- This topic has 1,202 replies, 1 voice, and was last updated 3 months ago by Dave.
June 8, 2020 at 12:58 #54794Clark
The origin of SARS-CoV-2 debate.
Extensively referenced article in The Bulletin of the Atomic Scientists, 27 May 2020, by Milton Leitenberg, a senior research associate at the Center for International and Security Studies at the University of Maryland (CISSM):
I reach the same three conclusions as I have done consistently.
1) Secrecy kills. All surveillance systems point in entirely the wrong direction. They snoop on the public, and deliver that data into the control of organisations. Those organisations are variously private/corporate or governmental. But organisation itself is the greatest amplifier of human ability, for good or for ill. Organisations must be permitted no secrecy, no concealment. If their work produces good, disclosure will distribute that good. If their work results in danger or damage, the people of the world have a right to know that, and understand everything about it. Competition is killing us and our world.
2) Biological laboratory security is hopelessly inadequate. These facilities must be in remote places, with live-in accommodation and on-site quarantine.
3) The US political mud-slinging over CoVID-19 is utterly hypocritical because this strongly appears to be yet another outsourcing issue:
– “Details of the most recent National Institute of Allergy and Infectious Diseases (NIAID) grant for WIV bat coronavirus surveillance and WIV bat coronavirus gain of function research are publicly available” – NIAID is part of the US NIH. Article citation number 28:
Project Number: 2R01AI110964-06
Title: UNDERSTANDING THE RISK OF BAT CORONAVIRUS EMERGENCE
It seems to me that both the US and Chinese governments are seeding conspiracy theories to divert attention from their own contributions to what was a collaborative project.
Here’s another article on the same topic, with some simple explanation:June 9, 2020 at 20:38 #54838SA
It all still remains circumstantial and all of what this author is saying is pointing out possibilities in an opinion piece, looking at existing evidence.
But let me add something else to fuel this fire. The Chinese discovered and sequences this virus in record time. They knew very well and feared its potential so much so that they took extreme measures to suppress it and managed to do so.
Some other countries were slow with much more disastrous consequences. Does this mean that the Chinese new more about the virus from the very beginning than they let on?June 9, 2020 at 21:00 #54842Clark
Hmm, there are indications both ways. Yes the genome was sequenced fast, suggesting that maybe they had a head start from existing knowledge of the virus and the way SARS-CoV-2 had been derived, but even China’s extreme measures were late, and if the joint US-Chinese NIAID project was the source, you’d have expected word to have got back to the US, yet the US’s responses have been among the worst. Mind you, maybe word did get back, but the Trump administration…June 10, 2020 at 05:51 #54857SA
There you are. We have just got a step towards getting to the realisation that part of the problem is that there are unknown unknowns and also unknowable Unknowns.June 10, 2020 at 19:45 #54895Clark
– “But possibly, the biggest problem with the 4% difference argument is that it relies on RaTG13 being exactly what WIV says it is. If we are to seriously consider the lab leak hypothesis, we must concede that it does not make sense to blindly trust the data released by the very lab suspected of the leak. If the leak did occur, as is the premise of the lab hypothesis, then the description of what RaTG13 is could be furthering the goal of covering up the leak.
– Again, I am not claiming with certainty that is what is happening here. All I am saying is that this is what could have happened, and we need a lot more evidence before we can reach a definitive conclusion. One thing that could help rule out tampering with RaTG13 is having independent labs sequence the 2013 Yunnan samples that She Zhengli extracted RaTG13 from. WIV must still have them if they re-sequenced RaTG13 in 2020.”June 17, 2020 at 18:19 #55218SA
Coronavirus breakthrough: dexamethasone is first drug shown to save lives
In a large trial the drug was found to reduce the mortality in severe cases of covid-19 on ventilators or those needing oxygen therapy by 20-30%.
Dexamethasone is a steroid which is widely used and cheap and with few side effects. There is a good experience of using this drug in ITU and in some cancers. It supresses the hyperreactive immune response that is seen in patients with severe disease. The drug has no effect in milder cases.June 19, 2020 at 12:33 #55310SA
Some observations on today’s snapshot figures
What is apparent is that the rate of diagnosed infections vary between .005 %(China) and 1.2% (Chile).
The CFR vary from 1.4% (Russia) to 15.4% (France) with UK high at 14%. But so far as these figures show, density of population does not appear to be a major cause of increased infection.June 20, 2020 at 12:48 #55377Clark
SA, some questions: what is your source for the figures, and what is the formula for the O rate?
