4 ms·

Very impressive! To be clear, this is not the smallest known bacterial genome; only the smallest known archaeal bacterial genome, at 238k base pairs. In the ar

Very impressive! To be clear, this is not the smallest known bacterial genome; only the smallest known archaeal bacterial genome, at 238k base pairs. In the article they mention C. ruddii, with a smaller 159k base pair genome. But according to wikipedia, it seems N. deltocephalinicola, at 112k base pairs, may be the smallest known bacterial genome. https://en.wikipedia.org/wiki/Nasuia_deltocephalinicola https://en.wikipedia.org/wiki/Nasuia_deltocephalinicola

flobosg 10mo ago
A nitpick: Although similar in some aspects, archaea are not bacteria; they are classified under their own phylogenetic domain.
api 10mo ago
[flagged]
- smallmancontrov 10mo ago
  1. Autocatalytic RNA reaction networks -- "soup producing more soup" -- are easily replicated in the lab, subject to Darwinean processes, and are at the center of ongoing study. "0 to Darwin" is now easy, "Darwin to Life" is the new focus, and God of the Gaps must retreat once again. 2. Spores hitchhiking on impact ejecta sounds exotic until you realize that anywhere life is present at all spores will be everywhere and extremely sturdy. That desktop wallpaper you have of planets crashing together and kicking off an epic debris cloud? Everything not molten is full of spores. 3. Religious explanations are not in the same universe of seriousness as 1 and 2. Opening with a religious talking point and closing with a false equivalence is mega sus.
  - bavell 10mo ago
    Would love to see some sources for #1. #2 sounds plausible but speculative?
    - smallmancontrov 10mo ago
      RNA World is really cooking: https://pubmed.ncbi.nlm.nih.gov/39358873/ https://pubmed.ncbi.nlm.nih.gov/39358873/ Ejection: https://link.springer.com/chapter/10.1007/3-540-25736-5_3 https://link.springer.com/chapter/10.1007/3-540-25736-5_3 Reentry: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132611 https://journals.plos.org/plosone/article?id=10.1371/journal... Not to mention the constant trickle of "X survived in space" stories that we get every time someone bothers to collect and culture a sample. The amount of success at every stage with, frankly, very little effort spent tuning the conditions, multiplied by "bacteria are everywhere" makes hitchhiking less crazy than it sounds. Our intuition misleads us because bacteria are so much better at handling acceleration (easy if you're small) and dessiccation (everywhere is a desert if you're small) than anything we are used to thinking about.
      - Egret 10mo ago
        https://pmc.ncbi.nlm.nih.gov/articles/PMC1892545/ https://pmc.ncbi.nlm.nih.gov/articles/PMC1892545/ An upper bound probability for the RNA world hypothesis is 10^-1018. A reasonable interpretation is that the RNA world hypothesis is impossible in the real world.
        avadodin 10mo ago
        A superficial reading doesn't inspire much confidence in this peer-reviewed article but I agree that RNA-world is a thought experiment at best. There is no evidence of these RNA structures in actual lifeforms. RNA encodes proteins. The most parsimonious explanation is that proteins(likely incapable of true replication by themselves) preceded RNA even if an RNA-based system can be designed in theory. I won't make claims of probability of unknown processes but proteins exist that can assemble spare nucleotides and proteins exist that can assemble proteins out of nucleotide chains. All you need is a pair of them to come in the vicinity of each other and wait until RNA comes along that encodes a similar-enough pair.
        Egret 10mo ago
  - cozyman 10mo ago
    [flagged]
  - deleted 10mo ago
    [deleted]
- alonmower 10mo ago
  If you’re interested in this area I highly recommend “The Vital Question” by Nick Lane if you haven’t read it. The TLDR of his theory is that life originated in alkaline hydrothermal vents on the ocean floor, where natural energy gradients could have driven primitive metabolic reactions before the development of DNA. Book goes into a lot of layperson-accessible detail.
- ferfumarma 10mo ago
  > Still far, far too complex to occur "randomly," which is fascinating Why spend time making this point? Nobody believes that this occurred randomly: it occurred via evolution. The mutations are a random part of evolution, but the process overall is not random at all - no more so than your immune system (which randomly generates antibodies, then selects against those that target innate epitopes), or stable diffusion (which starts with random noise, then marches up a gradient toward a known target). It is the selection step that makes similar processes non-random, because a random selection step would just be noise.
  - threethirtytwo 10mo ago
