What's a virus, anyway? The bare-bones basics • Hacker News Board

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

#111

Post by johnohara » Fri, Apr 03, 2020, 3:53 AM UTC

titzer wrote: post #100

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?

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

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.

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

#112

Post by randlet » Fri, Apr 03, 2020, 4:00 AM UTC

titzer wrote: post #100

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?

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

Amazing. The mind boggles at how complex this is and the fact that humans have the tools to discover and understand the process. Thank you very much for sharing!

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

#113

Post by codekilla » Fri, Apr 03, 2020, 4:00 AM UTC

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.

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

#114

Post by akamoonknight » Fri, Apr 03, 2020, 4:00 AM UTC

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…

Not necessarily specifically RNA/DNA but a super accessible description of biology is The Machinery of Life (https://www.goodreads.com/book/show/6601267-the-machinery-of...). I can't get over much it makes me want to learn more, and as a lay-person, I think it gave me a much better idea of what's going on at pretty much an atomic level.

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

#115

Post by pedroguitarm4n » Fri, Apr 03, 2020, 4:01 AM UTC

titzer wrote: post #100

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?

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

That was brilliant -- be sure to watch it with the sound on. the ominous music makes the experience even better

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

#116

Post by nojvek » Fri, Apr 03, 2020, 4:09 AM UTC

JshWright wrote: post #99

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'd highly recommend the YouTube channel "Journey to the Microcosmos" for videos that do a great job of improving that intuition.

https://m.youtube.com/channel/UCBbnbBWJtwsf0jLGUwX5Q3g

^ here is the link. Pretty great animation. Thanks for the recommendation.

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

#117

Post by guscost » Fri, Apr 03, 2020, 4:12 AM UTC

twomoretime wrote: post #39

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…

It's like writing ultimate spaghetti code in a dynamic language. The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy. But through natural selection it seems to work. Like a totally incomprehensible compression algorithm learned by neural nets or…

And not only is it far worse than the most spaghettified and surprising program/meta-program you've ever seen, it's also a quine.

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

#118

Post by jyounker » Fri, Apr 03, 2020, 4:22 AM UTC

Viliam1234 wrote: post #54

twomoretime wrote: post #39

Earlier quoted context omitted.

It's like writing ultimate spaghetti code in a dynamic language. The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy. But through natural selection it seems to work. Like a totally incomprehensible compression algorithm learned by neural nets or…

This. Spaghetti code beyond human imagination. Once I tried to learn this stuff by asking a biochemist, but I soon became frustrated because it seems there are no 100% rules, only "it is usually like this" all the way down. Like, did they teach you at school that eukaryotes have two sets of chromozomes, one from each parent? Yeah, "usually". But then also: https://en.wikipedia.org/wiki/Polyploidy And similarly with e…

But the code and products are also pieces of spaghetti :)

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

#119

Post by nojvek » Fri, Apr 03, 2020, 4:35 AM UTC

Someone who is a molecular biologist, please correct my understanding.

DNA is a molecule, made out of 4 amino acids. ACTG. There are 18 different kinds of amino acids. Amino acids are made out of carbon, nitrogen, hydrogen, oxygen. Amino acids make proteins. Proteins are the structural bricks (like LEGO) that are combined in various sequences by enzymes to build more complex machinery.

The proteins make up cell organelles, which make up cells.

How much of how DNA turns into proteins and different proteins build different structures is understood? Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures?

How close are we for computer science folks to actually start writing compilers, debuggers, frameworks and simulation tools for DNA and man made cell machinery ?

How far away are we from making custom DNA + cells that act like 3D printers taking collagen and building nanometer precision complex structures?

It seems our cells already do nano manufacturing and computation, how do I tap into that ?

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

#120

Post by waterhouse » Fri, Apr 03, 2020, 4:43 AM UTC

johnohara wrote: post #111

titzer wrote: post #100

Earlier quoted context omitted.

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

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?)