Perceiving trends in this pandemic has so many problems of variability of accuracy of data; some counties have tested a much higher proportion of the population than others, and most countries’ rate of testing has presumably increased; testing is targetted in various ways, very little of it is random and thus a representative sample of the population; attribution of cause of death probably varies a lot; we don’t have any metrics for either imposition of social restrictions or actual public behaviour in social distancing.
Maybe proxy data would serve us better. For instance, when considering diverse countries, the overall excess death rate is probably more reliable than the covid-19 death rate.
Population density is an interesting one because the overall population density of a country tells us hardly anything about, for instance, how often people inhale each other’s breath. England has a population density of 430 per square kilometre, but obviously the potential for cross-infection varies hugely between 430 people out looking for mushrooms compared with 430 people attending a meeting in the village hall.
What would serve as a good proxy for social proximity distribution? And what about social mixing, ie. unusual meetings between people as opposed to repeated ones? I suppose transport use might help – a distribution curve of number of journeys and their distance.
It’s frustrating. The things to be considered are so mundane, yet quantifying them is so elusive. I can certainly see the temptation to modelling – just write a program, let the machine crunch the numbers, and ponder upon the output at leisure. But I expect that hammering out good parameters and directly measurable proxies for them would provide a better route to being able to think about the problem directly.June 20, 2020 at 16:34 #55383SA
Apologies for not explaining more the source of my data.
The data about no of cases reported per country and of deaths related to Covid-19 come from COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). The source for population and density come from World Population Review
The other figures are calculated by me. The Overall rate is the number of reported cases divided by the population of that country. The CFR is the number of deaths divided by number of cases. I guess the number of deaths divided by the population may also be useful.
Of course this is all governed by the robustness of the data in the first place as you point out and I agree that the excess death rates may be more indicative, but these are not easy to extract from the different countries. Of course the numbers of cases and deaths are also a function of where in the epidemic countries are. For example China is fairly advanced in this respect because they were the first and went through suppression and possible resurgence, whereas Russia and Brazil and other Latin American countries are very much on the steep rise arm.. Another piece of data worth looking at is the daily changes shown in my first link as a bar chart.
There are different patterns. Take a look at US. The chart shows that what has actually happened is very partial suppression and continuation at a high level.
Whereas the pattern for Italy shows a good suppression. UK is in between.
These charts are worth looking at because I think they reflect effectiveness of measures taken by each country. The initial firmness of the lockdown shown by countries like Spain, Italy, France, Austria and other European countries are seen in their charts, whereas the chart for Iran shows how relaxation of measures leads to a rebound.June 20, 2020 at 16:37 #55384SA
Sorry Clark, it looks that the links I tried to post to individual countries does not work it just goes back to the dashboard but you can look at figures by clicking on each country and then click at daily change in the bar chart at the bottom of the page on the right side.June 21, 2020 at 13:38 #55436Clark
SA, absolutely no apologies necessary; I asked you to clarify and you did; job done, unlike responses from so many commenters I could name.
Yes, the bar charts for daily figures show the effectiveness or otherwise of the suppression responses. I frequently refer to the charts at Worldometers, and the following page has all countries classified as red, amber or green by the effectiveness of suppression:
Something I’m fed up with from the denialists and minimisers are oversimplified legalistic interpretations, the most common of which is “Sweden has no lockdown, but…”. It’s public behaviour that affects the spread; emergency laws have only indirect effects.
Excellent new page at EndCoronavirus about green zones:June 21, 2020 at 15:21 #55438SA
Thank you. That is a good website and just provides the information I was looking for.June 23, 2020 at 22:11 #55682Clark
So. The “Vaccine Contaminants and Safety” thread comes to a shuddering halt. With fireworks…June 27, 2020 at 20:08 #55909SA
Have you seen Dr Edd’s last contribution from 26/06. I think it said it all.June 28, 2020 at 14:46 #55954Clark
SA, yes, I saw it.
I find the situation very sad. Conspiracy theory not only displaces political awareness; those who accept it become so suspicious that they won’t even discuss it, to compare it with other ways of thinking. Anyone challenging any claim of any conspiracy theory that has been accepted becomes themselves suspected of being part of the conspiracy. It is a self-reinforcing belief system.
It is hugely damaging. Not only does it provide a ready supply of supporters for crooks like Geier and his son, and David Noakes; it also polarises debate, thereby obstructing progress in exposing genuine scientific corruption.
