4 ms·

I am not under the impression folding proteins is a state-change, and it's also unclear to me if it is a chemical reaction, so I do not think I understand the r

by nawgz 5y ago

I am not under the impression folding proteins is a state-change, and it's also unclear to me if it is a chemical reaction, so I do not think I understand the relevance of this point. I specifically stated the parameters.

sp332 5y ago
It's not a chemical change. Neither is ice forming from water.
- nawgz 5y ago
  Yes, clearly ice <-> water is a state change and not chemical, but my point is mostly that prions / protein folding is neither a state-change nor a chemical change, so I don't see how it's relevant to the posited scenario.
  - beecafe 5y ago
    A prion causing other proteins to misfold can only occur if the misfolded state has lower energy than the correctly folded one. It does this by acting as a catalyst, lowering the potential energy barrier that was allowing the protein to persist in the correctly folded state, to the point where e.g thermal fluctuations allow it to cross that barrier. The equivalent could occur if there was a lower energy state for water (and an ice-9 like scenario could then occur if this lower energy state catalyzed further transitions to this lower energy state). We don't expect this to be possible though, as we can't make water decay by other ways of making it cross that hypothetical potential energy barrier by dumping energy into it (whereas for a protein you can e.g burn it, denature it, etc), and aren't aware of catalytic activity by any forms of water.
    - nawgz 5y ago
      Thanks for the comment. Thinking out loud, for prions is not the requirement that they "[act] as a catalyst, lowering the potential energy barrier ... to the point where e.g thermal fluctuations allow it to cross that barrier" also a guarantee against this type of ice-9 "infection" scenario, because the equilibrium of the environment itself would be so impacted and be absorbing that energy and then causing unfavorable conditions to the reaction at the reaction's frontier even? I more-or-less equate that to the "supercooled water + normal ice" reaction of how much energy delta you can create allows you to make a small energy explosion reaction/state-change/etc that isn't truly an "infection" but just a localized energy transfer. But okay, after stating this very interesting mechanism in that form, I see the point being made by others. This catalyst-style mechanism which can induce physical changes in the environment without itself changing could be exploited on scales that would allow one to "maliciously/adversarially" create a chemical / energized substance that would catalyze say a lake or an ocean into freezing / sublimating. However, I find it impossible to see how such a transition could be found for water though, and it seems to me the nature of the prion & proteins is that the prion requires some level of complexity in the matter it interacts with to cause this energy transition. For more exotic substances than water, or perhaps water which itself holds a large amount of solutes satisfying some characteristic, I could see it. I appreciate your insight into this matter clarifying the prion mechanism especially. I am also not well educated on these matters so hopefully it doesn't stink too bad :)
      - beecafe 5y ago
        It depends. Tin pest is an autocalaytic reaction that doesn't produce enough energy to destabilize its own progression. One could say the same for rust, as it flakes and is porous allowing further rusting. Or the chain reaction could proceed faster than the environmental changes destabilize it - like a nuclear chain reaction, or metastable vacuum collapse. Or it could self regulate into a steady state, like a nuclear reactor. Also consider that the energy released could itself cause further reactions - like a fire. See https://en.m.wikipedia.org/wiki/Autocatalysis https://en.m.wikipedia.org/wiki/Autocatalysis for more. Yes, it seems unlikely that any such transition exists for liquid water - a water molecule doesn't have any molecular degrees of freedom like a protein does, nor any easy way to extract energy from it (it's "already burnt"), and we haven't found any exotic structures of water that are stable at atmospheric pressures.
        nawgz 5y ago
        All very interesting points. Appreciate the insights.
rocqua 5y ago
Both are, essentially, about crystalline structure. That sounds quite similar to a phase change to me. Especially if we consider ice to have multiple phases.
- nawgz 5y ago
  Yes, I see your point. I disagree for water such a phase change could be discovered under earth-like conditions, but I can see how "sufficiently complex" substances with reasonable energy deltas in their phase-/structural-changes could be "attacked/exploited/triggered" to look like an infection-style reaction. My stream of conscious while realizing this is here: [0] [0] https://news.ycombinator.com/item?id=28925835 https://news.ycombinator.com/item?id=28925835

by nawgz 5y ago

sp332 5y ago

It's not a chemical change. Neither is ice forming from water.

