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Covid-19: The T Cell Story

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Re: Covid-19: The T Cell Story

#101
post #77

Earlier quoted context omitted.

I think it really depends on your underlying dynamics, but I just want to point out that f'/f going to zero does really not imply that f will converge. If for example you are in a still strongly growing (but no longer exponential) regime where you can approximate the currently infected number of persons as proportional to t^2 , and there is some constant IFR, then f'(t) is also proportional to t^2. f(t) will then be…

And I still politely ask you to just look at the data. There is nothing in the data that points to "somehow" and "maybe". It is just a straight linear line in the logscale. You may see some wobble caused by outbreaks here and there, but the mechanics of COVID-19 are always the same. Going to zero exponentially does mean it will converge mathematically. And t^-1 won't look like the things that can be observed. There i…

I'm not doubting that it looks like what you say for the area you looked at. I just wanted to make a more general point that it is not sufficient to look at f'/f and conclude that things will be fine if that is tending towards zero.

I'm not claiming that is what you were saying, I just wanted to call out this point in case other people read this that may come to this conclusion.

FWIW, the solution to f'/f = exp(-t) is f(t)=c*exp(-exp(t)), which actually looks like an epidemiological curve, but like any sigmoid it will be hard to determine the actual saturation point until after it has already passed the inflection point.

Re: Covid-19: The T Cell Story

#102
post #59

Earlier quoted context omitted.

> then some mass spreading events infecting many more The point is however that it is impossible that the choir selected their members based on the criteria of "members can be only these who will be easily infected with the at the moment still unknown disease." There the existence of the superspreading event to "80% of some random selection" disproves the hypothesis that "on average much less than 80% of the populati…

Just because the choir couldn't select its members on the basis of lower immunity, doesn't it mean it didn't select them (or they self-selected on) the basis of some characteristic(s) that happened to correlate with lower immunity, e.g. age, biological gender, ethnicity, socioeconomic status, etc. The same is true of any other sub-population this is not a true random sample of the global population, like prisons, car…

> I've not heard a convincing explanation for Germany's relative success based only on the quality of its healthcare system and interventions. That isn't to deny that they played an important role, just that they may not have been the whole story.

Of course "its healthcare system" is not the whole story alone. "Its healthcare system and interventions" is a good enough precondition, combined with the timing: it was since long obvious that the difference in timing of introducing the interventions immensely changes the number of deaths in the first peak: first order approximation: if the doubling time is 3 days, interventions of 2 weeks earlier compared to some other country could result in 2 ^ 4 = 16 times less deaths per capita. It's very primitive approximation but good enough to make such an argument (even if it's significantly off, it is to show how little time result in big changes). For more detailed elaboration there was recently a paper calculating the difference with more exact models, I believe for the UK. (edit: found one for the US https://www.medrxiv.org/content/10.1101/2020.05.15.20103655v... )

So the story for Germany is: luck, in having the early warning and the capability to act on it: Italy have had its spread earlier and it gave Germany enough of "early warning" which was effectively used. The bigger story is the failure of other countries who also practically had the same "early warning" and remained blind to it, until they recognized that they had do "do something" but with the resulting cost of more deaths.

Europe is a good enough field where a lot of effects could be clearly observed, all countries having in some important aspects significantly more sane health system than the U.S. We also know for sure that the excess deaths due to the all causes together can't be hidden in these countries (see https://euromomo.eu/graphs-and-maps/ ), so we now know exactly how bad which country was hit. Comparing the rich European countries and knowing how they function all the differences among them are indeed very explainable, I don't see any surprises: it's the interventions and learning from the experience of other countries that consistently worked.

U.S. was of course much less ready to learn from anybody. In spite of that, the deaths per million in the U.S. is still 362 while it's 500 in Sweden -- so we all have a good "negative example" from Sweden. Note also that Sweden did close universities and older classes in schools, and suggested everybody who can to work from home, and still got to be that bad -- only because their interventions were by design less strong compared to other European countries.

Reported daily deaths per million in USA, Sweden, Germany and Italy, "by number of days since 0.1 average deaths (per million) first recorded" compared:

https://ig.ft.com/coronavirus-chart/?areas=usa&areas=swe&are...

