Archive for the Covid-19 Category

Bad Statistics and COVID-19

Posted in Bad Statistics, Covid-19 with tags , , , on March 27, 2020 by telescoper

It’s been a while since I posted anything in the Bad Statistics folder. That’s not as if the present Covid-19 outbreak hasn’t provided plenty of examples, it’s that I’ve had my mind on other things. I couldn’t resist, however, sharing this cracker that I found on Twitter:

The paper concerned can be found here from which the key figure is this:

This plots the basic reproductive rate R against temperature for Coronavirus infections from 100 Chinese cities. The argument is that the trend means that higher temperatures correspond to weakened transmission of the virus (as happens with influenza). I don’t know if this paper has been peer-reviewed. I sincerely hope not!

I showed this plot to a colleague of mine the other day who remarked “well, at least all the points lie on a plane”. It looks to me that if if you removed just one point – the one with R>4.5 – then the trend would vanish completely.

The alleged correlation is deeply unimpressive on its own, quite apart from the assumption that any correlation present represents a causative effect due to temperature – there could be many confounding factors.

 

P.S. Among the many hilarious responses on Twitter was this:

 

Life going on..

Posted in Biographical, Covid-19 on March 26, 2020 by telescoper

I’ve had the feeling that this blog is in danger of turning into some sort of plague diary so I thought I’d pass on a couple of examples of life going on. It’s not quite business as usual, but there’s no point in us sitting around feeling sorry for ourselves.

As it happens I came onto campus today, mainly to check on the Library Cat (who was absent from his post, but well provisioned with food) but also to check the Departmental mail. Somebody has to deal with the invoices, or at least the minority of them that don’t come electronically. In fact there were only two.

Anyway, as I walked through campus I saw the building work on the Kilcock Road site continuing apace. It can’t be difficult to practice social distancing at the top of one of those cranes:

The last picture I took of the construction site was on St Patrick’s Day (17th March), just nine days ago:

It’s from a different vantage point, but you can still see they’ve added quite a lot in the past week and a bit. You can also see how much the weather has improved. In fact the last few days have been lovely!

Another thing worth reporting on is that there’s been a notable uplift in submissions to the Open Journal of Astrophysics recently. It’s almost as if some people have got some time on their hands to write papers! I’ll do a separate post about a few developments on the OJA front in due course but, for the time being, I will just mention that as a fully online journal all our processes run remotely anyway so we are, and will remain, fully operational throughout the Coronavirus emergency.

Well, now I have to get my act together and activate another remote computational physics laboratory session. Fingers crossed!

Shopping Mad

Posted in Biographical, Covid-19, Maynooth with tags , , , , on March 22, 2020 by telescoper

Empty shelves in Asda, Swansea

I don’t know how widespread scenes like that pictured above actually are, but there seems to be a lot of panic buying and/or stockpiling going on.

Worse still are scenes like this:

Social distancing doesn’t seem to be a priority among these people.

It all seems a bit ironic to see this demonstrable lack of public-spiritedness alongside the usual rhetoric about the “Dunkirk Spirit”. With the latter in mind I’ve updated Winston Churchill’s famous wartime peroration from 1940 in a manner more suitable for the 2020s:

We shall fight in Tesco, we shall fight in Aldi and Asda, we shall fight with growing panic and growing stupidity in the aisles, we shall defend our toilet rolls, whatever the cost may be. We shall fight for the pasta, we shall fight for the hand-wash…(continued, page 94)

Anyway for what it’s worth I still haven’t noticed any shortages of food or household goods where I’m living. It may be different elsewhere of course but Maynooth is doing fine in that regard.

This is not to say I haven’t changed my shopping habits at all. I’ve never been in the habit of doing big shopping trips. I live alone, don’t have a freezer and my fridge is quite small. I tend therefore to buy bits and pieces as I need them. I prefer fresh food and, usually eating lunch in the College when I’m at work, I don’t need a main meal in the evening.

