Coronavirus 33

Proof is a useful concept in formal logic and mathematics but has no place in science*, which is always provisional. Science seeks to describe and understand phenomena but descriptions and understandings are always subject to improvement. Scientists are always wrong but they share their findings so their work can be criticised and improved

It was government policy to keep their Scientific Advisory Group for Emergencies (SAGE) advice secret. 

The minutes of SAGE meetings and supporting documentation (scientific data and analysis used to inform SAGE discussions) are typically published at the conclusion of the relevant emergency. - wrote the Government.

That really stops it being science as it is not open to peer review and improvement, an essential part of the scientific method. Now that the minutes of some SAGE meetings have been published, there will be much scrutiny of any advice that may, with hindsight, be demonstrated to have been wrong, and the Government and its supporters will doubtless reinforce their message that the Government followed the science. This was their Big Lie.

Cherry-picking advice from their chosen scientists, whose work was undisclosed and not subject to peer review, is not within the scientific method.

And importantly, as Anthony Costello of The Independent SAGE points out "The minutes of SAGE meetings before the fateful March 12 press briefing have not been released." 

The 60,000 and more deaths so far represent a Government failure so don't blame scientists.

Karl Popper

*Proof has a rather different meaning and usage in the context of courts of law and this varies with jurisdiction, England and Scotland having differences. Bakers using yeast depend on proving their product too, but that is something else. 

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1. COVID-19 Test and Trace is a good thing.
2. It should have begun in late January
3. The abandonment of any attempt on 12th March was a National Disaster
4. Starting today distracts from Dominic Cummings. Well that's handy.

During yesterday's briefing at which we were introduced to Dido Harding, my wife asked "How do you get to be a baroness?". "Marry a baron I suppose", I answered cynically, "or do something really useful". I added, generously. I looked her up. Turns out there's a third way, choose your grandfather well.  What follows is informed by Wikipedia.

Diana Mary "Dido" Harding, Baroness Harding of Winscombe is the daughter of Lord Harding, and the granddaughter of Field Marshal John Harding, 1st Baron Harding of Petherton, who commanded the Desert Rats in World War II. She was raised on the family pig farm in Dorset. She graduated from the University of Oxford in Philosophy, Politics and Economics, where she studied alongside David Cameron.

Her business career involved being marketing director at Thomas Cook Group (they ceased trading last year) and commercial director at Woolworths Group (remember Woolies?). She then joined Tesco as international support director (Tesco pulled out of the USA in 2013).

It was her job at TalkTalk that brought her to public attention. In October 2015, TalkTalk experienced a "significant and sustained cyber-attack", during which personal and banking details of up to four million customers is thought to have been accessed. City A.M. described her responses as "naive", noting that early on when asked if the affected customer data was encrypted or not, she replied: "The awful truth is that I don’t know". Her "inflexible line" on termination fees was also criticised. Marketing ran a headline, "TalkTalk boss Dido Harding's utter ignorance is a lesson to us all". The Evening Standard noted that "It has been a tough week for TalkTalk boss Dido Harding, facing complaints from customers and calls for her head." The company admitted the hack had cost it £60 million and lost it 95,000 customers.

In February 2017, Harding announced she would stand down after seven years as CEO of TalkTalk in May 2017, to focus more on her public service activities. In October of that year she was appointed chair of NHS Improvement, which is responsible for overseeing all NHS hospitals, comprising foundation trusts and NHS trusts, as well as independent providers that provide NHS-funded care.

In January 2018 Harding, herself a racehorse owner and rider, became a member of the Jockey Club's Board of Stewards, which runs many of British horse-racing's most popular events, including the Cheltenham Festival.

What? I hear you scream. Yes, that's right, the Cheltenham Festival was one of the key turning points in this government's abject failure to control the pandemic, ensuring we would be like the USA rather than like New Zealand. In May 2020, Health Secretary Matt Hancock announced that Harding was to be put in charge of the "Track, Test and Trace" effort as part of the UK government's response to the COVID-19 pandemic. Of course it is just a coincidence that she has a connection with the decision not to cancel Cheltenham. And it is just a coincidence that the NHS was found to be woefully under-equipped to deal with a pandemic while on Harding's watch as chair of NHS Improvement.