But always remember that conspiracy theory is a symptom not the cause. Secrecy and opacity in all their forms are the underlying problem. Their form is less extreme in science than in foreign policy, but more widespread.July 11, 2020 at 05:24 #56409SA
So at last everyone seems to acknowledge that SARS-cov2 is a respiratory virus and that the predominant method of transmission is through aerosols and droplets. The predominant thrust of the prevention should have been social distancing, true quarantine in proper facilities of all diagnosed and suspected cases, wearing of face masks and avoidance of indoor crowding. Early diagnoses and contact tracing should then have been instigated but this can only be meaningful if proper wuarantine is implemented. Instead we went for a distraction of concentrating on hand washing and other rituals as a political distraction, being only a minor measure to reduce the infection rate. So much time was spent on sourcing expensive ventilators but little on prevention.
These are well tried and tested public health measures that are bread and butter of prevention of epidemics. Instead reliance was placed on high profile reliance on ‘data’ and ‘science’. Empty words used by ignorant politicians relying on unproven ‘modelling’ which of course is based on so many assumptions. No wonder the country and the planet are in such a state.July 11, 2020 at 05:27 #56411SA
This was all known by the Chinese and Koreans and other Asian countries in January 2020. Why did it take so long for this to be realised by the rest of the world?July 11, 2020 at 05:36 #56412SA
‘But always remember that conspiracy theory is a symptom not the cause.’
It is a reaction not a symptom. But now it is easy for governments to give out half truths and let the conspiracy theories make the rest of the case for them.
An example here is how incompetent our government has been in dealing with Covid-19 and some spent so much time instead concocting theories that it was just the flu, not only condoning actions by extreme right wing governments, but ignoring or even condoning their actions. We now have the major consequences of clamping down on dissent and secrecy in contract award produced by this emergency, and the anti- Vaxxers and Covid denialists have no comments to make.July 11, 2020 at 10:05 #56429Clark
Hello SA, good to see you back. I’ll reply as soon as I have time.July 12, 2020 at 16:30 #56471Clark
– “This was all known by the Chinese and Koreans and other Asian countries in January 2020. Why did it take so long for this to be realised by the rest of the world?”
Somebody else’s problem:
Hitchhiker’s Guide to the Galaxy: Somebody Else’s Problem field theory – YouTube (3m 32s)
Something I find highly ironic about the modelling is that you reach almost the same predicted number of fatalities just by multiplying the IFR by the population.
– – – – – – – – – –
– “But now it is easy for governments to give out half truths and let the conspiracy theories make the rest of the case for them”
I know. So disappointing, isn’t it?
– “…and the anti- Vaxxers and Covid denialists have no comments to make”
To be fair a couple of the most vocal managed to get themselves banned just in time.July 19, 2020 at 13:51 #56655SA
Australia is leading the way together with US and UK in ‘weaponising’ the SARS-Cov2 pandemic and also now the developement of vaccines.
“MELBOURNE (Reuters) – Australia on Sunday added to growing pressure on China over its handling of the novel coronavirus, questioning its transparency and demanding an international investigation into the origins of the virus and how it spread.”
This was the first shot started by the Australian government and robustly refuted by China.
But the most recent spat is the recent story that Russia is trying to sabotage or steal research on the vaccine. Apparaently Canadian and UK intelligence have uncovered a plot by Russia. But meanwhile, scientists involved in the actual vaccine research are more wary of the US buying anything for their sole use, and probably then selling it for extortionate prices.July 19, 2020 at 13:56 #56656SA
And Lisa Nandy has jumped on the Russian demonisation bandwagon and at the same time criticizing Corbyn. The woman is shameless.July 20, 2020 at 00:41 #56660Clark
Politics is broken, SA; join Extinction Rebellion! (If you haven’t already, of course.) You don’t have to get arrested; there are dozens of useful roles. At any action, the public come up and ask questions or argue or just get into conversations; anyone who can talk accurately about science will be busy all day.
The governments have broken and continue to break the social contract by not protecting the people; covid-19, climate change, ecological destruction, gross inequality or rampant poverty, it’s all the same thing. Governments’ power over the people has no legitimacy, which is why we peacefully break their laws, those of us who choose to getting arrested.
Come and join us. Love and Rage.July 20, 2020 at 19:16 #56696SA
Thanks for your answer and invitation. I admire those who give up a lot of their time and comfort in order to endure hardsguke you do. Sadly I can’t join for many reasons but I am with you in thoughts and spirit.July 20, 2020 at 23:36 #56699Lucinda Chalfant
I follow you on Consortium News and am very impressed with your investigative writing. A public comment posted today to an article by Caitlin Johnstone on 7/19/20 really stirred my interest. The commenter (Antisandman) said that Julian Assange was not targeted for exposing war crimes but for threatening the international private banking cartel. He gave a time-line with very convincing support for his theory. I wonder if you have any particular insight on this. If true, it would be great to see it exposed. Perhaps in an article on CN.
