[HN Gopher] A New Theory for the Assembly of Life in the Universe
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A New Theory for the Assembly of Life in the Universe
Author : isaacfrond
Score : 110 points
Date : 2023-05-05 10:01 UTC (12 hours ago)
(HTM) web link (www.quantamagazine.org)
(TXT) w3m dump (www.quantamagazine.org)
| ihm wrote:
| Sounds interesting. It's cool they found an OK way to approximate
| the assembly index given that it sounds like something
| uncomputable (will have to read the paper but it sounds like
| computing something like Kolmogorov complexity in some model of
| computation).
| mjreacher wrote:
| By the sounds of that article there needs to be more work done on
| applying abstract notions of complexity to the real world and
| developing suitable methods for this.
| TwoNineA wrote:
| Theory? The correct term should be 'hypothesis'.
| ordu wrote:
| I'm not sure how philosophers of science demarcate hypotheses
| from theories, but my own feeling that this is a theory. It is
| infallible, like Euclidean geometry. It can be falsified, but I
| think it can adapt to falsification attempts. Or it can detach
| itself from Real, it can go platonic, like Euclidean geometry
| does, and to speak about Ideal, like points, lines, planes and
| other objects that are not real. So it is more than a
| hypothesis, that to my mind must be falsifiable.
| jononomo wrote:
| The existence of life is definitive proof of the existence of
| God.
|
| It is laughable that people think it is irrational to believe in
| the virgin birth of Jesus Christ but then blithely believe that
| life itself was birthed from nothing for no reason.
|
| Natural Selection cannot even begin until life exists, which is
| like saying that you can't even start counting to one million
| until you're already at nine hundred and ninety-nine thousand
| nine hundred and ninety-nine.
|
| The existence of life is the only interesting question in the
| Universe because without life no other question can even arise.
| MrResearcher wrote:
| Covered in lots of details in Lex Fridman's podcast #279
| https://www.youtube.com/watch?v=SFxIazwNP_0 Unfortunately,
| transcript isn't available.
|
| Potentially has big practical applications as it allows for
| construction of chemical computers that compute through chemical
| reactions.
| tomviner wrote:
| https://www.transcriptforest.com/en/lex-fridman-podcast/8727...
| goodmachine wrote:
| Fascinating stuff. However: annihilating critique here
|
| "What they have proposed is a limited special case of an RLE-
| Huffman coding algorithm, which means their paper introduces a
| simpler version of what was already considered one of the
| simplest coding algorithms in computer science."
|
| The 8 Fallacies of Assembly Theory
| https://hectorzenil.medium.com/test-8f0be54817c4
|
| And https://arxiv.org/abs/2210.00901
| m3kw9 wrote:
| There is some reason why things in the universe are incentivized
| to replicate. The earliest life forms are all about replication,
| up to now. It's about more, everything we do is also about more.
| Maybe it's a way to create order, because if something is random
| chaos, you cannot count it. Maybe the math laws in our universe,
| especially addition is the basis for a lot of why things happen
| [deleted]
| visarga wrote:
| Language is also about replication. Ideas have a lifecycle,
| they get born, spread, evolve and die, but it's a different
| cycle from that of humans. We act like fertile grounds for
| language. Up until now language could self replicate only by
| humans and copying. With the advent of LLMs language gained
| another vector for replication.
| hobo_in_library wrote:
| It's more of a survival bias.
|
| Say, something new comes into existence every 1000 years on
| avg, with an average shelf life of 1 year.
|
| 0.001% of those things can self replicate. The rest can't.
|
| After a billion years: - 1,000,000 new objects have been
| created - 10 of them were self-replicating - There's a 0.1%
| chance that the current year contains at least one object that
| cannot self replicate. Chances are there won't be any non-self
| replicating objects existing in the current year. - There will
| be many, many copies/descendants of the 10 self-replicating
| objects
|
| Replication leads to survival bias
| toss1 wrote:
| It'll be interesting to see if this potentially very useful
| framework can play out.
|
| At least the article failed to dig deeper into this:
|
| >> by narrowing down relatively complex molecules to a small
| subset. Ordinary chemical reactions already "select" certain
| products out of all the possible permutations because they have
| faster reaction rates.
|
| Since the theory is about assembly all the way down the the
| bottom, does it seem the theory needs to account for the next
| level down (and below that from quantum foam to atoms), relative
| to this chemical selection process? Why is it, or what is it
| about the universe that causes this, or makes it inevitable?
