Author Topic: Covid 19 virus  (Read 68897 times)

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Offline cleanworkbench

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Covid 19 virus
« on: February 21, 2020, 07:28:53 pm »
Just had a thought , do you think the labs are using scanning electron microscopes to take a tour inside the  virus as virtual reality and tinker with it to view an outcome in real time ie accelerated graphics , i,m no expert but anyone reckon its feasible . 
 

Offline janoc

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Re: Covid 19 virus
« Reply #1 on: February 21, 2020, 09:20:23 pm »
No.

The labs that are doing the analyses have much better and more important things to do than to tinker with Hollywood style gadgets that wouldn't bring any benefit for their jobs.

Also, the fact that you can view a virus using a microscope and that there is a virtual reality helmet available doesn't mean that can just feed video from a microscope into a VR helmet and expect it to "work". You would get only a blurry low resolution mess that would make you nauseous and you wouldn't see anything more than what you can see on the screen of the microscope already anyway.

If you really wanted to do this, you would need to know how to:

a) Model the behavior of the virus (extremely complex task, notabene when it is something as new as this one where the knowledge is still very limited) so that it can be meaningfully simulated.

b) Make such simulations real-time. They aren't, not even close. We are talking typically hours and days of simulation time, and that is for chemical reactions, not a living system which is order of magnitudes more complex than a simple chemical reaction between molecules. In biology it is faster (and more accurate!) to do it in a petri dish than to simulate, especially when we don't even know how to simulate behaviour of anything of this complexity yet!

c) To develop an VR application that would interface with such simulation. We are talking enormous amounts of data which you can't simply load into a GPU and let the helmet display it. I did a visualization of chemical reactions in Li-ion batteries last year and about million particles (atoms/molecules) was pushing it already.

Even the simplest virus has orders of magnitude larger complexity if you want to simulate effects of e.g. a new drug on it. That would require a lot of very fancy and complex technology  to manage such visualization, not to mention the costs of the hardware to run it on.

E.g. this paper speaks about 6.5 millions of atoms in a capsid (shell) of a polio virus, which has been simulated for 200ns (!) using a supercomputer (only the capsid, without the virus) :
https://physicstoday.scitation.org/do/10.1063/PT.5.7117/full/


(develops VR applications for living)
« Last Edit: February 21, 2020, 09:35:34 pm by janoc »
 

Offline NiHaoMike

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Re: Covid 19 virus
« Reply #2 on: February 22, 2020, 12:48:21 am »
Doing biological simulations is what the Folding@Home project (and cryptocurrency that uses it for mining, as in Curecoin and Foldingcoin) does.
https://foldingforum.org/viewtopic.php?f=17&t=32124
Cryptocurrency has taught me to love math and at the same time be baffled by it.

Cryptocurrency lesson 0: Altcoins and Bitcoin are not the same thing.
 

Offline cleanworkbench

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Re: Covid 19 virus
« Reply #3 on: February 22, 2020, 11:46:01 am »
Well i learnt something there , very interesting many thanks .  So its down to good old fashion common sense and today,s technology to save us then .
 

Offline Rerouter

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Re: Covid 19 virus
« Reply #4 on: February 22, 2020, 12:15:25 pm »
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13510&postid=91696#91696

There is a lot of computing resources being thrown at the problem, and even then it will not be fast to discover its base structure, let alone then using that to attempt simulating how it interacts with everything, Its more a case of searching for what might be a chink in the armor that could them be used to damage it, or interrupt its replication.

Re the scanning electron mircoscope, viruses are just a bundle of DNA packaged in the shell, if the shell is closed, they look like popcorn chicken, if open, it is usually too well packaged to be able to take a 3D model of the interior structures.
 
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Offline cleanworkbench

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Re: Covid 19 virus
« Reply #5 on: February 22, 2020, 08:55:22 pm »
It sounds like a very weird world inner space ,lets hope they can crack the code .
 

Offline angrybird

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Re: Covid 19 virus
« Reply #6 on: February 24, 2020, 11:08:54 pm »
I wish they would put this much work into figuring out why nuthatch are so damn cute and distracting.
THE CAKE IS A LIE AND THESE NUTHATCH ARE WAY TOO DISTRACTING
 

Offline Nominal Animal

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Re: Covid 19 virus
« Reply #7 on: February 25, 2020, 12:22:32 am »
You don't do molecular dynamics simulations to find out how to stop viruses from replicating.  You work on the 1) the outer envelope of lipids to see how to get immune systems to recognize and attack the virus particles, 2) on the capsid or shell protecting the genetic information, for the same reason, or 3) on the DNA or RNA strands to find a way to stop the virus from replicating.

