Meanwhile, back to Covid…

So here we are, at the end of the 9th teaching week of Semester 2 at Maynooth University. There are three more weeks of lectures before the end of term, either side of a one-week break for Easter.

It was decided weeks ago that we all have to proceed on the basis that the Covid-19 pandemic is all over.

Case numbers are still very high though:

The above picture is a bit misleading because it shows only cases confirmed by PCR tests fewer of which are being done now than previously. The HSE data hub also records daily antigen tests which are typically of the same order but higher than the PCR results. The real level of infection is therefore at least twice the level shown in the picture. That’s the bad news. The good news is that positive results from both PCR and antigen tests do seem to be falling, as do hospitalizations and ICU admissions. The mortality rate has also remained low during this phase of the pandemic. The logical inference is that wall of protection afforded by vaccines is holding despite the high level of infections. We’re clearly in a less dangerous phase of the pandemic than we were last year.

But, equally clearly, the pandemic is not all over.

The number of absences due to illness or self-isolation is high for both staff and students. I’ve noted before on this blog that although third level institutions were put under great pressure to return to on-campus teaching, many students are just not attending lectures, tutorials and laboratories in person.

As well as having to look after their own health, many students haven’t been able to secure local accommodation for this Semester, partly because of a general shortage and partly because the 21/22 academic year started late and in chaotic fashion making it impossible for first years to sort out satisfactory living arrangements. It looks like this will happen next year too.

Third-level education isn’t the only sector feeling significant residual effects of the pandemic, but it is one in which problems have been exacerbated by the unrealistic expectations of Government and University managements.

Anyway, after so much disruption we approach the end-of-year examination period with considerable trepidation. For first- and second-year students these will be the first examinations they have taken on the campus; third-years will not have taken on-campus exams since January 2020. The style of our online examinations was necessarily different to the traditional format so in the Exam Halls the students will find themselves in very unfamiliar territory. In particular, we used “open-book” exams so students could use notes, textbooks and other resources to do the examinations. This won’t be the case in May.

How will the results turn out?

We can only wait and see.

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Two Years of Covid in Ireland

Trying to find something other than the conflict in Ukraine to write about, I thought I’d do a quick post to mark that we have reached the two year mark since the first “official” case of Covid-19 in Ireland was detected. It seems so long ago that I had forgotten that 2020 was a leap year and the date was 29th February, and the case was reported a day later on 1st March 2020.

It was to be another couple of weeks before we went into the first lockdown and I didn’t start keeping a log of all the cases and deaths until 27th March 2020, but you will find a complete record here (backdated to the date of the first case).

Here is the latest plot, with data complete up to today:

Today is the day that most Covid related restrictions are lifted. There is no longer a legal requirement to wear masks anywhere other than in healthcare settings, though at my University there is a recommendation to do so. I dropped into Dunnes this morning to buy a sandwich to have for lunch and I’d say a slight majority of shoppers (including myself) were still wearing masks, though all the staff I saw were unmasked (a fact which I found very disappointing).

I intend to carry on wearing a face covering in shops and, of course, in classrooms (and especially in labs) for the foreseeable future. I didn’t have any teaching this morning so I don’t know what the students are doing. We are told that if a student refuses to wear a mask then lecturers can’t make them, but peer pressure may do the job for us. We do have a significant number of students off and teaching staff unavailable due to Covid-19 infection but we just have to manage this as best we can.

The requirement to have a PCR test if you are symptomatic has also lapsed for most people in Ireland, but not for me. As I’m over the age of 55 I am still required to take a test if I have symptoms.

The drastic reduction in testing implied by the change in regulations will undoubtedly lead to a steep reduction in PCR-confirmed cases (currently running at a seven-day average of around 3500 per day) and in the light of this I’m not sure it’s worth carrying on plotting the data for much longer. I will persevere for the mean time though.

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All Change for Semester Two!

So here we are, then, at the start of Semester Two at Maynooth University. When I arrived in the Department of Theoretical Physics I noticed a few differences:

August 2020 versus January 2022

All the signage relating to physical distancing has been removed. We are no longer required to observe 2m spacing between individuals in labs or anywhere else. That solves my potential problem about constraints in the Computational Physics lab (to the left of the picture).

Our little kitchen is also now back in operation so we can share that space for lunch or coffee, sitting around the table which has now been put back in place. Staff meetings can be held in person, though the meeting of Academic Council I have to attend this afternoon will still be via Teams. I don’t actually start teaching until tomorrow and will be in the office most of the day so will have to wait until tomorrow until I find out how busy the campus seems; we expect there to be more students around than last term.

Students are still to wear face coverings in lectures etc but other than that all restrictions seem to have gone, including those on eating and social spaces on campus. Everyone seems to have decided that this pandemic is all over. Only time – and perhaps the next coronavirus variant – will tell whether they are right.

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End of Term Blog

Yesterday was the last day of teaching at Maynooth University for 2021 and, although I didn’t have any teaching to do, I walked to the Department partly to get a bit of fresh air having been stuck at home on Thursday after my booster jab, and partly to collect a few things before the break. I also discovered that a lovely parcel of goodies had been sent to me and I was anxious to collect the items before Christmas.

