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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

#91

Post by wesleywt »

gravelc wrote: post #82
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…

The reason why CS analogies don't work very well is that molecular biology is very context driven, and we often don't know what the context is. For example, in eukaryotes, the same piece of DNA can can produce different amounts of different proteins (i.e. with different amino acid sequences and different post-translational modifications), depending on things like DNA methylation (there's a number of different types),…

Analogies obviously don't hold for many cases. But it's a good entry point to explain some basic concepts such as the Central Dogma. I am a biologist who has to teach molecular biology to computer scientists in our Bioinformatics department. It was the only way to bridge the gap. Once we got it we could start on the more detailed stuff.

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

#92

Post by pushrax »

whatshisface wrote: post #13
boring_twenties wrote: post #9

Earlier quoted context omitted.

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!

Process reproduce (through forking) metabolize (stdin->stdout) and maintain homeostasis (garbage collection). How could they not be alive?

None of those things are necessary to consider something a process.

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

#93

Post by ggm »

biophysboy wrote: post #50
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…

Biophys grad student here. If I'm understanding your frustration correctly, you're basically saying: "yes for the 1000th time, I KNOW DNA is the recipe book, but who is the chef?" Well, I'm sorry to report that there are a lot of chefs. And to make things worse, every cell is different, so there are also a lot of restaurants. For this reason, it is not possible to make a book on any of the topics you listed above wit…

Yes: how can we make an omelette without breaking chefs?

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

#94

Post by ggm »

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?

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

#95

Post by koeng »

tomerico wrote: post #61
learnstats2 wrote: post #48

Earlier quoted context omitted.

DNA is literally only instructions for building proteins (each 'gene' commonly encodes one protein). It's a very low level code, then. The various proteins that are built are actually interacting with the environment. So, your desire to look at interaction with the environment might be better captured by a field other than genetics: maybe proteomics or molecular biochemistry.

Maybe you can help me understand a simple example - if there is a gene that controls the eye color, how does it express itself as eye color (vs something completely different)

Basically, the variance in melanin is what causes different eye colors. So, if you have a gene that produces melanin, and then turn it's expression down, then you might get bluer eyes.

The complicated part is that a lot of genes actually control for eye color - that is where the complications come. Each gene interacts with every other gene in a unique way.

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

#97

Post by xigency »

tomerico wrote: post #61
learnstats2 wrote: post #48

Earlier quoted context omitted.

DNA is literally only instructions for building proteins (each 'gene' commonly encodes one protein). It's a very low level code, then. The various proteins that are built are actually interacting with the environment. So, your desire to look at interaction with the environment might be better captured by a field other than genetics: maybe proteomics or molecular biochemistry.

Maybe you can help me understand a simple example - if there is a gene that controls the eye color, how does it express itself as eye color (vs something completely different)

A gene is like a DLL. Asking how it works would require a lot of know-how that’s specific to the usage.

When talking about how DNA is an instruction for making a protein, that protein is your data structure or a function. The next level of fundamental building block. Genes can contain a lot of information or non-information for proteins. Just like a program might have a lot of functions or data. The way they work together and interact is what creates a larger effect.

I think maybe the best starting point for understanding biology is learning about enzymes up close. They are proteins that act as “machines”. It gets down to physics and chemistry to determine how they work, so that’s probably when to drop the analogies.

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

#98

Post by Retric »

vikramkr wrote: post #70
Retric wrote: post #60

Earlier quoted context omitted.

It’s hard to disagree with what your saying, but analogies are fun. I think the best analogy is DNA is a series of automated assembly lines. The workers, raw materials, and signals to turn sections on or off are separate. Each nucleotide station is called A, T, C, or G and adds a single element at a time to long chains which then get folded up into useful tools. DNA can also be used to manufacture either more stands…

Edit - I'll concede that analogies are absolutely fun haha. They might be useful to come up with when you yourself are trying to better understand something by drawing connections to other things you know and all. But I don't think they're ideal for being taught the subject. And again, for a layperson, analogies are totally fine if you just want a surface level understanding of "oh, mitochondrias are powerhouses of t…

The problem with including codons in such a high level analogy of DNA is their context sensitive. DNA doesn’t care about those details and can be sliced an diced to completely change how it’s interpreted.

Also, you really should include activation sites etc, but soon your out of the realms of analogy and just describing the details.

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

#99

Post by JshWright »

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.

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

#100

Post by titzer »

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.
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