None of them are flashy research where one brilliant mind can solve the thing in hours like in movies.
We have a lot of data on how viruses work, but because living cells are so complex and varied, it is extremely hard work to find out how particular strains of a virus work, and how they can be disrupted.  It's much more like trying to find commonalities between the books from a couple of dozen authors, than people trying to think of creative ways to attack it directly.

Vaccines are essentially just ways of teaching immune cells what to track and attack.  Some antiviral treatments only reduce the replication enough for the body to keep up -- it's like the difference between nuclear fission in a reactor keeping it hot (requiring constant medication) and in a nuclear bomb.  Some antiviral treatments stop the replication, so that when the infected cells eventually die, the person is fully cured.

Viruses also mutate constantly.  When two (different!) viruses infect the same cell, they exchange DNA/RNA.  This is why it is extremely scary when a patient with a deadly virus infection gets infected with a more infectitious virus: the new combined one can be both deadly and infectitous.  We should also be more careful about the medication we use, because if you don't kill all of a virus, only most of it (to bring the viral load down to levels the body can manage on its own), the virus variants that survived the medication can spread.  This is exactly how superbugs came to be.

That is also why finding the "root" of the virus is sometimes important: you can find the commonalities before the mutations, so you can target the entire "descendant" set.  As an example, there are four influenza virus variants, three of which cause flu, but vaccination only protects for a year or so, and only for the chosen variant -- but since we don't know which of the three will be the major one next flu season, it's always a bit of a guess work.

For corvid-19, the reports that a person could have been reinfected very soon after recovery are the most alarming, because if so, we really have no hope for developing effective antiviral treatments for it; they all depend on the human immune system to do the heavy work, and if the human immune system doesn't develop any kind of immunity (for at least a couple of months), it means the immune system does not have a reliable way of recognizing the virus, and none of our antiviral treatments have much hope of working at all.

The most important thing here is that corvid-19 is not that special.  We know influenza becomes a worldwide epidemic killing millions about three times a century; and now it looks like coronaviruses can cause similar epidemics.  Corvid-19 is just a bit less infectitious and a bit more deadly.

What we should do, is to not stock food and resources until this epidemic passes, but to try and find ways of combating the spread of these viruses in the first place.  It may mean things like no more flights or public transport when you have a cold/flu/whatever; that wearing gloves becomes the norm for everybody throughout the year (that helps avoid flu already); and that sneezing, coughing, or spitting towards someone becomes bigger faux pas than saying a racial slur.

You see, while this too will pass, there will always be the next, and the next, and so on.  And since humans mix more than ever before, considering the ways viruses share genetic data, at least some of the future ones will be even worse.  This is not the end of the world (because 90% of the people who have gotten infected recover; so even if every human being on this planet were to be infected, 90% would still survive), so no need to panic; but this would be the optimum time to look at how we deal with epidemics and the spread of infectitious diseases as a planet-wide species.
 
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Offline cleanworkbench

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Re: Covid 19 virus
« Reply #8 on: February 26, 2020, 08:32:08 pm »
So does it matter which part of the planet a human is from as to whether the mutation would be a different type . In simplistic terms someone from China develops covid 19 and as it works its way around the world does it end up as something else but still covid 19 , is this the mutation that they appear to be chasing. ?.
 

Offline Nominal Animal

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Re: Covid 19 virus
« Reply #9 on: February 26, 2020, 08:48:05 pm »
So does it matter which part of the planet a human is from as to whether the mutation would be a different type.
No, we are all one species in this regard.

There are differences in how human bodies deal with the virus, though.  As an example, people with sickle cell anemia are much less likely to get malaria.  For coronaviruses, I am not aware of any regional differences in immunity or otherwise.  There could be some, we just don't know yet.  If there are any, it is probably related to inherited immunity from previous generations' encounters with the same family of viruses, coronaviruses, and not differences in humans per se.

In simplistic terms someone from China develops covid 19 and as it works its way around the world does it end up as something else but still covid 19 , is this the mutation that they appear to be chasing.
Each virus has its own typical mutation rate.  It does not matter whether it travels around the world, or slowly infects new people in the same region, they just tend to mutate at the same rate.  That is not the issue here.

The risk is that if it is true that the same person can get infected within weeks of recovering from the virus, the mutation rate is such that human immune system can't keep up.  The virus looks completely new to the immune system, so it doesn't recognise it as something it needs to fight/eat.  Fortunately, it now looks that this report was not that, but something like a misdiagnosis in the first place.

