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What's a virus, anyway? The bare-bones basics

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Re: What's a virus, anyway? The bare-bones basics

#141

Post by Hnrobert42 »

vikramkr wrote: post #35
dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

I wouldn't recommend trying to understand it through analogy to CS - I'm a biologist and know enough CS to feel uncomfortable really using any of the usual analogies. The problem is that they work ok for a layperson understanding, but are fundamentally wrong enough that if you want to understand it at the level of something like virology you'll be lead constantly astray. I dont know of a better recommendation than "w…

Can you recommend any sites like HN, but for biology?

Re: What's a virus, anyway? The bare-bones basics

#142

Post by mardifoufs »

waterhouse wrote: post #120
johnohara wrote: post #111

Earlier quoted context omitted.

Pity I only get 1 upvote. I'd triple-click if I could. 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.

I note that the virus depicted in the animation is HIV. How much of the lifecycle is different from HIV to SARS-CoV-2? One thing I noted is that it said the inserted viral DNA might remain dormant for years; surely that part is HIV-specific? (Or do we really bear viral infections for years after recovery, and—I presume—rely on the continued presence of antibodies to quash the remaining DNA?)

That part is mostly specific to retroviruses and DNA viruses. Retroviruses are special because even though they are RNA based they can "translate" their RNA into dna once inside the cell and embed that DNA into the cell's genome. That translation in itself is remarkable since it's the opposite of the normal DNA to RNA "translation" we see in almost every organism, hence the "retro".

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.

Re: What's a virus, anyway? The bare-bones basics

#143

Post by fiblye »

01100011 wrote: post #88
darkerside wrote: post #84

Earlier quoted context omitted.

So they're a parasite. There are insects that can only reproduce by laying eggs inside of another insect. They don't physically carry their own. Does that mean they're not alive?

You're describing an organism. What about its cells?

Cells divide on their own, but they often rely on other cells to supply them with the nutrients they need to divide.

Re: What's a virus, anyway? The bare-bones basics

#144

Post by hoseja »

matheusmoreira wrote: post #139
dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

> Is there a a good read on how RNA and DNA work for a Computer Scientist? DNA is source code. RNA is an intermediate representation. Enzymes compile DNA into mRNA. Ribosomes compile mRNA into proteins which can actually execute a wide variety of functions. Proteins may require post-processing before they're usable. The output of a ribosome is a primary protein: a linear, one-dimensional structure. By interacting wit…

Also the "source code" is an unaligned quaternary tape of hyper-optimized inter-dependent assembly monolith.

Re: What's a virus, anyway? The bare-bones basics

#145

Post by nullc »

mardifoufs wrote: post #142
waterhouse wrote: post #120

Earlier quoted context omitted.

I note that the virus depicted in the animation is HIV. How much of the lifecycle is different from HIV to SARS-CoV-2? One thing I noted is that it said the inserted viral DNA might remain dormant for years; surely that part is HIV-specific? (Or do we really bear viral infections for years after recovery, and—I presume—rely on the continued presence of antibodies to quash the remaining DNA?)

That part is mostly specific to retroviruses and DNA viruses. Retroviruses are special because even though they are RNA based they can "translate" their RNA into dna once inside the cell and embed that DNA into the cell's genome. That translation in itself is remarkable since it's the opposite of the normal DNA to RNA "translation" we see in almost every organism, hence the "retro". DNA based viruses don't have that…

> 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.

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

Re: What's a virus, anyway? The bare-bones basics

#146

Post by mseepgood »

dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

> Many vulgarization sources say that DNA is like the source code of life.

DNA is a tape archive of files (genes). They are not binary (base-2) encoded, but base-4 encoded. A reading head (polymerase) reads sections of the tape and copies them into working memory. A 3D printer (ribosome) receives these sections from the working memory and prints nano machines (proteins) based on these tape snippets. DNA is not source code, it does not contain conditions or jumps (loops), it's data for the 3D printer. (Actually it's just a 1D printer, but the result folds into a 3D shape).

Re: What's a virus, anyway? The bare-bones basics

#147

Post by mardifoufs »

nullc wrote: post #145
mardifoufs wrote: post #142

Earlier quoted context omitted.

That part is mostly specific to retroviruses and DNA viruses. Retroviruses are special because even though they are RNA based they can "translate" their RNA into dna once inside the cell and embed that DNA into the cell's genome. That translation in itself is remarkable since it's the opposite of the normal DNA to RNA "translation" we see in almost every organism, hence the "retro". DNA based viruses don't have that…

> 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. 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/Antigen…

Yep! That's what really makes influenza special, as I said the mutation rates are only part of why Influenza viruses rapidly change. Their ability to cross between species by combining easily with other types of influenza viruses are the key to their incredible variability

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

Re: What's a virus, anyway? The bare-bones basics

#148

Post by garmaine »

codekilla wrote: post #113
ggm wrote: post #94

Wise words a former cell biology aware PhD said to me once: a cell is at a scale where van der Waals forces means 'water' isn't behaving like you think and the 'liquid' of a cell is possibly more like a matrix than a fluid. Those high school cell models are very misleading. He basically said macro scale intuition was useless for what it means to pierce the cell wall, as an example. What does "pierce" even mean?

I think this was first written about at length in the book ‘Soft Machines’, which is a really good critique of some of the nanotechnology thinking at the time. I highly recommend the book.

Actually it was a terrible critique of nanotechnology, which doesn’t try to make things the same way as biology. But a good overview of the funkiness which comes part and parcel with life’s microbiology.

Re: What's a virus, anyway? The bare-bones basics

#149

Post by twic »

Balgair wrote: post #122
titzer wrote: post #100

Earlier quoted context omitted.

Agree! I found ( https://blogs.scientificamerican.com/observations/watch-the-... ) to be pretty mind-blowing.

Some other good ones: 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…

I think David Goodsell's beautiful paintings, in his book Machinery of Life, were the first serious attempt to depict how crammed a cell is (page down past the pictures of individual molecules to get the the cell cross-sections):

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.

Re: What's a virus, anyway? The bare-bones basics

#150

Post by djmips »

taylorlunt wrote: post #44
redindian75 wrote: post #14

> Is a virus a living thing? Maybe. Maybe Virus is akin to a SEED. Seeds are inert/dead by themselves, but it carries as all the code/DNA/instructions needed to spring to life, flourish & even reproduce infinitely when put in an friendly environment (nourished soil with water, O2 etc)

But a virus doesn't "spring to life." A virus is like a seed that just generates more seeds without ever making a plant.

When it takes over the cell, the cell is now the plant.
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