12 ms·

The Grayness of the Origin of Life

98 points by Breadmaker 5y ago

xor99 5y ago
So interesting! Some similar work on this area: https://www.nature.com/articles/s41467-021-23258-x https://www.nature.com/articles/s41467-021-23258-x https://ui.adsabs.harvard.edu/abs/2020AGUFMP001...01C/abstract https://ui.adsabs.harvard.edu/abs/2020AGUFMP001...01C/abstra...
NotSwift 5y ago
A nice article. It seems likely that we will never really know how life started. It is still very interesting to research this subject, because it might help us to learn more about the possibility of life on other planets.
- ExpiredLink 5y ago
  From a scientific point of view we can - not just will - never know the origin of life. Of course, popular science frames it differently.
  - mypalmike 5y ago
    What makes it fundamentally impossible to know the origin of life? It seems we are likely to develop and refine experiments and theories that approximate the initial conditions and processes by which life took hold. Some of the details of how it happened are certainly lost to time, but it seems there's a lot of room for exploration towards a fairly valid model.
    - meetups323 5y ago
      We can know an origin of some life, but never the origin of our own life. It's simply not testable, and without tests it's not science.
      - ReactiveJelly 5y ago
        But to say that we could find several plausible theories and not know _something_ of value is teetering on Last Thursdayism.
        meetups323 5y ago
        If I may use a programming analogy, the process described is akin to NPC agents in a browser based MMORPG Rowhammering a bunch of random bits into some exposed ArrayBuffer until a Counter div appears on the page, then claiming they have some deeper understanding of the origins of life in their universe. Do they have a deeper understanding? Perhaps. Have they come anywhere near the "origin of life"? Nope.
      - crazygringo 5y ago
        That's not how science works. You can't ever test anything in the past, so by your logic nothing in the past can be considered scientific. By your logic, plate tectonics can't explain the past movement of continents. Which is, of course, wrong. We can absolutely test aspects of a theory, verify its general validity, see that it best correlates with past evidence, and therefore infer past causes. Nothing of that is unscientific -- to the contrary, that's precisely how science works.
        meetups323 5y ago
        If all we had was observations of modern day plate tectonics it would be foolish to back-propagate the same motions billions of years in reverse and claim ones methods were "scientific". Luckily, we have things like fossil records to justify such conclusions. They provide the second point with which we can "fit a curve" when exploring history. With this "origin of life" stuff, we don't have that second point of confirmation. We think up a bizarre process, execute it, and see that it produced some molecules that we see in modern day life. We then have the gall to say that we've discovered "the origins of life"? Yeah right... https://news.ycombinator.com/item?id=27974369 https://news.ycombinator.com/item?id=27974369
    - posterboy 5y ago
      I think they may be arguing semantics of knowing versus believing, and especially the loss of information to the eventual increase of entropy. I don't think there's a calculation to prove it because it would require a very thorough definition in the first place, which could be taken as a sufficient answer in its own right. The answer is of course 42. On another note, at "17 hours ago" and no response I guess they are still writing trying to work it out, or gave up, if they are anything like me and my random blurts
- Koshkin 5y ago
  > we will never really know how life started A big bang of another sort.
- AprilArcus 5y ago
  I think in our lifetimes, we'll know enough about the preconditions for abiogenesis to perform experiments replicating portions of the process in vitro.
  - airstrike 5y ago
    I hope you're right, but at the same time I think I've expecting that since middle school and I'm now fast approaching my 40s...
  - NotSwift 5y ago
    We know that it has been a very, very slow process and we don't really know where and under which conditions it happened. I hope that you are right, that we might be able to replicate portions of it. It might help us understand something more about what we call life. It might also help us understanding alternative forms of life that might exist on other planets.
aazaa 5y ago
