6 ms·

I really do not understand viruses. Given that viruses do not have a metabolism and are not able to produce their own energy, how do these satellite viruses th

by alyx 3y ago

I really do not understand viruses. Given that viruses do not have a metabolism and are not able to produce their own energy, how do these satellite viruses then survive off of other viruses? I don't even understand how without energy producing mechanisms viruses can survive, propagate, etc. Can anybody recommend any good books on the matter?

quonn 3y ago
The propagate by entering cells that do produce their energy? Theoretically not producing spendable energy would not exclude activity either as long as some previously made energy is spent.
- alyx 3y ago
  How do you "enter a cell" without exerting energy?
  - dist-epoch 3y ago
    You convince the cell to bring you in. Or you "store" energy when you are built - sars-cov-2 is built with a coiled spring which is triggered by a cell receptor when it binds. This coiled spring releases mechanical energy to force merging between virus and cell wall: https://www.youtube.com/watch?v=e2Qi-hAXdJo https://www.youtube.com/watch?v=e2Qi-hAXdJo
  - OmarShehata 3y ago
    It's the same way chemicals have effects even though they have no energy/way to move themselves etc: they just diffuse in whatever medium they're in (like salt diffusing in water). No energy needed
  - fsckboy 3y ago
    cells are not dead lumps, they are living things driven by energy (food sugar), doing stuff all the time and reacting to their environment (even if their environment is inside your body). The surface of the cell, the cell membrane, is a wall that has little "doors" or "windows" that will open and close to let stuff IN (sugar to burn for example, and raw protein parts (amino acids) so they can make them into useful proteins, and they open the windows to let stuff OUT, waste products, the useful proteins they just made, CO2. There's another membrane doing a similar thing around the nucleus within the cell. The windows in these walls open and close automatically controlled a bit like a lock with magnets in it. If a "key" with the right combination of magnets is inserted in the lock, the lock magnets will align to open the window. Viruses carry keys that know how to get in your windows, pretending to be authorized but it's a forgery. The virus doesn't "do" anything, it doesn't know its not doing anything, it just hangs around till it fits a lock. Viruses that look like good keys get into the reproduction system and reproduce. Viruses that don't unlock anything don't. if your tea leaves have these viruses in them, adding water to the tea will spread the viruses around the same way the tea spreads, and they will come into contact with your tongue cells.
    - COGlory 3y ago
      Diffusion is typically passive, sometimes (rarely) guided. But actual genome delivery usually requires energy stored in the capsid. For membraneous viruses, it's usually energy stored in the spike/fusion protein, plus some help from the host. Note: I'm talking about energy stored in the 3D structure, not ATP molecules.
      - alyx 3y ago
        Where does the energy stored in the 3D structure come from? How does it get infused with said energy?
        COGlory 3y ago
        When the virus is made by the previous cell, as the virus is assembled, it is assembled into what is called a "metastable" state. This is a low, but not lowest energy state, or energy well. Typically the lowest possible energy state requires some additional input of energy to reach (it has to get over a small hump to find the deepest well). That energy often comes from an interaction with a new host.
  - rvba 3y ago
    When you move your body you shuffle stuff around. Blood also flows. There's also wind.
  - COGlory 3y ago
    The viral capsid, or the spike proteins/binding proteins, are in a metastable state. Upon interaction with the host/target, they use that energy to rearrange into a lower energy state. Genome delivery is usually associated with that state.
fsckboy 3y ago
The smallest things in your body that have a metabolism are your cells. Cells are much much bigger than viruses. The things in your body that are the same size as viruses also do not have a metabolism. It's sort of like there's an engine in your car. But there's not an engine in your engine, there are just parts that together make an engine. None of those parts have car-ness, but together they do. Your car has many parts all working together to make a comfortable and useful car. But the parts of the car if they are separated and just sitting on the bench, just sit there. Viruses are like those parts, car parts. When they are not in a cell, they just sit there. But if a virus part gets into your car, it gets to participate in the metabolism of the whole car, by acting like one of the other parts and just contributing its part-in-the-system. Unfortunately, the virus part's part-in-the-system is to turn your car into a factory/machine that makes more virus parts. This is how it spreads. This is why you do not want to get a virus. In this news story, a virus that is missing a piece of how to be a functioning part in your car, attaches to another virus that has that missing piece, and together they behave like a part that knows how to become one of your car parts.
- JadoJodo 3y ago
  This analogy was really great. Thank you.
- alyx 3y ago
  Okay so following your analogy, viruses are like subcomponents of an engine. How are subcomponents of an engine moving in space without ever exerting energy? I can imagine how this can happen infrequently but can't see how this propagation (movement without energy) is sustainable.
  - space_fountain 3y ago
    They’re like seeds in the wind. This also means most viruses will never infect a cell. Maybe thinking of them like infected usb drives strewn across the ground hoping some unsuspecting cell picks them up will help.
    - 3y ago
nomel 3y ago
> viruses can survive, propagate These are the same. Viruses are closer to self propogating exploitations of protein creation mechanisms. They cause their proteins to be replicated by these mechanisms, and statistics takes care of the rest, clicking the fragments together, creating a new virus, floating about, using other exploitations along the way, and the process repeats. In all stages, there're "just" bits of protein.
ethanbond 3y ago
It’s not really about viruses but I think it does give a really good (and fairly… shocking?) intuition for them: Richard Dawkins’ The Selfish Gene