nawgz 5y ago
Yes, clearly ice <-> water is a state change and not chemical, but my point is mostly that prions / protein folding is neither a state-change nor a chemical change, so I don't see how it's relevant to the posited scenario.
- beecafe 5y ago
  A prion causing other proteins to misfold can only occur if the misfolded state has lower energy than the correctly folded one. It does this by acting as a catalyst, lowering the potential energy barrier that was allowing the protein to persist in the correctly folded state, to the point where e.g thermal fluctuations allow it to cross that barrier. The equivalent could occur if there was a lower energy state for water (and an ice-9 like scenario could then occur if this lower energy state catalyzed further transitions to this lower energy state). We don't expect this to be possible though, as we can't make water decay by other ways of making it cross that hypothetical potential energy barrier by dumping energy into it (whereas for a protein you can e.g burn it, denature it, etc), and aren't aware of catalytic activity by any forms of water.
  - nawgz 5y ago
    Thanks for the comment. Thinking out loud, for prions is not the requirement that they "[act] as a catalyst, lowering the potential energy barrier ... to the point where e.g thermal fluctuations allow it to cross that barrier" also a guarantee against this type of ice-9 "infection" scenario, because the equilibrium of the environment itself would be so impacted and be absorbing that energy and then causing unfavorable conditions to the reaction at the reaction's frontier even? I more-or-less equate that to the "supercooled water + normal ice" reaction of how much energy delta you can create allows you to make a small energy explosion reaction/state-change/etc that isn't truly an "infection" but just a localized energy transfer. But okay, after stating this very interesting mechanism in that form, I see the point being made by others. This catalyst-style mechanism which can induce physical changes in the environment without itself changing could be exploited on scales that would allow one to "maliciously/adversarially" create a chemical / energized substance that would catalyze say a lake or an ocean into freezing / sublimating. However, I find it impossible to see how such a transition could be found for water though, and it seems to me the nature of the prion & proteins is that the prion requires some level of complexity in the matter it interacts with to cause this energy transition. For more exotic substances than water, or perhaps water which itself holds a large amount of solutes satisfying some characteristic, I could see it. I appreciate your insight into this matter clarifying the prion mechanism especially. I am also not well educated on these matters so hopefully it doesn't stink too bad :)
    - beecafe 5y ago
      It depends. Tin pest is an autocalaytic reaction that doesn't produce enough energy to destabilize its own progression. One could say the same for rust, as it flakes and is porous allowing further rusting. Or the chain reaction could proceed faster than the environmental changes destabilize it - like a nuclear chain reaction, or metastable vacuum collapse. Or it could self regulate into a steady state, like a nuclear reactor. Also consider that the energy released could itself cause further reactions - like a fire. See https://en.m.wikipedia.org/wiki/Autocatalysis https://en.m.wikipedia.org/wiki/Autocatalysis for more. Yes, it seems unlikely that any such transition exists for liquid water - a water molecule doesn't have any molecular degrees of freedom like a protein does, nor any easy way to extract energy from it (it's "already burnt"), and we haven't found any exotic structures of water that are stable at atmospheric pressures.
      - nawgz 5y ago
        All very interesting points. Appreciate the insights.

rocqua 5y ago

Both are, essentially, about crystalline structure. That sounds quite similar to a phase change to me. Especially if we consider ice to have multiple phases.

nawgz 5y ago
Yes, I see your point. I disagree for water such a phase change could be discovered under earth-like conditions, but I can see how "sufficiently complex" substances with reasonable energy deltas in their phase-/structural-changes could be "attacked/exploited/triggered" to look like an infection-style reaction. My stream of conscious while realizing this is here: [0] [0] https://news.ycombinator.com/item?id=28925835 https://news.ycombinator.com/item?id=28925835