> A more inclusive representation is to recognize a spectrum between the non-living and the living—a “grayness” resulting from the protracted evolutionary process that gave rise to life. The meaning of "grayness" would appear to have something to do with the fuzzy line between life and non-life. There is a footnote to the article "The Seven Pillars of Life": https://www.pps.net/cms/lib/OR01913224/Centricity/Domain/3337/SevenPillarsofLife.pdf https://www.pps.net/cms/lib/OR01913224/Centricity/Domain/333... But it doesn't mention grayness at all. This gets cleared up a little a few paragraphs in: > The ability to clearly distinguish between abiotic and biotic systems is considered by many a prerequisite for effective astrobiology studies. However, since no natural demarcation truly exists, there is a profound difficulty in advancing the field if we rely on a strict dichotomy. ...
macawfish 5y ago
I'm personally convinced at this point that most everyday distinctions between living and dead are arbitrary human categorizations. Even a "dead body" is teaming with life. As far as "inanimate matter" is concerned, all matter is ultimately part of a plethora of various different cycles and processes of transformation and recapitulation... even if something temporarily looks like it's static to us and our meager little narrow timeframe of experience, it's not. Just to clarify, I don't mean that these distinctions are meaningless, just that their meaning is inherently embedded in human experience.
- jollybean 5y ago
  That's a good thought - but worth considering that just because lines are fuzzy doesn't make them either 'arbitrary' or even 'subjective'. That a materialist perspective gives us some nice hard rules for understanding certain things, it also by definition struggles to help us understand the nature of other things, i.e. 'most important bit' which is 'life' itself, so maybe we should be thinking about that problem a little bit differently. 'Emergence' seems to be a least one idea, among many.
  - guerrilla 5y ago
    > That's a good thought - but worth considering that just because lines are fuzzy doesn't make them either 'arbitrary' or even 'subjective'. Interesting and plausible, but you didn't give an argument or any example for that.
    - jollybean 5y ago
      For most things in the real life that we categorize, the rules that distinguish those categories can be vague. It doesn't mean those categories are not valid, or a function of 'human perception'. We have difficulty with biological distinction, but we can still confidently categorize something as being a 'Horse' and 'Not A Horse' ... even if sometimes it's a little bit ambiguous, aka 'Kind of a Horse'. Edit: and as for 'other ways of thinking' it very quickly goes into metaphysics so it's hard to talk about because we don't spend much time in that realm. 'Emergence' and 'Biocentrism' are interesting ideas (fields?) that sit within more or less regular bounds of science and so they're just examples of what I'm referring to.
antattack 5y ago
Motor proteins look alive: https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8
- Koshkin 5y ago
  As do these: https://www.youtube.com/watch?v=hsLJdpjSJcM&t=15s https://www.youtube.com/watch?v=hsLJdpjSJcM&t=15s
- AprilArcus 5y ago
  I love this animation because it's beautiful, but I hate that it gives the impression of deliberate one-foot-in-front-of-the-other movement. In reality, when the "foot" of the motor protein is unbound, it is oscillating to and fro in a state of brownian motion until it happens to snap into place at the next (or, infrequently but inevitably, the previous) subunit. At this scale, quantum effects such as tunneling come into play, and it would be cool to visualize the organized thermodynamic chaos of the cell rather than the mechanical operation of a homunculus.
  - mncharity 5y ago
    > quantum effects such as tunneling come into play Really? I'd not have expected that. > but I hate that it gives the impression Oh yes. Rather than being towed, the payload explores its entire tethered configuration space between one step and the next. Not a donkey walking along a river towing a barge, but a mouse clinging to wire and a balloon a hurricane. The nanoscale moshpit from hell. It's like creating education content about human locomotion, for aliens completely unfamiliar with it, and with no sense of what's plausible, and showing them only one of those stop motion videos where someone floats along not touching the ground. An extremely biased selection of video frames to tell a very false narrative. Worse, this and other misconceptions engendered might be mitigated by very briefly including other representations... but the folks who created the video explicitly prioritize "pretty" over "do no harm". Which rather diminishes my appreciation of their beauty. > cool to visualize the organized thermodynamic Years ago I saw a video at a talk, of simulated viral icosahedral capsid assembly. The panels are tethered together, to maintain proximity, as they bounce and slam together and apart, incrementally assembling and misassembling. I wish I could link to it. If anyone knows of content to give a visceral feel for nanoscale dynamics, I'd appreciate hearing of it.
