[HN Gopher] Scientists discover new "origins of life" chemical r...
___________________________________________________________________
Scientists discover new "origins of life" chemical reactions
Author : geox
Score : 86 points
Date : 2022-07-29 14:09 UTC (8 hours ago)
(HTM) web link (www.scripps.edu)
(TXT) w3m dump (www.scripps.edu)
| wrycoder wrote:
| Keto acids[0] are a primary precursor.
|
| [0] https://en.m.wikipedia.org/wiki/Keto_acid
| gilleain wrote:
| What looks like the main (?) reaction (from the graphic on
| https://www.nature.com/articles/s41557-022-00999-w) :
|
| R-C(=O)COO -- (CO2, "NH3", CN-, H2O) --> R-Hydantoin (?) -->
| aminated amino acid --> alfa-amino acids
|
| where R = {H, CH3, CH2COO}.
|
| (ps : Apologies to any chemists reading this...)
| gilleain wrote:
| Oh ok, looks like this is called the
| https://en.wikipedia.org/wiki/Bucherer%E2%80%93Bergs_reactio...
| - mentioned in the abstract.
| yuan43 wrote:
| > After their success using cyanide to drive other chemical
| reactions, Krishnamurthy and his colleagues suspected that
| cyanide, even without enzymes, might also help turn a-keto acids
| into amino acids. Because they knew nitrogen would be required in
| some form, they added ammonia--a form of nitrogen that would have
| been present on the early earth. Then, through trial and error,
| they discovered a third key ingredient: carbon dioxide. With this
| mixture, they quickly started seeing amino acids form.
|
| This is all well and good, interesting chemistry even.
|
| However, a-keto acids are not the kinds of things just laying
| around. These are reactive species and so would interact in a
| variety of ways with environmental nuclophiles, oxidants, and
| other stuff.
|
| The article doesn't link to the study in question, which is
| unfortunate and inexcusable. It does link to a study on a
| different system earlier this year.
|
| Origins of life research has been plagued with efforts that
| front-load the problem in various ways. For example, how do we
| make proteins abiotically? How do we make sugars abiotically?
|
| Load up a flask with all the amino acids you want. Zap it with
| whatever you want in terms of energy. At the end of it you won't
| have much but a mess.
|
| There seem to be fundamental principles we're missing that go
| beyond reaction pathways. Not many people are working on that
| problem. It's extremely risky for both PIs and students, and
| almost impossible to fund.
| rlkjlk3 wrote:
| vkazanov wrote:
| I am not sure Discovery Institute is a reliable source.
| Wikipedia says that it's a non-profit created with a specific
| goal of promoting certain non-scientific ideas:
| https://en.m.wikipedia.org/wiki/Discovery_Institute
| trasz wrote:
| We can call it by name: a fringe theory spread by Christian
| extremists, a particular kind that's deranged even by most
| Christian extremist standards. Same disgusting human trash
| like the ones behind abortion ban.
| dang wrote:
| Religious flamewar is not ok here, so please don't take HN
| threads further into it.
|
| https://news.ycombinator.com/newsguidelines.html
|
| Edit: We've had to ask you this kind of thing many times
| before - here's a small sample:
|
| https://news.ycombinator.com/item?id=29916978 (Jan 2022)
|
| https://news.ycombinator.com/item?id=29687837 (Dec 2021)
|
| https://news.ycombinator.com/item?id=23578435 (June 2020)
|
| https://news.ycombinator.com/item?id=23578417 (June 2020)
|
| Edit 2: It looks like you've been using HN primarily for
| political and ideological (and religious) battle. We ban
| accounts that do this. It's not what this site is for, and
| it destroys what it is for.
|
| If you keep this up, we're going to have to ban you, so
| please review
| https://news.ycombinator.com/newsguidelines.html and use HN
| as intended. That means for _curious_ conversation on
| topics of intellectual interest.
| trasz wrote:
| It's not a flamewar: I can easily provide sources that
| support all my claims, and I'm following your advice
| about "two comments at most, three is too much". It also
| doesn't have much to do with religion as such, as even
| Catholic Church is officially against the "intelligent
| design" idea.
|
| Now, what the above is, it is pointing out an organized
| disinformation campaign, which uses religious beliefs for
| its purposes. I'm pretty sure that fighting propaganda
| used to be part of the hacker ethos. And we're not going
| to solve this problem by pretending this particular
| propaganda somehow deserves anyone's respect or that it
| is any different from others. Would you be opposed to
| comments against antivax theories? If not - can you
| explain where do you see the difference?