Secondary risk is that people with other viruses in their system, more dangerous but less virulent ones like a hemorrhagic fever, get infected.  In those cases, the two viruses may exchange genetic material, with completely new variants being "created" as a result.  It is not common, but it is known to happen.  If this virus came to be without human intervention, this is likely how it developed in some animal (a "mix" of two different coronaviruses, I mean; I've heard of similarities to some coronaviruses endemic/typical in bats and some other species), then jumped to a human being, and started to spread.

For now, the problem in treating covid-19 is that we have no way to tag the virus for the human immune system to detect it early.  It will detect it when you're already sick -- could be two to four weeks after initial infection, and you'll be spreading the virus during all that time.  We have no medicine that can help the body combat the virus; we can just treat the symptoms (pain, kidney failure) and keep the patients hydrated and so on.  If we could describe it to our immune cells -- that's what the flu vaccine does; the body remembers that particular description for a year or so, but as there are three different variants, it's always a bit of a guesswork which one to get/give -- they could attack it immediately, and prevent the virus from getting a foothold.

If the "native change rate", mutation rate, in the virus were so fast that the same person could be reinfected within weeks, there would be about zero hope of finding a way to tag the virus, as it changes faster than we could manufacture the tagging stuff.  Again, it does not look that way, although for a couple of days, I was quite alarmed about that.  (I'm a materials scientist, a physicist, not a doctor, though.)

The reason it is important to keep track of the path of the virus, is that two to four week incubation period.  If we know how the virus is passed on, we can prepare the medical facilities accordingly; basically make better guesses as to where resources are needed.  When "untraceable" infections pop up, it means there are carriers we don't know about, and when they get sick, there could be many of them in the same area; and then it can be very hard to get them help in time.  (Covid-19 seems to be particularly hard to the kidneys in the severe cases; many in intensive care are in dialysis, to reduce the stress on their kidneys.  Otherwise its symptoms are comparable to the flu.)
« Last Edit: February 26, 2020, 08:57:38 pm by Nominal Animal »
 

Offline imo

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Re: Covid 19 virus
« Reply #10 on: February 27, 2020, 04:16:57 pm »
Interestingly there is none child below 2-3 years of age infected. Why?
 

Offline blueskull

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Re: Covid 19 virus
« Reply #11 on: February 27, 2020, 04:18:03 pm »
Interestingly there is none child below 2-3 years of age infected. Why?

Double check your facts. The youngest report in China is freaking 5 days after birth.
 

Offline imo

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Re: Covid 19 virus
« Reply #12 on: February 27, 2020, 04:23:21 pm »
Do you have a statistics from 5days to 3years of age?
 

Offline blueskull

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Re: Covid 19 virus
« Reply #13 on: February 27, 2020, 04:26:56 pm »
Do you have a statistics from 5days to 3years of age?

Just sparse news reports from time to time.
 

Offline cleanworkbench

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Re: Covid 19 virus
« Reply #14 on: February 27, 2020, 06:56:27 pm »
Oh well folks thanks for the insight , i just hope there's a very clever and highly skilled team out there in a lab somewhere .
 

Offline Nominal Animal

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Re: Covid 19 virus
« Reply #15 on: February 27, 2020, 07:28:08 pm »
Oh well folks thanks for the insight , i just hope there's a very clever and highly skilled team out there in a lab somewhere .
It's actually more like "hope there is enough people working on this and coordinating with each other, because the 'haystack' they need to comb through is so vast".

The haystack being the genetic information in covid-19, and the "needle" being either some way of tagging it for immune system to attack, or a way to weaken the virus from infecting new cells or slowing or stopping the replication.  Lots of possibilities, but only very, very few of them actually work, and all need to be tested to find the ones that do work.
 

Online 0xdeadbeef

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Re: Covid 19 virus
« Reply #16 on: February 27, 2020, 08:03:22 pm »
While all of this becomes somewhat terrifying admittedly, it's important to keep the numbers in perspective. E.g. in Germany there are currently < 50 confirmed cases (numbers of the tracking sites are still quite old and vary around 26 but there were 20 new cases recently), thankfully still without any fatality. The number of confirmed influenza cases for this season is around 100k though with 161 fatalities and nobody really cares.
In the influenza season 2017/18, 25k (!) people died (about 0.03% of the population) in Germany and nobody panicked about that. And still lots of people don't even care about influenza vaccination.
So, yes. it's a serious thing, maybe a bit more serious than influenza if it really spreads worldwide but it's not the apocalypse. Just as with influenza, most people that die of it are either old or suffer from a serious pre-existing illness.
Trying is the first step towards failure - Homer J. Simpson
 