benlivengood 5y ago
I find it fascinating that abiotic chemical/physical cycles are considered an integral part of early life (e.g. if your nutrient transport is environmental osmosis/tides/whatever, you're still alive but the larger environment is an integral part of your biochemistry). From that perspective the freshwater cycle is still a major component of biochemistry (bulk ion transport) on Earth, despite arguably being a physical state change and not chemistry per se. The Sun provides photons that most cells need in order to live but Desulforudis audaxviator have decoupled themselves from that source of energy. In theory they could outlast the solar system or hitch a ride on a rogue planet.
- perl4ever 5y ago
  >The Sun provides photons that most cells need in order to live but Desulforudis audaxviator have decoupled themselves from that source of energy. In theory they could outlast the solar system or hitch a ride on a rogue planet. I suspect it's the opposite; first there was life and then it evolved to use sunlight. How did life arise on earth right after the rocks stopped being red hot? The only reasonable theory in my opinion is that the original life forms were inside the rocks on some jetsam that wasn't totally molten and if you go back further, lived off a little heat and water underground, quite possibly on a "rogue planet". One reason this seems obvious to me is that there must be orders of magnitude more planets without stars than with. Just like there are more asteroids than planets, more dim red stars than sun-like stars, etc. The other reason is that I think it helps a great deal with the Fermi paradox. If life just zapped into existence on Earth, 4.5 billion years ago, then it could've happened at any time, anywhere else, over the prior (almost) 10 billion years or so. But if it took most of that time, since the Big Bang, to develop what we think of as the most primitive life, in the much larger arena of rubble or rogue planets in deep space, then it looks more like we are the earliest life that could develop, and that's why we wouldn't have been overrun by space invaders. Looking the exponential development of life, even if you choose somewhat arbitrary milestones, it's basically a self-similar curve; each "step" takes a fraction of the previous one. Going backwards, each step should take the corresponding multiple. The great oxidation event was about 2.5 billion years ago. The first life we know about was about twice that. It seems to me a near perfect fit, timing wise, for the origin of that life to be about twice that ago, rather than suddenly arise from nothing in a few million years. What it comes down to is I think creationists who are skeptical of abiogenesis really have a good point, about how the simplest life is unbelievably complex, in spite of not having a viable theory to explain it. But I think the answer is staring us in the face. And of course panspermia isn't new or my idea particularly, but what bugs me is instead of saying there needs to be more evidence, it should be the default assumption. Our environment is just not representative of most of the universe even if you ignore non-baryonic dark matter.
divbzero 5y ago
A few offshoots from this line of thinking… Where do viruses sit on this scale of grayness? Yes, viruses have organic molecules, information storage systems, and compartmentalization. No, viruses do not have metal catalysis (correct me if I’m wrong) nor do they have energy currencies (they rely on hosts for energy). Viruses appear rather gray indeed. Can the grayness framework be modified/extended to describe superorganisms? Superorganisms like bee colonies are only mentioned in passing and the authors do not try to apply their grayness framework. Organic molecules and metal catalysis aren’t as relevant beyond the molecular scale, but information storage systems, energy currencies, and compartmentalization apply just as well to superorganisms. Perhaps those are the more generalizable attributes of life. I’m reminded of concepts from Schrödinger’s What Is Life?. Schrödinger describes local reduction of entropy to be a key feature — combining energy currencies with compartmentalization is one way to achieve that. Separately, he discusses the hereditary mechanism and suggests an “aperiodic crystal” could encode heritable information. What would be the contents of a sister article titled “The Grayness of the Origin of Consciousness”? I would love to see an outline.
- new299 5y ago
  > No, viruses do not have metal catalysis (correct me if I’m wrong) RNA viruses would generally have an RdRp polymerase which requires a metal ion.
amelius 5y ago
There is also grayness in the question "what is an individual organism?" For example, you can look at a single bacterium as an organism. But you can also look at a colony of bacteria as an organism.