Now I’m having lunch at home every day I need to buy a bit more, which is one change. Mindful that a stricter lock down might be coming soon, I have also begun buying a few things I wouldn’t normally buy. To my usual shopping I’ve added the odd item of tinned food but never more than a can or two at a time. I also bought some powdered milk in case fresh milk becomes unavailable.

I haven’t eaten any of the tinned goods I’ve bought yet: I am still eating fresh things as they seem to be readily available. Who knows when or if that will change.

I realise my personal situation makes coping with this social distancing malarkey rather easier than most but I think certain individuals are making it even more difficult for the others with their selfish behaviour. I suppose there will always be some.

Anyway, do feel free to share your own experiences of shortages or lack thereof through the comments box.

Farewell to Flybe

Posted in Biographical, Covid-19, Finance on March 20, 2020 by telescoper

Just for the record, I today received a full refund for the cost of my Flybe tickets via the Chargeback scheme. Thanks to AIB for processing this so quickly!

The collapse of Flybe happened on 5th March 2020, just over two weeks ago. Can it really have been so recent? It seems like ages ago.

telescoper's avatarIn the Dark

It had been on the cards for some time, but last night the airline Flybe collapsed and has now gone into administration. Let me just leave this Twitter announcement made in January by Transport Secretary Grant Shapps here:

It seems that Flybe has gone the inevitable way of every Tory promise.

I had bought a ticket to fly from Dublin to Cardiff at the end of next week as the following week is a study break that includes the St Patrick’s Day holiday. As a result I got this email this morning.

Obviously it’s an inconvenience for me as I’ll have to find another way to get to Cardiff, but I’ll probably get my money refunded by the Chargeback scheme so it’s not such a big deal. The same can’t be said of the 2000 people who worked for Flybe who have now lost their jobs, nor the many…

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A Note from Maynooth

Posted in Biographical, Covid-19, Education, Maynooth with tags , , , , on March 18, 2020 by telescoper

I’m indebted to colleagues from Maynooth University Special Collections & Archives for sending out the following bit of history.

It is now over 100 years ago the 1918 “Spanish ‘flu” influenza pandemic came to Maynooth College. It was officially closed from 8th November until 7th January and 60 students remained in the infirmaries. Over 500 students went home and sadly 11 of these did not survive the pandemic. More details below.

One difference between 1918 and 2020 is that the Spanish flu mainly affected the young. Covid-19 is remarkably different, as these grim mortality statistics from Italy demonstrate:

Nobody at all under the age of 30 has died (so far) of Covid-19 in Italy. It’s the mortality rate for those over 70 that is terrifying. This is just the rate so far. Many of those currently in intensive care won’t make it, so these figures will probably change significantly.

Last night the Taioseach Leo Varadkar gave an unusual address to the nation, which pointed out the gravity of the situation facing Ireland and indeed the world in genderal, which is even more serious that a century ago. In particular he stressed that the COVID-19 emergency would probably last well into the summer.

I don’t agree with Varadkar on many political issues but I think his speech last night was very good. He praised Ireland’s front line medical staff, but also found time to mention the teachers and lecturers who trying their best to deliver remote teaching. Above all, though, he was honest.

I feel very lucky right now, not only to be so far unaffected by Coronavirus but also to be living and working in a small University town in Ireland right now.

There are no obvious shortages of anything and my local (small) supermarket has put out hand wash and wipes for people to use on baskets and trolleys.

We’re also in a Study Week that has at least given us some time to figure out how to move to online teaching by next Monday when we are supposed to start again.

We are probably going to be in this for months rather than weeks but aat least we academics are in no imminent danger of losing our jobs. The same is not true for the folk working in local shops, restaurants and other businesses. We owe it to them to do what we can to support the local community and its economy as much as possible.

In particular, I’ve often remarked that we are lucky in a small town like Maynooth to have quite a few nice cafés and restaurants. Some of these have switched to takeaway or delivery mode during the emergency. I wouldn’t normally use a takeaway service but I will do now, and I suggest my colleagues and friends in Maynooth might do likewise. If we don’t support these establishments now we might lose them for good.

That goes for other local businesses too!