Thank youJuly 22, 2020 at 11:02 #56738cimarrón
Could you give the link to Caitlin Johnstone’s article, please. The only article of hers on 7/19/20 that I could find on Medium was about overpopulation.
On another matter, I did, however, come across this article by Caitlin on the Uighurs in China and the consequent western propaganda –
and the Twitter thread that relates to her article –
This thread is a reproduction for posterity of a good thread by @OohTheChilliOil, an account deleted by Twitter for unknown reasons, on the "Uighur Genocide". The only archives I've been able to find of this thread are damn near unreadable, so I'm piecing it back together here: pic.twitter.com/4ET5fjnjz9
— Caitlin Johnstone ⏳ (@caitoz) July 8, 2020July 22, 2020 at 11:17 #56740cimarrón
Sorry, I realise now that you meant Caitlin Johnstone’s article on Consortium News; I didn’t know she also wrote on that site. I still can’t find the article there – her last article is given as July 17th, 2020.July 31, 2020 at 03:07 #57023SA
This* is a good update of some of the findings relating to Covid 19 written in an easy to understand style.
The salient points are:
- The virus causes symptomatic disease in only a fifth of those infected and serious illness in only a quarter of those.
- The virus can affect other organs either by direct invasion of cells or indirectly by damage to blood vessels or inappropriate activation of the immune system or clotting system of the Blood.
- Long term immunity to virus still unknown.
- Some people may have long term sequelae.
- The multiplicity of organs affected is due to the ability of the virus to invade and multiply in cells using the ACE2 as a docking point, this receptor, involved in blood pressure regulation, is found in many cells and not just airways, the gut and heart muscle and most other organs.
* “We Thought It Was Just a Respiratory Virus: We were wrong” – UCSF Magazine (University of California San Francisco, Summer 2020)July 31, 2020 at 10:40 #57035Clark
Excellent, informative article. Thanks SA.August 12, 2020 at 17:17 #57514SA
The Moon of Alabama has a current thread about the Russian vaccine and MSM propagandistic distortions. Of course this was all preceded by the misinformation that the Kremlin had been trying to steal secrets of vaccines from U.K. and others.August 15, 2020 at 10:37 #57652N_
For the RT-PCR test:
* true positives (“sensitivity”) are around 70%.
* true negatives (“specificity”) are around 95%.
This info is from BMJ propaganda to low-level quacks (“Practice Pointer”), but still. So prevalence is being over-estimated.
The government recently decided to say it had actually tested 1.3 million fewer people than it “thought” it had. That’s 2% of the population.August 15, 2020 at 10:40 #57653N_
Although the 1.3m may have been for a different test. I dunno. I don’t believe a word of what the authorities or big business say about “statistics”. I take a Soviet view.August 15, 2020 at 11:29 #57654N_
“ICL’s “total infected so far” figure seems to match post-peak antibody studies within a factor of two, which is damn good modelling for a brand new disease.“
Only a small number of tests (say a few thousand) are needed to estimate incidence (“total infected so far” per population), assuming the test works reasonably well. With the new SARS strain this happened through the biowar defence network and was done covertly. All sorts of tests are done covertly all the time. One can hardly talk about serious biowar defence unless this happens, routinely, even when there is no particular reason to think a particular pathogen is abroad. Otherwise an opponent with good BW offence will wipe the floor with you. Back tests can be run on samples collected earlier too, probably going back several years. I am sure they have had reasonably reliable and constantly updated current figures for “total infected so far” with SARS-CoV2 since March at the latest.
Officially the authorities probably don’t admit that a single covert SARS-CoV2 test of material taken even from a single individual was ever conducted, let alone tests for other kinds of nasty. “Ethics” and stuff.
“The SAGE committee were witnesses that the government had seen the numbers, denying the government the option of claiming ignorance post-disaster.“
What mechanism would hold the authorities to account? Few who comment on this blog believe the media would. Nor a parliamentary committee either. An inquiry chaired by his ennobled lordship or her ennobled ladyship who spent their career as a “red” judge or a senior mandarin?
Anyway, wait a while…a cull is coming and not just in what remains of the “care homes” this time.
