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Prions are one of the things that makes me go, hey wait maybe we do live in a simulation. They're basically corrupted code (which we've yet to figure out how th

Prions are one of the things that makes me go, hey wait maybe we do live in a simulation. They're basically corrupted code (which we've yet to figure out how they get that way in the first place) that corrupts other code... what is that?!?! Reminds me a lot of the WoW 'corrupted blood incident'. I understand how something like bacteria or a virus enters a host and replicates, but an anomalous protein corrupting other protein is just so strange. I'm sure science will adequately explain it someday but until then it's a pretty WTF anomaly to me.

rantanplan 8y ago
We do live inside a simulation... of particles, called... the Universe.
AllegedAlec 8y ago
It's actually relatively simple. Proteins, very roughly speaking, are things that change other things into something we need. You could think of proteins required for breaking down sugar, which do more or less exactly that: they take a molecule of sugar, break a part off of it and hand it to the next protein in the chain. What makes prions so weird is that they are a protein that has been mismade (misfolded, generally). That something is being made broken isn't that weird in biology. Mostly, the body degrades them pretty quickly. However, prions, while not being able to do what they're meant to do, can take well-made versions of itself and break them in the same manner.
- ryanmercer 8y ago
  >What makes prions so weird is that they are a protein that has been mismade (misfolded, generally). And science doesn't know how they get misfolded in the first place then they basically go "hey other protein, boop you're like me now, let's burn this mother to the ground" and then you get something similar to the 'corrupted blood incident' https://en.wikipedia.org/wiki/Corrupted_Blood_incident https://en.wikipedia.org/wiki/Corrupted_Blood_incident except you lose your mind and die. As far as saying we know how proteins misfold, I'm going purely by what I've read both on and on wikipedia as I'm not an expert in proteins and amino acids... >It is not known what causes the normal protein to misfold Second sentence of: https://en.wikipedia.org/wiki/Prion https://en.wikipedia.org/wiki/Prion
  - Balero 8y ago
    There are plenty of ways that a protein could be mis-folded. There is a lot of bumpiness in a cell (though this is unlikely to lead to this). A random mutation (through some sort of radiation) could change a piece of DNA or RNA, causing the protein to be made incorrectly. All of these are frighteningly unlikely. But happen so often they are almost certain to do so in a large enough time, with a large enough population. The similarities to the 'corrupted blood incident' start and end with them both spreading to others in a local area. Prions don't really suggest that life is a simulation.
    - jerf 8y ago
      "Prions don't really suggest that life is a simulation." If life is a simulation, prions suggest either the simulation is run at an extremely high degree of verisimilitude, indeed simulating QM at a particle level for living things, or that the simulator has an incredible desire for accuracy, and has put a lot of non-trivial work into ensuring it. Almost anything you can think of that would reduce the computational load for simulating a human being would eliminate the possibility of prions arising in the first place, since "protein folding" is one of the first things you'd want to get rid of to cut the load down.
      - ryanmercer 8y ago
        >If life is a simulation, prions suggest either the simulation is run at an extremely high degree of verisimilitude, indeed simulating QM at a particle level for living things, or that the simulator has an incredible desire for accuracy, These are both somewhat my logic for even believing we live in a simulation. Obviously humans seem to be the largest factor on Earth given how we are rapidly changing the planet and directly, and indirectly, affecting all life on the planet. We already have things like folding@home, weather modelling, climate modelling, asteroids@home, cosmology simulations from universe sandbox to supercomputer level, etc etc so on and so forth. People love to immediately dismiss a simulation hypothesis "stuff is too detailed!" "why would someone use such specificity!". Well, why would anyone watch the Kardashians