I'd love to know what Harding's view, as a Jockey Club board member and chair of NHS Improvement, was on the decision to allow the Cheltenham Festival to go ahead,

Anyway, they say poachers make the best gamekeepers.

The UK Government, having first tried all the wrong policies, has at last got round to promoting the correct action. Our job is to make sure that Test and Trace works.

Coronavirus 31

Here is a graph. It was not shown at the Downing Street Briefing yesterday afternoon but it was reported by Chris Giles at The Financial Times.

Here are the numbers. This is where they come from: Office of National Statistics.

Week 13	14	15	16	17	18	19	20
27-Mar-20	03-Apr-20	10-Apr-20	17-Apr-20	24-Apr-20	01-May-20	08-May-20	15-May-20
11,141	16,387	18,516	22,351	21,997	17,953	12,657	14,573

The right hand bar, the last number, 14.573, is the one to think about. Maybe just some noise in the data and next week all will be well, but deaths lag behind infection and infection depends on behaviour. This uptick in the total deaths may reflect the change in behaviour around the VE Day bank holiday weekend and the mixed signalling from government about easing of the, already very leaky, lockdown.

All the talk is now about further easing of lockdown. Never mind driving to Barnard Castle to test our eyesight, we drive the country by watching in our rear-view mirror where we went three weeks ago. Only Cassandra is looking forwards.

Coronavirus 30A

Sunday 24th May 2020

This is a continuation of last night's post, Coronavirus 30. Please read it first. And if you skipped reading the article by Gian Volpicelli linked half way way through please read that too.

For the last several years I've been pointing out that we are on the road to fascism, the Brexit affair providing a particular boost to the journey. Of course few, if any, took the warning seriously, but the mistake, easily made, was to assume that a new fascism would look like the old fascism, would be recognised and stopped in its track. But no, though there is much that can be learnt from history, it does not repeat itself, at least not in the details.

In last night's bloglet I copied a thread of tweets from Carole Cadwalladr. She starts:

Why does the Cummings story matter? And what does it obscure? The real story is the huge transfer of government assets to private companies that he is overseeing under cover of a pandemic

Brexit gave much cover for this restructuring of British governance, economy and society to the neo-liberal agenda but SARS-CoV-2 has boosted the Bad Boys' cause enormously. For starters, the economic downside, for the all but a tiny minority, of Brexit is lost as noise in the catastrophe of the pandemic.

We can now be confident that the COVID-19 case fatality rate is in the region of 1%, as explained in my piece a few days ago, Coronavirus 29. At the beginning of February, the UK had the chance of avoiding pretty much any deaths. My piece on the 7th of February recommended stopping all incoming flights. Vietnam and New Zealand are two countries of enormous contrasts but had in common a determination to avoid deaths at any cost and knew that the first step was to stop the virus entering the land and second was to trace and eliminate any outbreaks where the first step failed. They succeeded in preventing almost all deaths. The UK could have been in the same position.

At the beginning of March the UK had the chance to learn from Italy being caught unawares. Germany did. They're deaths are a fraction of the UK's. But on the 12th March the UK government abandoned any moral sense. The tracking and tracing was abandoned and we were told to take it on the chin with the Big Lie of protecting the NHS (see again Coronavirus 29 ).

That was the turning point when the UK Government decided it was just fine to allow 1% of the population to die. Why?  As Carole Cadwalladr points out, to provide cover for the huge transfer of government assets to private companies that Dominic Cummings is overseeing.

This is the New Fascism. It has only just begun.

When it's all over, we'll need to thank Carole Cadwalladr.

Coronavirus 30

Saturday 23rd May 2020

Tonight I pass over this episode of the COVID bloglets to some of the most important tweets in twitter's history. Thank you Carole Cadwalladr @carolecadwalla

Why does the Cummings story matter? And what does it obscure? The real story is the huge transfer of government assets to private companies that he is overseeing under cover of a pandemic while restructuring the Cabinet Office into his & @michaelgove's private fiefdom

We have no insight into these contracts which did not go to tender but to Cummings's friends & associates. Including a massive transfer of our most private, intimate NHS data. The privatisation of essential state functions is happening in real time in almost complete darkness

Cummings made absolutely clear his conditions for working in govt were smashing civil service & rebuilding in his image & creating British 'ARPA' - an AI-driven research facility. That's exactly what he's doing right now in Cabinet Office with Gove his long-time co-conspirator

Sure, the hypocrisy & entitlement of Cummings is breathtaking but there's a far darker story that it obscures & it's why the focus must be on Johnson now & his decision to throw weight of his office - statement from No 10 - behind him.

