OT: The Evolution of Bacteria on a "Mega-Plate" Petri Dish (Kishony Lab)

[jim rozen]

The reason smallpox and polio can be eradicated is that there's no other reservoir for the viruses besides humans.

 

[Joe Gwinn]

Interesting, but I don't think the bacteria are mutating the same way as the virus. Check out the genomic map on page 6 of the link below, I had assumed that each variant was based on its preceding variant, but apparently that is not correct, omicrons roots are from the original strain.
https://www.gla.ac.uk/media/Media_829360_smxx.pdf

Your are certainty correct that COVID mutates somewhat differently than the ordinary bacteria used in the test, but the principle is the same, and bacteria on an agar plate are far easier to do time-lapse photography of.

The purpose of the time-lapse movie is to give one an instinctive understanding of the churn of such evolutionary processes.

The skipping seen in Omicron is universal, and also seen in the agar plates, but not pointed out as such in the youtube video.

 

[Trueturning]

Isn’t the new virus variant being studied in lab work beginning in mid Dec. and running for about seven weeks? They are testing and confirming things which need the lab setting. If any variant jumps from humans elsewhere then it will grow. Right now the origin of Covid has not been identified. It is not needed to produce vaccines.

It could very well be the virus has a few active variants going at one time. If we have not noticed a few they will eventually move on or dominate especially with vaccines working. They had been working on a delta booster I believe. Still they have persons being monitored in studies from the very start and still are monitoring them.

 

[boslab]

In 1962 there was a smallpox outbreak in the welsh valleys, my sister had been vaccinated but I was but a little thing, I hadn’t had it yet, turned out I didn’t have to wait long, she was a nurse, or training to be one and guess what, I bloody well contracted the dreaded pox, was not long before I was transferred to a place called “ hill house isolation hospital “ why were these places on hills I thought, because no one goes there, anyway I survived it, I’m now exempt ( I have a card!) from smallpox vaccinations, turns out if you live your rendered impotent immune but sometimes useful for clinical trials and as a blood puddle, last go off they slurped a pint a week for anti b or something
I’ve had covid, it didn’t really bother me much the first time, not at all the second go, however the government think sticking an experimental booster is going to be beneficial, the big question is to who?, I can still catch it, still spread it with impunity, it like buying a washing machine that doesn’t actually work, or being mandated to, the only winner there is the manufacturer, does you no good and potentially harms, before surgery they checked bloods and found gronkovirus19 antibodies aka immunity, why would you want to take anything more, why don’t I get a smallpox jab the same time, oh and chickenpox, I’ve had that too, the science is being distorted to suit the political will of the government who are being manipulated by big pharma,
We manufacture flow tests in the U.K., they aren’t authorised for use so they all get exported, we get ones made in the originator of the viruses factory’s
I smell a rat, this stinks of corruption
Mark

 

[1yesca]

why not just lock this thing down now before it becomes one big i am right your wrong 80 page ego trip

 

[Joe Gwinn]

Suppose the most successful viruses are massively contagious without harming (much) the host, lest successful kill the host before jumping to a new one. Seems common sense, ...

Yes, and backed up by much field experience, long before the current COVID pandemic.

... however goes wrong with a bit of gain of function tinkering by dr frankenfucky.

Much has been made of the gain-of-function experiments performed in Wuhan, but this is a standard kind of study does to get some idea where the pathogen will go next, because if it's easy to make in the lab, Mother Nature will soon get there as well, or may already be there unnoticed. As always.

Said another way, note that the ancient plagues and pandemics all emerged and ran their courses, eventually fading into the background, all long before the emergence of experimental biology as a science or engineering discipline. And as plagues go, COVID is small potatoes.

Immune systems first evolved long before multicellular animals evolved, long before humans and biologists were invented.

Coral animals have an immune system, and abutting coral reefs will fight one another, rather than merging. Each reef is a clone.

 

[Joe Gwinn]

I hope you're right but it still feels like a lot of wishful thinking pushed by people who so often seem to enjoy hearing their voices on TV more than they enjoy being right.

Well, I don't doubt this, but I don't watch the talking heads on TV, and so cannot comment. I prefer to spend the time reading original sources. And if the issue is very political, the most reliable sources are those that predate the political issue in question.

As far as I can tell evolutionary forces gives the virus 3 main objectives #1 evolve to evade immunities in the community #2 if at all possible try to become as infective as possible prior to being detected, and #3 make sure you don't kill the host off prior to replicating and infecting at least 3-7 others so as to hit an exponential reproduction cycle.

Not that viruses have objectives, but in general, yes. But it's #2 and #3 that are objectives, while #1 is a means to meet those objectives.

