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UK Govt Coronavirus Response: Sceptics Thread


sancho panza

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Talking Monkey
22 hours ago, sancho panza said:

https://lockdownsceptics.org/  

11/5/20

“Sue Denim” has been in touch to point out that several other people with similar levels of coding expertise have posted analyses of Neil Ferguson’s code that are as scathing as his. Take this one, for instance, by Chris von Csefalvay. He is an epidemiologist specialising in the virology of bat-borne illnesses, including bat-related coronaviruses. “It is very difficult to look at the Ferguson code with any understanding of software engineering and conclude that this is good, or even tolerable,” he writes. He notes that Ferguson apologised for the poor quality of the code on Twitter, explaining that he wrote it more than 13 years ago to model flu pandemics. Csefalvay responds as follows: “That, sir, is not a feature. It’s not even a bug. It’s somewhere between negligence and unintentional but grave scientific misconduct.”

Then there’s this review by Craig Pirrong, Professor of Finance and Energy Markets Director of the Global Energy Management Institute at the Bauer College of Business, University of Houston. “Models only become science when tested against data/experiment,” he writes. “By that standard, the Imperial College model failed spectacularly.”

https://chrisvoncsefalvay.com/2020/05/09/imperial-covid-model/

Of bits, bugs and responsibility in the public square

Chris von CsefalvayBy Chris von Csefalvay 3 days ago06957 views
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Usually, I wake to the sound of the bluejays in our spacious backyard. This morning, I woke to the ‘priority alert’ from my phone, indicating an urgent message. It was 0515 – early even by the standards of epidemiologists in these times. My friend’s message was terse but foreboding – “look at this”, followed by a link to Github.

At the end of the link was the codebase promised for weeks by Neil Ferguson, the computational epidemiologist who has advised the UK government on COVID-19 related steps until his recent resignation. I have previously been a staunch defender of Ferguson’s approach – his model was (and is) theoretically sound, and probably as good as such models will ever get. Prediction, of course, is difficult. Especially when it comes to the future, as Niels Bohr is credited of saying. Using a method that relies on simulating populations in cells and microcells, it combines the granularity and stochastics of agent-based models without requiring the resources typical for agent-based simulation. His model, versions of which were used in previous outbreaks, has been the de facto gold standard to the UK government.

And looking at the code, that raises some extremely serious questions. I would like to explore some of these issues, but will not go into a detailed analysis of the code, for one reason – the code eventually (and reluctantly) shared by Imperial College is almost definitely not the code used to generate forecasts for HM Government. We know that at some point, Github and even John Carmack (yes, that John Carmack!) has been involved in cleaning up some of the quality issues. Imperial, meanwhile, obstinately resists releasing original code – both via Github and under a valid FOIA request that Imperial’s lawyers are entirely misinterpreting.1) We can, however, safely assume from the calibre of the people who have worked on the improved version that whatever was there was worse.

The quality issue

First of all, the elephant in the room: code quality. It is very difficult to look at the Ferguson code with any understanding of software engineering and conclude that this is good, or even tolerable. Neil Ferguson himself attempts a very thin apologia for this:

 

That, sir, is not a feature. It’s not even a bug. It’s somewhere between negligence and unintentional but grave scientific misconduct.

For those who are not in the computational fields: “my code is too complicated for you to get it” is not an acceptable excuse. It is the duty of everyone who releases code to document it – within the codebase or outside (or a combination of the two). Greater minds than Neil Ferguson (with all due respect) have a tough enough time navigating a large code base, and especially where you have collaborators, it is not unusual to need a second or two to remember what a particular function is doing or what the arguments should be like. Or, to put it more bluntly: for thirteen years, taxpayer funding from the MRC went to Ferguson and his team, and all it produced was code that violated one of the most fundamental precepts of good software development – intelligibility.

The policy issue

When you write code, you should always do so as if your life depended on it. For us working in the field of modelling infectious diseases, lives being at stake is common, sometimes to the point of losing track of it. I don’t, of course, know whether that is what indeed happened, but I doubt anybody would want to trust their lives to thousands of lines of cobbled-together code.

Yet for some reason, the UK government treated Ferguson’s model as almost dogmatic truth. This highlights an important issue: politicians have not been taught enough about data-driven decision-making, especially not where predictive data is involved. There is wide support for a science-driven response to COVID-19, but very little scrutiny of the science behind many of the predictions that informed early public health measures. Hopefully, a Royal Commission with subpoena powers will have the opportunity to review in detail whether Ferguson intentionally hid the model from HM Government the way he hid it from the rest of the world or whether the government’s experts just did not understand how to scrutinise or assess a model – or, the worst case scenario: they saw the model and still let it inform what might have been the greatest single decision HM Government has made since 1939, without looking for alternatives (there are many other modelling approaches, and many developers who have written better code).

The community issue

Perhaps the biggest issue is, however, the response to people who dare question the refusal by Imperial to release the original source code. This is best summarised by the responses of their point man on Github, who is largely spending his time locking issues and calling people dumb & toxic:

0ACC7FA3-7240-4FF8-8A54-4E51ACD59A97.jpe

It may merit attention that the MRC is taxpayer-funded – the self-same taxpayer who is deemed unfit to even behold what he paid for. This is the worst of ‘closed science’, something many scientists (myself included) have worked hard to dismantle over the years. Publicly funded science imposes a moral obligation to present its results to the funder (that is, the taxpayer), and it should perhaps not be up to the judgment of a junior tech support developer to determine what the public is, or is not, fit to see. Perhaps as an epidemiologist, I take special umbrage at the presumption that everyone who wishes to see the original code base would be “confused” – maybe I should write to reassure Dr Hinsley that I do understand a little about epidemiology. It is, after all, what I do.