| fowtowmowcow wrote:
| I think that their theory might go something like this when
| extended:
|
| Whatever early state of the universe was in there was a huge
| set of possibilities but a smaller set assemble into anything
| and even smaller set can assemble into things such as atoms
| that have stable eletron orbits that can mix with other atoms
| giving rise to chemistry.
|
| It's not saying this option is inevitable but some option is.
| We happen to live in the option that gave rise to atomic matter
| that self interacts allowing to assemble more complex matter.
|
| Of course this doesn't include dark energy and dark matter
| which presumably doesn't interact chemically with the matter we
| are familiar with but none the less could still be a component
| needed/useful for life.
| at_a_remove wrote:
| My own not-even-a-hypothesis feeling about this is that cycles
| are required.
|
| Here me out: Earth life first put a surface around the seawater
| it was in. Each cell is really a bag of saline (unless you're a
| plant and then you have rigid walls) plus other stuff. That was
| encapsulated. Anyone who has kept saltwater fish knows that they
| only do well in a narrow range of temperatures, salinity, and so
| forth.
|
| Then creatures thermoregulated, carrying the necessary
| temperatures for life within themselves. Slow down at night.
| Basking in the sun: an innovation. Feathers, then fur. Brown fat
| cells. All this to keep our interior seawater just so.
|
| But what if what kickstarted life wasn't _just_ chemistry, but
| the cycles applied to the chemistry? A warm little pond, a soup
| all of its own. New unreacted chemicals (nutrients) rain in. A
| bit of tide washes out the chemicals at the bottom of the entropy
| chain (waste). Rain in, wash out, over and over, allowing for a
| concentration. Dump chemicals in an unmoving tank of water, they
| head toward equilibrium, but have them surging in and out, you
| can get interesting stuff. Rain in, wash out; inhale, exhale;
| eat, excrete; heartbeat. All cycles. Urea cycle, Krebs cycle,
| glyoxylate cycle. Once you step back to see that life works as
| repeated cycles of chemistry, well, we probably needed cycles to
| get started, just as we needed chemistry and other conditions to
| get started. We incorporated those cycles because life is not
| _static_ , it persists because it repeats.
|
| So perhaps -- and this is just a perhaps -- not only does life
| need one "set" of chemistry or another to begin (maybe arsenic
| instead of phosphorus, hydrogen sulfide instead of water), it
| needs cycles, interlocking cycles. So not just a year with
| seasons, but day and night (tidally locked planets need not
| apply), and even tides (hope you have a moon) would be needed.
| The more cycles to piggyback upon, the more opportunities for
| chemistry to capture, repeat, and encapsulate those cycles, to
| self-perpetuate.
|
| Just something I wonder about.
| evandale wrote:
| I love this theory and it seems very plausible. Cycles are
| everywhere in the world and it's impossible to avoid them.
|
| I wonder if that's why are brains want to find patterns all the
| time. We need cycles and patterns because they represent
| stability. Once you have stability then you can focus on
| improvements because you have a baseline. Your baseline is like
| your save file you reset to when your experiments go wrong.
|
| It really seems like you can apply this to almost anything in
| life.
| cmrdporcupine wrote:
| You might want to read some of Nick Lanes' work, he's a
| biochemist researching abiogenesis etc but has written a number
| of popular works, which I found very compelling
|
| https://nick-lane.net/
|
| He is in particular concerned with exactly the chemistry and
| physics aspect of the origin of life. In particular his summary
| of the theory of alkaline "warm" hydrothermal chemistry & the
| early earth and the origin of life is very compelling.
|
| Essentially such areas are theorized to have created physical
| protocells at the chemical and energy boundaries between the
| sea water and the alkaline hydrothermal vents. The naturally
| occurring molecules there apparently present aspects similar to
| a hypothetical early cell, and yes, bags of saline. But also
| the relevant point is the interaction of energy across this
| barrier. And eventually something "escaped" from this system
| that was able to "create" a similar system or sustain itself in
| other environments.
|
| https://www.ucl.ac.uk/news/2019/nov/deep-sea-vents-had-ideal...
| [deleted]
| alanbernstein wrote:
| Here's a rough metaphor for you: life is an engine (running
| cyclically) but it needs a manual kickstart (existing cycles)
| to get going.
| at_a_remove wrote:
| More or less, yes. Very sloppily at first.
