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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

#171

Post by ufo »

ses1984 wrote: post #135
ufo wrote: post #64

Earlier quoted context omitted.

The cliff notes version of it is that DNA encodes the information on how to build proteins. https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio... Proteins are built out of a chain of aminoacids. There are 20 different kinds of aminoacid, and the particular sequence of aminoacids determines the shape of the protein, and therefore its biological function. https://en.wikipedia.org/wiki/Amino_acid To build a pr…

Why do cells replicate virus rns so much, why don't we replicate out own rna out of control by the same mechanism?

The polymerase in most RNA viruses is an RNA-dependent RNA polymerase, an enzyme that makes copies of RNA. So what happens is: a single piece of viral RNA comes in the cell. Then it gets translated by the cell machinery, producing the polymerase enzyme. That polymerase then makes more copies of the viral genome. Which in turn gets translated into even more polymerase. Which then make even more copies of the virus... That is where the fork bomb analogy comes in.

https://en.m.wikipedia.org/wiki/RNA-dependent_RNA_polymerase

That kind of thing doesn't normally happen to us because we don't have those enzymes that can make copies of their own messenger RNA. Putting those fork bombs in production would be asking for trouble :)

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

#172

Post by codekilla »

garmaine wrote: post #148
codekilla wrote: post #113

Earlier quoted context omitted.

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.

Not sure which field of bionanotechnology (I assume you meant bionanotechnology ) you work in, but for the one I work in, the metaphor of biology and computer science is extremely intertwined—like very explicitly. Circuits, computation, the whole nine yards. If you’re talking about graphene or something that is an entirely different field. I can’t see how this book was a terrible critique of bionanotechnology—or at least an excellent discussion of the hardships faced.

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

#173

Post by learnstats2 »

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)

It's important that there isn't a gene that controls the eye colour.

Eye colour is modulated by several genes which haven't necessarily been identified - I understand this to be an open question.

I can give an example, though:

Eye colour is a function of what pigments are present in the iris, the most relevant pigment (in humans) being melanin, which also contributes to dark skin and tanning.

So, melanin is produced via the biochemical pathway 'melanogenesis'.

Among other things, the process of melanogenesis requires the enzyme tyrosinase, a protein which has a decent length wikipedia page.

If you are missing the TYR gene which codes for the protein tyrosinase, then you will likely be albino. This won't only affect your eyes, then.

I say you will 'likely' be albino only because it's hypothetically possible that a lack of tyrosinase could be compensated for with another biochemical pathway. And, of course, albinism could come about by some other break in melanin production.

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

#174

Post by ethbro »

Cogito wrote: post #151
ethbro wrote: post #105

Earlier quoted context omitted.

Would you not say they each have more purpose than a virus?

You're begging the question here; you need to establish they have any purpose before you can ask if one has more than the other.

No. I'm pointing to the relativity of the term.

Anything can be said to have, or not have a purpose, depending on how broadly or narrowly you scope the definition.

For use in this conversation, I think it's self evident that the level of purpose exhibited by higher-complexity organisms is several orders of magnitude different than that of basic organisms.

Wasn't sure if original poster would agree / disagree.

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

#175

Post by ethbro »

neuronic wrote: post #65
ethbro wrote: post #32

Earlier quoted context omitted.

IMHO, biology is most easily looked at as a recipe for order, from whatever ingredients happen to be laying around. Essentially, everything is in the service of increasing order. And maintaining it. Polymerase creates more genetic code out of raw ingredients. Genetic code creates proteins. Proteins perform all kinds of functions by leveraging physics and chemistry. Membranes prevent all of this from being blown away…

To me, what blows most comparisons and analogies out of the water, is the insane complexity to it all. That genes can influence and interact with each other. So gene expression (= gene -> protein) can change gene expression, e.g. based on environmental factors or folding of DNA etc... Gene A is responsible for property A is way way way too simplified.

True, but in the same way that all engineering can be complex.

Which is to say, you can use quantum mechanics to augment Newtonian physics, but the latter dominates results in most usages.

Biology does have the quirk that sometimes (I guess because exponential growth / propagation?) nuances dominate observed result.

But usually things proceed as expected. Otherwise, we'd be killing people left and right with pharmaceutical side effects!

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

#176

Post by johnohara »

usrusr wrote: post #140
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.

> 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-Co…

Seems impossible but from observation obviously is not.

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.

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

#177

Post by ethbro »

cowboysauce wrote: post #169
ethbro wrote: post #105

Earlier quoted context omitted.

Would you not say they each have more purpose than a virus?

Definitely not. Viruses perform key roles in ecosystems, particularly in ocean ecosystems. Their infection and subsequent killing of organisms provides a vital mechanism for cycling nutrients. They also help keep algal blooms in check. Viruses kill 20% of bacteria in the oceans everyday. Viruses also provide a mechanism for horizontal gene transfer. A protein that is critical to the formation of the human placenta ha…

Granted, but to me those seem like side effects.

The virus has no intentionality in doing them. They're a consequence of replication.

In contrast, I think a much stronger case could be made for a chimpanzee, duck, mosquito, or even amoeba evaluating multiple options, choose one to the exclusion of others, and pursueing it.

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

#178

Post by nikofeyn »

chadcmulligan wrote: post #127
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.

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…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

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

#179

Post by cowboysauce »

nikofeyn wrote: post #178
chadcmulligan wrote: post #127

Earlier quoted context omitted.

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…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

Actually game theory is probably the better place to look. Though the concept of natural selection already tends to cover the big picture. Organisms need resources to reproduce. Those that can obtain more resources (or use what they have more efficiently) reproduce more and eventually drown out those who cannot reproduce as much. Taking from another organism (whether by hunting, parasitism, etc) is just one way of obtaining more resources.

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

#180

Post by twangist »

ramraj07 wrote: post #129
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 simil…

"Oracle's DB2" - Do you mean Oracle's DBMS? DB2 is an IBM product.
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