The science issue

None of these issues are, of course, anywhere near as severe as what this means – a massive leap backwards, erosion of trust and a complete disclaimer of accountability by publicly funded scientists.

There is a moral obligation for epidemiologists to work for the common good – and that implies an obligation of openness and honesty. I am reminded of the medical paternalism that characterised Eastern Bloc medicine, where patients were rarely told what ailed them and never received honest answers. To see this writ large amidst a pandemic by what by all accounts (mine included) has been deemed one of the world’s best computational epidemiology units is not so much infuriating as it is deeply saddening.


One of my friends, former Navy SEAL Jocko Willink, counseled in his recent book to “take the high ground, or the high ground will take you”. Epidemiology had the chance to seize and hold the narrative, through openness, transparency and honesty about the forecasts made. It had the chance, during this day in the sun of ours, to show the public just how powerful our analytical abilities have become. Instead, petty academic jealousy, obsessions with institutional prestige and an understandable but still disproportionate fear of being ‘misinterpreted’ by people who ‘do not understand epidemiology’ have given the critics of forecasting and computational epidemiology fertile breeding ground. They are entirely justified now in criticising any forecasts that come out of the Imperial model – even if the forecasts are correct. There will no doubt be public health consequences to the loss of credibility the entire profession has suffered, and in the end, it’s all due to the outdated ‘proprietary’ attitudes and the airs of superiority by a few insulated scientists who, somehow, somewhere, left the track of serving public health and humanity for the glittering prizes offered elsewhere. With their abandonment of the high road, our entire profession’s claim to the public trust might well be forfeited – in a sad twist of irony, at a time that could well have been the Finest Hour of computational epidemiology.

And while we may someday regain the respect of the public we swore to serve (perhaps after a detailed inquiry into what went wrong), for now there will be never glad confident morning again.

 

https://streetwiseprofessor.com/code-violation-other-than-that-how-was-the-play-mrs-lincoln/

May 10, 2020

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Code Violation: Other Than That, How Was the Play, Mrs. Lincoln?

Filed under: CoronaCrisis,Economics,Politics,Regulation — cpirrong @ 3:03 pm

By far the most important model in the world has been the Imperial College epidemiological model. Largely on the basis of the predictions of this model, nations have been locked down. The UK had been planning to follow a strategy very similar to Sweden’s until the Imperial model stampeded the media, and then the government, into a panic. Imperial predictions regarding the US also contributed to the panicdemic in the US.

These predictions have proved to be farcically wrong, with deaths tolls exaggerated by one and perhaps two orders of magnitude.

Models only become science when tested against data/experiment. By that standard, the Imperial College model failed spectacularly.

Whoops! What’s a few trillions of dollars, right?

I was suspicious of this model from the first. Not only because of its doomsday predictions and the failures of previous models produced by Imperial and the leader of its team, Neil Ferguson. But because of my general skepticism about big models (as @soncharm used to say, “all large calculations are wrong”), and most importantly, because Imperial failed to disclose its code. That is a HUGE red flag. Why were they hiding?

And how right that was. A version of the code has been released, and it is a hot mess. It has more bugs than east Africa does right now.

This is one code review. Biggest take away: due to bugs in the code, the model results are not reproducible. The code itself introduces random variation in the model. That means that runs with the same inputs generate different outputs.

Are you fucking kidding me?

Reproducibility is the essence of science. A model whose predictions can not be reproduced, let alone empirical results based on that model, is so much crap. It is the antithesis of science.

After tweeting about the code review article linked above, I received feedback from other individuals with domain expertise who had reviewed the code. They concur, and if anything, the article understates the problems.

Here’s one article by an interlocutor:

The Covid-19 function variations aren’t stochastic. They’re a bug caused by poor management of threads in the code. This causes a random variation, so multiple runs give different results. The response from the team at Imperial is that they run it multiple times and take an average. But this is wrong. Because the results should be identical each time. Including the buggy results as well as the correct ones means that the results are an average of the correct and the buggy ones. And so wouldn’t match the expected results if you did the same calculation by hand.

As an aside, we can’t even do the calculations by hand, because there is no specification for the function, so whether the code is even doing what it is supposed to do is impossible to tell. We should be able to take the specification and write our own tests and check the results. Without that, the code is worthless.

I repeat: “the code is worthless.”

Another correspondent confirmed the evaluations of the bugginess of the code, and added an important detail about the underlying model itself:

I spent 3 days reviewing his code last week. It’s an ugly mess of thousands of lines of C (not C++). There are hundreds of input parameters (not counting the fact it models population density to 1km x 1km cells) and 4 different infection mechanisms. It made me feel quite ill.

Hundreds of input parameters–another huge red flag. I replied:

How do you estimate 100s of parameters? Sounds like a climate model . . . .

The response:

Yes. It shares the exact same philosophy as a GCM – model everything, but badly.

I recalled a saying of von Neumann: “With four parameters I can fit an elephant, with five I can make him wiggle his trunk.” Any highly parameterized model is IMMEDIATELY suspect. With so many parameters–hundreds!–overfitting is a massive problem. Moreover, you are highly unlikely to have the data to estimate these parameters, so some are inevitably set a priori. This high dimensionality means that you have no clue whatsoever what is driving your results.

This relates to another comment:

No discussion of comparative statics.

So again, you have no idea what is driving the results, and how changes in the inputs or parameters will change predictions. So how do you use such a model to devise policies, which is inherently an exercise in comparative statics? So as not to leave you in suspense: YOU CAN’T.

This is particularly damning:

And also the time resolution. The infection model time steps are 6 hours. I think these models are designed more for CYA. It’s bottom-up micro-modelling which is easier to explain and justify to politicos than a more physically realistic macro level model with fewer parameters.