    This is technically random. The entire creationist argument is that complexity cannot come from randomness but evolution is the method in which it does. Evolution is just a sort of way for low entropy structures to form from randomness. It’s still random all the way down. The man is just trying to reconcile a belief in god with the scientific reality. He needs to bend the evidence to fit his identity he cannot bend his identity to fit the evidence because that could break his identity. The fact he commented here on this topic is sort of unhinged. It seems like the article presented evidence that is strikingly against his world view and he needed to justify something in order to prevent his identity from rearranging itself according to external reality.
    - cozyman 10mo ago
      [flagged]
      - threethirtytwo 10mo ago
        Easy. Covid evolved forms. The genes are different. There are measurable differences in DNA. These are slight. So from real time observation we know viruses and bacteria can mutate and have small delta changes in their DNA. From this we can deduce that over long period of time many small changes can equate to big changes in DNA. Because we know DNA describes macro characteristics of all living beings and effects behavior, physicality and speciation by logic we know that through induction many many small changes together equals big change and thus evolution can result in speciation and different creatures. This is the literal conclusion through Direct observation and the inescapable logic of induction. Not to mention it's inline with fossil evidence AND covid is clearly not the only species where we observe mutations. Mutations are observed everywhere, including humans. Cancer is mutation and selection as well.
- 0134340 10mo ago
  >Still far, far too complex to occur "randomly," which is fascinating I don't see the word "random" anywhere in the article. By random maybe you mean it's seemingly indeterministic? Regardless of the nature of the underlying process, at the classical level, the environment acts as a deterministic filter, ie, other chemical processes.
- estimator7292 10mo ago
  Good news: the primordial oceans were so vast (literally planet-scale) and persisted for so long (millions to billions of years) that you can run a trillion trillion individual random reactions. You are being severely restricted by your imagination. You seem to have presupposed that random abiogenesis is impossible and reconstructed the facts to support that claim because you can't conceive of the alternative. Planets are really, really big. Any one chemical reaction is on the scale of molecules. If you let those figures compound for a long time, the number of total reactions gets very, very large. Far larger than you imagine. Many times more.
  - reedlaw 10mo ago
    The probability space of a 140-nucleotide chain is 10^84. The estimated number of atoms in the universe is 10^80. The hypothesized RNA self-replicator is far simpler than the 238,000 base pair archaeal genome. But how are they formed? Even the most favorable prebiotic lab conditions have only produced short nucleotide chains. Direct chemical synthesis only recently achieved chains over 1700 nucleotides long [1]. 1. https://www.chemistryworld.com/news/first-direct-chemical-synthesis-of-a-gene-over-1700-nucleotides-long/4020938.article https://www.chemistryworld.com/news/first-direct-chemical-sy...
    - oskarkk 10mo ago
      To go through all 10^84 possible combinations in a billion years, around 10^67 combinations would have to be "tried" per second. So yeah, it doesn't seem feasible to have one and only correct combination of 140 nucleotides spontaneously appear. But if the "solution" could be composed of a couple of separate smaller parts, that would be stable and linger for a long time, it would be much easier. 40 nucleotides have 10^24 combinations, so only 10^7 tries per second would be needed... over a billion years. And all of the necessary parts would need to be created and then meet in the same place and somehow combine. So, still not easy, but this case doesn't sound so outrageously improbable. In the end, maybe it is extremely improbable for life to happen, and only one in 10^n suitable planets develops life, and Earth was just very lucky to experience this peculiar phenomenon.
  - 10mo ago
oersted 10mo ago
That’s interesting. The main difference seems to be that those other tiny organisms only encode how to produce some metabolic products for the host but cannot reproduce independently, so they are quite close to being organelles. Instead, this new one pretty much only produces the proteins it needs to reproduce and nothing for the host. The new one with 238 kbp: > Sukunaarchaeum encodes the barest minimum of proteins for its own replication, and that’s about all. Most strangely, its genome is missing any hints of the genes required to process and build molecules, outside of those needed to reproduce. Referencing the 159 kbp one: > However, these and other super-small bacteria have metabolic genes to produce nutrients, such as amino acids and vitamins, for their hosts. Instead, their genome has cast off much of their ability to reproduce on their own.