|
| Also, I can't help but notice that while comments that
| are openly racist are widely tolerated here, pointing it
| out is an "ideological battle" - as evidenced by your own
| examples above. Don't you find it a bit... curious? I'm
| pretty sure I'm not the only person frustrated with it.
| dang wrote:
| Flamewar has nothing to do with providing sources or not.
| Nor does it have to do with being right or not. It's easy
| to be both right and replete with sources and still be
| doing the name-calling, snark, aggression, and other
| things that the HN guidelines ask commenters to avoid.
|
| It has to do with inflaming discussion to the point where
| people angrily hurl talking points and attacks at each
| other. That's far removed from the curious conversation,
| respectful across differences, that we want here.
|
| This is not a difficult concept for anyone familiar with
| internet threads. Moreover, the ways that you've been
| breaking the site guidelines are not borderline cases.
| Please just fix this.
|
| Pointing fingers at the bad behavior of others doesn't
| seem relevant to this point. You've been breaking HN's
| rules badly for a long time now, and we've asked you to
| stop a lot. If you first fix this, and then have
| something to say about other people's bad behavior, or
| about moderation failures, I'd be happy to address it.
|
| By the way, you've also posted lots of good comments that
| are perfectly within the site guidelines. I appreciate
| that, and I definitely don't want to ban you.
| Unfortunately, bad comments do more damage than good
| comments add value; plus they add to existential risk
| (since the default fate of most internet forums is self-
| destruction, sooner or later). So we need to do something
| about the bad comments.
|
| https://news.ycombinator.com/newsguidelines.html
| beefok wrote:
| The Discovery Institute's only purpose[1] is to push
| creationism into public education under the guise of
| 'Intelligent Design'. Of course they never specify 'what' or
| 'who' the 'designer' is, but we all know what they are pushing.
|
| Their only way of providing 'evidence' for an Intelligent
| Designer is fallacious at best [2]. Like all creationists, they
| can only provide bad faith arguments of ignorance and the god
| of the gaps. They can't even differentiate between what is
| 'designed' and what is 'natural', what's worse, they think
| everything is designed in the first place.
|
| Let's say the modern synthesis of the theory of evolution is
| wrong, and the evidence put forth is wrong (160+ years of
| evidence.) If this were the case, neither creationism nor
| intelligent design is suddenly the alternative.
|
| Intelligent design does not have any scientific merit. It does
| not explain _anything_ about the abundance of evidence we
| actually have. It cannot make predictions, nor can it be
| falsified. It 's a worthless unscientific mess that should have
| been put to rest many times over by now.
|
| If there was ever evidence of 'design', that's evidence of
| 'design', not evidence of a designer. Before anything, you
| would first have to meet the burden of proof on the _designer_.
|
| [1] https://en.wikipedia.org/wiki/Wedge_strategy
|
| [2] https://www.americanprogress.org/article/the-flaws-in-
| intell...
| Calavar wrote:
| I have always felt that applying the label "origins of life"
| research on amino acid/nucleic acid synthesis is extremely
| misleading.
|
| An analogy would be writing an article about the natural
| abundance of silicon on beaches and calling it "how computers are
| made."
|
| We have a decent idea of how the first nucleic acids may have
| been synthesized, and we have a decent framework for how life
| evolved from protobiont to prokaryote to eukaryote to
| multicellular organisms. But there is an absolutely staggering
| gap between the synthesis of individual nucleotides and the
| synthesis of the first RNA replicase that we know nearly nothing
| about.
| TrapLord_Rhodo wrote:
| The whole point of the article was discussing how RNA isn't the
| orgin of life and we need to push our ideas back further.
|
| RNA-Peptide coevolution is the spontaneous immergence of
| 'replicating' matter. No one molecule in the system has all the
| requisites for life, but as a whole they do. (I.E.amino acids
| and nucleobases can transmit information, replicate, move and
| 'sense' about the world). Pushing this idea of self-replicating
| orgiins of life back may illuminate the issue. RNA generation
| doesn't have to be random, it can be selected for like any
| other evolutionary proceses.
|
| Finally, Listen to what you are saying... The rhetoric was much
| different 10 years ago.
|
| We have scientifically narrowed the limit of what we can't
| explain, and this very small gap in our knowledge is what's
| left. We are making progress in understandng the origins of
| life.
| Thorentis wrote:
| There is also a staggering gap between nucleic acids existing,
| and just random atoms existing. And then an even more
| staggering gap between atoms existing, and nothing existing.