There's so much misogyny directed at @bbclaurak who mostly does extraordinarily difficult job with grace & professionalism. But the 'lobby' system of embedding journalists in the heart of government is a busted flush & any serious society would undertake an honest review of it

Because none of this is acceptable. And which came first?The decision to centralise UK's response to COVID-19 which so many public health experts say is at the heart of its failure? Or the private contracts to the friends of ministers & advisors?

There's so much more to say about this. And how it is eclipsing the news we learned yesterday that government is ignoring its own scientists. But job of holding both Cummings & No 10 to account is in hands of journalists who rely every day on Cummings & No 10 as 'sources'

I'm obsessed with knowing what happened on March 12. The critical day when Britain moved from containment to delay. But did nothing to shut down the country. It just let the virus rip. This is what Cummings was doing on the evening of March 11.

[Vitally important link: https://www.wired.co.uk/article/dominic-cummings-coronavirus-big-tech ]

The next day, Boris Johnson told us our loved ones would die. But did nothing to protect care homes, shut down mass events or shield elderly & vulnerable. It's this decision that's at the heart of the government's failure. That has seen 63,000 people die. And we need answers

This is what I tweeted on March 12. To massive pushback. But Cummings’s role as interface between scientists of SAGE, friends & associates in private tech sector & decisions of government is key. And this is where our focus needs to be. And on those who enable & cover for him 

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Friday 22nd May 2020

Yesterday in the Downing Street Briefing the Health Secretary, Matt Hancock, said:

"antibody tests suggest that 17% of people in London and 5% in the rest of the country may have had coronavirus."

5% of UK population is 3,350,000. Add some more for the higher rate in London and we have a rough figure of 4 million people having had the virus. We've had over 63,600 deaths according to the Chris Giles / Financial Times estimate or 36,042 according to the government. Choose your preferred number but this at last allows us to do a calculation of the case fatality rate. Either way, we get figures of just under 1% or about 1.5%.

For a so-called 'herd immunity' of 80% we need getting on for a million deaths. That's the Government plan is it? It's not my plan.

Remember they said 'Protect the NHS'. 'Flatten the curve'. New Zealand, Vietnam and others took a different approach - 'We will not let our people die'.

Protect the NHS was a Big Lie. The NHS is there to protect the people, not t'other way round. Flattening the curve was not about avoiding COVID-19 deaths but spreading the deaths out through time.

We must not accept that half a million or a million more deaths are inevitable. The Government may have done everything wrong for the last three months but that is no reason to keep doing everything wrong. There must, even now, be a change in strategy.

We must eliminate the virus.

From Vietnam

to New Zealand

other approaches to dealing with COVID-19 are available.

Coronavirus 28

Saturday May the 16th 2020, just two weeks to go and then the UK Government, at least in England, intends to reopen schools. The British Medical Association said yesterday "...until we have got the case numbers much lower, we should not consider reopening schools." Also yesterday we learnt that the R value is likely to have increased, an assessment based on data from before the Government morphed the 'Stay at Home Message' to 'Alert'. New cases are recorded daily in their thousands.

The Government's plan is to open schools partially, with smaller than normal class sizes, 'social distancing' and other precautions. The precautions give the impression that the government is, well, cautious. Good, one thinks. But what it actually shows is that the Government knows that there is a risk that some children and teachers may be carrying the disease. 

The keep two metres apart rule may make some sense when doing the necessary tasks of shopping for food where encounters with potentially infected people will be brief. The same rule is less useful when asking children to sit in the same room as an infected person for five hours per day, five days per week.

The Government knows that reopening schools, even on a limited basis, will increase the R value, prolong the pandemic and increase the eventual total of deaths.

The time to reopen schools is when the prevalence of the virus is so low that it is very unlikely that a child meets an infected person. That's what the doctors are saying. We will know that time has arrived when 'social distancing' and other precautions are not needed.

Parents will be more confident of the safety of their children after they see 650 MPs crowded into the House of Commons. And they will know it is safe when the bars on the right of this graph dwindle to next to nothing.

