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Government of Ontario weekly growth 2020-05-09

Government of Ontario weekly growth numbers.  Note Ontario which began “re-opening” remains at R=~ 1


Written by Colin Henderson

May 9, 2020 at 12:13

Posted in Uncategorized

He said in some parts of the province, the reproduction number or R0 has fallen to about 0.8

In more positive news, Williams said that for the first time, Ontario’s basic reproduction number has fallen below one, meaning that on average, each newly infected person is passing the virus on to less than one other person.

He said in some parts of the province, the reproduction number or R0 has fallen to about 0.8, but in other parts, it remains well above 1, closer to 1.3.

The 477 new cases confirmed on Friday translate into a positive rate of about 2.9 per cent on the more than 16,000 tests conducted. That’s up marginally from a positive rate of around 2.6 per cent on about 1,000 thousand fewer tests one day prior but is down from May 6 when there were 412 confirmed cases on just under 13,000 tests.

Written by Colin Henderson

May 9, 2020 at 09:13

Posted in Uncategorized

6 countries, 6 curves: how nations that moved fast against COVID-19 avoided disaster

Hassan Vally, La Trobe University

To understand the spread of COVID-19, the pandemic is more usefully viewed as a series of distinct local epidemics. The way the virus has spread in different countries, and even in particular states or regions within them, has been quite varied.

A New Zealand study has mapped the coronavirus epidemic curve for 25 countries and modelled how the spread of the virus has changed in response to the various lockdown measures.

Read more: Latest coronavirus modelling suggests Australia on track, detecting most cases – but we must keep going

The research, which is yet to be peer-reviewed, classifies each country’s public health response using New Zealand’s four-level alert system. Levels 1 and 2 represent relatively relaxed controls, whereas levels 3 and 4 are stricter.

By mapping the change in the effective reproduction number (Reff, an indicator of the actual spread of the virus in the community) against response measures, the research shows countries that implemented level 3 and 4 restrictions sooner had greater success in pushing Reff to below 1.

R0 can be viewed as an intrinsic property of the virus, whereas the Reff takes into account the effect of implemented control measures. The Conversation, CC BY-ND

An Reff of less than 1 means each infected person spreads the virus to less than one other person, on average. By keeping Reff below 1, the number of new infections will fall and the virus will ultimately disappear from the community.

Conversely, the larger the Reff value, the more freely the virus is spreading in the community and thus the faster the number of new cases will rise. This means a higher number of cases at the peak of the epidemic, a greater risk of the health system becoming overwhelmed, and ultimately more deaths.

Here are some of study’s findings from states and nations around the world:

New South Wales, Australia

The effect of Australia’s strict border control measures, implemented relatively early in the pandemic, can clearly be seen in the graph below. Federal and state governments introduced strict social distancing rules; schools, pubs, churches, community centres, entertainment venues and even some beaches were closed.

This prompted the Reff value to drop below 1, where it has stayed for some time. Australia is rightly regarded as a success story in controlling the spread of COVID-19, and all states and territories are now mapping their paths towards relaxing restrictions in the coming weeks.

The Conversation, CC BY-ND

Read more: 90% out of work with one week’s notice. These 8 charts show the unemployment impacts of coronavirus in Australia


Italy was relatively slow to respond to the epidemic, and experienced a high Reff for many weeks. This led to an explosion of cases which overwhelmed the health system, particularly in the country’s north. This was followed by some of the strictest public health control measures in Europe, which has finally seen the Reff fall to below 1.

Unfortunately, the time lag has cost many lives. Italy’s death toll of over 27,000 serves as a warning of what can happen if the virus is allowed to spread unchecked, even if strict measures are brought in later.

The Conversation, CC BY-ND

United Kingdom

The UK’s initial response to COVID-19 was characterised by a series of missteps. The government prevaricated while it considered pursuing a controversial “herd immunity” strategy, before finally ordering an Italy-style lockdown to regain control over the virus’s transmission.

As in Italy, the result was an initial surge in case numbers, a belatedly successful effort to bring Reff below 1, and a huge death toll of over 20,000 to date.

The Conversation, CC BY-ND

New York, USA

New York City, with its field hospital in Central Park resembling a scene from a disaster movie, is another testament to the power of uncontrolled virus spread to overwhelm the health system.

Its Reff peaked at a staggeringly high value of 8, before the city slammed on the brakes and went into complete lockdown. It took a protracted battle to finally bring the Reff below 1. Perhaps more than any other city, New York will feel the economic shock of this epidemic for many years to come.