98 points by Breadmaker 5y ago

So interesting! Some similar work on this area: https://www.nature.com/articles/s41467-021-23258-x https://www.nature.com/articles/s41467-021-23258-x https://ui.adsabs.harvard.edu/abs/2020AGUFMP001...01C/abstract https://ui.adsabs.harvard.edu/abs/2020AGUFMP001...01C/abstra...

NotSwift 5y ago

A nice article. It seems likely that we will never really know how life started. It is still very interesting to research this subject, because it might help us to learn more about the possibility of life on other planets.

ExpiredLink 5y ago
From a scientific point of view we can - not just will - never know the origin of life. Of course, popular science frames it differently.
- mypalmike 5y ago
  What makes it fundamentally impossible to know the origin of life? It seems we are likely to develop and refine experiments and theories that approximate the initial conditions and processes by which life took hold. Some of the details of how it happened are certainly lost to time, but it seems there's a lot of room for exploration towards a fairly valid model.
  - meetups323 5y ago
    We can know an origin of some life, but never the origin of our own life. It's simply not testable, and without tests it's not science.
    - ReactiveJelly 5y ago
      But to say that we could find several plausible theories and not know _something_ of value is teetering on Last Thursdayism.
      - meetups323 5y ago
        If I may use a programming analogy, the process described is akin to NPC agents in a browser based MMORPG Rowhammering a bunch of random bits into some exposed ArrayBuffer until a Counter div appears on the page, then claiming they have some deeper understanding of the origins of life in their universe. Do they have a deeper understanding? Perhaps. Have they come anywhere near the "origin of life"? Nope.
    - crazygringo 5y ago
      That's not how science works. You can't ever test anything in the past, so by your logic nothing in the past can be considered scientific. By your logic, plate tectonics can't explain the past movement of continents. Which is, of course, wrong. We can absolutely test aspects of a theory, verify its general validity, see that it best correlates with past evidence, and therefore infer past causes. Nothing of that is unscientific -- to the contrary, that's precisely how science works.
      - meetups323 5y ago
        If all we had was observations of modern day plate tectonics it would be foolish to back-propagate the same motions billions of years in reverse and claim ones methods were "scientific". Luckily, we have things like fossil records to justify such conclusions. They provide the second point with which we can "fit a curve" when exploring history. With this "origin of life" stuff, we don't have that second point of confirmation. We think up a bizarre process, execute it, and see that it produced some molecules that we see in modern day life. We then have the gall to say that we've discovered "the origins of life"? Yeah right... https://news.ycombinator.com/item?id=27974369 https://news.ycombinator.com/item?id=27974369
  - posterboy 5y ago
    I think they may be arguing semantics of knowing versus believing, and especially the loss of information to the eventual increase of entropy. I don't think there's a calculation to prove it because it would require a very thorough definition in the first place, which could be taken as a sufficient answer in its own right. The answer is of course 42. On another note, at "17 hours ago" and no response I guess they are still writing trying to work it out, or gave up, if they are anything like me and my random blurts
Koshkin 5y ago
> we will never really know how life started A big bang of another sort.
AprilArcus 5y ago
I think in our lifetimes, we'll know enough about the preconditions for abiogenesis to perform experiments replicating portions of the process in vitro.
- airstrike 5y ago
  I hope you're right, but at the same time I think I've expecting that since middle school and I'm now fast approaching my 40s...
- NotSwift 5y ago
  We know that it has been a very, very slow process and we don't really know where and under which conditions it happened. I hope that you are right, that we might be able to replicate portions of it. It might help us understand something more about what we call life. It might also help us understanding alternative forms of life that might exist on other planets.