From the Independent SAGE Report:
"11. The government should take steps to ensure all children, irrespective of their backgrounds, have access to technology and internet at home, and where required additional learning support which does not rely on parents at home. The government should also ensure that resources are available for schools to conduct remote learning"

Update 17th May 2020

Here's some recently published research that might be relevant for people talking to each other in rooms, as they do in schools.

The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission

Speech droplets generated by asymptomatic carriers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are increasingly considered to be a likely mode of disease transmission.

Valentyn Stadnytskyi, Christina E. Bax, Adriaan Bax, and Philip Anfinrud
PNAS first published May 13, 2020 https://doi.org/10.1073/pnas.2006874117

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On Tuesday 12th of May 2020 the first Report of The Independent SAGE was published.

The Report, (36 page pdf file) can be downloaded here.

The Press Conference can be viewed here.
(if you've been watching the daily Downing Street Briefings you will see a remarkable difference here, the contrast between the the answers given to the journalists' questions by these scientists and the government's people is extraordinary).

Follow the discussion on Twitter here.

Sir David King has convened a group of scientists of impeccable credentials and appropriate expertise. They have produced a report of unequivocal importance, damning of the Government's handling of the Covid catastrophe so far and clear in its recommendations for the future.

Extraordinarily, what should have dominated the afternoon's Briefing from Downing Street, but wasn't, was further ignored by some of the main stream media, with no mention on the BBC's main TV news at 10 pm or Newsnight.