To summarize: these models are absolute crap. Bad code. Bad methodology. Farcical results.

Other than that, how was the play, Mrs. Lincoln?

But it gets better!

The code that was reviewed in the first-linked article . . . had been cleaned up! It’s not the actual code used to make the original predictions. Instead, people from Microsoft spent a month trying to fix it–and it was still as buggy as Kenya. (I note in passing that Bill Gates is a major encourager of panic and lockdown, so the participation of a Microsoft team here is quite telling.)

The code was originally in C, and then upgraded to C++. Well, it could be worse. It could have been Cobol or Fortran–though one of those reviewing the code suggested: “Much of the code consists of formulas for which no purpose is given. John Carmack (a legendary video-game programmer) surmised that some of the code might have been automatically translated from FORTRAN some years ago.”

All in all, this appears to be the epitome of bad modeling and coding practice. Code that grew like weeds over years. Code lacking adequate documentation and version control. Code based on overcomplicated and essentially untestable models.

But it gets even better! The leader of the Imperial team, the aforementioned Ferguson, was caught with his pants down–literally–canoodling with his (married) girlfriend in violation of the lockdown rules for which HE was largely responsible. This story gave versimilitude to my tweet of several days before that story broke:

It would be funny, if the cost–in lives and livelihoods irreparably damaged, and in lives lost–weren’t so huge.

And on such completely defective foundations policy castles have been built. Policies that have turned the world upside down.

Of course I blame Ferguson and Imperial. But the UK government also deserves severe criticism. How could they spend vast sums on a model, and base policies on a model, that was fundamentally and irretrievably flawed? How could they permit Imperial to make its Wizard of Oz pronouncements without requiring a release of the code that would allow knowledgeable people to look behind the curtain? They should have had experienced coders and software engineers and modelers go over this with a fine-tooth comb. But they didn’t. They accepted the authority of the Pants-less Wizard.

And how could American policymakers base any decision–even in the slightest–on the basis of a pig in a poke? (And saying that it is as ugly as a pig is a grave insult to pigs.)

If this doesn’t make you angry, you are incapable of anger. Or you are an idiot. There is no third choice.

 

Reading the above this Ferguson chap really looks like the Emperor with no clothes. A model with 100s of parameters, generating random results for the same inputs.

None of his code/workings were reviewed prior to the government taking the huge decisions, even though his modelling during foot and mouth had been so catastrophically wrong. There was no attempt to get a dozen or so 'world class' epidemiologists  with differing viewpoints on a call to debate/challenge the various scenarios that they thought could unfold

The really crazy part is the US went with his models when they must have dozens of top guys in this field at their top unis. 

The whole lockdown points to some other agenda, I don't know what but the sheer destruction caused by it points to something else. Now that the true lethality of covid is apparent the speed to lift lockdown is extremely slow almost as if the economic and social destruction is being maximised

Edited by Talking Monkey
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sancho panza
2 hours ago, Talking Monkey said:

Reading the above this Ferguson chap really looks like the Emperor with no clothes. A model with 100s of parameters, generating random results for the same inputs.

None of his code/workings were reviewed prior to the government taking the huge decisions, even though his modelling during foot and mouth had been so catastrophically wrong. There was no attempt to get a dozen or so 'world class' epidemiologists  with differing viewpoints on a call to debate/challenge the various scenarios that they thought could unfold

The really crazy part is the US went with his models when they must have dozens of top guys in this field at their top unis. 

The whole lockdown points to some other agenda, I don't know what but the sheer destruction caused by it points to something else. Now that the true lethality of covid is apparent the speed to lift lockdown is extremely slow almost as if the economic and social destruction is being maximised

As I've said to @dnb24 up until now,the only certainty in this mess was the $5 trillion bail out package.Now the mess of fergusons code is coming out, we'll see govts covering their backsides trying to pretend it was worse than it was because they have to double down.I mean absolutely HAVE TO.Anything other than that would be admitting that they'd got it badly wrong and very few govts -excpet maybe people like the Swedes and Dutch would do that.

Mrs P was asking me this morning who's going to pay for the bail out and I pointed to our 2&3 year old kids.That's the sad truth.Johnson will be off performing in old folks homes by  the time they start paying the bill.

This is a Dutch study I put up on the main delfation thread.Truly stunning.Apparently,this concurs roughly with data from the UK.

image.png.af8fd6579132029e895d6670ee047c5d.png

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sancho panza
2 hours ago, Talking Monkey said:

Reading the above this Ferguson chap really looks like the Emperor with no clothes. A model with 100s of parameters, generating random results for the same inputs.

None of his code/workings were reviewed prior to the government taking the huge decisions, even though his modelling during foot and mouth had been so catastrophically wrong. There was no attempt to get a dozen or so 'world class' epidemiologists  with differing viewpoints on a call to debate/challenge the various scenarios that they thought could unfold

The really crazy part is the US went with his models when they must have dozens of top guys in this field at their top unis. 

The whole lockdown points to some other agenda, I don't know what but the sheer destruction caused by it points to something else. Now that the true lethality of covid is apparent the speed to lift lockdown is extremely slow almost as if the economic and social destruction is being maximised

A lot fo them were telling them to not to lock down-Prof John Nicholls,Prof Ioannidis,Prof Guptha,Prof Bakdi.

They'll make a movie about this.