| photochemsyn wrote:
| It's unlikely that RNA replicases ever existed in the absence
| of short amino acid polymers. The primordial ribosome might be
| the concept your looking for - an association between short RNA
| sequences and short amino acid sequences capable of self-
| replication via various RNA reactions and amino-catalyzed
| reactions.
|
| This may be the original article discussing this hypothesis:
|
| "The ribosome as a missing link in the evolution of life"
| (2015) Root-Bernstein & Root-Bernstein, J. Theoretical Biology
|
| https://sci-hub.se/10.1016/j.jtbi.2014.11.025
|
| > "Evolvable entities existing between self-replicating
| polymers and fully functional cells would presumably have many,
| though not all, of the functions of a cell, yet be
| significantly simpler in composition and organization. These
| entities would be able to self-organize and replicate
| themselves; store information and replicate that information;
| translate the information into the components necessary to
| produce their functional structures; capture metabolic
| components and energy; and transform these into useful
| biochemical networks. Norris and his colleagues have called
| functional forms of organization midway between macromolecules
| and cells "hyperstructures" (Norris et al., 2007). Such
| hyperstructures had to be instantiated as evolvable entities,
| meaning that their components would be subject to variation,
| replication and natural selection."
| gliptic wrote:
| If we truly didn't know how computers came about, it's
| certainly progress to figure out the silicon can come from
| sand.
|
| How is it not origins of life research to attack every step in
| the process?
| dieselgate wrote:
| Just a clarifying question but when you use "attack" do you
| mean from a "critically minded research focused lens" or a
| "skeptical" one?
| trasz wrote:
| Calavar wrote:
| It's progress, but the degree of progress is vastly oversold
| by the media, and sometimes even by academics. Kind of
| similar to those "amazing new semiconductor" articles that
| come out every 6 months.
| soco wrote:
| Maybe you mean the regular amazing new battery
| breakthrough?
| Calavar wrote:
| Adding to my previous comment:
|
| If a student asked "how did life originate?" a response
| about about nucleic acid synthesis would be a bit
| disingenuous, because that covers only very, very tiny
| fraction of the surface area of the problem. The more
| honest answer would be that there are so many large gaps in
| our knowledge that we truly don't know.
|
| To be clear, I'm not trying to cast skepticism on the whole
| of biology. There are other questions that we have much
| better answers to, like the evolutionary pathway from
| single cellular life to multicellular life. Or the
| evolutionary link between humans and great apes. But
| abiogenesis is not one of those questions.
| mannykannot wrote:
| > If a student asked "how did life originate?" a response
| about about nucleic acid synthesis would be a bit
| disingenuous...
|
| As the article title does not say or imply that the
| answer to this question has been found, let alone that it
| will be revealed in the article, this is at least beside
| the point.
|
| In attempting to brush aside gliptic's pertinent
| question, you have switched to a general (and somewhat
| subjective) claim that does not seem to hold up in this
| specific case.
| RosanaAnaDana wrote:
| Also, and imo fundamentally, it doesn't define a natural
| process of system where this reaction is
| thermodynamiccally favorable.
|
| That, imo, is far more important.
| marcosdumay wrote:
| > The more honest answer would be that there are so many
| large gaps in our knowledge that we truly don't know.
|
| Are the gaps really that large? We know that some
| configurations of nucleotids are enough to create a full
| metabolism, we know that they arrange at random, and we
| know how most of them appeared.
|
| Except for the few nucleotides that we don't know how
| they existed, we do know that if you have enough of them
| on enough places, some kind of life will appear. So looks
| like the open question here is how those molecules
| appeared.
| dathanb82 wrote:
| But RNA / DNA isn't sufficient for life, right? How are
| proteins synthesized from that string of nucleotides
| without ribosomes? And nucelotides randomly reshuffling
| certainly doesn't explain how ribosomes would be created.
|
| It's theorized that under the right conditions amino
| acids will bond to become proteins without needing the
| mediation of a ribosome. So it's certainly possible that
| with enough primordial soup you could get proteins. But
| that doesn't explain how the nucleotide string ends up
| getting treated as a reusable blueprint for proteins.
|
| That seems like a pretty big gap.
| marcosdumay wrote:
| Ribosomes are mostly RNA, and there is good evidence that
| they evolved from something that was purely RNA. The
| aminoacid transport and encoding mechanism is also
| basically composed of RNA, with some evidence that
| something like them would work without any of the protein
| parts.