The Conversation, CC BY-ND


Sweden has taken a markedly relaxed approach to its public health response. Barring a few minor restrictions, the country remains more or less open as usual, and the focus has been on individuals to take personal responsibility for controlling the virus through social distancing.

This is understandably contentious, and the number of cases and deaths in Sweden are far higher than its neighbouring countries. But Reff indicates that the curve is flattening.

The Conversation, CC BY-ND


Singapore is a lesson on why you can’t ever relax when it comes to coronavirus. It was hailed as an early success story in bringing the virus to heel, through extensive testing, effective contact tracing and strict quarantining, with no need for a full lockdown.

But the virus has bounced back. Infection clusters originating among migrant workers has prompted tighter restrictions. The Reff currently sits at around 2, and Singapore still has a lot of work to do to bring it down.

The Conversation, CC BY-ND

Read more: This is why Singapore’s coronavirus cases are growing: a look inside the dismal living conditions of migrant workers

Individually, these graphs each tell their own story. Together, they have one clear message: places that moved quickly to implement strict interventions brought the coronavirus under control much more effectively, with less death and disease.

And our final example, Singapore, adds an important coda: the situation can change rapidly, and there is no room for complacency.

Hassan Vally, Associate Professor, La Trobe University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Written by Colin Henderson

May 3, 2020 at 10:49

Posted in Uncategorized

Brussels goes bike friendly before end of lockdown

Brussels goes bike friendly before end of lockdown

Written by Colin Henderson

May 1, 2020 at 11:52

Posted in Uncategorized

New model released by Province of Ontario

New covid-19 model released by Province of Ontario.

Written by Colin Henderson

April 20, 2020 at 11:46

Posted in Uncategorized

COVID-19 has its own syndromes not the least of which is survival with the same person 24/7.

COVID-19 has its own syndromes not the least of which is survival with the same person 24/7.

So what do the experts think and who are the experts.

The Times suggests Nuns.

I normally link only or quote but given the pervasive result of lockdown I trust The Times will permit an exception with full attribution.