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sancho panza

https://lockdownsceptics.org/2020/05/13/latest-news-29/

A reader has flagged up an excellent presentation by Numis Healthcare Research Team – a real tour de horizon of what we know about the pandemic. Lots of great graphs, including the one below. Orange lines for countries that have lockdowns, black lines for those that don’t:

image.png.c115208ae19e7bc1412c8083853616b0.png

The Telegraph has published a very damning piece by Ambrose Evans-Pritchard. His assessment of the Government’s response to the crisis is withering, and much of it is based on an email he received from a “Covid cardiologist at a top London hospital”. Here’s Ambrose’s summary of the email, as well as some direct quotes from it:

Basically, every mistake that could have been made, was made. He likened the care home policy to the Siege of Caffa in 1346, that grim chapter of the Black Death when a Mongol army catapulted plague-ridden bodies over the walls.

“Our policy was to let the virus rip and then ‘cocoon the elderly’,” he wrote. “You don’t know whether to laugh or cry when you contrast that with what we actually did. We discharged known, suspected, and unknown cases into care homes which were unprepared, with no formal warning that the patients were infected, no testing available, and no PPE to prevent transmission. We actively seeded this into the very population that was most vulnerable.

“We let these people die without palliation. The official policy was not to visit care homes – and they didn’t (and still don’t). So, after infecting them with a disease that causes an unpleasant ending, we denied our elders access to a doctor – denied GP visits – and denied admission to hospital. Simple things like fluids, withheld. Effective palliation like syringe drivers, withheld.”

“The striking thing is how consistently the government failed, in every single element of the response, everywhere you turn (the Army excepted),” writes the doctor. “This is probably the most expensive series of errors in the country’s history.”

Reading this doctor’s email helped clarify for me that the case against the lockdown isn’t just that the loss of life it will bring about from other causes will be far greater than the number of people it has supposedly saved from dying of COVID-19 (if any). It’s also that the lockdown itself has exacerbated the loss of life from COVID-19. The fact that NHS hospitals discharged elderly patients diagnosed with coronavirus and sent them back into care homes is an appalling scandal. As Dominic Lawson wrote in the Sunday Times, it shames the nation. Heads must roll.'

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11 hours ago, PaulParanoia said:

That may be true but where would it leave us.  We'd not be able to open our borders again until a vaccine (which may never arrive) was available.  The UK would truly become an island, cut off from the rest of the world indefinitely.

Even if we did take that approach, I suspect the virus would eventually find it's way into the population.  That's what viruses specialise in after all.

Spanish flu died after 2 years and 10 million dead..

i have no idea if this virus will do the same eventually but the past is usually the best indicator of the future..

it could mutate though in to a deadlier strain.. then we are proper fucked

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56 minutes ago, sancho panza said:

The Telegraph has published a very damning piece by Ambrose Evans-Pritchard.

Jesus...

Releasing known cases back into care homes, that's horrific.

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sancho panza
1 hour ago, macca said:

Spanish flu died after 2 years and 10 million dead..

i have no idea if this virus will do the same eventually but the past is usually the best indicator of the future..

it could mutate though in to a deadlier strain.. then we are proper fucked

From what I've read ,as the viruses mutate they get weaker,but I'm not a specialist.

 

1 hour ago, Hardhat said:

Jesus...

Releasing known cases back into care homes, that's horrific.

I suspect the evidence of bumbling incompetence on the part of our govt will become more compelling as the months go on re covid. Since this thread started we've heard about cancer patients being taken off treatment, operations being cancelled,A&E attendances for strokes and chest pain being substntially down.

I've never seen the hospitals so empty which means one of two things,people either have stopped getting ill or they're not being treated.

The lack of testing for NHS staff is one of the big blunders.Lack of a random sample testing regime so we weren't relying on Mr Magoo from Imperial College etc etc.

 

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3 minutes ago, sancho panza said:

From what I've read ,as the viruses mutate they get weaker,but I'm not a specialist.

 

I suspect the evidence of bumbling incompetence on the part of our govt will become more compelling as the months go on re covid. Since this thread started we've heard about cancer patients being taken off treatment, operations being cancelled,A&E attendances for strokes and chest pain being substntially down.

I've never seen the hospitals so empty which means one of two things,people either have stopped getting ill or they're not being treated.

The lack of testing for NHS staff is one of the big blunders.Lack of a random sample testing regime so we weren't relying on Mr Magoo from Imperial College etc etc.

 

202 UK doctors and nurses dead

0 German doctors and nurses dead..

Something is very very wrong.. 

not sure if its true but apparently HcUNT reduced PPE stockpiles by 40% to save money..

 

additionally this might also blow the chief medical officer out of the water on fp3 masks..

 

Why do doctors wear FP3 masks if apparently the public dont need them? they must work or why do doctors bother.. just wear gloves.. 

 

think they are telling lies as always

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sancho panza
55 minutes ago, macca said:

202 UK doctors and nurses dead

0 German doctors and nurses dead..

Something is very very wrong.. 

not sure if its true but apparently HcUNT reduced PPE stockpiles by 40% to save money..

 

additionally this might also blow the chief medical officer out of the water on fp3 masks..

 

Why do doctors wear FP3 masks if apparently the public dont need them? they must work or why do doctors bother.. just wear gloves.. 

 

think they are telling lies as always

The big issue re clinical staff is something Prof John Nicholls referred to on the first post in thread re staff training.He said the only public place he'd wear a mask was the tube possibly.The issue is mainly viral load I believe,which as I understand means people at risk of being on the receiving end of higher doses should PPE up.

I think the stats you refer to really do raise some serious questions.That's a lot of staff dying.Italy's losses were substantial too.

I'd be interested to know how their protocols differed if you have any links.

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1 hour ago, sancho panza said:

The big issue re clinical staff is something Prof John Nicholls referred to on the first post in thread re staff training.He said the only public place he'd wear a mask was the tube possibly.The issue is mainly viral load I believe,which as I understand means people at risk of being on the receiving end of higher doses should PPE up.