|
| Also, people have created RNA-only self replicating
| mechanisms that could quite well appear at random, with
| extremely low odds. Life probably comes from some
| structure with higher odds that we don't know about, but
| that's not a huge gap.
| bobthechef wrote:
| sterlind wrote:
| I wish I recalled better, but I saw a hypothesis that
| centered around tRNA rather than the ribosome as the
| origin of replication. after all, the ribosome simply
| catalyzes the binding of tRNA to mRNA, and amino acid
| linkage.
|
| iirc the idea centered around the tRNA "code" having a
| pattern to it - one shaped by its binding affinity to
| part of the sequence that codes for the tRNA-
| aminoacyltransferase enzyme itself. I wish I remembered
| enough to find the reference.
|
| edit: ah! think I remembered. the hypothesis was that the
| codon sequence had some sort of binding affinity to the
| amino acid it codes for. that there's a relationship
| between them, suggesting a world where codons attracted
| amino acids to bind to them without an enzyme linking
| them.
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924937/
| RosanaAnaDana wrote:
| In the context of building computers and defining
| computation, silicon can be considered an afterthought.
|
| We already had adding machines and the philosophy necessary
| for digital logic.
|
| It may well be the case with the original system that
| initiated the process we call life. RNA (and by extension
| DNA) may have been a complete afterthought.
|
| I'm always disappointed when I see this research outside of a
| systems context. Like, sure we can show these things happen,
| but show me a thermodynamic systems, in place,where this can
| happen.
|
| In you metaphor about sand and beaches, this may be like
| taking some one to a dune field and saying 'see all this
| sand. That's where computers come from'.
| oneoff786 wrote:
| Is that really a staggering gap? The nucleotides jumble
| together until they randomly hit a config that leads to a
| pattern that leads to more of that config. We don't know what
| that path is exactly but we can be pretty sure it's the result
| of random mumbling through a series of random searches in an
| organic chemistry space.
|
| Computers don't arise randomly (without annoying semantic
| arguments).
| NateEag wrote:
| > Computers don't arise randomly (without annoying semantic
| arguments).
|
| If you believe the human brain's processes are computable,
| and you believe evolution is a random process, then you
| believe that computers arise randomly.
|
| Is that what you mean by "annoying semantic arguments"?
| oneoff786 wrote:
| Yes. That is an annoying semantic argument. The intended
| discussion is pretty clearly a purposefully manufactured
| device made of silicon and how understanding how that
| instantiates by watching silicon is not at all like
| watching how nucleotides arrange into rna.
|
| Discussions of what constitutes a computer in this context
| or whether an nth order effect of a "random" process are
| just distracting.
| jdthedisciple wrote:
| Are you saying you are certain that human DNA was not
| purposefully manufactured?
| oneoff786 wrote:
| Human DNA is a lonnnng way down below the timelines and
| processes we're talking about buddy.
| tengbretson wrote:
| > Computers don't arise randomly
|
| You are right. They don't.
| rmbyrro wrote:
| > we can be pretty sure it's the result of random mumbling
|
| If you throw construction materials up 1 quadrillion times,
| how many times can they randomly fall in the form of a house?
|
| My response is zero. Building a house is not a product of
| randomness, it's a product of intelligence and will.
|
| Life also can't be a product of randomness. There's some
| intelligence and will going on in nature's laws to make life
| happen.
| bglazer wrote:
| Are you arguing that there was some direct intervention
| during the origins of life? Like, an intelligent being
| stuck a probe into a chemical mixture and tipped it towards
| generating cells?
|
| Or, perhaps you're arguing that the rules of the universe
| were designed in a way that guaranteed that life would
| arise?
|
| Something else?
| rmbyrro wrote:
| More on line of the second thought, yes.
|
| To me, Universal laws aren't random. If they were, I'd
| expect them to change from time to time.
|
| These laws are immutable and inexorable. They respect,
| interact and cooperate perfectly with each other.
|
| How did they come to exist and be that way if not by
| intelligence and will?
|
| I have no idea how this works or came to exist, but it
| definitely doesn't look random to me.