The Times Apr 20th, 2020

How to survive lockdown, by the nuns who do it 24/7

You may be climbing the walls after a few weeks inside, but for enclosed nuns this is a way of life — so what can we learn from them?
April 19 2020, The Times
If the past few weeks have had you praying for divine intervention . . . well, that would be rather fitting. Because while life in lockdown may be a whole new experience for most of us, there is one section of the population who have lived this way for years — nuns.
“We don’t leave the convent unless we absolutely have to,” says Sister Pat, 67, a member of the enclosed order of the Poor Clares in Arundel, West Sussex. “When I entered here in 1982 we didn’t even go to the dentist or the doctor — they came to us. Now, though, we do go out if we need to for these reasons, which means a minimum of once every six months for a dental check. We’re also allowed to go for a walk on the South Downs once a month. But otherwise we stay within the confines of the house and garden.”
The question is, what can we learn from them?
Unholy rows will ensue
Or at least they will if you don’t quickly decide who does what in the chores department. Even nuns aren’t immune to a little bickering, says Sister Julian, who has been a member of the Stanbrook Abbey Benedictine community since 1978 (their convent was originally in Worcestershire, but they moved to Yorkshire just over a decade ago).
“It’s no good thinking everyone will chip in because they won’t — it will all fall on the shoulders of one kind-hearted soul, and then she’ll feel resentful. And since we believe that thou shalt not kill, we certainly can’t have that.”
The solution? A rota, of course. “When you’ve suddenly been forced into isolation, you’ll have lost many of the things you normally have. Everyone needs a job, everyone needs to be given a responsibility.”
She thinks rotas at home for families will also be “an enormous opportunity for adults to trust young people to do more than they normally would”. Something to tell teenage children the next time they kick up a fuss.
Say sorry first
Of course, some disagreements are inevitable. “What makes for a happy convent is reconciliation, forgiveness and listening to one another,” says Sister Aelred, 76, a member of the Arundel community. “You can’t sweep things under the carpet; it’s much better to have a row than to let things go underground.”
“Sort things out before sunset,” is the advice of Sister Julian. “If you’ve had words with someone, have a conversation or send them a note before the end of the day. Sometimes here you see a couple of sisters having a hug at the end of the cloister and you know they’re making up after an argument.”
Sister Pat agrees. “I’d had a big row with another sister, and I knew we couldn’t go to Mass without making up. I said to her, ‘I’m sorry I’ve upset you.’ And to my surprise she said, ‘It wasn’t you, it was me.’ When you say sorry, often the other person opens up. Even if you believe you didn’t do anything wrong, you can say you’re sorry about how the other person is feeling — it’s about breaking the ice.”
The less said the better
Given the above, it may pay to know when to keep your counsel. Most enclosed communities speak only when necessary during the day, and they keep what they call the “great silence” from 8pm to about 10am the next morning. “People need a certain amount of space from one another, and silence,” says Sister Philippa, 73, of the Stanbrook Abbey community. Words to live by. Or, rather, the opposite.
Stop lazing about — and start microscheduling
Too much sleeping in late and wafting around without purpose has limits. What we need, Sister Philippa says, is a timetable. At Stanbrook Abbey the day starts at 5am and finishes after the office of evening prayer or Compline at 8pm. Between those times it is split into one or two-hour windows for meals, prayer, household work, income-generating work (book-binding, calligraphy, weaving, painting, photography and handicrafts), reading and shared time or recreation. “It means we don’t have acres of unstructured time we can just fritter away,”Sister Philippa says.
It appears nuns cottoned on to the Silicon Valley trend for “microscheduling” — that is, dividing your day into ever tinier increments — centuries ago. Sister Aelred agrees: “We don’t do anything for too long, and we alternate between work and prayer and reading and enjoying one another’s company. We stick to a timetable, and that gives our lives variety.”
Dust off your fitness DVDs — or sing in the shower
At the Poor Clare convent in Arundel the sisters do yoga to a DVD, and they have an exercise bike. “We also have walks round the garden because being outside is always good,” Sister Pat says.
Dancing is popular too. “We did a Brazilian water dance just the other morning,” Sister Aelred says.
Make your own fun
“We look for opportunities for fun,” Sister Julian says. “We do a lot of homegrown entertainment — we’ll have an evening where sisters recite poetry or tell stories. I’m rather keen on doing magic tricks myself.”
She also recommends trying your hand at crafts. “Recently we had a decorate-your-coat-hanger competition,” she says. “Everyone has a coat hanger, and everyone can be creative. It was loads of fun.”
After all, Sister Aelred says, you have to take your kicks where you can get them. “One evening a week we’re allowed to cook for ourselves, and you get sisters who make food they really miss and love,” she says. “And we only get toast and marmalade on a Sunday, and I look forward to it so much and really enjoy it. Because treats are relative, aren’t they?”
Read poetry at breakfast (really) 
Can some Wordsworth with your eggs cure the lockdown blues? Maybe. “Often I’ll read a poem first thing in the morning — it doesn’t have to be religious. It’s like having your breakfast at a deeper level than the breakfast you eat, because it’s nourishing you in a different way.”
In lieu of rhyming couplets, the nuns recommend finding time to practise thankfulness for the good things we do still have in our lives. “You’re going to be banged up with people for weeks on end, and I’d say be open to conversations about spirituality and what life means — and also build in time to be thankful,” Sister Julian says.
“People think of isolation and confinement as negative,” Sister Philippa says. “But our way of life has demonstrated that the concentration you get from this existence allows a true focus on the positive — sometimes in ways you’ve never experienced before.”

Written by Colin Henderson

April 20, 2020 at 09:10

Posted in Uncategorized

Where is the evidence to suggest that the covid peak is here?

With all the talk of opening up the economy because we have reached the peak, there is nothing to validate that statement in the data of new case growth.

You don’t need to focus on any particular country to see that all are still growing in cases, and there is no perceptible new trend of a tipping point having been reached.

Written by Colin Henderson

April 16, 2020 at 07:31

Posted in Uncategorized

Harvard research points out that physical distancing could be around until 2022 – 2024

Harvard research points out that physical distancing will be around for a lot longer even based on an antidote.

It is urgent to understand the future of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) transmission. We used estimates of seasonality, immunity, and cross-immunity for betacoronaviruses OC43 and HKU1 from time series data from the USA to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained since a resurgence in contagion could be possible as late as 2024

Covid-19 Exit Strategy

I think the key point is that flattening the curve should not be confused with eliminating the tail of the curve.

The Harvard model takes into account:

  • the impact of the tail of the curve
  • the impact of multiple covid waves, which could be this iteration or future mutations

The paper considers a host of issues which is not something I can evaluate here. This observation is typical:

Highly-effective distancing could reduce SARS-CoV-2 incidence enough to make a strategy based on contact tracing and quarantine feasible, as in South Korea and Singapore. Less effective one-time distancing efforts may result in a prolonged single-peak epidemic, with the extent of strain on the healthcare system and the required duration of distancing depending on the effectiveness

The reference to SARS-CoV-2 is covid-19 or coronavirus.