“We tried loosening up a bit and giving the dirty proles the benefit of the doubt, treating them like adults, but they all went to Spain and came back with the lergy, and the blacks don’t listen anyway and reasoning with them won’t stop them partying in the streets”. These are the kind of extremely ugly attitudes that are prevalent among low-level managers of different types…August 15, 2020 at 14:32 #57657N_
* true negatives (“sensitivity”) are around 70%.
* true positives (“specificity”) are around 95%.
Just for background…
Let’s assume the above figures and that 6% of people are infected.
A person is chosen from the population at random.
They test positive.
Before the test, the probability they were infected was 6%.
After they test positive, what is the probability they are infected?
Any NHS medics reading this might like to have a go at answering (without checking any “practice notes” or calling your insurer to check whether you’re covered for ballsing it up) …
…and the answer is…
the probability is 16.8%.
prior odds = 0.06 / 0.94 = 0.0638298
Bayes factor = likelihood ratio = true positive / false negative = 0.95 / 0.3 = 3.1666667
posterior odds = prior odds * LR = 0.2021277
convert odds to probability:
posterior probability = (prior odds) / (1 + prior odds) = 0.2021277 / 1.2021277
= 0.1681416August 16, 2020 at 09:01 #57680SA
The accuracy of the test in clinical practice does not mean that the test itself is useless, it means that there are other factors such as the way swabs are taken, the number of samples, the timing of the swabs and where the swabs come from, nasal swabs, urine BAL etc… Also as stated a positive result is more significant than a negative result. This is not really a reflection on the test itself. In a fast moving situation, practice evolves and what this paper is saying is that the practice of swabbing and the interpretation of results is important.
So if you are well today and have a swab which is negative then you become ill two days later and the swab then is positive, it does not mean that any of these tests were unreliable, it just means that there was not enough virus two days ago to be picked up on testing on the first occasion.
I am not sure what the reference for the bit on the block quotes is, could you please provide one?August 16, 2020 at 09:09 #57681SA
It is sometimes difficult to follow your arguments mainly because you seem to be against everything, the science, the medicine and the politics. Whereas science and medicine are more open to scrutiny, politics, especially under the current ‘regime’ is not and as we know is often deliberately twisted. The politics is also trying to recruit some of the ‘science’ both as a defense for their arbitrary action, but ultimately as a fall guy. It weakens your case if you attack everyone because what we should really attack is the government’s handling of this both in the general sense but specifically in the economic sleazy sense.August 16, 2020 at 11:46 #57700N_
I messed up “sensitivity” and “specificity” because I am more into pure maths than applied maths and more used to the terms “true positives” and “true negatives” which are more self-explanatory. So I will redo the calculation below. My apologies for this.
“Sensitivity” and “specificity” are deliberately confusing terms meant to be memorised by medical students and then used mostly within the “profession” to exclude those who are outside the racket. (This happens in all “professions”, not just among charlatans such as NHS GPs who allow the plebs to think they have doctorates and local solicitors who “specialise” in conveyancing, “helping” senile elderly ladies manage their bequests whether in property or financial assets, and remortgaging.) “True positive rate” is a much clearer term that indicates how many % of people who test positive actually have what is supposed to be have been tested for. Nobody will confuse “true positive” with “true negative” as I unfortunately did “sensitivity” with “specificity”.
The aide memoire “I’m positive that I’m sensitive” seems a good way to remember which way round it is 🙂
The figures for 70% sensitivity (true positives) and 95% specificity (true negatives) (which I have checked) come from the “practice note” in the British Medical Journal that I linked to. The BMJ, owned by Elsevier, is a vehicle for Big Pharma propaganda – see the relevant pages of Edward Bernays’s great (absolutely must-read) book “Propaganda” on how “trade journals” create and manage “opinion” within a “trade”, and also Vance Packard’s “Hidden Persuaders” in which – going by memory – I seem to recall he talks about the marketing of librium which medics were told should be prescribed “whatever the diagnosis”. Things are done more subtly nowadays. Nowadays there is little leftwing critique of how say “flu jabs” were marketed until they became “normal”, although that would be extremely interesting knowledge to have at the present time. (Perhaps there are some loony-right articles about it, mixed up with assertions such as that the Sandy Hook massacre was fake. By such means is clear critique obstructed. This kind of method developed after Bernays wrote.) Similarly “everyone” talks of “Oxford” research, “Cambridge” research, and “Imperial College” research, rather than whichever drug companies are really calling the shots. At Oxford it’s Astra Zeneca. At Cambridge it’s Glaxo Smith Kline. I don’t know who it is at Imperial.