flobosg 10mo ago

A nitpick: Although similar in some aspects, archaea are not bacteria; they are classified under their own phylogenetic domain.

api 10mo ago

[flagged]

smallmancontrov 10mo ago
1. Autocatalytic RNA reaction networks -- "soup producing more soup" -- are easily replicated in the lab, subject to Darwinean processes, and are at the center of ongoing study. "0 to Darwin" is now easy, "Darwin to Life" is the new focus, and God of the Gaps must retreat once again. 2. Spores hitchhiking on impact ejecta sounds exotic until you realize that anywhere life is present at all spores will be everywhere and extremely sturdy. That desktop wallpaper you have of planets crashing together and kicking off an epic debris cloud? Everything not molten is full of spores. 3. Religious explanations are not in the same universe of seriousness as 1 and 2. Opening with a religious talking point and closing with a false equivalence is mega sus.
- bavell 10mo ago
  Would love to see some sources for #1. #2 sounds plausible but speculative?
  - smallmancontrov 10mo ago
    RNA World is really cooking: https://pubmed.ncbi.nlm.nih.gov/39358873/ https://pubmed.ncbi.nlm.nih.gov/39358873/ Ejection: https://link.springer.com/chapter/10.1007/3-540-25736-5_3 https://link.springer.com/chapter/10.1007/3-540-25736-5_3 Reentry: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132611 https://journals.plos.org/plosone/article?id=10.1371/journal... Not to mention the constant trickle of "X survived in space" stories that we get every time someone bothers to collect and culture a sample. The amount of success at every stage with, frankly, very little effort spent tuning the conditions, multiplied by "bacteria are everywhere" makes hitchhiking less crazy than it sounds. Our intuition misleads us because bacteria are so much better at handling acceleration (easy if you're small) and dessiccation (everywhere is a desert if you're small) than anything we are used to thinking about.
    - Egret 10mo ago
      https://pmc.ncbi.nlm.nih.gov/articles/PMC1892545/ https://pmc.ncbi.nlm.nih.gov/articles/PMC1892545/ An upper bound probability for the RNA world hypothesis is 10^-1018. A reasonable interpretation is that the RNA world hypothesis is impossible in the real world.
      - avadodin 10mo ago
        A superficial reading doesn't inspire much confidence in this peer-reviewed article but I agree that RNA-world is a thought experiment at best. There is no evidence of these RNA structures in actual lifeforms. RNA encodes proteins. The most parsimonious explanation is that proteins(likely incapable of true replication by themselves) preceded RNA even if an RNA-based system can be designed in theory. I won't make claims of probability of unknown processes but proteins exist that can assemble spare nucleotides and proteins exist that can assemble proteins out of nucleotide chains. All you need is a pair of them to come in the vicinity of each other and wait until RNA comes along that encodes a similar-enough pair.
        Egret 10mo ago
- cozyman 10mo ago
  [flagged]
- deleted 10mo ago
  [deleted]
alonmower 10mo ago
If you’re interested in this area I highly recommend “The Vital Question” by Nick Lane if you haven’t read it. The TLDR of his theory is that life originated in alkaline hydrothermal vents on the ocean floor, where natural energy gradients could have driven primitive metabolic reactions before the development of DNA. Book goes into a lot of layperson-accessible detail.
ferfumarma 10mo ago
> Still far, far too complex to occur "randomly," which is fascinating Why spend time making this point? Nobody believes that this occurred randomly: it occurred via evolution. The mutations are a random part of evolution, but the process overall is not random at all - no more so than your immune system (which randomly generates antibodies, then selects against those that target innate epitopes), or stable diffusion (which starts with random noise, then marches up a gradient toward a known target). It is the selection step that makes similar processes non-random, because a random selection step would just be noise.
- threethirtytwo 10mo ago
  This is technically random. The entire creationist argument is that complexity cannot come from randomness but evolution is the method in which it does. Evolution is just a sort of way for low entropy structures to form from randomness. It’s still random all the way down. The man is just trying to reconcile a belief in god with the scientific reality. He needs to bend the evidence to fit his identity he cannot bend his identity to fit the evidence because that could break his identity. The fact he commented here on this topic is sort of unhinged. It seems like the article presented evidence that is strikingly against his world view and he needed to justify something in order to prevent his identity from rearranging itself according to external reality.