|
| My "look for life _here_ " candidates are basically planets
| (or moons!) where a liquid solvent is present (so you can
| have chemistry happen more readily), warmer (faster reaction,
| so you can have the chemistry happen faster, and therefore
| again and again), and with cycles (not tidally locked, a moon
| helps).
|
| I'm still something of a carbon chauvinist, but I am open to
| different solvents and other chemistries.
| _nhynes wrote:
| And that units of computation are called cycles is no
| coincidence right?
| marstall wrote:
| seems like he's thinking in the same space as Andreas Wagner, who
| writes about these ideas in his book, "arrival of the fittest".
|
| Wagner also talks about the "probability space" of organic
| molecules being too high for life to emerge through true
| randomness.
|
| For even the simplest components of life, like the citric acid
| cycle, to come into existence is something like everybody in the
| world hitting the lottery number every day for a billion years.
| or something.
|
| I don't remember how he brings his theory down to earth because I
| didn't finish the book, but a cool thing to think about.
| quacked wrote:
| I am a little religious (deist and Quaker background) so it's
| easy for me to hand-wave away the origins of life as divine,
| but I often think about how life could have arisen completely
| randomly. This line:
|
| > everybody in the world hitting the lottery number every day
| for a billion years. or something.
|
| is something I totally agree with, but the amusing confounding
| factor is that if "time" is infinite, then this exact scenario
| would happen infinity times.
|
| Whatever the origins of life are, I'm certainly glad to be
| here.
| chasd00 wrote:
| yeah on a long enough timeline all probabilities = 1
| kevinventullo wrote:
| Yet the earth is widely believed to be only a few billion
| years old!
| TeMPOraL wrote:
| Enter the anthropic principle. Our Earth is one planet out
| of some hundreds of billions of planets the galaxy likely
| has, out of however many billions of galaxies are there.
| Earth is just the planet (likely one of many planets) that
| won the lottery.
| HarHarVeryFunny wrote:
| Early terrestrial chemistry can't have stayed random for too
| long though - given the goldilocks conditions of multiple
| energy sources (solar, geothermal), mechanical agitation (lunar
| tides) and abundant water facilitating mixing/migration of
| chemicals. Chemical complexity must gave progressed fairly
| quickly, especially in environments (e.g. thermal vents,
| seashores) where factors like these were more pronounced.
|
| The precursors to instruction-based biochemical factories like
| modern cells would have started out with things as simple as
| catalysts that favored certain reactions, and gradually grew in
| complexity (maybe via multi-product catalysts?) to encode the
| production of more and more specific chemical products.
|
| The story here would be one of ever-increasing chemical
| complexities and ever-increasingly complex cells/proto-cells.
| Chemical products, and cycles, that may have been infinitely
| unlikely to have been created under initial conditions of
| randomness would eventually become incorporated into the
| chemistry of the cell whose production was encoded for and
| inevitable. Complexity would have grown with simpler
| biochemicals being combined into more complex ones,
| simple/shorter cycles growing into longer ones, etc.
| LesterTheMolest wrote:
| The Universe is computational per Scott Aaronson.
| slowmovintarget wrote:
| He's wrong, per Roger Penrose, if you're making an appeal to
| authority.
|
| If you're actually examining the reasoning, Penrose points
| simply to a non-computational quantum phenomenon that we
| observe in the real world and uses that to say "therefore, the
| universe is non-computational."
| memling wrote:
| > Penrose points simply to a non-computational quantum
| phenomenon that we observe in the real world
|
| Do you have an example?
| Koshkin wrote:
| But he is only a part of the Universe...
| photochemsyn wrote:
| From the associated paper:
|
| > "Our central thesis is that molecules with high MA [Molecular
| Assambly Index] are very unlikely to form abiotically, and the
| probability of abiotic formation goes down as MA increases, and
| hence experimental determination of MA is a good candidate for a
| life detection system. If our hypothesis is correct, then life
| detection experiments based on MA can indicate the presence of
| living systems, irrespective of their elemental composition,
| assuming those living systems are based on molecules."
|
| You could get a false positive from a pre-biotic but molecularly
| complex planet, such as Earth in the 100 million years before the
| origin of the first self-replicating genetic-information-
| containing entity. Such an environment would contain many complex
| molecules, whose sites of formation/sources could include metal-
| rich hydrothermal vents, metal-rich clays, meteorite inputs,
| ocean surface photochemistry, etc.