The BMJ article, entitled “Interpreting a covid-19 test result”, says the 70% and 95% figures are at the lower ends of reviews and that they are approximate. I am not trying to be an “expert” who produces a super-accurate estimate of how many people have had SARS-CoV2. I have no particular opinion on what the real figure is. I am just trying to pick at what a heap of flimsy rubbish the officially encouraged lines of thought are where testing is concerned.
The stuff in the block quote is just me applying Bayes’s Theorem. Feed in the rate of true positives and the rate of true negatives, and you get the “likelihood ratio” (“Bayes factor”) that tells you how to alter the whole-population incidence rate (i.e. the probability that a person chosen at random has the problem) to get the post-test probability (one figure for if it’s positive, another for if it’s negative) that the tested person has the infection. This is the principle of how you get from ANY medical test result to an estimate of the probability that the person has the infection or other problem. Of course you are right that other indicators should be accounted for, which is why I said let’s take the person at random from the population.
In the real world, testing is not done at random. Two cases in particular are interesting: first, when people who do have “the symptoms” are NOT tested, and second, when people who don’t have the symptoms (or who at least have only a high temperature or basically a cold) ARE tested. In Britain I reckon both groups include a lot of people.
“Covid-19” is a collection of flu-type symptoms. (Impairment of smell and taste also happens with the common cold which is usually a much less severe illness than flu.) Many who have had these symptoms have never been tested for SARS-CoV2. If I recall correctly, these include our host on this blog and his wife. If the ill people are in “care homes for the elderly” (mostly rented by wide boys from companies they are connected with that are registered offshore), they have usually been left without any hospital treatment. Ambulance teams have been told not to attend to them, but to spend hours cleaning and re-cleaning their ambulances instead, Nero-style. If they then die, many are recorded on their medical certificates of the cause of death (MCCDs) as having died with Covid-19 even if they were never actually tested for SARS-CoV2. (How many of the 40000+ deaths “with Covid-19” in Britain does this account for, I wonder?) I.e. they were recorded as having died with Covid-19 because they had flu symptoms, and then probably many of them died of pneumonia (another collection of symptoms that can have many causes) inside care homes, pneumonia that was brought to the care homes by patients who caught it in hospital and were then discharged back into the care homes. (If you want to murder loads of people in a care home, this is a way to do it.) The policy is one of “involuntary euthanasia”. In Germany the extermination policy did not start with Jews, gays, Jehovah’s witnesses, recidivist criminals, etc. – it started with the physically and mentally disabled. There haven’t been many press articles about how the homeless have been getting along in Britain since they were cleared off the streets in March either.
One of the most important provisions in the Coronavirus Act (sections 11-13) is the provision for indemnifying designated people from liability when patients die. Now that the petty-official manager stuck-up types who infest this country have been entrained into spouting “coronavirus”-themed bullsh*t by their higher-ups and the media, bullsh*t that directly contradicts what is going on often in front of their eyes, and what they could in any case work out if they were used to applying a teensy bit of logic in a sensible way undirtied with any poncy “I’m an expert” role-playing, they basically have the taste for blood. It’s a twist on the Stanford Prison Experiment or Stanley Milgram’s electroshock experiment.
It’s very scary indeed and the prognosis doesn’t look good. The economic background is one of very heavy over-employment, as anyone who has walked past an office building can attest. We are at the early stage of a cull which is likely to exceed greatly what has happened so far.
(See the “toilet paper” story. Exciting to Daily Mail readers because it’s about bums, and also about dirt, this was deliberate misdirection by the government in order to make shortages look amusing and to direct attention to this particular commodity, a shortage of which is certainly annoying but is nowhere near as problematic as shortages of food. In March, various food items were similarly put on private-sector ration and similarly ran short on the shelves, but it was “wiping your bum” that got most of the media attention. As a piece of psychological warfare it was a bit of a practice on a shooting range. One can also remark on the functioning of the NOTION of “panic” – not actual “panic” but the notion of it.)
Now to the calculation. I am taking 6% as the incidence rate because it was mentioned here.