Offline SilverSolder

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Re: Covid 19 virus
« Reply #17 on: February 27, 2020, 08:09:45 pm »
While all of this becomes somewhat terrifying admittedly, it's important to keep the numbers in perspective. E.g. in Germany there are currently < 50 confirmed cases (numbers of the tracking sites are still quite old and vary around 26 but there were 20 new cases recently), thankfully still without any fatality. The number of confirmed influenza cases for this season is around 100k though with 161 fatalities and nobody really cares.
In the influenza season 2017/18, 25k (!) people died (about 0.03% of the population) in Germany and nobody panicked about that. And still lots of people don't even care about influenza vaccination.
So, yes. it's a serious thing, maybe a bit more serious than influenza if it really spreads worldwide but it's not the apocalypse. Just as with influenza, most people that die of it are either old or suffer from a serious pre-existing illness.

Also, let's not forget about ~40,000 traffic fatalities each year (USA) that we are completely OK with...
 

Offline donotdespisethesnake

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Re: Covid 19 virus
« Reply #18 on: February 27, 2020, 08:19:45 pm »
"One person's death is a tragedy, a million deaths is just a statistic".

I hope it stays purely a statistic for you.
Bob
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Offline Stray Electron

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Re: Covid 19 virus
« Reply #19 on: February 28, 2020, 01:54:03 am »
While all of this becomes somewhat terrifying admittedly, it's important to keep the numbers in perspective. E.g. in Germany there are currently < 50 confirmed cases


   Germany today is China two months ago.  How is that for perspective?

  The public and the govenments in the US, Europe and the rest of the world should have already realized what is happening in China today is something that we're going to have to deal with in the very near future.

   If you need a reminder of how quickly this can spread and at what the medical and economic effects are just look at Italy or at South Korea over the last two weeks. And this virus is just getting started! 

    Think is this as being December 1917 and the 1918 Spanish flu is just beginning to be noticed.
 
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Offline Bud

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Re: Covid 19 virus
« Reply #20 on: February 28, 2020, 02:03:53 am »
While all of this becomes somewhat terrifying admittedly, it's important to keep the numbers in perspective. E.g. in Germany there are currently < 50 confirmed cases (numbers of the tracking sites are still quite old an died (about 0.03% of the population) in Germany and nobody panicked about that. And still lots of people don't even care about influenza vaccination.
Call us when coronavirus Death will knock Your door and let is know if ignorance and denial helped scare her away.
Facebook-free life and Rigol-free shack.
 

Online 0xdeadbeef

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Re: Covid 19 virus
« Reply #21 on: February 28, 2020, 10:07:24 am »
You guys really know how to turn a calm and rational statement into something coldhearted and misanthropic. Please try to read whole sentences or even paragraphs before trying to blame other people of a horrible attitude.
Trying is the first step towards failure - Homer J. Simpson
 

Offline donotdespisethesnake

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Re: Covid 19 virus
« Reply #22 on: February 28, 2020, 10:30:01 am »
You guys really know how to turn a calm and rational statement into something coldhearted and misanthropic. Please try to read whole sentences or even paragraphs before trying to blame other people of a horrible attitude.

Well, you said "it's nothing to worry about, and anyway mostly old and sick people will die". Neither statements is factual. Since no one has a crystal ball, the rational statement is "we don't know how bad it will get".

If you said "I'm not worried about it", that would be a valid opinion. But you tried to dress it up as "you should not be worried because <made up reasons>". Not rational at all.
Bob
"All you said is just a bunch of opinions."
 

Online 0xdeadbeef

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Re: Covid 19 virus
« Reply #23 on: February 28, 2020, 11:30:32 am »
Well, you said "it's nothing to worry about, and anyway mostly old and sick people will die". Neither statements is factual. Since no one has a crystal ball, the rational statement is "we don't know how bad it will get".
No, that's not what I said. That's what you decided to read into it. Which says a lot about your perception of yourself and other people but nothing about what you falsely quoted.
Trying is the first step towards failure - Homer J. Simpson
 
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Offline donotdespisethesnake

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Re: Covid 19 virus
« Reply #24 on: February 28, 2020, 01:01:41 pm »
Well, you said "it's nothing to worry about, and anyway mostly old and sick people will die". Neither statements is factual. Since no one has a crystal ball, the rational statement is "we don't know how bad it will get".
No, that's not what I said. That's what you decided to read into it. Which says a lot about your perception of yourself and other people but nothing about what you falsely quoted.

If you really think that is not what you said, you really need to be a lot more careful about how you write things. But no need to get your panties in a bunch, it's not the apocalypse, right?

Anyway, at least you agree it is something serious which needs people's attention, and will affect people of all ages.
Bob
"All you said is just a bunch of opinions."
 


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