If you don't believe me look at the AIDS virus that thing never got less deadly with time and was perfectly happy killing off the host. Good thing that one didn't spread thru airborne transmission or I bet humanity would look quite different.

Well, HIV is a very different case. HIV is a RNA retrovirus, while COVID is just a RNA virus.

The difference is immense - retroviruses transcribe themselves into the genome of the host, and so cannot be stamped out so easily. HIV's RNA copy mechanism is famously sloppy, so the HIV population in a given host is a quasi-species, with far too much variation and rate of change for vaccines to be effective. The anti-viral drugs that do work do so by jamming various unique and critical enzymes up, preventing viral reproduction.

Sexual transmission is also very different than aerosol transmission.

Seems like the whole level of severity and how the virus effects the host is just a luck of the draw type of thing. Assuming the virus doesn't kill the host too quickly - how we feel after our infection is of little concern to the virus.

Yes, there is definitely a great deal of luck involved.

 

[Joe Gwinn]

Bacteria =/= viruses.

True, but evolution is evolution.

Did smallpox become less virulent over time?

Nope. it was vaccinated out of existence.

Likewise Polio. These two viruses evolve very slowly, and have no animal hosts, and so can be cornered and eliminated.

But this is not the most common case.

 

[Joe Gwinn]

More research on the origins of omicron
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant - ScienceDirect

I just downloaded the article, and will read it. But I notice two things:

1. The authors all live and work in China, and so they are by definition interested parties.

2. In Figure 3, the ellipses for Bat and Dog are similar, and are perpendicular to that of Mouse. But mice and bats are closer genetically than either is to dog, so I'm perplexed. Also, there may be some other animals that get COVID or related viruses, such as the Pangolin, which isn't listed.

 

[dalmatiangirl61]

I just downloaded the article, and will read it. But I notice two things:

1. The authors all live and work in China, and so they are by definition interested parties.

2. In Figure 3, the ellipses for Bat and Dog are similar, and are perpendicular to that of Mouse. But mice and bats are closer genetically than either is to dog, so I'm perplexed. Also, there may be some other animals that get COVID or related viruses, such as the Pangolin, which isn't listed.

#1. It has been peer reviewed, and I'm pretty sure the chinese know more about this than anyone else

#2. It appears to me (not a scientist) that a lot of what is talked about in that paper is still hypothetical and needs more research.

 

[boslab]

Bat, pangolin, humanised mice, hardly probable in nature at a guess however the biolonutters seemed rather determined to get the bat bug into humans at all costs ( can be calculated in millions I suppose) the argument of preventing a pandemic by GOF research seems bit backwards, the CCP are hardly the right folk to trust with WMDs just because it was made illegal to carry out this kind of research in the US and Europe, even trusting them, building a L4 lab ( thanks to mr Jean Claude Barnier and Mr macron) seems foolhardy at the extreme, our leaders were and are complacent it the destruction of our economy, freedom and way of life.
Should we continue to trust them, I think not sociopathic megalomaniac with a touch of psychopath seems probable
Mark

 

[MrStretch]

Evolution?
Just wind in sails.
Everybody knows that the world was created less than 6000 years ago by the baby Jesus, our lord & savior. He created Noah who was kicked out of the garden and then made an ark out of dictionaries with his friend Webster.

 

[GregSY]

"why not just lock this thing down now before it becomes one big i am right your wrong 80 page ego trip"

Yes! Nothing worse than open discussion and the factual exchange of information. Too much talking can only lead to....dissent and instigation.

Reminds me...I need to burn my copy of The Gulag Archipelago....

 

[dgfoster]

I wonder if people will be able to allow this thread to continue as an interesting, polite, and science-based discussion. Or will the “evolution” post above, intended to start a fight, (we need more of that!) successfully derail it. It’ll be interesting to see if that poster’ cheap shot can be ignored and he be denied the attention he craves.

Thanks to those who posted interesting information above.

Denis

 

[Demon69]

A question I have for Joe Gwinn, perhaps Denis too.

I had Covid june/july last year. While I had symptoms id test myself most days with lateral flow tests to see when the viral load was on the decline. Out of curiosity I thought to attempt to test breath condensate. Using clean glass I collected samples from normal and heavy breathing, swabbing and testing the condensate yielded negative results despite me still testing strongly positive using the normal procedure.

Any ideas as how meaningful this result is? Ive read papers that suggest either way that covid is/isn't in tidal breath.

Cheers
D

 

[dgfoster]

A question I have for Joe Gwinn, perhaps Denis too.