So we have
prior probability = incidence rate = 0.06
convert to odds: prior odds = 0.06 / 0.94 = 0.063830
true positive rate = sensitivity = 0.70
true negative rate = specificity = 0.95
false negative rate = 1 – 0.95 = 0.05
likelihood ratio = Bayes factor = true positive rate / false negative rate = 0.70 / 0.05 = 14
posterior odds = prior odds * likehihood ratio = 0.063830 * 14 = 0.893617
convert to probability: posterior probability = 0.893617 / 1.893617 = 0.471910
a positive test result from “RT-PCR” test, carried out on person chosen randomly, indicates that
the probability they are infected with SARS-CoV2 is 47%
As I said, many may have had SARS-CoV2 but were never tested. But there are also many who have been tested, and who tested positive, and who probably did not have SARS-CoV2. If these were all people who were tested only because they had the whole collection of specified symptoms, then the above figure 47% doesn’t tell us much, because it rests on an incidence figure of 6% which is (supposedly) for the whole population. However, they were NOT all people who displayed the said symptoms. Many of them were probably as fit a fiddle or at least had no more than a minor cold for a day or two. They include many who work in the NHS. The official advice is get tested if you have any one of the three famous symptoms. NHS advice:
You can get a test:
(…) if you have coronavirus symptoms now (a high temperature, a new, continuous cough, or a loss or change to your sense of smell or taste)
Note the use of “or” rather than “and”. A minor sniffle will give you the third of these symptoms.
It’s relevant that tests have been given out like smarties to NHS staff, because I would imagine that now that most hospital wards have been shut down the managers don’t want loads of nurses and other employees running around all over the place with nothing to do other than “makework”.
Last, while I’m here, going by official figures and interpretations it seems that many have caught SARS-CoV2 and successfully fought it off, in some cases without even getting symptoms. Their immune systems have defeated it, sometimes even before their antibodies have been called out! That’s good news! In many individuals, it’s been a case of Evolved Human Biology 1, The Nasty Virus 0. And not all of these people are children. Reason suggests that on average they have had a smaller viral load than those who have died from the virus, but the point is that their immune systems have fought the virus and won.
This makes it a disgrace that there has been absolutely no “public health advice” telling people how to strengthen their immune systems. (Cryzine make this point well in their footnote 7 here.) I could make a list of foods and substances but will mention only iron, zinc, and vitamin C (e.g. in orange juice) for the time being. Many middle class and lower middle class bureaucratic types assume that whatever they are not ordered to say to “the public” is material that “the public” shouldn’t hear, and doubtless they could come up with a dozen reasons why advice about “how to strengthen your immune system” would be “inappropriate” to give to people, would be misinterpreted, would cause more harm than help, would cause the sky to fall in, and so on and so forth, ad nauseam – a string of bullsh*t “reasons”.August 16, 2020 at 13:34 #57704SA
There is a lot here that you wrote and I do not presume to even try and answer you point by point. To start on a light note: “Why is there a shortage of loo paper?” “Because every time one person coughs, a hundred shit themselves”.
But let is analyse some of what I perceive to be known about SARS Cov2 and Covid 19.
SARS Cov2 is the recently described virus which has been associated with a set of clinical conditions from being completely asymptomatic, to having mild cold like or flu like symptoms, to being severely ill, to requiring ventilation support and at the extreme to dying of multiorgan failure.
Covid-19 on the other hand is the disease caused by the virus which constitutes only about 20% of all those who encounter the virus according to several studies. So not everyone who is infected with SARS Cov2 develops Covid 19, in fact 80% go around their business merrily and do not even notice. This is not unique to this virus because disease caused by many agent, whether microbiological, neoplastic, inflammatory or chemically induced, are manifested by the combination of the presence of the agent, the amount or dose of exposure, the timescale of the exposure, the state of the immune system at the time of exposure, genetic makeup of the individual, dietary factors and so on.
In the case of Covid 19 some observations so far have shown some of the factors associated with severe disease. There is a very strong correlation with age and certain comorbidities, including heart disease, diabetes, factors such as obesity, ethnic origin and sex. These all contribute to the variability of the disease in any one group of cases.
What has also been known from the outset is that the most extreme end of the spectrum, respiratory failure is associated with what is medically known as ARDS, whereby fluid accumulates in the lung and the patients literally drown in their own secretions. Ventilation in these cases has a limited effect because you can’t force oxygen through all the inflammatory fluid in the alveoli, but is used purely as a holding measure. It has been shown, in the case of Covid-19 and also other diseases associated with ARDS, as well as multiorgan failure, that this situation is caused by an overreaction of the immune system (known as a cytokine storm) to the virus that occurs in some cases. Why this is the case, is not known. One of the practical outcomes of this knowledge is that dexamethasone, an immunosuppressive agent, used in medicine to treat various conditions associated with dysregulated immunity, but also cancers of the immune system, has been shown to have some beneficial effects in patients at this severe end of disease increasing their chances of survival.
Also unlike some expectations, some patients with immunosuppression due to their cancers were found to be surprisingly less susceptible to severe disease.