bigbillheck 3y ago
How about a youtube series? From the 2023 Columbia U. virology course for undergrads by Vincent Racianello (of microbe.tv, discussed above): https://www.youtube.com/playlist?list=PLGhmZX2NKiNkAKAp3BynockFLUiCkZ8aJ https://www.youtube.com/playlist?list=PLGhmZX2NKiNkAKAp3Byno...
jryb 3y ago
They do have energy producing mechanisms: cells! The key to understanding this is, in my mind, to not put labels on things, and just consider how information encoded in genomes moves around. Also, all of the interactions that I've read about between virophages and phages occur inside of a prokaryotic cell, where there are plenty of molecules for making more viruses and powering chemical reactions. Honestly I'm not sure what to recommend you in terms of books. When I was a biology undergrad I had a biochemistry textbook that, at the time, I found to be mostly inscrutable. Then as a grad student I was going back through it to refresh my memory for a class I was TAing and remarked, "this is incredibly straightforward and clear" and immediately realized how much I must have changed. All of this to say - learning biology via text is pretty hard and takes a long time. I've never used it, but smart biology (https://www.smart-biology.com/ https://www.smart-biology.com/) looks very promising. I think the biggest way that the field of biology fails humanity is that we communicate relationships between these incredibly complex machines with little cartoons of a circle and triangle bumping into each other or something like that. Once you get the intuition for how things behave on a molecular level it's a super efficient means of communicating, but for people joining the field it's just brutal. But if you want to understand viruses you really need to understand biochemistry and molecular biology first. If you already have that background then I can ask around for book recommendations, if not, I would try smart biology, or if you really want a book, Lehninger is the classic biochemistry book, Alberts Molecular Biology of the cell is the classic cell biology book. These aren't intro books though, you typically wouldn't get them until your 2nd or 3rd year in a university program. It's easy to find free PDFs on the internet if you find their outrageous prices a bit high.
mncharity 3y ago
> I really do not understand viruses. You stand overlooking a giant office park with lots of stand-alone offices. A storm swirls trash among them, though trash doesn't last long in the wind and wet. Your goal is to create steady-state trash. So you design a packet. An envelope with tape (so it sticks when blown against glass front doors), and an address label (to get it carried inside, rather than being ignored as trash, or trashed as spam). And then you fold that envelope around hopefully-persuasive instructions for photocopying envelope and instructions, and assembling new packets. Then you make a lot of them. Few will reach doors, few will get inside, few will be executed. There are a bunch of design tradeoffs. The address can spam or spear-fish. A "<blur> Trucking" address works well with trucking companies, and poorly with others. A "<blur> Accounts Dept" works less well, but more broadly. You can include helpful envelope folding templates, but that means making fewer larger packets with more to go wrong when assembling them. You can go for stealth, only one person in the corner making packets and tossing them out the window, or even getting the instructions inserted into to the company process manual. Or you can go for fast private-equity zombie-apocalypse takeover, where the whole company dedicates itself to production until it explodes, scattering scads of packets to the wind. Zombies are the common case. Our human genome manual is littered with inserts. You might put an inter-departmental envelope within the envelope with a specific destination - trading lack of generality for performance. You might include a photocopier how to - buying "no worries, I've brought my own" generality at a cost of size and complexity. But the complexity budget is tight. Each extra badly-photocopied page ups the odds of a broken packet. Offices don't want to become zombies. So they keep their sprinklers running, to degrade packet trash. They toss out port-a-potties that feel like front doors to decoy packets. People run around the office with scissors, chopping up paper that looks spamish - you might want your instructions to fire them early on. Employees refuse instructions that don't look right. Out of common cause with sister offices, if someone notices the office going zombie, they may pull a fire alarm, burning down the office. It's a hard hard life being spam. And not easy being an office either. Looking out over a shallow coastal city... it's a burning trash-filled hellscape warzone. The half-life of functional packets is like an hour. The half-life of bacterial office buildings is only a couple of days. Asides: Some envelopes can punch a hole through the door to inject instructions. The time between insertion and resistance-is-only-a-delaying-action can be short - seconds to minutes. The zombie buildings explode within an hour or day. > how do these satellite viruses then survive off of other viruses? Small and simple, and easy to build, are nice design goals. As simple as possible but no simpler - taking over offices is hard after all. But what if the office is already being taken over, by someone else? The C-suite has been sent golfing, and the scissor snippers fired. Now in that altered environment, your even simpler or more general instructions might survive and grab a slice of production, or even takeover the takeover. Parasite parasites. Think of the ecological interactions of memes - "I might not have believed <improbable A> yesterday, but now, after encountering <conspiracy theory B> this morning...". And if two different packet designs are being photocopied at the same time, hey, mixups happen. Or consider a label of "Important Mandatory Instructions from the Fire Marshall - OPEN IMMEDIATELY" - highly persuasive... when someone else is causing nearby offices to burn down. The complex interactions of living in a warzone.
huytersd 3y ago
You have to think of a virus as a flash drive. It can just sit there with nothing happening for years and years. If it happens to coincidentally get plugged into a PC it immediately starts executing a program that hijacks the entire computer to start producing more copies of that same flash drive. In this analogy the computer is your cell.

