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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

#121

Post by adrianmonk »

boring_twenties wrote: post #9
tcgv wrote: post #5

> Is a virus a living thing? Maybe. I remember 20 year ago, at school, when the biology teacher was presenting this dilemma. Ever since, when I hear someone saying "doing this will kill the virus", it triggers my brain into this subject, since you can't kill something if it's not alive ;) Somewhat related, I also like the concept of the "Viruses of the Mind" [1], which makes an analogy between the spreading of a biol…

If you can kill a process, or a proposal I don't see why you shouldn't be able to kill a virus -- alive or not!

For that matter, you can kill a vibe or a conversation.

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

#122

Post by Balgair »

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.

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 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

[1] https://www.youtube.com/watch?v=Zg-GHmvtIeI

[2] https://www.youtube.com/watch?v=xG-meaGqg-M

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

#123

Post by achenatx »

nojvek wrote: post #119

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 organ…

DNA is made out of nucleic acids. Each sequence of 3 DNA nucleotides codes for an amino acid. There are 21 amino acids.

How DNA -> proteins is well understood. Protein folding though is incredibly complex to model.

It is easy to know the amino acid sequence, but hard to know how the protein will end up folding.

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

#124

Post by timy2shoes »

nojvek wrote: post #119

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 organ…

DNA is made of nucleic acids (deoxyribonucleic acids), not amino acids. DNA is translated to amino acids, except when it encodes long-noncoding RNAs, or miRNAs, or piRNAs, or untranslated regions, or intergenic regions, or transposons, or psuedogenes.

And the protein coding sequences are coded into proteins, except when there are alternative splicing sites, or anti-sense RNAs.

And then the protein sequence folds into their minimum free energy state, except when they are assisted by other proteins, or when they exist as disordered proteins.

And it's not always DNA -> protein. Sometimes proteins make other proteins, for example circular proteins can only be made from other proteins.

Then there are post-translational modifications, which change the RNA sequence between DNA to RNA and RNA to protein. And then there's RNA interference, where miRNAs interfere with RNA to protein translation.

And then there's epigenetics such as DNA methlyation or histone modifications (histones are protein which compress DNA) which change what genes can be expressed when.

Really, for every rule that you've been taught, there is an exception. Biology is so much more complicated than we understand. And understanding how to make a biological computer (different from the biological computing of Adelman, yes the same Adelman as RSA) would involve understanding how all the pieces fit together.

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

#125

Post by achenatx »

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 have a microbiology degree and an EE degree (but more like comp E).

DNA truly is a blue print. (almost) Every cell in your body has the source code for your entire body.

"this gene or set of genes are responsible for that outcome" is generally going to be a true statement.

The equivalent wouldnt necessarily be a processor instruction.

If you wanted an analogy, a cell is like an entire minimal computer. Power supply, processor, memory, and I/O. Each computer can run different parts of the code, but every computer has the entire code base.

Within the computer are specialized "organelles" for storage, graphics, network, etc. These are comparable to organelles such as mitochondria, nucleus, endoplasmic reticulum etc.

DNA acts like code in that it produces outputs (messages) and receives inputs. Proteins are also like code in that they produce outputs and receive inputs.

It might be that DNA is like the executable source code that is stored as files and proteins are more like in memory processes such as services and actively running programs that get spawned from the files to perform various tasks.

Viruses are like hostile code in bound in an email or coming through as tainted packets. They cant actually do anything on their own - they are inert, but once the processor starts executing the code, they hijack the processor. Sometimes to spawn more malicious code to other computers in a trusted network

To carry the analogy further, departments in a company are a bit like organs. The computers in that department all roughly do the same thing. Imagine if IT imaged every computer in the company the exact same way, but what software was actually used would be based on your department.

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

#126

Post by [deleted] »

nojvek wrote: post #116
JshWright wrote: post #99

Earlier quoted context omitted.

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.

[deleted]

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

#127

Post by chadcmulligan »

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.

I picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard.

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

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

#128

Post by ramraj07 »

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?

Want to point out that this still slightly depends on what cell you are talking about - a mammalian cell is a thousand times larger than a bacterial cell, which in turn is a hundred or thousand times larger than a virus. An apt comparison is if you were a cell in your body, a bacteria is at best the size of a pea and a virus the size of an ant. Viruses are so small that you can sometimes just crystallize them to study their structure with crystallography as if the entire thing is a single molecule.

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

#129

Post by ramraj07 »

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 have discussed this exact analogy with a couple colleagues from a CS background. If someone said the genome is the source code that's very wrong. The more accurate analogy is that your genome is a compiled, highly compressed executable file (more or less 200 MB in size?) Where the optimizer blindly reuses variables and memory locations for multiple routines that may or may not be related. It probably is quite similar to oracle's DB2 codebase, where all this shit is in C, and you change some variable here and hell breaks loose somewhere else. For the most part though, if you don't tinker with it, it runs like a well oiled machine because a blind watchmaker programmer (with great intuition but no CS organization fundamentals) has debugged and patched it for billions of years, patch on top of patch millions of times over.

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

#130

Post by FPGAhacker »

RivieraKid wrote: post #49
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…

Part I of Molecular Biology of the Cell is the best read in my opinion, regardless whether you have a CS background.

https://archive.org/details/MolecularBiologyOfTheCell5th/mod...
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