https://www.youtube.com/watch?v=7Hk9jct2ozY
https://www.youtube.com/watch?v=B_zD3NxSsD8
The GP is right in that our intuitions aren't cutting it down at the bottom.
All these animations tend to edit out the water molecules so that the audience can understand better. The proteins aren't colored blobs at all. At these scales you'd clearly see individual atoms instead of blobs. But watching a bunch of really detailed atomic ball-stick models would be confusing. And not only are the H2Os battering everything like TIE fighters in the Hoth asteroid field [0], there are ions in there too (Na, K, Cl, etc) that really effect the cell. The membranes are also edited, as many cells are porcupined with receptors like an over crowded wave pool [1]. In addition to the water/saline being edited out, most of the other proteins, vesicles, and interior membranes are also gone for the sake of clarity. There is nearly no free 'space' in the cell, think of a really crammed subway car [2], with the air being like the water/saline. But only much much tighter.
The cell is more like a frantically efficient liquidy crystaly thingy than a wonky wobbly blobby poofed-up juice box. And each one is utterly deeply profoundly fascinating.
[0] https://www.youtube.com/watch?v=C_DnrceDEI8
https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedi...
Here's an interview with him, explaining and showing his process:
https://www.youtube.com/watch?v=f0rPXTJzpLE
Here's his recent painting of a coronavirus protease:
https://pdb101.rcsb.org/motm/242
The other thing missing from those videos is any indication of how random these processes are. At one point, an actin filament assembles by having monomers fly directly at the tip and stack neatly together. It's not like that. In reality, there are all sorts of molecules just randomly moshing around, and occasionally, an actin monomer will bump into the tip of the filament and stick, because it has a binding site. But sometimes one will bump into the tip and not stick! Sometimes, the tip of the filament will fall off! The growth is purely statistical: monomers are more likely to stick than to fall off, and more likely to stick than some random unrelated protein is to stick.
This animation enables one to visualize a single SARS-CoV-2 virion binding with the ACE2 enzyme, entering the host cell, and replicating 4-5 new virions.
One SARS-CoV-2 virion is 125 nanometers wide. By the time it shows up on a CT scan we are talking many, many billions.
It's seems impossible anyone could test positive and still be asymptomatic.
Why? Most symptoms are part of the body's response switching into overdrive and not a direct consequence of cells getting subverted into virion farms. If the immune system wins without resorting to state of emergency measures like a fever you won't notice, but in the meantime there is a phase of viral replication in the throat.
With SARS-Cov-2 there is even the pattern that detection drops already in the throat of patients that still have a pneumonia raging in their lung (probably because the throat, as a battlefield in this war, somehow favors the immune system more than the lung?), so it's not even a subset/superset relation between symptoms and positive throat PCR, it's a partial overlap.
Comorbidity is the issue with SARS-CoV-2. It is interesting that some patients testing positive report losing the sense of taste and/or smell while others report digestive problems prior to the onset of acute respiratory problems or even sore throat.
DNA based viruses don't have that unique mechanism but the result is conceptually the same: you get a virus that is extremely hard to completely cure/remove due to it being present in some of your own DNA. Herpes is a DNA based virus and that's why you can't ever be fully cured from it.
That's also why retroviruses like HIV can only be suppressed. It's also why antiretroviral drugs try to inhibit the replication phases of the virus, which makes managing the disease possible but can't remove the virus itself. Still, a cocktail of those inhibitors is an amazingly powerful treatment against AIDS and leads to HIV becoming basically dorment in the body.
A ribovirus (which is what coronaviruses are) is RNA based but it doesn't embed itself into our genome. It never translates it's RNA and since RNA is fundamentally less stable of a molecule than DNA, you get really high mutation rates. That "instability" is caused by the lack of a built in error checking mechanism in RNA. Those random mutations are part of why Influenza is hard to build immunity against. But it's also why RNA based viruses are generally either too virulent and mortal to allow for effective spread, or rapidly evolve towards less lethal forms.
Keep in mind that I've generalized a lot and that there are a lot of exceptions and outliers when it comes to viruses. For example, Hepatitis C is a ribovirus but it has a special protection mechanism that protects it's core genetic material from mutations even if it's RNA based.