Note that "it lasted longer in Italy" for almost 20 days -- that was the early warning available to other countries. Some used it. Pity that FT doesn't display simply all the curves based only on the dates. Also, too big entities like the whole USA or China aren't a good comparison, the big less infected areas (due to them being simply less reachable) move the averages down too much -- a better base for comparison would be the entities on the order of 10 millions. E.g. in the USA, NY is definitely a phenomenon that is worth observing separately etc.

Re: Covid-19: The T Cell Story

#103
post #40

Earlier quoted context omitted.

Yeah, experts won't get everything right so let's listen to the ignorants... Pretty sure there is a phallacy that describes this line of thought. Multiple ones, probably.

Why don’t we listen to the information too, and decide for ourselves by thinking critically? Maybe even change our own minds sometimes? None of that is beyond my reasoning abilities, and I have a hard time believing that it is beyond yours. By the way the GP is criticizing the “appeal to authority” fallacy, and you are criticizing a form of the “argument to moderation” fallacy.

"Appeal to authority" -- which is a huge red flag when it's brought up in a discussion, because it's usually an attempt to elevate nonsense as if all voices are equal and things like expertise and training/dedication aren't pertinent -- has zero relevance, and seems to be misunderstood a hundred times for every time it is actually understood.

An appeal to authority is disputing widely understood information by citing an authority as if it is an override. e.g. "my doctor told me that vaccines don't work": Against hundreds of thousands of experts and professionals, and a widely understood body of evidence, someone cites a dubious authority as a counter argument.

"My plumber says that lead makes you grow strong bones" "My accountant says that compounded interest is a myth". "My cousin has a chemistry degree and he says that global warming isn't real".

Does that somehow mean that every layperson needs to fill the world with their hot take of noise about COVID-19? No, not at all. This does not follow.

The argument to moderation claim makes even less sense, and I'm not sure you understand what it even is because it's woefully out of place.

Re: Covid-19: The T Cell Story

#104
post #100
post #80

Earlier quoted context omitted.

> while I agree with your general advice about sources, I don't find your "apparently" to be apparent at all. "Apparently" was used in the sense "I haven't seen and verified the sources myself" (i.e. the specific scientific material that supports the conclusion of an expert) but at least I took the effort to get the claim about that conclusion from a recognized expert directly." That is, I can't give you the ultimate…

You should look for the better source for your claims than some podcasts. It is already estblished that those who had COVID develop immunity for it, just not entirely clear how long lasting it is. But given its similarity to the original SARS it should last quite a long time.

> It is already estblished that those who had COVID develop immunity for it

Who claimed something opposite to that and where? I don't understand why you write that at all.

I'm arguing that getting the coverage directly from the experts who do reflect the knowledge of the whole fields (and who don't promote some narrow agenda like Ioannidis) is provably better than getting it from the politicians or the press. The goal is always to recoginize these who introduce a bias which distorts the truth.

What are your "better" sources (as in, more expert and less biased) that cover this pandemics?

Re: Covid-19: The T Cell Story

#105
post #40

Earlier quoted context omitted.

Why don’t we listen to the information too, and decide for ourselves by thinking critically? Maybe even change our own minds sometimes? None of that is beyond my reasoning abilities, and I have a hard time believing that it is beyond yours. By the way the GP is criticizing the “appeal to authority” fallacy, and you are criticizing a form of the “argument to moderation” fallacy.

"Appeal to authority" -- which is a huge red flag when it's brought up in a discussion, because it's usually an attempt to elevate nonsense as if all voices are equal and things like expertise and training/dedication aren't pertinent -- has zero relevance, and seems to be misunderstood a hundred times for every time it is actually understood. An appeal to authority is disputing widely understood information by citing…

> an attempt to elevate nonsense as if all opinions are equal

This is precisely the “argument to moderation” fallacy.

I disagree with the rest, and will not comply with any part of your recommendation. If you think my opinion is “noise” then it is probably best for you to ignore it.

Re: Covid-19: The T Cell Story

#106
post #38

Earlier quoted context omitted.

I mentioned Armin/Invecto since they are looking at T-cell responses to pathogens. Much of the prolonged antibiotic treatment is no longer common practice. It damages the GI, suppresses portions of the immune system and is in many cases bypassed by 2 resistant forms of Lyme (round body starvation form & biofilm colonies). Most of my testing has been through Igenex, which has a lot of experience with antibody testing…

Curious about your thoughts on a patient that tested both the Quest and IgeneX immunoblots at the same time. The Quest showing 5 positive bands. And the IgeneX no positive bands. Then repeated the same two tests four months later at the same time with the same results. So Quest repeatedly CDC positive, IgeneX repeatedly negative. How would you interpret that?