or eat hair (Trichophagia) or smoke cigarettes because none of these things are rational... however having a highly detailed simulation has all sorts of potential applications from seeing how ancestors may have evolved to seeing how a designer organism might potentially play out on a sterile world you plan to seed to being someone's incredible version of the Sims. I mean, WE have the desire to do this sort of stuff. The above mentioned distributed computing and supercomputer applications shows some level of desire for this sort of thing but then you have games like SimLife from 1992 that allowed players to simulate an ecosystem and to modify the genetics of the plants and animals in the game. 'Junk' DNA, prions, viruses, erm consciousness, burning fossil fuels to the tune of roughly 40 gigatons of carbon dioxide emissions this year, living in coastal cities at or below sea level even AFTER disasters do considerable damage, the rapid adoption of social media and reality television, all of these things seriously make me wonder if we in fact are some sort of simulation just to see how a species can deal with both environmental and self-caused disasters. Throw in many other things like the fact we've not detected life off-world, we've yet to detect any signs of another intelligent species (mind you we're just starting to really look), the rapid advances we've made in technology just in the 33 years of my life, technology allowing for us to fake audio and video of people that enough reference data exists for and things like this Chinese virtual news anchor, etc and it becomes really easy to go "huh, maybe we DO live in a simulation".
mrob 8y ago
At the molecular scale, everything is effectively made of springs (molecular and intermolecular bonds). Proteins are a big complicated tangle of springs, and that means they have multiple possible configurations they can spring to if you let them relax. If you bump another protein of the right shape against them, you can nudge them into a different spring configuration. Think of "slap bracelets", those curved metal strips that spring around your wrist. If you push two straight ones together, nothing happens. But if you push a curled one against a straight one it will make the straight one curl up too. The curled slap bracelet is acting like a prion.
- ryanmercer 8y ago
  >Think of "slap bracelets", those curved metal strips that spring around your wrist Wow, I've not heard someone mention those in probably 2 decades.
hannasanarion 8y ago
But prions aren't code. DNA is code. Proteins are factory robots, and the prion protein is a factory robot involved in the process of making factory robots. Neural proteins are very complicated, so they need other proteins to help them fold properly. One of these protein-folding-proteins (PRNP) can be mis-folded in such a way that it mis-folds other proteins in the same way that it is mis-folded itself. When most factory robots break, they simply stop working and they get recycled. But when a robot-making robot breaks in just the right way, it starts producing robot-making-robots that are broken just like itself.
- ryanmercer 8y ago
  >But prions aren't code. It was an analogy and reading https://en.wikipedia.org/wiki/Proteopathy#Seeded_induction https://en.wikipedia.org/wiki/Proteopathy#Seeded_induction it sounds very much like they act like a piece of code corrupting another piece of code >Some proteins can be induced to form abnormal assemblies by exposure to the same (or similar) protein that has folded into a disease-causing conformation, a process called 'seeding' or 'permissive templating' That sounds a lot like many computer viruses >A computer virus is a type of malicious software that, when executed, replicates itself by modifying other computer programs and inserting its own code
lolc 8y ago
Protein chains are used by all living cells to manufacture the molecules we're made of. They arrange soure material into new molecules. Many proteins are intended to manufacture themselves. This capability is usually tightly regulated by availability of the source materials within cells. Prions are proteins too. And they can create themselves from source material too. But their source material are proteins which are not intended for processing. As such, prions are defined like weeds in a garden: They're not supposed to be there. Marvel at the wonderful world that is biology: https://en.wikipedia.org/wiki/Protein https://en.wikipedia.org/wiki/Protein