Written by Colin Henderson

April 14, 2020 at 17:15

Posted in Uncategorized

What is different about covid-19 and earlier pandemics

What is different about covid-19 ?

There are technical differences in covid-19 which suggest it is smarter than earlier viruses in some respects. For those technical details, see the article.

One result is the infection rate of covid-19 is higher than bird and swine flu.

Basically R-nought is a value that indicates the numbers of people that will be infected by someone with the virus. One target is to keep this value below 1.0, however covid-19 is roughly estimated at 2.0 to 2.5.

The H1N1 flu was also less contagious than the novel coronavirus. The basic reproduction number, also called the R-nought value, is the expected number of individuals who can catch the virus from a single infected person. For the 2009 H1N1 virus, the mean R-nought value was 1.46, according to a review published in the journal BMC Infectious Diseases. For the novel coronavirus, the R-nought value is estimated to be between 2 and 2.5, at the moment.

The R-nought value of covid-19 is what introduces the level of contagion and transmission speed we see.

In that context here is a series of quotes (paywall temporarily lifted by FT on the complete article by French Philosopher Simon Schama).

The few people he saw, he wrote, looked as if they had “taken leave of the world”. He moved amid Buriers and Searchers, often elderly women assigned the dangerous job of examining the dead for signs of the plague, carrying long white wands to warn people to keep their distance as they went about their gloomy work. It was getting closer. His physician and the waterman who ferried him daily had both died, and Pepys decided to make a will.

Pepys took it hard when one of his favourite taverns, The Angell on Tower Hill, in common with many others, closed. He and many like him exemplified Aristotle’s conviction that humans are, above all else, social animals; and that the vital energy of cities in particular comes from gatherings — in public squares, theatres, sports stadiums
A standard feature of the “Dances of Death” imagery that became popular after the arrival of the Black Death in Europe in 1348 was the indifference of the plague to rank, wealth and authority, indiscriminately mowing down popes and emperors at the height of their powers, along with peasants and beggars.

The similarities of the Plague (1665) and the Black Death (1348) are remarkable and troubling. We have learned nothing it would appear.

The constant desire to blame other nations is a common thread. Most often blamed are Asians.

The root cause of the older plagues were caused by local inefficiencies of basic cleanliness.

 physician John Snow conclusively traced back the cholera infection of 1854 to those who had used a single water fountain at Broad Street in Soho, and established that the water company servicing that pump had been using dangerously tainted water from the sewage-riddled gunk of the Thames, his principal argument that the disease was conveyed in faecally polluted water took a while to be accepted.

Some examples of the pieces and behaviours noted in pandemics over the last 800 years that are evident in 2020 covid-19:
– [ ] local authority is both useful to day to day management, and a blind spot to identification of important causes
– [ ] closing of borders / exclusion of outsiders and that strategy lack of success over time
– [ ] relative success of ‘lockdown’ whether by authority or from self protection
– [ ] blaming other nations
– [ ] disbelief this is happening to ‘me’ and interfering with ‘my’ lifestyle

More on blaming other nations:

Certainly the more recent pandemics originated in bats and other wildlife in China experiencing ‘spillover’ to humans.

Clearly some clean up of behaviours is needed in that area such as eliminating ‘Wet Markets’, but this is still short term thinking.

Are we certain it ends there? This article with a reference to an early 2000’s paper on the source of SARS and that highlights a cave whose location is being kept secret in Spain.

The article points out the proximity in China to similar caves as well as hunting habits are included in the reason for ‘spillover’. Yet the underlying root cause is not limited to China. Viruses are ‘learning’ organisms and addressing one physical location will not address root cause.

All this to say I found the Schama article thought provoking as it touched on so many similarities in covid-19 to Pandemics for which we have documented history over 800 years time span.

So what did we learn?

Written by Colin Henderson

April 11, 2020 at 11:00

Posted in Uncategorized

Google and Apple are co-operating in a key component of covid-19

Apple and Google team up to contact trace Covid-19

Apple and Google are co-operating in a key component of covid-19 mitigation.
Their contact-tracing method would work by using a smartphone’s Bluetooth signals to determine to whom the owner had recently been in proximity for long enough to have established contagion a risk.
If one of those people later tested positive for the Covid-19 virus, a warning would be sent to the original handset owner.

No doubt the privacy brigade will have issues but this approach makes great sense to me.

It does leave the question of what you are to do when you get the warning. Ideally there will be some co-ordination with the contact tracing team whereby they could track the results.

Written by Colin Henderson

April 11, 2020 at 09:29

Posted in Uncategorized

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