An insanely detailed molecular simulation of HIV infection is extremely illustrative:
https://blogs.scientificamerican.com/observations/watch-the-...
What's a virus, anyway? The bare-bones basics
101–110 of 202 posts
Re: What's a virus, anyway? The bare-bones basics
#102Earlier quoted context omitted.
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.
That's why I figured an analogy would include nucleotides as letters that make up words rather than acting on their own to be able to encompass all that (and I love that in trying to help craft better analogies in a chain where im also railing against analogies)
Re: What's a virus, anyway? The bare-bones basics
#103Wise 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.
Thanks for sharing this link. Saw this video once and was COMPLETELY blown away but didn't know where it was from.
Re: What's a virus, anyway? The bare-bones basics
#104Is 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…
Imagine a machine learning algorithm to write Perl.
This algorithm is allowed to run for 4.5 billion years, and it has produced, through random iteration, a very good CMS.
The CMS works great most of the time, but there's a bug which rarely happens, which crashes the whole system.
This bug has been correlated with lines 4632486 and 434876365 in module132413.pl being executed, but it is not exactly clear how.
Your job is to figure out what these lines of code do, and how they cause the bug. Here they are, and you can download the whole source on github:
module132413.pl:4632486: $a4918732 = $b13rqw9 && chomp $dfadfaadf4r;
module132413.pl:434876365: print;
Good luck with the debugging!
Re: What's a virus, anyway? The bare-bones basics
#105Re: What's a virus, anyway? The bare-bones basics
#106They say there is a part 2. Where is the said part 2, I couldn’t find the link.
Looks like it hasn't been posted yet. This article came out today, this is the most recent article from that author, and google didn't turn up anything. It's strange how the end implies that part 2 already exists though.
Re: What's a virus, anyway? The bare-bones basics
#107Wise 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.
Thanks for sharing. The lifecycle was much more sophisticated than I assumed.
Re: What's a virus, anyway? The bare-bones basics
#108> 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…
It reminds me of something I read in response to that question (I can’t remember where): People love to place things in tidy categories; nature doesn’t.
Every second, we are constantly and automatically distilling insane quantities of internal and external stimuli into much simpler -- but still incredibly complex -- webs of categories, associations, and relationships. Each moment of awareness is composed entirely from these mental constructions.
We also analyze and modify our representations in various ways, both consciously and unconsciously. Science is one of the more explicit processes for doing so.
Of course, much of reality is lost and distorted in the process. But we do the best we can :) I like to think we make better maps of reality now and then.
I suppose, at the very least, some of the maps we currently possess can be used to enact more dramatic change in the world around us than ever before, which must say something about their truthiness.
Re: What's a virus, anyway? The bare-bones basics
#109Wise 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?
Also, on that scale individual molecules are bouncing around inside the cell faster than you can run or bike. It is a metaphorical froth of seething sliding movement.
Re: What's a virus, anyway? The bare-bones basics
#110> 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.
The seed analogy may be onto something.
Some viruses don't directly cause the host to create new viruses. Instead they direct the creation of virus creating factories, which create the virus.
Then you get virophages which are even tinier than normal viruses, which infect the virus factories of other viruses.