Here's the Executive Summary:Our Independent SAGE focuses on the priorities for measures to be taken to support a gradual release from social distancing measures through a sustainable public health response to COVID-19. This will be essential in suppressing the virus until the delivery of an effective vaccine with universal uptake. We do not address, except as it is directly relevant, the clear structural and procedural weaknesses that contributed to the current situation as we expect these to be addressed in a future inquiry. We draw extensively on the policy considerations proposed by the World Health Organization, which provides a clear structure on which an effective policy should be based given the inevitability that the virus will continue to cross borders.
Our main recommendations are:
1. The government should take all necessary measures to control the virus through suppression and not simply managing its spread. Evidence must show that COVID-19 transmission is controlled before measures are relaxed. We detect ambivalence in the government’s strategic response, with some advisers promoting the idea of simply ‘flattening the curve’ or ensuring the NHS is not overwhelmed. We find this attitude counter-productive and potentially dangerous. Without suppression, we shall inevitably see a more rapid return of local epidemics resulting in more deaths and potentially further partial or national lockdowns, with the economic costs that will incur.
2. The government should refocus its ambition on ensuring sufficient public health and health system capacities to ensure that we can identify, isolate, test and treat all cases, and to trace and quarantine contacts. Quarantine should be for 14 days and not seven. The government must develop a clear quarantine and messaging policy which takes account of the diversity of experiences of our population, variations in household structures, and with appropriate quarantine facilities in the community. This should be accompanied by real time high quality detailed data about the epidemic in each local authority and ward area.
3. Government ministers, NHS bodies and their officials should adhere to the Code of Practice for Statistics and the UK Statistics Authority should reports breaches of the code. There is concern about the inaccurate, incomplete and selective data presented by government officials rather than the statisticians responsible for them at the daily PM press briefings. The Office for Statistics Regulation should publish further assessments of them. The UK Statistics Authority, an independent body responsible for oversight of the statistics produced by the Office for National Statistics and other government departments and public bodies has a Code of Practice. The Code requires i) trustworthiness: confidence in the people and organisations that produce statistics and data, ii) quality: data and methods that produce assured statistics and iii) value: statistics that support society’s needs for information. It is vital the public has trust in the integrity and independence of statistics and that those data are accurate, timely and meaningful.
4. The government evaluates alternatives to complement conventional epidemiological modelling, such as dynamic causal modelling—e.g., via the expertise established by the RAMP initiative. Dynamic causal modelling (DCM) enables real-time assimilation of data quickly and efficiently to estimate the current levels of infection and ensuing reproduction rates (R). The computational efficiency of DCM may allow pressing questions to be answered; for example, would a devolved social distancing and surveillance policy—based on local prevalence estimates—be more efficacious than a centralised approach? In short, there is a pressing need to evaluate alternative approaches (and hypotheses) that may support real-time policy-making.
5. Recognising the centrality of human behaviour in transmission, the government should ensure that as social distance measures are eased, measures are taken to enable population-wide habit development for hand and surface disinfection, using and disposing of tissues for coughs and sneezes and not touching the T-zone (eyes, nose and mouth).
6. Outbreak risks must be minimised in high vulnerability and institutional settings. No-one should be discharged from hospital to another high-risk setting such as a care home without having been tested and found to be non-infected. The government should rapidly invest in the elimination of transmission in the currently recognised “high risk” settings, including but not limited to social care and health service facilities, prisons and migrant detention facilities, homes in multiple occupancy, and households that are overcrowded or contain multiple generations. This includes staffing, testing, protective equipment and guidance for effective household isolation. Community facilities and requisitioned hotels are likely to be needed to house a significant proportion of infected people and their contacts.
7. Ensure preventive measures are established in workplaces, with physical distancing and support to enable personal protective behaviours. Health and safety regulations appropriate for COVID -19 suppression and adequate surveillance should be agreed with trade unions and other staff representatives, with sanctions that are large enough to deter unsafe practices. There should also be a facility for workers to report unsafe working conditions, with no victimisation for those using it.
8. The procurement of goods and services in order to ensure responsive and timely supply of goods for primary and secondary care, and community infection control, in anticipation of a second wave of infection. Reform should learn as much as possible from the document challenges and failures of procurement over the last three months.
9. Manage the risk of importing cases from other countries, with consequent high-risk of transmission. This should be introduced as soon as possible, treating Great Britain and the island of Ireland as distinct health territories. We welcome the government’s recent commitment to establish a port control and quarantine strategy as an adjunct to other control measures. Managing the testing, thermal assessment, collection of contact details and quarantine facilities, such as requisitioned hotels, will be essential to stop imported cases.
10. Communities and civil society organisations should have a voice, be informed, engaged and participatory in the exit from lockdown. This pandemic starts and ends within communities. Full participation and engagement of those communities on issues such as childcare and public transport will assist with enabling control measures. Conversely, a top-down approach risks losing their support and trust. We are deeply concerned about the effects of the infection and the lockdown on BAME, marginalised, and low-income groups. There is an urgent need for government to demonstrate such active participation from communities from around the country.
11. The government should take steps to ensure all children, irrespective of their backgrounds, have access to technology and internet at home, and where required additional learning support which does not rely on parents at home. The government should also ensure that resources are available for schools to conduct remote learning. The closure of schools due to the COVID-19 pandemic has caused unprecedented challenges for everyone involved – students, teachers and parents, but we are particularly concerned about the detrimental impact (and widening of educational inequalities) of long term social distancing measures on learning for children from lower socioeconomic backgrounds. Education is a human right which should not be compromised in the context of COVID-19.
12. The government must ensure that health and social care services are planned, strengthened, and prepared for future waves of infection while continuing to provide the full range of services to all. For health services, this will require planning to ensure there are capacity and resources to meet need safely and to resume elective services including hospital, mental health and community health services. For social care this will require having accurate data on all staff and needs of residents; making good the serious shortages in staffing, increasing qualified staffing levels, and ensuring all staff terms and conditions of services include full sickness benefits when they fall ill.
13. The government should rapidly strengthen the social safety net, including addressing low income benefits and housing, thereby ensuring protection of the most vulnerable in our population. It is 7 now clear that COVID-19 has disproportionately affected older people, low income groups living in deprived areas, BAME communities, and those who are otherwise marginalised. We also note the over-representation of BAME communities as low paid care workers in health and social care settings which makes them vulnerable to COVD-19-related infection and deaths.
14. The management of often multi-organ COVID-19 disease has been based in hospital and ICU settings. Hospitals have had to radically alter non-COVID patient flows in order to deal with these pressures, and Nightingale facilities have also needed to be developed. There is clear evidence of increasing non-COVID mortality in association with the pandemic. The government should work with the Royal Colleges and professional societies to ensure that capacity and treatment guidance is updated and disseminated as evidence emerges.
15. There should be a re-evaluation of current plans to reduce overall hospital beds in the NHS per head of population and consider ICU bed and staffing requirements to provide future surge capacity. We also recommend a rapid engagement with primary care and community health settings to support those recovering from COVID-19 disease, and sequelae, including mental health problems, as well as support to rapidly identify and manage future local outbreaks.
16. The government should urgently review and improve co-ordination in the response to the pandemic across the multiple bodies tasked with pandemic planning, both within England, including different government departments, the NHS, PHE, and local authorities, and others, and among the Westminster and devolved administrations, the government should review and improve co-ordination.
17. In order to underpin our recommendations, the future long-term management of the pandemic should be based on an integrated and sustainable public health infrastructure. The government has adopted a top-down approach with vertical structures for test and trace programmes. The overdependence on outsourcing of key operational functions limits the sustainability of this approach. A more appropriate infection control response will require adaptation for local needs. Leadership from local public health and primary care professionals is essential. We do not specify which organisations should be responsible for these roles and functions as this will vary in the four nations of the United Kingdom but, in each of them, there should be a clear system map setting out responsibilities, accountability, and lines of communication.
18. In the longer term we recommend that legislation to enable an integrated National Health and Social Care System for England is considered, along the lines of the NHS in Scotland and Wales and the integrated NHS and social care system of Northern Ireland.
19. The Independent SAGE will continue to meet to consider some of these specific recommendations and to offer constructive solutions to government to ensure that the coronavirus is suppressed, that lives are saved and that the economy is able to recover as rapidly as possible.