rantanplan 8y ago

We do live inside a simulation... of particles, called... the Universe.

AllegedAlec 8y ago

It's actually relatively simple. Proteins, very roughly speaking, are things that change other things into something we need. You could think of proteins required for breaking down sugar, which do more or less exactly that: they take a molecule of sugar, break a part off of it and hand it to the next protein in the chain. What makes prions so weird is that they are a protein that has been mismade (misfolded, generally). That something is being made broken isn't that weird in biology. Mostly, the body degrades them pretty quickly. However, prions, while not being able to do what they're meant to do, can take well-made versions of itself and break them in the same manner.

ryanmercer 8y ago
>What makes prions so weird is that they are a protein that has been mismade (misfolded, generally). And science doesn't know how they get misfolded in the first place then they basically go "hey other protein, boop you're like me now, let's burn this mother to the ground" and then you get something similar to the 'corrupted blood incident' https://en.wikipedia.org/wiki/Corrupted_Blood_incident https://en.wikipedia.org/wiki/Corrupted_Blood_incident except you lose your mind and die. As far as saying we know how proteins misfold, I'm going purely by what I've read both on and on wikipedia as I'm not an expert in proteins and amino acids... >It is not known what causes the normal protein to misfold Second sentence of: https://en.wikipedia.org/wiki/Prion https://en.wikipedia.org/wiki/Prion
- Balero 8y ago
  There are plenty of ways that a protein could be mis-folded. There is a lot of bumpiness in a cell (though this is unlikely to lead to this). A random mutation (through some sort of radiation) could change a piece of DNA or RNA, causing the protein to be made incorrectly. All of these are frighteningly unlikely. But happen so often they are almost certain to do so in a large enough time, with a large enough population. The similarities to the 'corrupted blood incident' start and end with them both spreading to others in a local area. Prions don't really suggest that life is a simulation.
  - jerf 8y ago
    "Prions don't really suggest that life is a simulation." If life is a simulation, prions suggest either the simulation is run at an extremely high degree of verisimilitude, indeed simulating QM at a particle level for living things, or that the simulator has an incredible desire for accuracy, and has put a lot of non-trivial work into ensuring it. Almost anything you can think of that would reduce the computational load for simulating a human being would eliminate the possibility of prions arising in the first place, since "protein folding" is one of the first things you'd want to get rid of to cut the load down.
    - ryanmercer 8y ago
      >If life is a simulation, prions suggest either the simulation is run at an extremely high degree of verisimilitude, indeed simulating QM at a particle level for living things, or that the simulator has an incredible desire for accuracy, These are both somewhat my logic for even believing we live in a simulation. Obviously humans seem to be the largest factor on Earth given how we are rapidly changing the planet and directly, and indirectly, affecting all life on the planet. We already have things like folding@home, weather modelling, climate modelling, asteroids@home, cosmology simulations from universe sandbox to supercomputer level, etc etc so on and so forth. People love to immediately dismiss a simulation hypothesis "stuff is too detailed!" "why would someone use such specificity!". Well, why would anyone watch the Kardashians or eat hair (Trichophagia) or smoke cigarettes because none of these things are rational... however having a highly detailed simulation has all sorts of potential applications from seeing how ancestors may have evolved to seeing how a designer organism might potentially play out on a sterile world you plan to seed to being someone's incredible version of the Sims. I mean, WE have the desire to do this sort of stuff. The above mentioned distributed computing and supercomputer applications shows some level of desire for this sort of thing but then you have games like SimLife from 1992 that allowed players to simulate an ecosystem and to modify the genetics of the plants and animals in the game. 'Junk' DNA, prions, viruses, erm consciousness, burning fossil fuels to the tune of roughly 40 gigatons of carbon dioxide emissions this year, living in coastal cities at or below sea level even AFTER disasters do considerable damage, the rapid adoption of social media and reality television, all of these things seriously make me wonder if we in fact are some sort of simulation just to see how a species can deal with both environmental and self-caused disasters. Throw in many other things like the fact we've not detected life off-world, we've yet to detect any signs of another intelligent species (mind you we're just starting to really look), the rapid advances we've made in technology just in the 33 years of my life, technology allowing for us to fake audio and video of people that enough reference data exists for and things like this Chinese virtual news anchor, etc and it becomes really easy to go "huh, maybe we DO live in a simulation".

mrob 8y ago

At the molecular scale, everything is effectively made of springs (molecular and intermolecular bonds). Proteins are a big complicated tangle of springs, and that means they have multiple possible configurations they can spring to if you let them relax. If you bump another protein of the right shape against them, you can nudge them into a different spring configuration. Think of "slap bracelets", those curved metal strips that spring around your wrist. If you push two straight ones together, nothing happens. But if you push a curled one against a straight one it will make the straight one curl up too. The curled slap bracelet is acting like a prion.

ryanmercer 8y ago
>Think of "slap bracelets", those curved metal strips that spring around your wrist Wow, I've not heard someone mention those in probably 2 decades.

hannasanarion 8y ago

But prions aren't code. DNA is code. Proteins are factory robots, and the prion protein is a factory robot involved in the process of making factory robots. Neural proteins are very complicated, so they need other proteins to help them fold properly. One of these protein-folding-proteins (PRNP) can be mis-folded in such a way that it mis-folds other proteins in the same way that it is mis-folded itself. When most factory robots break, they simply stop working and they get recycled. But when a robot-making robot breaks in just the right way, it starts producing robot-making-robots that are broken just like itself.

ryanmercer 8y ago
>But prions aren't code. It was an analogy and reading https://en.wikipedia.org/wiki/Proteopathy#Seeded_induction https://en.wikipedia.org/wiki/Proteopathy#Seeded_induction it sounds very much like they act like a piece of code corrupting another piece of code >Some proteins can be induced to form abnormal assemblies by exposure to the same (or similar) protein that has folded into a disease-causing conformation, a process called 'seeding' or 'permissive templating' That sounds a lot like many computer viruses >A computer virus is a type of malicious software that, when executed, replicates itself by modifying other computer programs and inserting its own code

lolc 8y ago

Protein chains are used by all living cells to manufacture the molecules we're made of. They arrange soure material into new molecules. Many proteins are intended to manufacture themselves. This capability is usually tightly regulated by availability of the source materials within cells. Prions are proteins too. And they can create themselves from source material too. But their source material are proteins which are not intended for processing. As such, prions are defined like weeds in a garden: They're not supposed to be there. Marvel at the wonderful world that is biology: https://en.wikipedia.org/wiki/Protein https://en.wikipedia.org/wiki/Protein