| giva wrote:
| https://en.wikipedia.org/wiki/Anthropic_principle
| 323 wrote:
| There is a physical theory which postulates that life is
| inevitable and a consequence of the laws of physics:
|
| > _The thermodynamic dissipation theory thus assgins an
| explicit thermodynamic function to life; the dissipative
| structuring, proliferation, and evolution of molecular
| pigments and their complexes from common precursor carbon
| based molecules under the impressed short wavelength
| solar photon potential to perform the explicit
| thermodynamic function of dissipating this light into
| long wavelength infrared light (heat). In a general
| sense, the origin of life is no different than the origin
| of other dissipative structuring processes like
| hurricanes and the water cycle, except that these latter
| processes deal with structuring involving hydrogen
| bonding while life deals with structuring involving
| covalent bonding. The external photon potential supplied
| continuously by the environment (our Sun), and its
| dissipation into heat by the assembly of dissipative
| structures, are, therefore, both integral components
| necessary for understanding life._
|
| https://encyclopedia.pub/entry/6923
|
| > _The formula, based on established physics, indicates
| that when a group of atoms is driven by an external
| source of energy (like the sun or chemical fuel) and
| surrounded by a heat bath (like the ocean or atmosphere),
| it will often gradually restructure itself in order to
| dissipate increasingly more energy. This could mean that
| under certain conditions, matter inexorably acquires the
| key physical attribute associated with life._
|
| https://www.quantamagazine.org/a-new-thermodynamics-
| theory-o...
| tcmart14 wrote:
| Wouldn't this also have to assume a single universe. If
| our universe is just one of many, then randomness can
| still play an affect. We just happen to live in the
| universe with these laws. But the universe next door
| might have gotten a significantly different dice roll.
| Does that mean life isn't present there? No exactly, but
| I imagine it would look much different than us.
| throwoutway wrote:
| Our universe is single. The many concept is/was an
| attempt to make a square fit in a round hole when looking
| at some perplexing results. To me, Occam's Razor points
| to intelligence arguments as simpler rather than the
| "multi universe" arguments
| sterlind wrote:
| how do neural networks learn? is it by intelligence and
| will?
|
| no, it's by backpropagation. error is propagated and
| minimized. simple equations lead to emergent complexity.
|
| canyons form as water follows paths of least resistance,
| and incrementally erode rock. the water doesn't use its
| intelligence and will to construct a canal, even though
| the resulting river system looks like a max flow
| solution.
|
| the intelligence and will emerges from the math. simple
| systems with enough feedback can become very
| sophisticated.
| oneoff786 wrote:
| Whether universal laws are self evident, random or
| intelligently designed is irrelevant to the discussion at
| hand though. The laws are there. It is through these laws
| that life arose. We have a procedural generation
| algorithm and a seed.
|
| Even if you claim there is a single god that created both
| of these things, backwards deriving the seed necessary to
| generate the current state, it still routes through this
| physical process which is describable with physics and
| could be extrapolated to other starting conditions or
| future scenarios that humans can utilize.
|
| It makes no difference.
| trasz wrote:
| They don't cooperate perfectly; they cooperate somehow.
| They could be entirely different, and the life would look
| different - but there's no reason to think it wouldn't
| work.
| oneoff786 wrote:
| That's my point. Organic chemistry is not like your
| construction materials (or silicon computers). The organic
| chem functionality for nucleotides to begin organizing into
| repeating patterns exists. We know it does. And while we
| might not know the exact reactions that it took, they are
| highly likely to exist, and were arrived upon randomly.
|
| If you arrange your biological soup a large number of times
| randomly, you will eventually land on a pattern that causes
| other nucleotides to arrange in a similar or improved
| pattern around it.
|
| Not too dissimilar from thinking about the creation of
| specific atoms through various astronomical processes.
|
| Even if you need to believe in god for some reason, it's
| not incompatible with god defining the organic chemical
| reactions that enabled life to form via random interactions
| of nucleotides until they happened to land on god's lucky
| number
| rmbyrro wrote:
| And why is it that they can combine?
| oneoff786 wrote:
| Because that's how organic chemistry works.
| chris_overseas wrote:
| > There's some intelligence and will going on in nature's
| laws to make life happen.
|
| And how do you suppose the intelligence you refer to
| originated? You're not offering a solution, you're merely
| adding another layer of complexity that still needs an
| explanation along the same lines.
| rmbyrro wrote:
| I'm not trying to explain, just expressing that, to me,
| randomness also doesn't explain. The fact that I see
| intelligent processes going on is what makes me conclude
| that.
| dalmo3 wrote:
| > If you throw construction materials up 1 quadrillion
| times, how many times can they randomly fall in the form of
| a house?
|
| It depends on what you call a house.
|
| It will probably never fall in any given expected shape.
|
| It may very well fall into multiple configurations that
| someone arriving at the scene after the fact, and without
| prior knowledge of what you expected when you run the
| experiment, would call a "house".