The Independent SAGE came up with their own 3-phrase slogan, but unlike the Government's version, and very importantly, saving lives comes first. As it should.

Save lives,
suppress the coronavirus
and get the economy moving again.

Coronavirus 26

All the talk is of lifting the lockdown, when, how....?

We need to understand how pandemics spread and where the uncertainties lie.
For instance, what difference does varying the R make?

Pluck some input number out of the air: say number of infections is 250000 and infection-fatality rate is 1%

R ~Total deaths
>1    Half a million soon
1      Half a million eventually
0.9 22500
0.8 10000
0.7 5800
0.6 3750
0.5 2500
0.4 1670
0.3 1070
0.2 625
0.1 280

That, of course, is stupidly simple, but perhaps gives an inkling of what is meant when it is said the R needs to be below 1 and that 0.5 is much better than 0.9

Marcel Salathé & Nicky Case have produced an excellent tool to understand the thing properly.

Simple yet sophisticated. Simplicity, like minimalism, takes sophistication.

Please, please, devote the time necessary to go through it and then share it with everybody else. Understanding such things should be the duty of every citizen capable of understanding such things.

What Happens Next?COVID-19 Futures, Explained With Playable Simulations

This is Marcel Salathé

This is Nicky Case

Coronavirus 25

Right from the start of the pandemic, I've pretty much ignored the government's daily announcement of the number of cases, since they reflect the amount of testing and who is being tested, rather than give much useful information about the disease.

It's all been a smokescreen, diverting attention from a government policy that has caused tens of thousands of avoidable deaths. This came to a head with the excitement over whether Matt Hancock's totally arbitrary round number of 100,000 tests per day by the end of April would be met. (It was, but only by counting tests that hadn't happened yet. Only about 73,000 people were tested that day.)

As BBC Reality Check @BBCRealityCheck pointed out:
It's also worth pointing out that of the 122,347 tests announced by the Health Secretary, the number of people tested was 73,191 (according to the DHSC) This can be down to some people having to be tested twice for clinical reasons.

Much more important are questions of who is being tested and why. Had testing been of a random sample of the population then we might have learnt something useful.

Richard Horton, editor of the Lancet put it succinctly: "Daily UK deaths this wk: 813, 413, 360, 586, 765, 674, 739. We may be “past the peak”, but the number of daily deaths is a human catastrophe. Many of these deaths were preventable. News headlines should not be about meeting the 100K testing target. They should be about these deaths."

This article by Van Savage, explains the point. It is part of the Santa Fe Institute's Transmission series, transmitting insights into the COVID-19 pandemic from the world of complexity science. It's well worth a gander.

But whenever you read the words 'flattening the curve' do remember that given the policies applied in Vietnam, New Zealand, Taiwan, and South Korea, there would be no curve to flatten. And neither should there be in the UK, had the government actually followed the science instead of telling lies.