct tRNA and connect the amino acid that the tRNA has. I guess that the part that makes the connection assumes the correct handiness of the amino acids.
Going down the rabbit hole I found https://en.wikipedia.org/wiki/Nonribosomal_peptide that explains that some peptides (that are like small proteins) are formed by special enzymes instead of ribosomes, and some of them have D-amino acids or other weirs stuff.
Ah, neat. That was the step where I worried about coding being infeasible, too, coding for R amino acids wouldn't do any good if you couldn't distinguish them. I did know there was plenty of room in the encoding scheme.
You could go down all sorts of rabbit holes and none of them would truly be falsifiable unless you observed an enantiomeric lifeform on some distant planet.
Seriously. It would be a pretty good selector, and said “alien” need be no more than a snippet of RNA - and it would be entirely gone from earth now, eliminated by us sinister life forms.
The only evidence would be the ubiquitous absence of R-entantiomers in life.
I think I might be lifting from Asimov - The Left Hand of the Electron.
Why one specific handedness "won"? What caused the other one to be food? How can we be sure it was by chance?
Lots of questions.
Place two competitors at the origin on the number line. On any given turn they walk either to the left or to the right, with exactly 50% odds of each. First competitor to +100 wins.
> What caused the other one to be food?
Basic chemistry.
> How can we be sure it was by chance?
We can't. If the odds are sufficiently close, we probably can't be sure it wasn't chance, either. If we go to space and find a planet with life with the other handedness, it was probably chance.
How do you know the evolutionary model of these early organisms? How do you know that a competition had taken place?
If you can't know if it is by chance of not, why hypothesize it?
Suffice it to say all of the best models are reasonably plausible, and like everything in chemistry operates on the principle of chance molecular motions.
When I think of "chance molecular motions", I don't immediatelly jump to "well, that leads to biological evolution". I don't understand how you connected the two ideas. I mean, there's a path there, but a whole theory is missing. I searched for it but couldn't find it.
I really don't know organic chemistry, but I'm fascinated by the mystery. You don't need to write here, just give me some good links or references I can read that support your case.
It asserts:
> L-proteins need not emerge from a D-RNA World
So if more than one amino acid chirality could have emerged, why did we get the one we got and not several?
From the paper in the parent comment:
> Achiral linearly polarized light interacts with chiral objects and their enantiomers differently. An interesting example is a light-driven motor. Linearly polarized light can rotate a gammadion-shaped gold structure embedded in a silica block as a motor.
Imagine you were using some kind of optical tweezers to manipulate chiral molecules. I wonder if there's a reason that such a device would work better if you had a sample which had the same chirality. Suppose so...
If one of your samples made its way to Earth and replicated... Well that would be a reason for earth proteins to be biased in one direction, despite the laws of physics not prescribing such a bias.
I suppose there’s no reason you couldn’t use circularly polarised light to achieve the effect you’re talking about.
I clicked the hyperlink for OSIRIS-REx samples, and it didn’t contain any information about what kinds of materials were found, but this statement suggests amino acids were collected from OSIRIS-REx—did I miss this news? Were there proteins found on an asteroid?
https://www.hou.usra.edu/meetings/lpsc2024/pdf/1219.pdf
1: https://www.space.com/amino-acid-tryptophan-perseus-molecula...
https://en.m.wikipedia.org/wiki/Ice-nine
More explanation here.
>Oftentimes both the left- and right-handed versions of, for example, an amino acid, were found in equal amounts—exactly what might be expected. But in many cases, one or more organic molecule was found with an excess of one hand, sometimes a very large excess. In each of those cases, and in every meteorite studied so far by other researchers in the field, the molecule in excess was the left-handed amino acid that is found exclusively in life on Earth.
not in the panspermia theory
> ScholarlyArticle: "Amplification of electromagnetic fields by a rotating body" (2024) https://www.nature.com/articles/s41467-024-49689-w
>> Could this be used as an engine of some kind?
> What about helical polarization?
If there is locomotion due to a dynamic between handed molecules and, say, helically polarized fields; is such handedness a survival selector for life in deep space?