I think the stats you refer to really do raise some serious questions.That's a lot of staff dying.Italy's losses were substantial too.

I'd be interested to know how their protocols differed if you have any links.

Well they are a manufacturing nation which as always seems to give a very fast response in times of crisis..

China to test 11 million people in 10 days in Wuhan..

Germany equally were testing 250'000 per day months ago.. UK cant even supply nurses with adequate PPE that is required, with government asking them to re use items, testing here is up and down not the 100'000 promised..

The viral load i have seen mentioned several times, as the quantity of virus seems to be a significant factor.. I wonder if that's true why they cant just give people a micro load to trigger an immune response,  that's kind of how a vaccine works.. Since the large number of dead nurses and doctors are not all 70 year olds with diabetes.. I remember in the beginning seeing some dead Chinese doctors and nurses and thinking they are not that old..

Guy at work has a sister in law that has had it, 6 weeks being ill, she is a GP receptionist.. So front facing to sick people entering the practice..

Cough and breathing problems but no hospital stay..  

I have no idea how this all ends.. hopefully it will disappear like the Spanish flu did, that lasted 2 years and was gone.. although it did kill an estimated 10 million people..

It worries me how 33'000 dead just roles of the tongue, when people are saying open the economy they are somehow inhumane as to not recognise these are lives that have ended prematurely.. we need names and faces printed in papers.. that's the best way to stop people going out.. numbers are nothing.. photos like the little boy washed up on the beach during the refugee crisis trigger a much stronger public response that people can relate too

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Talking Monkey
13 hours ago, sancho panza said:

https://lockdownsceptics.org/2020/05/13/latest-news-29/

A reader has flagged up an excellent presentation by Numis Healthcare Research Team – a real tour de horizon of what we know about the pandemic. Lots of great graphs, including the one below. Orange lines for countries that have lockdowns, black lines for those that don’t:

image.png.c115208ae19e7bc1412c8083853616b0.png

The Telegraph has published a very damning piece by Ambrose Evans-Pritchard. His assessment of the Government’s response to the crisis is withering, and much of it is based on an email he received from a “Covid cardiologist at a top London hospital”. Here’s Ambrose’s summary of the email, as well as some direct quotes from it:

Basically, every mistake that could have been made, was made. He likened the care home policy to the Siege of Caffa in 1346, that grim chapter of the Black Death when a Mongol army catapulted plague-ridden bodies over the walls.

“Our policy was to let the virus rip and then ‘cocoon the elderly’,” he wrote. “You don’t know whether to laugh or cry when you contrast that with what we actually did. We discharged known, suspected, and unknown cases into care homes which were unprepared, with no formal warning that the patients were infected, no testing available, and no PPE to prevent transmission. We actively seeded this into the very population that was most vulnerable.

“We let these people die without palliation. The official policy was not to visit care homes – and they didn’t (and still don’t). So, after infecting them with a disease that causes an unpleasant ending, we denied our elders access to a doctor – denied GP visits – and denied admission to hospital. Simple things like fluids, withheld. Effective palliation like syringe drivers, withheld.”

“The striking thing is how consistently the government failed, in every single element of the response, everywhere you turn (the Army excepted),” writes the doctor. “This is probably the most expensive series of errors in the country’s history.”

Reading this doctor’s email helped clarify for me that the case against the lockdown isn’t just that the loss of life it will bring about from other causes will be far greater than the number of people it has supposedly saved from dying of COVID-19 (if any). It’s also that the lockdown itself has exacerbated the loss of life from COVID-19. The fact that NHS hospitals discharged elderly patients diagnosed with coronavirus and sent them back into care homes is an appalling scandal. As Dominic Lawson wrote in the Sunday Times, it shames the nation. Heads must roll.'

The level of incompetence needed to discharge infected or suspected infected old people from hospitals to old peoples home is beyond belief. In that process chain there are highly experienced medical personnel involved, at no point did anyone raise the alarm on the potential consequences, and on the care home end were no alarms raised by experienced professionals in the care industry. The whole thing has a sinister undertone in that it looks like steps were taken to actively get the number of deaths from covid up. Added to which all the stories of giving the cause of death as covid for people who clearly had died from strokes, heart attacks, cancer etc. 

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sancho panza
On 31/03/2020 at 14:48, sancho panza said:

Laymen's explanation of acquired/innate immune response and viral load.

For those interested,the explanation of viral load will likely explain the high mortality rate amongst Italian Medics who possibly weren't using the correct PPE or sufficiently trained in dealing with Covid.This also refers back to the earlier video where Prof John Nicholls discusses his reccomendations on adeqaute training of staff in respect of Covid.

Highlights are mine.

https://www.sciencemediacentre.org/expert-reaction-to-questions-about-covid-19-and-viral-load/

March 24, 2020

expert reaction to questions about COVID-19 and viral load

 

There have been questions from journalists about viral load ad the COVID-19 outbreak.

 

Comments sent out on Thursday 26 March 2020

 

Dr Michael Skinner, Reader in Virology, Imperial College London, said:

“Some comments on virus dose, load and shedding.

“Viruses are not poisons, within the cell they are self-replicating. That means an infection can start with just a small number of articles (the ‘dose’). The actual minimum number varies between different viruses and we don’t yet know what that ‘minimum infectious dose’ is for COVID-19, but we might presume it’s around a hundred virus particles.

“When that dose reaches our respiratory tract, one or two cells will be infected and will be re-programmed to produce many new viruses within 12-24 hours (for COVID-19, we don’t yet know how many or over how long). The new viruses will infect many more nearby cells (which can include cells of our immune defence system too, possibly compromising it) and the whole process goes around again, and again, and again.