I had Covid june/july last year. While I had symptoms id test myself most days with lateral flow tests to see when the viral load was on the decline. Out of curiosity I thought to attempt to test breath condensate. Using clean glass I collected samples from normal and heavy breathing, swabbing and testing the condensate yielded negative results despite me still testing strongly positive using the normal procedure.

Any ideas as how meaningful this result is? Ive read papers that suggest either way that covid is/isn't in tidal breath.

Cheers
D

First my answer: no idea.

Comment: You tried an interesting experiment that seems relevant to transmission concerns. Good on you! But you need more test kits and glasses—-first just breathe on the glass for a period of time, then sing a medium-pitched note onto the glass, hold the glass at various distances etc. Of course, I am being facetious. But, speaking vs quiet breathing has been shown to cause much more droplet spread/transmission. (As a side note, my wife had been a member of the singing group in Skagit County where one of the early outbreaks occurred).

Hopefully, someone with some actual knowledge (that’s not me) can answer your question.

Like you, I did briefly search on aerosol transmission of Covid/SARS. There are lots of interesting studies.

Denis

 

[EmGo]

Like you, I did briefly search on aerosol transmission of Covid/SARS. There are lots of interesting studies.

But you were probably looking for information, instead of just trying to justify your cockamamie fantasies ...

 

[Joe Gwinn]

#1. It has been peer reviewed, and I'm pretty sure the Chinese know more about this than anyone else

Yes it has been peer reviewed, and it's in a credible journal as well.

The problem is that the Chinese Government manages the news, so articles pointing towards a Chinese origin of COVID are often suppressed. This particular article talks about Africa, so is safe.

#2. It appears to me (not a scientist) that a lot of what is talked about in that paper is still hypothetical and needs more research.

That is my take as well. Anyway, I read the article this morning, and am convinced that their theory, that Omicron evolved during a stint in the mouse population of Africa, could well be true. It will require more work to refute or prove it.

As for the Principal Components of Figure 3, I now see what they are doing, and it depends of the genome of the viruses of that family, and not on how related bats are to mice.

More generally, it is not the case that variant N must have come from variant N-1. They very much can jump around, and most variants never achieve clinical significance, and so are never named.

 

[Demon69]

First my answer: no idea.

Comment: You tried an interesting experiment that seems relevant to transmission concerns. Good on you! But you need more test kits and glasses—-first just breathe on the glass for a period of time, then sing a medium-pitched note onto the glass, hold the glass at various distances etc. Of course, I am being facetious. But, speaking vs quiet breathing has been shown to cause much more droplet spread/transmission. (As a side note, my wife had been a member of the singing group in Skagit County where one of the early outbreaks occurred).

Hopefully, someone with some actual knowledge (that’s not me) can answer your question.

Like you, I did briefly search on aerosol transmission of Covid/SARS. There are lots of interesting studies.

Denis

I was firmly in the 'it's in your breath camp'. There was an article about a study on flu, it involved a 'Gesundheit Machine'. In pre covid times students who had symptoms sat faced into cone and breath was vacuumed away and analysed, coughing was allowed iirc. The conclusion was positive.
The test I did involved normal breathing, and 100% effort. Both were negative. Unfortunately I didnt think to try coughing before 'd recovered. I was surprised tbh, perhaps the tests arnt sensitive enough being aimed at throat and nose swab samples.

 

[Joe Gwinn]

I had Covid june/july last year. While I had symptoms id test myself most days with lateral flow tests to see when the viral load was on the decline. Out of curiosity I thought to attempt to test breath condensate. Using clean glass I collected samples from normal and heavy breathing, swabbing and testing the condensate yielded negative results despite me still testing strongly positive using the normal procedure.

Any ideas as how meaningful this result is? Ive read papers that suggest either way that covid is/isn't in tidal breath.

The lateral-flow tests are not sensitive enough to detect COVID in exhaled fog or droplets. But if you breathe enough of those droplets in, you will likely get infected.

My wife contracted Omicron a week or two ago, and I soon developed it as well, even though we are both fully vaccinated and boosted.

I administered the BinaxNow lateral-flow test to my wife, who had a scratchy cough and needed lots more sleep than normal, and she was strongly positive. (I didn't test myself on the assumption that I already know the answer - I had developed the same cough and sleep demand.)

In this test, one scrubs the inside of both nostrils up to 3/4" (19mm) in with a swab, collecting whatever is right on the mucosal skin that lines the nostril, and becomes a home for COVID. This is far more direct than sampling the droplets emitted while speaking. The scrubbing doesn't really hurt, but is maddeningly ticklish.

She probably got it from her immediate family, many of whom came down with Omicron as well. (There was a lot of travel because there was a death in the family.) In the immediate family, all are vaccinated and none of these infections were serious, none requiring medical attention.