Are chiral molecules more likely to land on earth?
> "Chiral Colloidal Molecules And Observation of The Propeller Effect" https://pmc.ncbi.nlm.nih.gov/articles/PMC3856768/
> Sugar molecules are asymmetrical / handed, per 3blue1brown and Steve Mould. /? https://www.google.com/search?q=Sugar+molecules+are+asymmetr... https://www.google.com/search?q=Sugar+molecules+are+asymmetr...
> Is there a way to get to get the molecular propeller effect and thereby molecular locomotion, with molecules that contain sugar and a rotating field or a rotating molecule within a field?
Methane + Gamma radiation => Guanine && Earth thunderstorms => Gamma Radiation https://news.ycombinator.com/item?id=42131762#42157208 :
> A terrestrial life origin hypothesis: gamma radiation mutated methane (CH4) into Glycine (the G in ACGT) and then DNA and RNA.
Creator -> left-handed
conclusion...
That being the state of things at the moment, I lean towards the evidence. Also, this is a scientific oriented discussion forum, so you must expect that many people here are going to disagree with you. Could you be correct? Sure, but we just don’t have reason to believe that at this point.
Define “naturally”. However you define it, that is precisely what some people call “divinely”.
the amount of text (considering this is a hardware/software community) i read here defending psychoanalys/acupuncture & the likes as well some opinions on ecology/nutrition makes me pretty agnostic of scientific orientation from users... we are (most of the times) just a bunch of laypersons often only reading titles & conclusions of most papers we read
Unless you're thinking of panspermia, in which case most any hard evidence would do. But that doesn't really sound like your thing.
- a former creationist
By contrast, the epistemological picture for creationism is a trash fire. It requires an ever increasing amount of special pleading to explain all the other evidence. And you don't get to complain that "abiogenesis is entirely unproven", about an event that necessarily happened long before recorded history under entirely different conditions, unless your own theory can stand up to a higher standard of evidence. Which it can't. Speaking, again, as someone who grew up under creationism and had to lever myself out of it piece by piece of evidence.
(Oh, and if you think "nobody has a clue" how abiogenesis worked, you're out of date. Try reading about the work of Nick Lane and Jeremy England, IIRC.)
If anybody has a clue how abiogenesis works, then they should prove it by doing it. Manufacture some bacteria out of sand. Claiming “it takes a trillion years of primordial soup” is an another wild unsubstantiated claim that anyone can make. That’s the same thing as saying: ”wait a few centuries and God will show you.”
By the way, evidence for natural evolution does not contradict creationism, because God could’ve created some things through a process of natural evolution — it’s a false dichotomy to assume that evidence for evolution is evidence against creationism; it’s not. Whether or not natural evolution happened is tangential to the claim of creationism.
The epistemological picture for creation is quite sound. Fermi’s paradox is clear evidence we’re special. Logically, we can define God as existence itself, and the existence of “anything” is proof of Him. It simply can’t be any other way. The fact that we have intentionality is also proof that intentionality “exists” and that in turn is proof that Existence is intentional.
> If anybody has a clue how abiogenesis works, then they should prove it by doing it. Manufacture some bacteria out of sand.
Naturally the only way to demonstrate "having a clue" is to jump straight to accomplishing your favorite chemically implausible but snappily-phrased challenge, that requires full understanding of life itself as well as advanced experimental manufacturing facilities. This is definitely how science works, and there's no way you would turn around and claim that because it was an orchestrated experiment under controlled conditions, it doesn't actually prove anything about the early earth. Anyway, give them time, they're working on it.
> Claiming “it takes a trillion years of primordial soup” is an another wild unsubstantiated claim that anyone can make. That’s the same thing as saying: ”wait a few centuries and God will show you.”
Good thing no one is actually claiming that then, huh? You should really catch up on the science. You sound like you stopped reading ICR tracts in the 90s.
Moving on, I notice you're already jumping into the classic "the creator could have created things in a way consistent with evolution" brand of special pleading. This is 3/4 of the way to admitting that the evidence clearly favors evolution.
Your last paragraph is too divorced from actual logic and evidence to be worth dissecting. Suffice to say, you fallacy is non sequitur.