I would ask which Quest lab specifically ran the test as lab quality can vary. I have not seen mainstream labs return all of the antibody stains present in some time, they usually indicate (+/-) for IgM (less likely) or IgG (more likely). The count is also usually indicated (titer level). It also depends which antibody proteins are present. Many of them overlap with other pathogens (IE: 41 covers most of the spirochete class: Borellia, Leptospirosis, Syphilis, etc). It depends on current & historical symptoms and markers like C3a/TGF-b/MMP-9/CD57,8 and would probably try other tests for markers, possibly another Lyme specific test at a different, but specialized lab like Galaxy Diagnostics (well known for Bart), Fry labs or another in NY whose name escapes me.

Re: Covid-19: The T Cell Story

#107

Earlier quoted context omitted.

And I still politely ask you to just look at the data. There is nothing in the data that points to "somehow" and "maybe". It is just a straight linear line in the logscale. You may see some wobble caused by outbreaks here and there, but the mechanics of COVID-19 are always the same. Going to zero exponentially does mean it will converge mathematically. And t^-1 won't look like the things that can be observed. There i…

I'm not doubting that it looks like what you say for the area you looked at. I just wanted to make a more general point that it is not sufficient to look at f'/f and conclude that things will be fine if that is tending towards zero. I'm not claiming that is what you were saying, I just wanted to call out this point in case other people read this that may come to this conclusion. FWIW, the solution to f'/f = exp(-t) i…

Yes, it's important to go down exponentially - which exactly is the thing it is doing - not just in one place...

Good luck that most countries on the planet have already passed the inflection point, so finding the saturation point isn't that difficult anymore.

Interesting to see that just asking people to look into this will generate downvotes. It's just basic mathematics. And it really isn't that hard to verify...

Re: Covid-19: The T Cell Story

#108

Earlier quoted context omitted.

I'm not doubting that it looks like what you say for the area you looked at. I just wanted to make a more general point that it is not sufficient to look at f'/f and conclude that things will be fine if that is tending towards zero. I'm not claiming that is what you were saying, I just wanted to call out this point in case other people read this that may come to this conclusion. FWIW, the solution to f'/f = exp(-t) i…

Yes, it's important to go down exponentially - which exactly is the thing it is doing - not just in one place... Good luck that most countries on the planet have already passed the inflection point, so finding the saturation point isn't that difficult anymore. Interesting to see that just asking people to look into this will generate downvotes. It's just basic mathematics. And it really isn't that hard to verify...

I think the downvotes were not for asking people to look at it, but because the comment can come off as overly dismissive of the severity of the situation.

Re: Covid-19: The T Cell Story

#109

Earlier quoted context omitted.

Yes, it's important to go down exponentially - which exactly is the thing it is doing - not just in one place... Good luck that most countries on the planet have already passed the inflection point, so finding the saturation point isn't that difficult anymore. Interesting to see that just asking people to look into this will generate downvotes. It's just basic mathematics. And it really isn't that hard to verify...

I think the downvotes were not for asking people to look at it, but because the comment can come off as overly dismissive of the severity of the situation.

Maybe, I'm not really a polite person. I think using a working formula for f would greatly help to evaluate the consequences of actions and helps to detect outbreaks early.

In my area they made masks mandatory and cut down the protection of hospitals - now we have an infected nurse. I think politicians currently are using seriously wrong models for their actions.

I had a discussion with one of the "official" epidemiologists. It went like the discussion with you - just at the point where we are now he decided to go into all-caps swearing, said that he will never look into this, called his models perfect and then blocked me.

Re: Covid-19: The T Cell Story

#110
post #67

Earlier quoted context omitted.

> https://i.imgur.com/zZ7UGVW.png I'm assuming the peaks and valleys correspond to weeks, but why are deaths correlating so strongly with the day of the week?

That's probably an artifact of the reporting process. Most hospitals don't report during the weekends.

I also wouldn't be surprised if there seasonality in medical care, like people receive worse care certain days, for some reason.
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