| rmbyrro wrote:
| Would electricity from the grid run through wires into a
| power outlet?
| dalmo3 wrote:
| Is photosynthesis a requirement for life?
| wussboy wrote:
| It will never form a house. But it doesn't need to, and
| expecting it to is a misunderstanding of evolutionary
| processes.
|
| What it needs to form is any kind of a shelter that is
| better than not a shelter. A 4x8 sheet of plywood that
| happens to lean against a brick forming a roof is all that
| is required for a first house.
|
| Life is a product of randomness. There is no intelligence
| or will going on in nature's laws. Neither of those things
| are required.
| rmbyrro wrote:
| With that line of reasoning, would we conclude that
| having H2O formed in the planet 4 billion years ago was a
| form of life better than not a life?
|
| Would we conclude that everything in the Universe is
| alive?
|
| I think that's a pretty interesting way of seeing things.
| And (to me, personally) it strengthens my view that there
| are intelligent processes going on in the Universe.
| ako wrote:
| There is intelligence: solutions can replicate itself,
| with small variations, and the best variations will be
| more successful going forward. It's not complete
| randomness, it's an optimizing algorithm.
| wussboy wrote:
| I was going to disagree with your definition of
| intelligence. But Wikipedia says "to retain it as
| knowledge to be applied towards adaptive behaviors within
| an environment or context", and certainly, in a way,
| evolutionary processes do indeed retain specific ways to
| do things that can be applied towards adaptive behaviors.
| So, yeah! :)
| shockeychap wrote:
| Throwing up materials that randomly fall into the shape
| of a crude shelter can certainly happen. But without a
| LOT of evolutionary mechanisms already in place, that
| crude shelter will just fall apart, and it certainly
| won't turn itself into something more sophisticated.
|
| What is necessary for life to arise from a random stew of
| disorganized chemicals is far more than just a good
| arrangement of a few molecules that exhibit some
| characteristics of life. Since all life dies as part of
| the never-ending march toward entropy, you also need to
| be capable of some form of reproduction and able to carry
| out reproduction at a faster rate than death. What is the
| minimum complexity involved in such a thing? I'd argue
| that it's probably more complicated than any house in
| existence.
| achenatx wrote:
| not really, any structure that can absorb energy and
| replicate could initiate life.
|
| nucleotides spontaneously form, then start to bind to
| each other in chains. Those chains spontaneously fall
| apart and reform.
|
| amino acids start to bind to the nucleotide chains and
| cause them to be more stable. Nucleotide chains bound to
| the amino acids have a longer life expectancy than those
| not bound to amino acids. The amino acids start to bind
| to each other (they naturally do). The RNA binding makes
| them slightly more energy efficient essentially
| catalyzing the reaction.
|
| over millions or billions of years, random chaining of
| nucleotides leads to random chaining of proteins that are
| slightly more energy efficient. Those forms "outcompete"
| alternate forms.
|
| Once a particular type of amino acid chain exists, it can
| influence other amino acid chains to follow the same
| structure. For example prions are extremely short but
| binding to normally folded versions of the protein causes
| the normal version to change patterns.
| joshuahedlund wrote:
| > over millions or billions of years
|
| one of the interesting constraints is you don't have
| billions of years. Life appeared on Earth within 100
| million years of the planet cooling down enough to have
| standing water, possibly even less, depending on your
| reading of the evidence that gets more disputed the
| farther back you go.
|
| It took 2 billion years for prokaryotes to turn into
| eukaryotes, and it took another billion for eukaryotes to
| go multi-cellular, but somehow the initial development of
| a self-replicating cell with a code took less than a
| tenth of that.
| gls2ro wrote:
| Evolution is not randomness. It is running smaller
| incremental multiple randomlike experiments and only few
| pass to the next increment where again a lot of variations
| will be generated and again selected only some few for the
| next stage ...
|
| So in your example with the house here is how it might be:
|
| Throwing 1 quadrillion times materials will they arrange in
| a fundation? Of course. Then throw again and will there be
| some kind of wall or pillar?
|
| Then you now have foundation and pillars. Throw again a
| huge number of times, will there be materials that might
| form a wall?
|
| Please also take into consideration that evolution is not
| only in a vertical progression (from materials to house)
| but also running horizontally (like creating multiple types
| of walls of all shapes before going for a roof).
|
| But more importantly evolution will not create a house as
| long as there is not need for one.