“At some time quite early in infection, our ‘innate immune system’ detects there’s a virus infection and mounts an innate immune response. This is not the virus-specific, ‘acquired immune response’ with which people are generally familiar (i.e. antibodies) but rather a broad, non-specific, anti-viral response (characterised by interferon and cytokines, small proteins that have the side effect of causing many of the symptoms: fever, headaches, muscle pain). This response serves two purposes: to slow down the replication and spread of the virus, keeping us alive until the ‘acquired immune response’ kicks in (which, for a virus we haven’t seen, is about 2 to 3 weeks) and to call-up and commission the ‘acquired immune response’ which will stop and finally clear the infection, as well as laying-down immune memory to allow a faster response if we are infected again in the future (this is the basis of the expected immunity in survivors and of vaccination).

“With COVID-19, these two arms of the immune system (innate and acquired) obviously work well for 80% of the population who recover from more or less mild influenza-like illness.

“In older people, or people with immunodeficiencies, the activation of the acquired immune system may be delayed. This means that the virus can carry on replicating and spreading in the body, causing chaos and damage as it does, but there’s another consequence. Another job of the acquired immune system is to stand-down the innate immune system; until that’s done the innate immune response will keep increasing as the virus replicates and spreads. Part of the innate immune response is to cause ‘inflammation’. That is useful in containing the virus early in an infection but can result in widespread damage of uninfected tissue (we call this a ‘bystander effect’) if it becomes too large and uncontrolled, a situation named ‘cytokine storm’ when it was first seen with SARS and avian influenza H5N1. It is difficult to manage clinically, requiring intensive care and treatment and carries with it high risk of death.

“The scenarios described above describe what happens following infection with ‘normal’ doses of virus, both in those who make a recovery, those who require intensive care and those (mainly elderly and/or immunosuppressed) who might succumb. Those with other comorbidities probably succumb due to additional stress of their already compromised essential systems by virus and/or cytokine storm.

“It is unlikely that higher doses that would be acquired by being exposed to multiple infected sources would make much difference to the course of disease or the outcome. It’s hard to see how the dose would vary by more than 10 fold. (Although differences have been seen in lab animal infections with some viruses, those animals are inbred (genetically similar to respond in the same way). It’s unlikely that we’d see the differences as statistically significant in out-bred humans.)

“We must be more concerned about situations where somebody receives a massive dose of the virus (we have no data on how large that might be but bodily fluids from those infected with other viruses can contain a million, and up to a hundred million viruses per ml), particularly through inhalation.

“Unfortunately, we don’t yet know enough about the distribution of the COVID-19 virus throughout the body of the infected patients in normal, and unusual situations.

“Under such circumstances the virus receives a massive jump start, leading to a massive innate immune response, which will struggle to control the virus to allow time for acquired immunity to kick-in while at the same time leading to considerable inflammation and a cytokine storm.

“For most of us, it’s hard to see how we could receive such a high dose; it’s going to be a rare event. In the COVID-19 clinic, the purpose of PPE is to prevent such large exposures leading to high dose infection. Situations we should be concerned about are potential high dose exposure of clinical staff conducting procedures on patients who are not known to be infected. I read about a Chinese description of an early stage COVID-19 infection of the lung, which only came about because lung cancer patients (not known to be infected) had lobectemies. There have been suggestions that such situations contributed to the deaths of medics in Wuhan, who were conducting normal procedures (including some that could generate aerosols of infected fluids) before the spread and risk had been appreciated.

“Obviously, testing of patients for infection should now be a priority for any such procedures. Some of the relevant elective procedures have been postponed or scaled back (for patient and staff safety) but we can’t do the same for non-elective procedures (especially in emergency and maternity departments).”

 

Prof Wendy Barclay, Action Medical Research Chair Virology, and Head of Department of Infectious Disease, Imperial College London, said:

“In general with respiratory viruses, the outcome of infection – whether you get severely ill or only get a mild cold – can sometimes be determined by how much virus actually got into your body and started the infection off.  It’s all about the size of the armies on each side of the battle, a very large virus army is difficult for our immune systems army to fight off.

“So standing further away from someone when they breathe or cough out virus likely means fewer virus particles reach you and then you get infected with a lower dose and get less ill.  Doctors who have to get very close to patients to take samples from them or to intubate them are at higher risk so need to wear masks.

“The fewer people in the room, the less likely it is than one person is coughing or breathing out infectious virus at any one time, so mixing with as few people as possible is the safest way.

“But there is no evidence for any suggestion that if everyone in a family is already sick they can they reinfect each other with more and more virus.  In fact for other viruses once you are infected it’s quite hard to get infected with the same virus on top.”

 

Prof Jonathan Ball, Professor of Molecular Virology, University of Nottingham, said:

“We know that the likelihood of virus transmission increases with duration and frequency of exposure of an uninfected individual with someone infected with the virus.  We also suspect that the amount of virus that an infected individual is producing – sometimes referred to as the viral load – and potentially shedding, will also impact on transmission; the higher the viral load the more infectious someone is likely to be.

“It is also possible that individuals with pneumonia who have a higher viral load might develop more serious disease, but disease development is complex and no doubt many factors will have an impact.”

 

Comments sent out on Tuesday 24 March 2020

Professor Willem van Schaik, Professor in Microbiology and Infection at the University of Birmingham, said:

“The minimal infective dose is defined as the lowest number of viral particles that cause an infection in 50% of individuals (or ‘the average person’). For many bacterial and viral pathogens we have a general idea of the minimal infective dose but because SARS-CoV-2 is a new pathogen we lack data. For SARS, the infective dose in mouse models was only a few hundred viral particles. It thus seems likely that we need to breathe in something like a few hundred or thousands of SARS-CoV-2 particles to develop symptoms. This would be a relatively low infective dose and could explain why the virus is spreading relatively efficiently.