Public Health and Open Science – Updated

Posted in Covid-19 with tags , , , on March 16, 2020 by telescoper

Preface: I wrote this on Monday 16th March, before the release of a report from Imperial College admitting that the previous modelling was based on incorrect assumptions. Most of what I argued still stands but I have updated a few points.

–o–

The current Coronavirus outbreak is posing a great many questions not only about how governments should act but also about how they should communicate with the public. One aspect of this issue that came up last week was an open letter (now closed) asking the UK Government to release the data and models underpinning its COVID-19 strategy. In the interest of full disclosure, I didn’t sign it but only because I’m no longer based in the UK.

Although this letter received many signatures, I was very surprised by the negativity with which it was greeted from some corners of the scientific community. Those of us who work in astrophysics are of course used to open sharing of data and models being the norm. Some of us even see it as an essential component of the scientific method, so I was a bit shocked to see hostility from some other scientists. I think the reason was largely that it wouldn’t help to people without expert knowledge playing around with the data, getting hold of the wrong end of the stick, and jumping to erroneous conclusions. There is of course a danger of that, but in the absence of openness people are jumping to conclusions anyway and conspiracy theories are rife.

For what it’s worth, my view is that if governments can’t get those with scientific training on board then it has no chance with the general population. Astrophysicists, for example, at least understand what an exponential curve really means. Those of us who have a scientific background will not stop asking questions – nor, I think, should we. That’s how we view the world and for many equations and numbers are how we make sense of things.

So, undaunted by the calls that I should shut up because I’m not an expert, but prefaced by a clear admission that I am not an expert, I’m going to comment on a question that a lot of people are asking: why is the UK Government’s Coronavirus strategy so different from that adopted in other countries?

I didn’t watch the press conference last week that ignited this question, but I have listed to clips. The controversial issue is that of so-called herd immunity. Here is a quote by Sir Patrick Vallance, the UK’s chief scientific advisor:

Our aim is to try to reduce the peak, broaden the peak, not suppress it completely; also, because the vast majority of people get a mild illness, to build up some kind of herd immunity.

Now in the absence of a vaccine there isn’t going to be herd immunity in the sense that I understand it, but (as I have already said) I am not an expert. I think the key words are `some kind of’ in the above quote. What is envisaged is a large number of people getting infected, hopefully only contracting mild symptoms, but in any case subsequently acquiring immunity. It would be bad news for this line of thought if it turns out that people can be reinfected, as indeed seems to be the case.

After listening to the press briefings, however, it seems to me that this idea isn’t a key driver of the science policy and that Vallance simply used the phrase `herd immunity’ inadvisedly.

So if that’s not the reason why would the UK’s approach be so different from other countries? Again I preface this by admitting that I’m not an expert.

At the core of a public health strategy to combat a pandemic will be mathematical models of the spread of infection. I only know a little bit about these but I’d guess that most government agencies will have similar models (though there might be different choices of parameters reflecting different populations). But that’s not all the strategy will be based on. Among the other factors are:

  1. the resources available for treating infected persons; and
  2. the likely behaviour of the population (and hence the infection rate) as a result of any measures taken.
  3. A decision about what it means for a strategy to be ‘optimal’.

In the first of these the UK is clearly in a very different situation from most of the rest of the world: the National Health Service has (per capita) far fewer hospital beds and, most importantly, far fewer intensive care unit facilities than other developed nations. The latter, in any case, run at close to capacity even at normal times so the resource available is severely limited. The need to `flatten the curve’ would therefore seem to be even more pressing for the United Kingdom than in many other nations.

Update: the Imperial College report explains that previous models made unrealistically optimistic assumptions about the number of infected persons requiring critical treatment. The old strategy would have led to upwards of 250,000 deaths as the NHS would have been swamped. This was exactly what was being pointed out by ‘inexpert’ commenters on social media.

Here is a dramatic confirmation of this:

The red line represents UK current critical care capacity. No amount of ‘flattening’ will be enough to avoid the NHS being overwhelmed.

That is a difference in input, but it doesn’t explain why the UK is not taking more stringent measures on social distancing. Quite the opposite, in fact. Apparently the Government has already accepted that hospitals are going to be overrun and that things are going to be very grim indeed for a long time.