aazaa 5y ago

> A more inclusive representation is to recognize a spectrum between the non-living and the living—a “grayness” resulting from the protracted evolutionary process that gave rise to life. The meaning of "grayness" would appear to have something to do with the fuzzy line between life and non-life. There is a footnote to the article "The Seven Pillars of Life": https://www.pps.net/cms/lib/OR01913224/Centricity/Domain/3337/SevenPillarsofLife.pdf https://www.pps.net/cms/lib/OR01913224/Centricity/Domain/333... But it doesn't mention grayness at all. This gets cleared up a little a few paragraphs in: > The ability to clearly distinguish between abiotic and biotic systems is considered by many a prerequisite for effective astrobiology studies. However, since no natural demarcation truly exists, there is a profound difficulty in advancing the field if we rely on a strict dichotomy. ...

macawfish 5y ago

I'm personally convinced at this point that most everyday distinctions between living and dead are arbitrary human categorizations. Even a "dead body" is teaming with life. As far as "inanimate matter" is concerned, all matter is ultimately part of a plethora of various different cycles and processes of transformation and recapitulation... even if something temporarily looks like it's static to us and our meager little narrow timeframe of experience, it's not. Just to clarify, I don't mean that these distinctions are meaningless, just that their meaning is inherently embedded in human experience.

jollybean 5y ago
That's a good thought - but worth considering that just because lines are fuzzy doesn't make them either 'arbitrary' or even 'subjective'. That a materialist perspective gives us some nice hard rules for understanding certain things, it also by definition struggles to help us understand the nature of other things, i.e. 'most important bit' which is 'life' itself, so maybe we should be thinking about that problem a little bit differently. 'Emergence' seems to be a least one idea, among many.
- guerrilla 5y ago
  > That's a good thought - but worth considering that just because lines are fuzzy doesn't make them either 'arbitrary' or even 'subjective'. Interesting and plausible, but you didn't give an argument or any example for that.
  - jollybean 5y ago
    For most things in the real life that we categorize, the rules that distinguish those categories can be vague. It doesn't mean those categories are not valid, or a function of 'human perception'. We have difficulty with biological distinction, but we can still confidently categorize something as being a 'Horse' and 'Not A Horse' ... even if sometimes it's a little bit ambiguous, aka 'Kind of a Horse'. Edit: and as for 'other ways of thinking' it very quickly goes into metaphysics so it's hard to talk about because we don't spend much time in that realm. 'Emergence' and 'Biocentrism' are interesting ideas (fields?) that sit within more or less regular bounds of science and so they're just examples of what I'm referring to.

antattack 5y ago

Motor proteins look alive: https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8

Koshkin 5y ago
As do these: https://www.youtube.com/watch?v=hsLJdpjSJcM&t=15s https://www.youtube.com/watch?v=hsLJdpjSJcM&t=15s
AprilArcus 5y ago
I love this animation because it's beautiful, but I hate that it gives the impression of deliberate one-foot-in-front-of-the-other movement. In reality, when the "foot" of the motor protein is unbound, it is oscillating to and fro in a state of brownian motion until it happens to snap into place at the next (or, infrequently but inevitably, the previous) subunit. At this scale, quantum effects such as tunneling come into play, and it would be cool to visualize the organized thermodynamic chaos of the cell rather than the mechanical operation of a homunculus.
- mncharity 5y ago
  > quantum effects such as tunneling come into play Really? I'd not have expected that. > but I hate that it gives the impression Oh yes. Rather than being towed, the payload explores its entire tethered configuration space between one step and the next. Not a donkey walking along a river towing a barge, but a mouse clinging to wire and a balloon a hurricane. The nanoscale moshpit from hell. It's like creating education content about human locomotion, for aliens completely unfamiliar with it, and with no sense of what's plausible, and showing them only one of those stop motion videos where someone floats along not touching the ground. An extremely biased selection of video frames to tell a very false narrative. Worse, this and other misconceptions engendered might be mitigated by very briefly including other representations... but the folks who created the video explicitly prioritize "pretty" over "do no harm". Which rather diminishes my appreciation of their beauty. > cool to visualize the organized thermodynamic Years ago I saw a video at a talk, of simulated viral icosahedral capsid assembly. The panels are tethered together, to maintain proximity, as they bounce and slam together and apart, incrementally assembling and misassembling. I wish I could link to it. If anyone knows of content to give a visceral feel for nanoscale dynamics, I'd appreciate hearing of it.