The coronovirues have a proofreader mechanism, which is interesting.
And influenza has more potent evolved countercountermeasures than just high mutation rates: https://en.wikipedia.org/wiki/Antigenic_shift
One of the distinguishing trait of CoVs are their special RNA replication/transcription mechanisms that results in less errors, which is really important considering the large size of their genomes compared to other RNA based viruses. Though, and correct me if I'm wrong, aren't they still extremely less stable than DNA viruses? Which is why only short/medium term immunity is usually possible? I don't know a lot about the synthesis of coronavirus RNA but it looks super interesting
That's correct. Worse, the proofreader doesn't have to protect all parts equally...
> Which is why only short/medium term immunity is usually possible?
No. For some viruses active immunity just doesn't last particularly long for reasons we don't understand (or at least it was described as not understood in every paper I've seen on the subject). For some viruses you can be reinfected months later with exactly the same virus. This is the case for several cold causing viruses.
All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary world in front of you, everythings eating each other and trying to not be eaten. If you're thinking of getting a telescope (I had one), think of a microscope they open up a new world, its incredibly easy to see things - I thought it would be a lot more work.
Probably there's so many on line resources now to - this guy is a great start - microbe hunter https://www.youtube.com/channel/UCDpKY8-oz5PWlBPNzNsbLug
and your last statement isn't getting to why. it's just what happens.
Anyway... The 'why' is trivial-seeming to me. Once one organism can consume ready-made nutrients from another organism for less energy cost than producing, it will, or it will be out competed by others who do. So carnivores exist everywhere. Even deer happily eat baby birds that they come across, and rabbits eat their own.
Almost Tragedy of the Commons?
Organisms that consume plants are capable of more complex behaviour and growth because the amount of energy and nutrients etc. is greater that they receive by conauming things that photosynthesize.
every living organism has some way of perpetuating itself, either by growing indefinitely or by making copies of itself. there's no reason "why", other than that organisms that can't do this get filtered out very early in the game. this implies having some sort of "strategy" for traveling up the energy gradient.
short of somehow evolving the biological capability to fuse/split atoms, all the usable energy on earth comes from the sun. so the first link in the chain has to be something like photosynthesis, where you collect and store energy directly from the sun (ie, "building a house"). but in doing this, you change the gradient, creating an opportunity for other organisms take your stored energy for themselves. in some sense, it's much "easier" for a rabbit to eat a plant in one minute than it was for the plant to collect all that energy over its entire life. there's only so much solar radiation per square meter, which limits a plants energy budget. a rabbit can eat many plants in a day, effectively multiplying the area of the solar radiation it can capture (and spend on acquiring even more). but then the rabbit creates an opportunity for a predator to harvest its stored energy and the cycle continues...
it seems like you're maybe asking "why can't all life just cooperate"? this would probably look like a planet full of plants (or a similar lifeform at a different scale). the problem is that this leaves a huge opening for the first "defector"; it's an unstable equilibrium. life does not evolve to leave opportunities on the table.
In short, energy gradients (ie, on hydrothermal vents) can cause matter to organize itself into structures that more efficiently dissipate this energy. You can see how the creation of this structure would in turn enable the creation of a new kind of structure that lives on top of that.
^ here is the link. Pretty great animation. Thanks for the recommendation.
Another interesting thing: cells are packed so tightly (not just a bag of water) that proteins grind against each other and against their ligands, increasing the "activity" (even the free energy of ATP hydrolysis isn't the standard 7.3kcal/mol.
Yes, macro-scale intuition isn't great (although people pierce cell walls with tiny needles all the time), but if you spend enough time looking at cells under a microscope, you start to build an intuition about cell and molecule behavior.
Because of Richard Smalley that money went towards material science and chemical research instead of the molecular manufacturing it was promised for. Even though, as you point out, in terms of fact the critique only applied to life-like bionanotechnology.
The history of this is laid out pretty well—with a surprisingly minimal amount of sour grapes—in Drexler‘s book Radical Abundance.