By way of support for this interpretation, Boris Johnson recently announced that the elections scheduled for May 2020 will be postponed for a whole year, rather than the six months recommended by the Electoral Commission. It is a reasonably inference that the Government does not believe that this will be anywhere near over by the end of 2020. That signals that it won’t be able to put extra resources in place on the timescale needed to deal effectively with COVID-19 as China and South Korea seem to have done.

It seems, then, that the reason for not enforcing stricter policies now is item 2 above, and it is a judgment based on behavioural psychology: that severe social distancing measures would not be effective because people would get bored or there would be widespread social unrest if folk were asked to endure them for many months. That very pessimistic view of the likely behaviour of the UK population may well be realistic but assuming it has serious implications for mortality.

My interpretation of this is that the Government thinks people won’t really pay enough attention to social distancing instructions until the body count starts to become very scary indeed which, with exponential growth leading to a doubling of cases, every 2-3 days, won’t take very long.

So that brings me the reason why I think there is no way the UK Government is going to release its modelling calculations, namely that they contain numbers for how many people are going to die over the next few months. It won’t do that because it thinks the numbers would just cause people to panic. That may be a correct call too. Those of us who work in subjects like astrophysics don’t have to worry that releasing our data and models will terrify people.

There’s also point (3) about what defines an optimal strategy, as constrained by (1) & (2). The criterion could be overall mortality, but one can imagine that a government might decide to include economic cost as well or instead. One can certainly imagine the UK Government making such a choice.

I’ll add one final comment.

Here in Ireland the HSE has increased the level of testing in recognition of the evidence that community transmission seems to be more probable than previously thought. A surge in the number of confirmed cases of COVID-19 is expected.

Meanwhile, in the United Kingdom, the National Health Service is no longer carrying out any community testing:

I suspect the reason for this is a combination of (1) and (2). Counting deaths rather than infections is arguably a more reliable indicator of the growth of the epidemic and it is certainly cheaper. Moreover, one way of keeping the numbers down to avoid frightening people is to stop counting them…

Update: As of yesterday Germany had 5813 COVID cases and had 13 deaths; Norway had 1356 cases and only 3 deaths. The UK claimed 1391 cases but 35 deaths. These numbers provide drastic evidence of undercounting cases in the UK.

Sax and the Single Man

Posted in Biographical, Covid-19, Music with tags , on March 16, 2020 by telescoper

I heard on Friday that my upstairs neighbours were going away for a few days for the St Patrick’s Day break, so I took the opportunity afforded by this solitude to take this baby out of its box and have a bit of practice.

I don’t have my usual tenor sax with me in Maynooth: it’s in safe (?) keeping elsewhere (that’s a long story). Here it is, pictured a few years ago in my house in Cardiff:

 

The soprano sax may be a much smaller and lighter instrument than the tenor but it is more of a handful to play in tune. I always thought this was my own incompetence but it seems to be agreed by proper musicians.

My usual practice is to warm up with scales and other exercises then play along a bit with some backing tracks made for the purpose with just a rhythm section. Playing simple riffs on the chords is a good way to settle in, then you can start to improvise properly.

I wouldn’t say my attempts to revive my long neglected musicianship have been very successful so far – not least because they were never very good in the first place – but it’s a nice diversion.

I suspect that many people will be looking for things to do to stop them getting bored over the next few weeks and months.

Business (Cards) as Usual

Posted in Biographical, Covid-19, Education, Maynooth with tags , , on March 15, 2020 by telescoper

One of the things that happened just before Maynooth University closed down last week was that I received delivery of my new business cards:

I’m sure they will prove useful at some point in the future, but I can’t see myself handing any out for a while!

I have subtly removed the telephone numbers from the above image because I was warned that people could use my number to do nefarious things, such as trying to contact me. They are my work numbers, of course, so I never answer them anyway, but you can’t be too careful.