by alyx 3y ago

quonn 3y ago

The propagate by entering cells that do produce their energy? Theoretically not producing spendable energy would not exclude activity either as long as some previously made energy is spent.

alyx 3y ago
How do you "enter a cell" without exerting energy?
- dist-epoch 3y ago
  You convince the cell to bring you in. Or you "store" energy when you are built - sars-cov-2 is built with a coiled spring which is triggered by a cell receptor when it binds. This coiled spring releases mechanical energy to force merging between virus and cell wall: https://www.youtube.com/watch?v=e2Qi-hAXdJo https://www.youtube.com/watch?v=e2Qi-hAXdJo
- OmarShehata 3y ago
  It's the same way chemicals have effects even though they have no energy/way to move themselves etc: they just diffuse in whatever medium they're in (like salt diffusing in water). No energy needed
- fsckboy 3y ago
  cells are not dead lumps, they are living things driven by energy (food sugar), doing stuff all the time and reacting to their environment (even if their environment is inside your body). The surface of the cell, the cell membrane, is a wall that has little "doors" or "windows" that will open and close to let stuff IN (sugar to burn for example, and raw protein parts (amino acids) so they can make them into useful proteins, and they open the windows to let stuff OUT, waste products, the useful proteins they just made, CO2. There's another membrane doing a similar thing around the nucleus within the cell. The windows in these walls open and close automatically controlled a bit like a lock with magnets in it. If a "key" with the right combination of magnets is inserted in the lock, the lock magnets will align to open the window. Viruses carry keys that know how to get in your windows, pretending to be authorized but it's a forgery. The virus doesn't "do" anything, it doesn't know its not doing anything, it just hangs around till it fits a lock. Viruses that look like good keys get into the reproduction system and reproduce. Viruses that don't unlock anything don't. if your tea leaves have these viruses in them, adding water to the tea will spread the viruses around the same way the tea spreads, and they will come into contact with your tongue cells.
  - COGlory 3y ago
    Diffusion is typically passive, sometimes (rarely) guided. But actual genome delivery usually requires energy stored in the capsid. For membraneous viruses, it's usually energy stored in the spike/fusion protein, plus some help from the host. Note: I'm talking about energy stored in the 3D structure, not ATP molecules.
    - alyx 3y ago
      Where does the energy stored in the 3D structure come from? How does it get infused with said energy?
      - COGlory 3y ago
        When the virus is made by the previous cell, as the virus is assembled, it is assembled into what is called a "metastable" state. This is a low, but not lowest energy state, or energy well. Typically the lowest possible energy state requires some additional input of energy to reach (it has to get over a small hump to find the deepest well). That energy often comes from an interaction with a new host.
- rvba 3y ago
  When you move your body you shuffle stuff around. Blood also flows. There's also wind.
- COGlory 3y ago
  The viral capsid, or the spike proteins/binding proteins, are in a metastable state. Upon interaction with the host/target, they use that energy to rearrange into a lower energy state. Genome delivery is usually associated with that state.