To go back to some of your points and calculating the possibility of finding a positive or negative results. This is in the realms of experimental or theoretical mathematics and may be used for algorithms or other guidelines in public health planning. But in the glaring daylight of frontline medicine the positive PCR for SARS cov2 means with a 100% certainty that you have the virus in your secretions. The test has a very high degree of specificity because it is looking at unique sequences and amplifying them. False positive results arise nevertheless mainly because of the possibility of contamination because of the high sensitivity of the test and hence the 5% error rate. Nevertheless in a well controlled laboratory with rigorous procedures the a positive result should mean that the virus has been detected in that individual. Rigorous internal and external quality controls are used in order to validate and accredit laboratories.
So moving on to symptoms of covid-19. I think there is a subtlety that escapes the layman, say about certain symptoms. To take an example, loss of smell and taste. The mechanisms that operate in this symptom and in covid-19 are completely different. It has been added as a specific symptom, because it often predates any coryzal symptoms, such as sneezing or a bunged up nose, and even occurs in the absence of these. In the common cold, loss of smell and taste is relative, and is due to inflammatory secretions around the taste and smell organs, but in covid-19 it appears to be due to an effect on the nervous system that transmits the perceptions of taste and smell from these receptors to the brain. Also the cough in typical covid-19 is often dry and associated with breathlessness much before there are any other respiratory symptoms, unlike in flu for example, where the shortness of breath, due to secondary bacterial pneumonia happens later in the disease.
Just to take one or two other points you make: The care homes death from covid-19 was at the early stages markedly underreported and there was no testing of care homes or even of elderly patients in hospital with early discharges to care homes, which then led to this tragedy of care home deaths. To mix this up only gives leeway to Johnson and co who want to absolve themselves of any responsibility.
The other point about statistics and % positives I wish to make, which I am sure you know, is that the positive rate is a shifting one because of the variability of number and symptomatic groups of people tested, but also because of the shifting infection rates. This moving target makes it difficult to make too many assumptions at present.August 17, 2020 at 11:57 #57747Clark
N_, August 15, 11:29, #57654:
– “Only a small number of tests (say a few thousand) are needed to estimate incidence (“total infected so far” per population), assuming the test works reasonably well.”
(a) I would expect this to be true for an infection that is near equilibrium in a population, ie. it has been around long enough to be distributed throughout the population – a proportion having sufficient immunity, a proportion having insufficient immunity but not a recent chance to be infected, and a proportion with the infection; all three groups distributed among each other.
(b) I would expect it to be untrue for a novel infection (1) to which the population begins with no immunity and (2) which spreads very fast.
A “few thousand tests” is a sample of the population; hopefully a random sample. In case (a), a random sample should yield a result representative of the randomly distributed infection, but in case (b) infection will be very clustered around the initial seeding infections, and by definition, the locations of these are unknown.
The fast spread is also significant, as the timescale for performing the tests and collating the results is similar to or exceeds the doubling time of the infection; the results will be out of date by the time they are ready for publication.
– “With the new SARS strain this happened through the biowar defence network and was done covertly. All sorts of tests are done covertly all the time.”
N_, do you have insider knowledge of this or are you guessing? To me this seems an unlikely approach, since the type of pathogen to test for would be unknown. As a first guess, if I were designing such a biowar detection/monitoring system, I would suggest monitoring of health databases to detect any sudden surges in a broad variety of symptoms, and to produce distribution maps of them to indicate clusters.August 17, 2020 at 12:54 #57754Clark
N_, I think too much significance can be placed upon testing, just as too much can be placed upon modelling. As SA points out, it is the medical staff who have direct experience of the effects of covid-19 upon actual individuals. It is medical staff who learn what works under which circumstances to improve given sufferers’ conditions, or fails to.
Yes, there will be errors both ways, but different reporting systems in different regions and countries will also extenuate those errors one way or the other. The situation is changing fast, and people are learning fast. In a few years time much will be realised in retrospect…
…In the meantime, we should all exercise patience and tolerance. Please pardon me for saying so, but you seem highly critical and indeed angry with entire professional groups. Such groups of course consist of diverse individuals, some better some worse, but all conditioned and habituated to various extents under the corrosive and abusive system that we have all been suffering under increasingly during its ascendency over the course of decades.
Ultimately, we need unity and communality among people, whereas the toxic system both exploits and encourages division between us. In the current socio-political environment, forgiveness, tolerance and respect become revolutionary attitudes.
Love and Rage to you, N_.
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