|
| On the other hand, as we are poaching the limits of
| science: how do you know that given a close to infinite
| number of arrangements those materials will not arrange
| into a house?
| dragonwriter wrote:
| > Evolution is not randomness.
|
| Darwinian evolution in the narrow sense is duplication
| _of_ life plus random variation plus filtering (that may
| also be random, but which at a minimum contains some bias
| which is, if not _consistent_ over time, at least usually
| changes very slowly compared to the rate of random of
| variation.)
|
| Darwinian evolution in the broad sense is the same thing,
| but without the "of life" part.
|
| But abiogenesis is not Darwinian evolution in the narrow
| sense, and may or may not significantly involve Darwinian
| evolution in the broad sense, so arguing about what
| evolution is or is not in the context of the initial
| creation of life as opposed to the explosion of diversity
| of life after its initial creation is, at best, skipping
| steps.
| uoaei wrote:
| Assembly theory from Sara Walker et al. takes a principled
| stab at questions like this using a combinatorial
| "assembly" framework of small constructions that recombine
| into larger ones. The model requires only Markov conditions
| so fits into this description of probabilities of observing
| certain assemblages.
|
| Intelligence fits into this in interesting ways. One way to
| consider it is as a guide to the assembly process from less
| complex from more complex.
| pfdietz wrote:
| Where do the nucleotides come from?
| jdthedisciple wrote:
| > Computers don't arise randomly
|
| As if, contrary to that, humans do/did.
| Calavar wrote:
| No, it's not as simple as that. The probability of self-
| replicating RNA arising by random assembly of bases is very
| low. There was a good Nature article [1] published a couple
| years back that digs through some of the numerical issues.
| (And a good, more layperson oriented summary as well [2].)
| The gist is that a self-replicating RNA sequence would have
| to be at least 40 nucleotides (and possibly even as long as
| 100), but the probability of randomly synthesizing a
| 40-nucleotide long sequence that happens to be self-
| replicating anywhere in the visible universe over the span of
| 13 billion years is effectively zero.
|
| To be fair, the probability gets closer to one if you expand
| your view to include the entire universe and assume that it
| is many, many orders of magnitude larger than the visible
| universe. But my take away, at least, is that we are not
| dealing with a situation where random assembly of RNA is so
| likely to generate self-replicating sequences that
| abiogenesis was effectively an inevitability. That was the
| narrative I was sold in grade school and undergrad, but it
| appears to be wrong.
|
| There are a good number of free parameters in the journal
| article that I linked: The fraction of RNA sequences that are
| self-replicating, the fraction of planets that are habitable
| for life, the average decay rate of RNA on a habitable
| planet, etc.
|
| You take can take issue with the empirical estimates for
| those parameters, but that points to missing pieces in the
| framework: Was there a chemical process on early earth that
| stabilized RNA oligomers that no longer exists? Are self-
| replicating RNA sequences more common than we believe? If so,
| why haven't we encountered more of them in nature? And so on.
| In my opinion, these are the truly interesting questions, not
| whether nucleotides and amino acids can form spontaneously.
|
| [1] https://www.nature.com/articles/s41598-020-58060-0
|
| [2] https://mathscholar.org/2020/05/the-origin-of-life-in-an-
| inf...
| trasz wrote:
| >The probability of self-replicating RNA arising by random
| assembly of bases is very low.
|
| But it parallelizes extremely well - throughout the entire
| universe for billions of years.
| JJMcJ wrote:
| Or here on Earth over say 100 million years with
| trillions of little globs of organic chemicals, likely
| with even simpler replication mechanisms that are not
| understood currently.
| adgjlsfhk1 wrote:
| What this is missing is that it assumes way too little
| structure. You don't have to generate a self replicating
| set of RNA. Many RNA strands (maybe most?) will do
| something, so all you need is to generate a strand of RNA
| that will eventually produce a self replicating set of RNA
| which is likely much easier.
| oneoff786 wrote:
| Undiscovered mechanisms of self replicating RNA arising by
| chance seems very likely though. That's my point. I agree
| there's a lot of good questions to be answered. I think it
| is likely that we will answer them by staring at nucleotide
| soup.
| skupig wrote:
| >the probability [...] is effectively zero
|
| Is that meaningful? No matter how unlikely our existence
| is, here we are.
| lisper wrote:
| > Are self-replicating RNA sequences more common than we
| believe?
|
| Almost certainly yes.
|
| > If so, why haven't we encountered more of them in nature?