  - cozyman 10mo ago
    [flagged]
    - threethirtytwo 10mo ago
      Easy. Covid evolved forms. The genes are different. There are measurable differences in DNA. These are slight. So from real time observation we know viruses and bacteria can mutate and have small delta changes in their DNA. From this we can deduce that over long period of time many small changes can equate to big changes in DNA. Because we know DNA describes macro characteristics of all living beings and effects behavior, physicality and speciation by logic we know that through induction many many small changes together equals big change and thus evolution can result in speciation and different creatures. This is the literal conclusion through Direct observation and the inescapable logic of induction. Not to mention it's inline with fossil evidence AND covid is clearly not the only species where we observe mutations. Mutations are observed everywhere, including humans. Cancer is mutation and selection as well.
0134340 10mo ago
>Still far, far too complex to occur "randomly," which is fascinating I don't see the word "random" anywhere in the article. By random maybe you mean it's seemingly indeterministic? Regardless of the nature of the underlying process, at the classical level, the environment acts as a deterministic filter, ie, other chemical processes.
estimator7292 10mo ago
Good news: the primordial oceans were so vast (literally planet-scale) and persisted for so long (millions to billions of years) that you can run a trillion trillion individual random reactions. You are being severely restricted by your imagination. You seem to have presupposed that random abiogenesis is impossible and reconstructed the facts to support that claim because you can't conceive of the alternative. Planets are really, really big. Any one chemical reaction is on the scale of molecules. If you let those figures compound for a long time, the number of total reactions gets very, very large. Far larger than you imagine. Many times more.
- reedlaw 10mo ago
  The probability space of a 140-nucleotide chain is 10^84. The estimated number of atoms in the universe is 10^80. The hypothesized RNA self-replicator is far simpler than the 238,000 base pair archaeal genome. But how are they formed? Even the most favorable prebiotic lab conditions have only produced short nucleotide chains. Direct chemical synthesis only recently achieved chains over 1700 nucleotides long [1]. 1. https://www.chemistryworld.com/news/first-direct-chemical-synthesis-of-a-gene-over-1700-nucleotides-long/4020938.article https://www.chemistryworld.com/news/first-direct-chemical-sy...
  - oskarkk 10mo ago
    To go through all 10^84 possible combinations in a billion years, around 10^67 combinations would have to be "tried" per second. So yeah, it doesn't seem feasible to have one and only correct combination of 140 nucleotides spontaneously appear. But if the "solution" could be composed of a couple of separate smaller parts, that would be stable and linger for a long time, it would be much easier. 40 nucleotides have 10^24 combinations, so only 10^7 tries per second would be needed... over a billion years. And all of the necessary parts would need to be created and then meet in the same place and somehow combine. So, still not easy, but this case doesn't sound so outrageously improbable. In the end, maybe it is extremely improbable for life to happen, and only one in 10^n suitable planets develops life, and Earth was just very lucky to experience this peculiar phenomenon.
- 10mo ago

oersted 10mo ago

That’s interesting. The main difference seems to be that those other tiny organisms only encode how to produce some metabolic products for the host but cannot reproduce independently, so they are quite close to being organelles. Instead, this new one pretty much only produces the proteins it needs to reproduce and nothing for the host. The new one with 238 kbp: > Sukunaarchaeum encodes the barest minimum of proteins for its own replication, and that’s about all. Most strangely, its genome is missing any hints of the genes required to process and build molecules, outside of those needed to reproduce. Referencing the 159 kbp one: > However, these and other super-small bacteria have metabolic genes to produce nutrients, such as amino acids and vitamins, for their hosts. Instead, their genome has cast off much of their ability to reproduce on their own.