benlivengood 5y ago

I find it fascinating that abiotic chemical/physical cycles are considered an integral part of early life (e.g. if your nutrient transport is environmental osmosis/tides/whatever, you're still alive but the larger environment is an integral part of your biochemistry). From that perspective the freshwater cycle is still a major component of biochemistry (bulk ion transport) on Earth, despite arguably being a physical state change and not chemistry per se. The Sun provides photons that most cells need in order to live but Desulforudis audaxviator have decoupled themselves from that source of energy. In theory they could outlast the solar system or hitch a ride on a rogue planet.

perl4ever 5y ago
>The Sun provides photons that most cells need in order to live but Desulforudis audaxviator have decoupled themselves from that source of energy. In theory they could outlast the solar system or hitch a ride on a rogue planet. I suspect it's the opposite; first there was life and then it evolved to use sunlight. How did life arise on earth right after the rocks stopped being red hot? The only reasonable theory in my opinion is that the original life forms were inside the rocks on some jetsam that wasn't totally molten and if you go back further, lived off a little heat and water underground, quite possibly on a "rogue planet". One reason this seems obvious to me is that there must be orders of magnitude more planets without stars than with. Just like there are more asteroids than planets, more dim red stars than sun-like stars, etc. The other reason is that I think it helps a great deal with the Fermi paradox. If life just zapped into existence on Earth, 4.5 billion years ago, then it could've happened at any time, anywhere else, over the prior (almost) 10 billion years or so. But if it took most of that time, since the Big Bang, to develop what we think of as the most primitive life, in the much larger arena of rubble or rogue planets in deep space, then it looks more like we are the earliest life that could develop, and that's why we wouldn't have been overrun by space invaders. Looking the exponential development of life, even if you choose somewhat arbitrary milestones, it's basically a self-similar curve; each "step" takes a fraction of the previous one. Going backwards, each step should take the corresponding multiple. The great oxidation event was about 2.5 billion years ago. The first life we know about was about twice that. It seems to me a near perfect fit, timing wise, for the origin of that life to be about twice that ago, rather than suddenly arise from nothing in a few million years. What it comes down to is I think creationists who are skeptical of abiogenesis really have a good point, about how the simplest life is unbelievably complex, in spite of not having a viable theory to explain it. But I think the answer is staring us in the face. And of course panspermia isn't new or my idea particularly, but what bugs me is instead of saying there needs to be more evidence, it should be the default assumption. Our environment is just not representative of most of the universe even if you ignore non-baryonic dark matter.

divbzero 5y ago

A few offshoots from this line of thinking… Where do viruses sit on this scale of grayness? Yes, viruses have organic molecules, information storage systems, and compartmentalization. No, viruses do not have metal catalysis (correct me if I’m wrong) nor do they have energy currencies (they rely on hosts for energy). Viruses appear rather gray indeed. Can the grayness framework be modified/extended to describe superorganisms? Superorganisms like bee colonies are only mentioned in passing and the authors do not try to apply their grayness framework. Organic molecules and metal catalysis aren’t as relevant beyond the molecular scale, but information storage systems, energy currencies, and compartmentalization apply just as well to superorganisms. Perhaps those are the more generalizable attributes of life. I’m reminded of concepts from Schrödinger’s What Is Life?. Schrödinger describes local reduction of entropy to be a key feature — combining energy currencies with compartmentalization is one way to achieve that. Separately, he discusses the hereditary mechanism and suggests an “aperiodic crystal” could encode heritable information. What would be the contents of a sister article titled “The Grayness of the Origin of Consciousness”? I would love to see an outline.

new299 5y ago
> No, viruses do not have metal catalysis (correct me if I’m wrong) RNA viruses would generally have an RdRp polymerase which requires a metal ion.

amelius 5y ago

There is also grayness in the question "what is an individual organism?" For example, you can look at a single bacterium as an organism. But you can also look at a colony of bacteria as an organism.