fsckboy 3y ago

The smallest things in your body that have a metabolism are your cells. Cells are much much bigger than viruses. The things in your body that are the same size as viruses also do not have a metabolism. It's sort of like there's an engine in your car. But there's not an engine in your engine, there are just parts that together make an engine. None of those parts have car-ness, but together they do. Your car has many parts all working together to make a comfortable and useful car. But the parts of the car if they are separated and just sitting on the bench, just sit there. Viruses are like those parts, car parts. When they are not in a cell, they just sit there. But if a virus part gets into your car, it gets to participate in the metabolism of the whole car, by acting like one of the other parts and just contributing its part-in-the-system. Unfortunately, the virus part's part-in-the-system is to turn your car into a factory/machine that makes more virus parts. This is how it spreads. This is why you do not want to get a virus. In this news story, a virus that is missing a piece of how to be a functioning part in your car, attaches to another virus that has that missing piece, and together they behave like a part that knows how to become one of your car parts.

JadoJodo 3y ago
This analogy was really great. Thank you.
alyx 3y ago
Okay so following your analogy, viruses are like subcomponents of an engine. How are subcomponents of an engine moving in space without ever exerting energy? I can imagine how this can happen infrequently but can't see how this propagation (movement without energy) is sustainable.
- space_fountain 3y ago
  They’re like seeds in the wind. This also means most viruses will never infect a cell. Maybe thinking of them like infected usb drives strewn across the ground hoping some unsuspecting cell picks them up will help.
  - 3y ago

nomel 3y ago

> viruses can survive, propagate These are the same. Viruses are closer to self propogating exploitations of protein creation mechanisms. They cause their proteins to be replicated by these mechanisms, and statistics takes care of the rest, clicking the fragments together, creating a new virus, floating about, using other exploitations along the way, and the process repeats. In all stages, there're "just" bits of protein.

ethanbond 3y ago

It’s not really about viruses but I think it does give a really good (and fairly… shocking?) intuition for them: Richard Dawkins’ The Selfish Gene

bigbillheck 3y ago

How about a youtube series? From the 2023 Columbia U. virology course for undergrads by Vincent Racianello (of microbe.tv, discussed above): https://www.youtube.com/playlist?list=PLGhmZX2NKiNkAKAp3BynockFLUiCkZ8aJ https://www.youtube.com/playlist?list=PLGhmZX2NKiNkAKAp3Byno...