“On the basis of previous work on SARS and MERS coronaviruses, we know that exposure to higher doses are associated with a worse outcome and this may be likely in the case of Covid-19 as well.  This means that health care workers that care for Covid-19 patients are at a particularly high risk as they are more likely to be exposed to a higher number of viral particles, particularly when there is a lack of personal protective equipment (PPE) as is reported in some UK hospitals (https://www.theguardian.com/society/2020/mar/22/nhs-staff-cannon-fodder-lack-of-coronavirus-protection).

“It seems unlikely that people can pick up small numbers of viruses from others (e.g. in a crowd) and that will tip the infection over the edge to become symptomatic as that must happen around the same time. In the current lockdown situation this seems even less likely as gatherings of more than two individuals are banned. Because the infectious dose is probably quite low, it is more likely that you will be infected by a single source rather than from multiple sources. Transmission can take place through small droplets in the air (like the ones that are produced after sneezing and which stay in the air for a few seconds). You can breathe in these droplets or they can land on surfaces. Unfortunately, SARS-CoV-2 survives reasonably well on most surfaces, so if somebody touches these and then touches their mouth or nose, there is a very real risk that they will be infected with the viruses. This is the main reason why hand washing is promoted as a precautionary measure.”

 

Dr Edward Parker, Research Fellow in Systems Biology at the London School of Hygiene and Tropical Medicine, said:

“After we are infected with a virus, it replicates in our body’s cells. The total amount of virus a person has inside them is referred to as their ‘viral load’. For COVID-19, early reports from China suggest that the viral load is higher in patients with more severe disease, which is also the case for Sars and influenza. 

“The amount of virus we are exposed to at the start of an infection is referred to as the ‘infectious dose’. For influenza, we know that that initial exposure to more virus – or a higher infectious dose – appears to increase the chance of infection and illness. Studies in mice have also shown that repeated exposure to low doses may be just as infectious as a single high dose.

“So all in all, it is crucial for us to limit all possible exposures to COVID-19, whether these are to highly symptomatic individuals coughing up large quantities of virus or to asymptomatic individuals shedding small quantities. And if we are feeling unwell, we need to observe strict self-isolation measures to limit our chance of infecting others.”

 

From Prof Richard Tedder, Visiting Professor in Medical Virology, Imperial College London:

What is “viral load”?

“This is a specific term used in medical virology which usually refers to the amount of measurable virus in a standard volume of material, usually blood or plasma. It is very commonly used to define how HIV responds in a patient to antiviral drugs; a patient taking such drugs would be pleased to know that their ‘viral load’ is reduced.”

What does viral load mean for Sars CoV 2 (aka Covid19 virus)?

“It is probably better to use the term ‘viral shedding’ which is actually in effect influenced by the amount of virus in the material being shed by an infected patient. In practice one could say that the virus load generated by the patient in whatever excreta they shed defines ‘shedding’ and its risk.

“From looking broadly at the overall data on the material which comes from a nose swab the amount of virus varies over a 1 million fold range. This is probably influenced by the stage of the disease, the efficiency with which the infection has colonised the patient at the time of sampling, and the amount of nasal sample on the swab. The amount of virus which comes from an infected person is influenced by two factors: the ‘load’ in the excreta and the volume of the excreta.

Why does the amount of virus shed matter?

1. “The inoculum, i.e. the infecting dose of virus is more likely to lead to infection in the “recipient” the higher the amount of the virus there is in the excreta.

2. The virus will survive and remain infectious outside the body, as viruses do; BUT infectivity will fall away with time. How quickly this fall occurs is measured as the time taken for virus infectivity to reduce by half. This is termed ‘half life’ or T1/2 and for this virus is measured in hours. In fact this is best thought of as ‘rate of decay’.

3. The rate of decay is fastest on copper with a T1/2 around 1 hour, in air as an aerosol T1/2 is also around 1 hour, cardboard is 3 and 1/2 hours, plastic and steel T1/2 is around 6 hours.

“For example, if one million viruses were placed on various surfaces it would require 20 half lives to become undetectable and non-infectious, so 20 hours if in an aerosol, 20 hours on copper, 60-70 hours on cardboard and finally 120-130 hours on plastic and steel.

“Of course, when one deals with infectivity rather than detectability, extinguishing infectivity is far quicker.  Studies with cultured virus starting at relatively high levels have shown loss of infectivity within around 12-15 hours on copper, under 10 hours on cardboard, around 50 hours on steel and 70 hours on plastic. The data for infectivity in aerosols were not comparable and were of a different time course.”

@macca explanation of viral load from page 1.

 

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sancho panza
9 hours ago, macca said:

 

The viral load i have seen mentioned several times, as the quantity of virus seems to be a significant factor.. I wonder if that's true why they cant just give people a micro load to trigger an immune response,  that's kind of how a vaccine works.. Since the large number of dead nurses and doctors are not all 70 year olds with diabetes.. I remember in the beginning seeing some dead Chinese doctors and nurses and thinking they are not that old..

Guy at work has a sister in law that has had it, 6 weeks being ill, she is a GP receptionist.. So front facing to sick people entering the practice..

Cough and breathing problems but no hospital stay..  

I have no idea how this all ends.. hopefully it will disappear like the Spanish flu did, that lasted 2 years and was gone.. although it did kill an estimated 10 million people..