- The Earth seems like the perfect planet but looking out into the sky there are trillions of planets that aren't perfect at all.
- Most likely the universe also appears "perfect" for the same reason - there must be a graveyard of universes where the parameters just didn't work out for life.
- Evolution is much the same - many mutations occur all the time, most are fixed by cellular machinery, most that aren't are deleterious, but once in a while a helpful mutation emerges. Take a moment to understand the timescale involved. Don't just handwave away 3.8 billion years as some number - feel it, starting at 1 year and stepping up each order of magnitude. You will realize that a million years is essentially "forever ago", and we had 3800 of those to get here. Consider how many species exist that aren't civilizational sentient intelligence.
Firstly, we have zero evidence for multiverse. Some scientists even argue that the idea is untestable and unfalsifiable.
When you said:
> there must be a graveyard of universes where the parameters just didn't work out for life
You just committed inverse gambler's fallacy. It's like:
> You wake up with amnesia, with no clue as to how you got where you are. In front of you is a monkey bashing away on a typewriter, writing perfect English. This clearly requires explanation. You might think: “Maybe I’m dreaming … maybe this is a trained monkey … maybe it’s a robot.” What you would not think is “There must be lots of other monkeys around here, mostly writing nonsense.” You wouldn’t think this because what needs explaining is why this monkey—the only one you’ve actually observed—is writing English, and postulating other monkeys doesn’t explain what this monkey is doing.
— https://www.scientificamerican.com/article/our-improbable-ex...
It's hard to consider something "so improbable that it must have been God" when we look out at a universe so incomprehensibly bigger that the real question becomes why we haven't evidence of it happening more.
It often starts with an argument between a creationist (could also be an advocate of intelligent design, but I'll just call them the creationist) and an evolutionist. The creationist says, look, the origin of life by purely naturalistic means is ridiculously improbable (and therefore it's reasonable to consider the possibility that God did it). They trot out some generally-accepted scientific principle, do a back-of-the-envelope calculation, and come up with a number that is, in fact, ridiculously improbable.
The evolutionist responds with the anthropic principle - if no life had arisen in this universe, we would not be here arguing about how life arose. This is clearly logically correct. It is also completely irrelevant.
The creationist didn't argue that life couldn't have arisen in this universe. They argued that it could not have arisen by purely naturalistic means. They're arguing about how, not about whether. The creationist might answer: "Yes, I agree that if life had not arisen in this universe, either by creation or by naturalistic processes, then we would not be here having this conversation. But the question is, which way did life begin?" The anthropic principle doesn't address that issue whatsoever.
It doesn't address that issue unless you add an assumption - that life had to begin by purely naturalistic means, that is, that the probability of creation is precisely zero. Then the anthropic principle is relevant, but then there's a new issue, that of begging the question.
I suspect that this assumption is present on the side of everyone on the evolution side that pulls out the anthropic principle in an argument with a creationist, but I have never heard it explicitly stated. I'm not even sure the evolutionist realizes they're making an assumption - it's so ingrained in their world view that they can't think that the alternative might be possible.
I grant you that the universe is huge and the evidence available is small. But that can turn into an "evolution of the gaps" argument quite easily, so I'm not sure you want to seriously use it.
"Nonsense! You wouldn’t have asked the questions if you hadn't survived."
Questions stand alone, regardless of whether someone or something exists to ask them.
In all the zillions of galaxies that exist, the ones where intelligent life developed are more likely to be observed by intelligent life. Therefore, intelligent life can't make any arguments based on probability that intelligent life developed, because our observation of the phenomenon is not independent.
And maybe some people have used it to avoid explanation, but it also doesn't really conflict with any effort to explain either.
Saying that we wouldn't be here to ask the question is not an answer to anything because we are here and we need to understand how and why.
1. "What the mechanisms or rules that explain or seem to govern this observable phenomenon?"
2. "The rules behind our own existence seem unique or low-probability, can I use our N=1 sample to safely assume we are inherently special and/or the existence of a god?"
Those are fun questions.
Edit: the follow up question is "why isn't the universe just a shell script?"