[alyx]

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?

[fsckboy]

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.

[earthboundkid]

“You, sir, have been reared in great luxury as becomes your noble birth. How did you come here, by foot or in a chariot?”

“In a chariot, venerable sir.”

“Then, explain sir, what that is. Is it the axle? Or the wheels, or the chassis, or reins, or yoke that is the chariot? Is it all of these combined, or is it something apart from them?”

“It is none of these things, venerable sir.”

“Then, sir, this chariot is an empty sound. You spoke falsely when you said that you came here in a chariot. You are a great king of India. Who are you afraid of that you don’t speak the truth?”

https://en.wikipedia.org/wiki/Milinda_Panha

[chatmasta]

The Buddhist Ship of Theseus?

[earthboundkid]

It’s a little different. Theseus is about identity over time. This is about identity of wholes from parts. No part of your engine is itself an engine, nor is a collection of engine parts in the wrong arrangement an engine. You need the right parts and the right relationship between the parts. But “right relationship” is not an entity over and above the parts either.

[alyx]

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]

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.

[fsckboy]

>They’re like seeds in the wind.

I like this analogy, I'll just take it a bit further: they are seeds in the wind where the wind is a snuffly and moist sneeze aaachoooooo, spraying the seeds all around.

some viruses can sit and survive on a door handle and get passed that way (your hand on then handle, then you rub your eyes) This is called "fomite transmission". Other viruses cannot survive sitting on a door handle outside of your body. The HIV virus can only be passed directly from one person to another in moist body fluids, and not "through" normal dry skin. From this we can see why cold and flu spread so easily, and even though HIV does not, it still has very little trouble finding pathways to transmit.

early in Covid, it was unknown how it spread. In certain ways we still don't know. Do masks work? A lot or a little? the whole thing became so politicized it's still hard to get good information.

[imchillyb]

> Do masks work? A lot or a little?

I truly don't believe this is the relevant question.

The questions society should be asking is this: "What percentage of the populace properly handles and dons masks? What percentage of the populace replaces or washes those masks thoroughly enough to prevent transmission? What percentage of the populace refuses to don a mask?

Answering these questions truthfully would provide a better coverage graph and allow researchers to find ways to increase the coverage and educate the public accordingly.

[fsckboy]

I was not trying to answer or even ask the mask question, I was using something the newbies (to virology) here would already be familiar with to point out that even though we know a good bit about viruses, experts still don't automatically know things like "how does this virus propagate", it takes time to tease out the answers and they don't always come.

It's a bit like yesterday's story here about massive amounts of evaporation of water occurring by a mechanism that science never knew about, just to point out that there is much to know that we don't know yet, and not to go deeper into evaporation where science is already struggling.

[autoexec]

> "What percentage of the populace properly handles and dons masks? What percentage of the populace replaces or washes those masks thoroughly enough to prevent transmission? What percentage of the populace refuses to don a mask?

While those questions are somewhat useful, ultimately masks still help in any case.

If half the population doesn't wear a mask, masks won't work as well as they would if 100% of the population did, but they would still make a difference. If people don't wear or care for masks correctly it still doesn't make those masks useless because putting literally anything in front of somebody's virus spewing face holes helps a lot regardless.

This is why we teach children to "vampire cough", not because every single person on earth is going to do it 100% of the time, or because people's elbow pits provide N95 levels of protection, but because neither of those things is necessary for it to make a massive difference in the spread of illness.

[dylukes]

Sheer random chance.

I had this same question while working on structural resolution of a certain RNA polymerase.

I asked "okay so if this ratcheting mechanism allows the protein to zipper along the nucleotide strand... what's pushing it along?"

The answer is that nothing is pushing it along. It's just random movement and enough time (milliseconds) plus a ratcheting mechanism to ensure it doesn't go backwards.

Our low level processes are not so different from viruses in this respect!

[jagraff]

Movement without energy is possible due to diffusion. Imagine you had a room with cellophane separating one side from another. Each side has a different gas, but both gasses are at the same pressure and at room temperature. Then, the cellophane is removed. Without adding any energy to the system, these gasses will mix until the whole room is a perfect mixture of the two gasses, simply because they both diffuse through the entire room. Something similar happens to allow viruses to move through your body (and, if they can be aerosolized, through the air).

[IIAOPSW]

Using the analogy, they are like loose screws or other basic machine parts that fell down the pipe, got in the engine, jammed a bunch of things cause they aren't supposed to be there, and consequently a bunch more misc scrap metal got sneezed out the exhaust pipe.

[JadoJodo]

This analogy was really great. Thank you.

[jryb]

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/) 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.

[ethanbond]

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

[huytersd]

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.

[bigbillheck]

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=PLGhmZX2NKiNkAKAp3Byno...

[nomel]

> 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.

[quonn]

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]

How do you "enter a cell" without exerting energy?

[fsckboy]

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]

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]

Where does the energy stored in the 3D structure come from? How does it get infused with said energy?

[COGlory]

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.

[OmarShehata]

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

[dist-epoch]

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

[COGlory]

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.

[rvba]

When you move your body you shuffle stuff around. Blood also flows.

There's also wind.

[mncharity]

> 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.