|
| In a planet with established life, particularly one with oxygenic
| photosynthesis , these processes don't allow organic molecules,
| amino acids etc., to accumulate in high amounts because every
| system is full of microbial scavengers that take up almost every
| complex molecule they come across, with a few exceptions (the
| 'persistent organic fraction' derived from tree lignin etc.).
| Also, free molecular oxygen is a kind of bleach that eventually
| degrades many organic molecules.
|
| However, in an abiotic system these complex molecules could
| persist for hundreds or thousands of years, particulary in the
| absence of free oxygen. Such a complex molecular soup would then
| provide many opportunities for the generation of simple living
| systems.
|
| Incidentally, the most plausible current theory of the origin of
| life puts the protein-producing rRNA-based ribosome at the
| center, and the concept is that abiotically produced amino and
| nucleic acids formed conglomerates, and these bodies developed
| the ability to replicate themselves by pairing up with free
| abiotically produced amino and nucleic monomers and catalyzing
| bond formation (May 2022):
|
| https://www.nature.com/articles/d41586-022-01303-z
|
| > "Structure that links amino acids suggests that early organisms
| could have been based on an RNA-protein mix."
| svnt wrote:
| The article is confused but the theory (and it is a theory,
| albeit an early one) is a useful restatement of a lot of
| intuitive understanding in a way that allows it to co-articulate
| with evolution in particular.
|
| The introduction to one of the linked papers is far more
| informative and frankly readable than the article:
|
| > Biological systems have access to a lot of information--
| genetically, epigenetically, morphologically, and metabolically--
| and the acquisition of that information occurs via evolutionary
| selection over successive cycles of replication and propagation
| [7]. One way to look at such systems is by comparing the self-
| dissimilarity between different classes of a complex system,
| allowing a model-free comparison [8]. However, it has also been
| suggested that much of this information is effectively encrypted,
| with the heritable information being encoded with random keys
| from the environment [9]. As such, these random keys are recorded
| as frozen accidents and increase the operative information
| content, as well as help direct the system during the process of
| evolution, producing objects that can construct other objects
| [10].
|
| https://www.mdpi.com/1099-4300/24/7/884
| cryptonector wrote:
| I think what the last sentence is saying by "and increase the
| operative information content" is that if you're comparing
| disparate systems' information content, but all you have is
| ciphertext and the keys but not the encryption algorithm, then
| it's as if the systems have a lot more information than the
| plaintext would have. Yes?
| hn_throawlles wrote:
| matter is the basis of all finally generates yields as the
| ultimate 'output': The as 'completed' scientific discipline
| called chemistry
|
| the point being how they (chemistry as a cultural institution)
| owns so much technical know-how without which we cannot live
| like we do, and this knowledge is not innovating, nor nothing
| of the sort, it's in maintenance mode. this what I mean by
| "completed" discipline.
|
| energy is the basis of all:
|
| same as above but physics are the 'ultimate output'; as the
| completed discipline. I suppose this 'goal of 'completing
| physics' is not fully realized yet.
|
| Except in some sub-disciplines like civil engineering (built on
| physics-science).
|
| information is the basis of all:
|
| still working on it. some mix of logic, philosophy, physics,
| and computer engineering/science must all output another
| 'completed scientific 'discipline. or completely re-draw
| physics as a cultural institution.
|
| this article is all about this 'information'-awareness going
| over old biology
|
| > _a useful restatement of a lot of intuitive understanding_
|
| now with more 'information' as a substance guiding the
| intuition.
| eimrine wrote:
| So empty article on the main page. All you need to read is
| following:
|
| Not surprisingly, such an ambitious project has aroused
| skepticism. Its proponents have not yet made clear how it might
| be tested in the lab. And some scientists wonder whether assembly
| theory can even deliver on its more modest promises to
| distinguish life from nonlife, and to think about complexity in a
| new way.
| DennisP wrote:
| > But others feel that these are still early days for assembly
| theory, and there's a real chance that it might bring a fresh
| perspective to the question of how complexity arises and
| evolves...Paul Davies, a physicist at Arizona State agrees,
| calling it "a novel idea with the potential to transform the
| way we think about complexity."
|
| If you're only interested in mature, well-tested science, then
| ignore this. But if actual scientists did that, then scientific
| progress would slow down by a lot, because anyone with a new
| hypothesis would have to labor in solitude.
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