Incidentally, today the Taoiseach Leo Varadkar announced that pubs and bars in Ireland should close down until March 29th, which will include the St Patrick’s Day holiday on Tuesday. I don’t know why this wasn’t done earlier and wonder how many people have been infected with Coronavirus because of the delay.

Anyway, after a weekend of not working, tomorrow we resume working from home. Fortunately it’s Study Week so we don’t have to try doing remote teaching until next week.

Working from Home

Posted in Biographical, Covid-19, Maynooth on March 13, 2020 by telescoper

Today was my first day of “working from home” after the closure of Maynooth University campus yesterday. As I live close to the campus I did venture out from home to perform various duties thereon (see picture).

Before the closure yesterday I was told some grim stories about panic buying in Maynooth but when I went to the local Supervalu around 7pm there was plenty of stuff on the shelves. I treated myself to some nice wine after a very stressful day.

This morning I did indeed work from home, getting on with some writing until lunchtime while still in my dressing gown.

Working from home isn’t that easy. Without the discipline imposed by having to go to work at a specific time it’s tempting just to potter about uselessly. You have to force yourself to focus but also remember to take breaks, which you don’t usually have to do during the course of a working day as, e.g., lunch is part of the regular timetable.

I’ve found that what works for me when working at home, is to divide a say into two-hour blocks, after which I break for 30 minutes to have a cup of tea or a snack.

I did two such blocks this morning, after the second of which I checked my email while having a sandwich. The deluge of messages in my inbox contained a number that I needed stuff from my office to deal with (including the publication of an Open Journal paper).

When I got there campus was quiet, unsurprisingly, but there were a few people around, including some of our research students. It all felt a bit unreal, but I think it might be the reality for some time now.

I have been pretty effective at self-isolation and social distancing for many years now, so I think I’ll be OK with this.

Break Points

Posted in Biographical, Covid-19, Education, Maynooth with tags , on March 11, 2020 by telescoper

It is now Week 6 of the Spring Semester at Maynooth University.  My lectures on Engineering Mathematics take th place on Monday, Tuesday and Wednesday so today I gave the 18th of the semester, which means I am halfway through the module. Next week is a scheduled Study Week so there are no lectures planned after this Friday until 23rd March. Just two days to go before the breaking

It remains to be seen whether teaching does indeed resume on that day. If the coronavirus situation in Ireland gets much worse we may stay closed for a longer period.

There is a subdued mood around campus, and the number of students in my class this afternoon was significantly lower than usual. I don’t know whether that is because of coronavirus or because some students have headed home early for the break or because they didn’t fancy learning about curves and tangent vectors!

Last night the University issued updated guidance. The main thing is that we stay open but the Conferring Ceremonies for postgraduate degrees scheduled for Thursday and Friday next week have been postponed indefinitely.  The students will formally receive their degrees in absentia although they will (hopefully) be able to attend a ceremony to get their certificates in person at some point in the not-too-distant future.

I blogged on Monday about contingency planning and I’ve been spending quite a lot of time this week making the best arrangements possible for students in case we don’t reopen on 23rd March. That includes getting all the notes and examples sheets ready for Engineering Mathematics, which is now done.

My other module is Computational Physics. For that one there’s a small project that the students do (usually) in pairs. I published the list of projects for the students to pick from earlier than originally planned and will hopefully be able to allocate them before the end of this week. That way, if there’s a campus closure they can at least get on with their projects. Fortunately Python is free so they can run code on their laptops. All the other resources for that module will be available online too so disruption shouldn’t be too bad: even if we have to cancel the laboratory sessions the students can still work through the scripts on their own.

What will happen with examinations is not yet clear, but those don’t take place until May so they’re not the immediate priority!

I asked the students in my Engineering Mathematics at the end of this afternoon’s lecture please to keep an eye on their email and social media for announcements about changes in the situation. The positive message for students is that they are actually at very low risk of serious illness themselves (although they should of course take precautions to ensure they don’t infect others).

I feel a bit guilty for thinking about the positive message for staff, but I do have quite a bit of writing-up to do and a nice long campus closure would seem to provide an ideal opportunity to `self-isolate’ and get on with it. For the time being, though, it’s business as usual…