jryb 3y ago

They do have energy producing mechanisms: cells! The key to understanding this is, in my mind, to not put labels on things, and just consider how information encoded in genomes moves around. Also, all of the interactions that I've read about between virophages and phages occur inside of a prokaryotic cell, where there are plenty of molecules for making more viruses and powering chemical reactions. Honestly I'm not sure what to recommend you in terms of books. When I was a biology undergrad I had a biochemistry textbook that, at the time, I found to be mostly inscrutable. Then as a grad student I was going back through it to refresh my memory for a class I was TAing and remarked, "this is incredibly straightforward and clear" and immediately realized how much I must have changed. All of this to say - learning biology via text is pretty hard and takes a long time. I've never used it, but smart biology (https://www.smart-biology.com/ https://www.smart-biology.com/) looks very promising. I think the biggest way that the field of biology fails humanity is that we communicate relationships between these incredibly complex machines with little cartoons of a circle and triangle bumping into each other or something like that. Once you get the intuition for how things behave on a molecular level it's a super efficient means of communicating, but for people joining the field it's just brutal. But if you want to understand viruses you really need to understand biochemistry and molecular biology first. If you already have that background then I can ask around for book recommendations, if not, I would try smart biology, or if you really want a book, Lehninger is the classic biochemistry book, Alberts Molecular Biology of the cell is the classic cell biology book. These aren't intro books though, you typically wouldn't get them until your 2nd or 3rd year in a university program. It's easy to find free PDFs on the internet if you find their outrageous prices a bit high.

mncharity 3y ago

> I really do not understand viruses. You stand overlooking a giant office park with lots of stand-alone offices. A storm swirls trash among them, though trash doesn't last long in the wind and wet. Your goal is to create steady-state trash. So you design a packet. An envelope with tape (so it sticks when blown against glass front doors), and an address label (to get it carried inside, rather than being ignored as trash, or trashed as spam). And then you fold that envelope around hopefully-persuasive instructions for photocopying envelope and instructions, and assembling new packets. Then you make a lot of them. Few will reach doors, few will get inside, few will be executed. There are a bunch of design tradeoffs. The address can spam or spear-fish. A "<blur> Trucking" address works well with trucking companies, and poorly with others. A "<blur> Accounts Dept" works less well, but more broadly. You can include helpful envelope folding templates, but that means making fewer larger packets with more to go wrong when assembling them. You can go for stealth, only one person in the corner making packets and tossing them out the window, or even getting the instructions inserted into to the company process manual. Or you can go for fast private-equity zombie-apocalypse takeover, where the whole company dedicates itself to production until it explodes, scattering scads of packets to the wind. Zombies are the common case. Our human genome manual is littered with inserts. You might put an inter-departmental envelope within the envelope with a specific destination - trading lack of generality for performance. You might include a photocopier how to - buying "no worries, I've brought my own" generality at a cost of size and complexity. But the complexity budget is tight. Each extra badly-photocopied page ups the odds of a broken packet. Offices don't want to become zombies. So they keep their sprinklers running, to degrade packet trash. They toss out port-a-potties that feel like front doors to decoy packets. People run around the office with scissors, chopping up paper that looks spamish - you might want your instructions to fire them early on. Employees refuse instructions that don't look right. Out of common cause with sister offices, if someone notices the office going zombie, they may pull a fire alarm, burning down the office. It's a hard hard life being spam. And not easy being an office either. Looking out over a shallow coastal city... it's a burning trash-filled hellscape warzone. The half-life of functional packets is like an hour. The half-life of bacterial office buildings is only a couple of days. Asides: Some envelopes can punch a hole through the door to inject instructions. The time between insertion and resistance-is-only-a-delaying-action can be short - seconds to minutes. The zombie buildings explode within an hour or day. > how do these satellite viruses then survive off of other viruses? Small and simple, and easy to build, are nice design goals. As simple as possible but no simpler - taking over offices is hard after all. But what if the office is already being taken over, by someone else? The C-suite has been sent golfing, and the scissor snippers fired. Now in that altered environment, your even simpler or more general instructions might survive and grab a slice of production, or even takeover the takeover. Parasite parasites. Think of the ecological interactions of memes - "I might not have believed <improbable A> yesterday, but now, after encountering <conspiracy theory B> this morning...". And if two different packet designs are being photocopied at the same time, hey, mixups happen. Or consider a label of "Important Mandatory Instructions from the Fire Marshall - OPEN IMMEDIATELY" - highly persuasive... when someone else is causing nearby offices to burn down. The complex interactions of living in a warzone.

huytersd 3y ago

You have to think of a virus as a flash drive. It can just sit there with nothing happening for years and years. If it happens to coincidentally get plugged into a PC it immediately starts executing a program that hijacks the entire computer to start producing more copies of that same flash drive. In this analogy the computer is your cell.