It worries me how 33'000 dead just roles of the tongue, when people are saying open the economy they are somehow inhumane as to not recognise these are lives that have ended prematurely.. we need names and faces printed in papers.. that's the best way to stop people going out.. numbers are nothing.. photos like the little boy washed up on the beach during the refugee crisis trigger a much stronger public response that people can relate too

It's really difficult dealing with death. As I've said before, people suffering with shortness of breath is quite horrific to witness and not a method of passing I'd choose for myself if I have an option.

A lot of the reasons for opening up the economy and society more widely aren't to do with the 33,000 dead but the 67 million that are left.There are people I know with terminal cancer who've had their treatment suspended for 12 weeks due to covid. There are lots of people with current problems that could shorten their lives considerably for which they're being neither diagnosed or treated.A&E attendances for strokes and cardiac issues are down now as I've said,either those problems have stopped occurring or those patients are staying away.There's no third option.

In terms of the 67 million and the economy,it's important to understand that things like unemployment have a massive effect on both people's physical health and their mental health.I grew up in the 80's.For me,opening the economy/society/hospitals is about people's health primarily and on a secondary level,so that we can then fund the treatments we need for the 67 million.

 

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sancho panza
1 hour ago, Talking Monkey said:

The level of incompetence needed to discharge infected or suspected infected old people from hospitals to old peoples home is beyond belief. In that process chain there are highly experienced medical personnel involved, at no point did anyone raise the alarm on the potential consequences, and on the care home end were no alarms raised by experienced professionals in the care industry. The whole thing has a sinister undertone in that it looks like steps were taken to actively get the number of deaths from covid up. Added to which all the stories of giving the cause of death as covid for people who clearly had died from strokes, heart attacks, cancer etc. 

The problem is that when orders come from the top,they tend to get obeyed no matter what anyone says.People will likely have raised objections-for instance I heard a good few people in the NHS questioning why we weren't being tested as a matter of priority given that we may be infecting people-but the reality is that they will have been ignored.As I've said,lots of top Professors of Epidemiology had their advice overlooked because the govt wanted to listen to Imperial.

The truth will out over the next year and I think it's safe to say it will be very depressing.

Edited by sancho panza
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Talking Monkey
2 minutes ago, sancho panza said:

The problem is that when orders come from the to,they tend to get obeyed no matter what anyone says.People will likely have raised objections-for instance I heard a good few people in the NHS questioning why we weren't being tested as a matter of priority given that we may be infecting people-but the reality is that they will have been ignored.As I've said,lots of top Professors Epidemiology had their advice overlooked because the govt wanted to listen to Imperial.

The truth will out over the next year and I think it's safe to say it will be very depressing.

Makes sense SP,  the consequences of these orders has been devastating. The truth will come out eventually on who at the top was issuing the idiotic orders and what idiocy was involved in formulating them

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So, in a nutshell, we killed thousands to protect the unmasked NHS who then sung and danced in empty wards.

I feel sick.

Edited by Harley
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sancho panza
1 hour ago, Harley said:

So, in a nutshell, we killed thousands to protect the unmasked NHS who then sung and danced in empty wards.

I feel sick.

Dare I say it but I'd hazard a guess that a lot of the excess deaths aren't down to covid but the fact that a lot of very sick people have been turfed out of hospital.

The dancing is a sign that people have time on their hands.Time is normally in short supply at the hospitals I usually work at.Just saying.

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11 hours ago, Talking Monkey said:

The level of incompetence needed to discharge infected or suspected infected old people from hospitals to old peoples home is beyond belief. In that process chain there are highly experienced medical personnel involved, at no point did anyone raise the alarm on the potential consequences, and on the care home end were no alarms raised by experienced professionals in the care industry. The whole thing has a sinister undertone in that it looks like steps were taken to actively get the number of deaths from covid up. Added to which all the stories of giving the cause of death as covid for people who clearly had died from strokes, heart attacks, cancer etc. 

it might have something to do with the 7.5 billion cut to adult social care by the CONs

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12 hours ago, macca said:

it might have something to do with the 7.5 billion cut to adult social care by the CONs

Traditional party politics is soooo pre CV!

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sancho panza

https://lockdownsceptics.org/

 

image.thumb.png.2d3b9047c3c1c4986728d018b9ab61ec.png

The Mirror leads with the preprint I flagged up yesterday estimating that by the end of April 29% of the UK population may have already had the virus (29% of 66 million is ~19 million). If we assume that roughly 50,000 people in the UK will have died from COVID-19 by May 21st – allowing for the three-week lag time between infection and death – that gives an infection fatality rate (IFR) of ~0.076%, less than half the IFR of seasonal flu.

My Lockdown Sceptic of the week is Luke Johnson, former chairman of Pizza Express and Channel 4, who was on Question Time last night. He dared to suggest the lockdown will cause a greater loss of life that it will prevent and duly reaped the whirlwind. One of the points he made is that if you’re under 60 with no underlying health conditions you’re more likely to drown than die of COVID-19. You can watch Johnson firing off truth bullets here.

A regular contributor to this site – anonymous, but one of the best financial journalist in the country – has done a bit of analysis based on the “response tracker” that Oxford’s Blavatnik School of Government has created. This is a tool that enables you to compare and contrast different countries according to what non-pharmaceutical interventions they’ve put in place in an attempt to mitigate the impact of the virus:

The Blavatnik School of Government provides an estimate of Lockdown “stringency” (100 being complete lockdown). I put the numbers for a few countries into a spreadsheet. What you find is that there is no statistical relationship between the stringency of lockdown (at the end of March) and a country’s rate of COVID-19 infections and deaths (per million of population – numbers from Our World in Data). There is, as you would expect, a stronger statistical relationship between the degree of stringency and projected fiscal deficits (estimated by the IMF, and already massively understating the problem).

Never have some many sacrificed so much for so little…

 

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