|
| Because they can't compete with modern life. Nearly all of
| the biomass on earth is in use. A primitive replicator,
| even if it arose today, would have to compete for resources
| against all the existing life on earth. It wouldn't stand a
| chance. This is the reason there is only one universal
| common ancestor. It's not necessarily that abiogenesis only
| happened once, it's that only the descendants of one common
| ancestor survive today. All traces of all other abiogenesis
| events have been obliterated.
|
| You have to compute the abiogenesis odds for an environment
| that, by definition, does not yet include life. Here is a
| rough back-of-the-envelope approximation: the biomass of
| earth is about 2^52kg. Avogadro's number is 2^76. So there
| is the potential for the early earth to have 2^120
| nucleotide bases and amino acid molecules floating around.
| If the complexity of a simple replicator is around O(100)
| bits then the odds of finding one by chance when you are
| rolling that many dice in parallel approaches 1 in just a
| few million years. After that, evolution takes over.
| pfdietz wrote:
| Back up from that... how are the nucleotides formed? And
| don't they need energetic polyphosphate groups on them to
| drive the polymerization? And how does this work in an
| impure solution with all sorts of variant nucleotides and
| other cruft?
| JJMcJ wrote:
| To my thinking, that means that self replicating systems
| arose in an even simpler chemical environment and even RNA
| was a later development.
| rojobuffalo wrote:
| Dr. Nick Lane is my favorite author on this subject. My reduced
| summary of a slide he presented titled "what is life" goes:
|
| - free energy powers growth
|
| - growth is thermodynamically favorable
|
| - heredity is growth, doubling by exact copying
|
| - growth combines carbon and energy metabolism
|
| - growth is driven by environmental disequilibria
|
| That doesn't explain away the mystery of the first RNA
| replicase, but I really like how it explains growth and
| doubling as a form a growth. That's copy-pasted from a
| newsletter draft I'm writing. It'll be posted next week on
| https://0123.substack.com
| kabdib wrote:
| If you like Nick Lane's writing, I also recommend David
| Dreamer's _Assembling Life_. It gets a good deal more
| technical (chemical?), and has more depth about possible ways
| that membranes were "invented".
|
| Paul Falkowski's _Life 's Engines_ is also quite good.
| pfdietz wrote:
| > We have a decent idea of how the first nucleic acids may have
| been synthesized,
|
| Really? Nucleotides are already too complex to have been
| produced in any valid OoL experiment at more than vanishingly
| small concentrations. Experiments that demonstrate some
| chemical X can be produced, and then lead to another experiment
| where X is made available in pure form at high concentration
| (and then rinse and repeat down the synthesis chain), don't
| tell us anything interesting at all.
| jbj wrote:
| For those who find this subject fascinating and want more origin
| of life chemistry, I recommend to find a video of Jack Szostack
| giving a presentation after he got his Nobel price.
| gnatman wrote:
| 2nd video down on this page (first is the introduction):
|
| https://www.nobelprize.org/prizes/medicine/2009/szostak/lect...
| nomel wrote:
| I highly recommend the Lex Fridman podcast with Lee Cronin
| (#269), about the origins of life and complexity theory [1].
|
| The discussion is really incredible. It really changed my naive
| perspective of life, and the universe.
|
| 1. https://www.youtube.com/watch?v=ZecQ64l-gKM
| hsnewman wrote:
| We don't have a clear defination of life, for example, James
| Lovelock's Gaia theory says the earth is alive. How can one
| discover something when that something is undefined?
| nomel wrote:
| It's incorrect to say it's "undefined" which means "without
| definition". The "problem" is that it has a "fuzzy definition",
| or you could rightly claim "multiple definitions", depending on
| the context.
|
| But, a good definition must come _after_ understanding, not
| before. And, just because something doesn 't have a precise
| definition or understanding doesn't mean that understanding
| can't be _improved_ , or even _branched_ , in the form of a
| _discovery_ , to create some new label that better fits the
| concept.
|
| Until then, we have to live with something fuzzy, with the
| understanding that it is somewhat incorrect (which anyone
| familiar with biology will happily tell you). Lack of
| definition, which is lack of understanding, doesn't impede
| discovery. Lack of definition and understanding are necessary
| _requirements_ for discovery.
| mcphage wrote:
| > We don't have a clear defination of life
|
| We don't even have a clear definition of tall--is a person 6'
| 4" tall? How about 6' 3"? Or 6' 2"? Or 6' 1"? And yet a
| building 6' 4" high would be tiny. What about a rock--is a rock
| high 6' 4" tall?
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