I’ll be keeping myself to myself over the break, apart from the odd trip to the shops, and am glad to be doing so. We are yet to see the steep increase in Covid-19 cases associated with the omicron variant happening in the UK and elsewhere in Europe. If anything case numbers are currently declining slowly. But the new wave will undoubtedly hit Ireland soon.

UPDATE: not half an hour after I posted this, the HSE announced 7333 new cases of Covid-19 in Ireland, more than double yesterday’s figure and the highest number seen since early January. And this is before the Christmas surge.

The jury is still out on whether omicron is more or less dangerous than previous variants but it is clearly more transmissible, and I don’t see the point of taking chances, so I agree with the Irish Government on the need to take precautions. I don’t think the latest restrictions go anywhere near far enough though.

Yesterday we received at work an email from University management that said, among other things, that

At present the aim is to resume teaching on 31 January, as in Semester 1.

The phrase “as in Semester 1” means that large lectures will be online-only but everything else will be face-to-face. That is a reasonable starting point because the extent of the omicron wave is as yet unknown, but I think it’s more likely than not that in the end we’ll find ourselves doing everything online. I just hope a decision on that is made in reasonable time for us to put Plan B into action. We don’t start lectures again until January 31st and there should be enough data by then to make an informed decision.

I don’t want to sound unduly pessimistic but I don’t see any sign that we are anywhere near the end of this pandemic. With a bit of luck we might find that we’re roughly halfway through, but as long as governments allow large pools of virus to circulate, mutations will continue to occur and new variants will continue to emerge. To end this cycle will require a majority of the world’s population to be vaccinated, and I don’t see that happening soon.

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The Coronavirus Vaccine Effect

When I was updating my Covid-19 page today I thought I would try something a bit different. Here are the cases and deaths (in the form of 7-day rolling averages) as I usually plot them:

You can see a slight recent downturn – the latest 7-day average of new cases is 4214.3; it has been falling for a few days. A log plot like this shows up the changing ratio between deaths and cases quite well, as in l if you multiply a quantity by a factor that manifests itself as a constant shift upwards or downwards. There is clearly a bigger shift between the orange and blue curves after 500 days than there is, say, between, 300 and 400.

(I don’t think you can read much into the gap between the curves at the beginning (up to around 100 days in) as testing coverage was very poor then so cases were significantly underestimated.

Anyway, to look at this a bit more clearly I plotted the ratio of daily reported deaths to daily confirmed cases over the course of the pandemic. This is the result:

The sharp downward glitches occur whenever the number of reported deaths is zero, as log of zero is minus infinity. The broader downward feature after about 300 days represents the period in January 2021 when cases were climbing but deaths had not caught up. To deal with that I tried plotting the deaths recorded at a particular time divided by the cases two weeks earlier. This is that result:

The spike is still there, but is much decreased in size, suggesting that a two week lag between cases and deaths is a more useful ratio to look at. Note the ratio of deaths to cases is significantly lower from 500 days onwards than it was between 200 and 400 (say), by a factor a bit less than ten.

This obviously doesn’t translate into a direct measure of the efficacy of vaccines (not least because many of the recent cases and deaths are among the minority of unvaccinated people in Ireland) but it does demonstrate that there is a vaccine effect. Without them we would be having death rates up to ten times the current level for the same number of daily cases or, more likely, we would be in a strict lockdown.

On the other hand if cases do surge over the Christmas period there will still be a huge problem – 10 % of a large number is not zero.

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Back to Online Examinations Again

This afternoon teaching staff at Maynooth University were informed of changes to the plans for the January examination session: all examinations will now be held remotely, apart possibly from those for some final-year modules; for the latter the lecturer will decide whether they should be on campus or remote.

It’s worth mentioning that a petition set up recently by the Maynooth University Students Union urging the University to switch exams online attractive over 4,000 signatures.

As I said a while ago I think this is a very sensible move. I was chatting to some students before a lecture earlier today and I think they will all be relieved that a decision has been taken and they can make sensible plans for the Examination Period. I am teaching one module for first-year students and one for second-years this semester so both of these will definitely be going online.

We now have done three full cycles of online examinations since the pandemic started: May 2020, January 2021 and May 2021, plus two sets of repeats. I think we have a pretty good idea what we are doing with them and have got three weeks before the end of term to make any changes to the papers we have written for January. Since the online examinations are effectively open-book tests we tend to exclude bookwork – stating results which the students could easily look up – and concentrate instead on problem-solving tasks. Online examinations done this way are certainly no easier than in-person papers, and emphasize what is probably the most useful skill we try to develop.

I am glad we have some clarity on the examinations. We still have three weeks of teaching to finish before the end of term, though, and no changes have been announced to plans for lectures and tutorials. I told my class this afternoon however that as of Wednesday 8th December I will have exceeded 6 months since my second Pfizer dose. There is very little chance I will get a booster dose by then so I will be working from home from that date until the end of term. That means I’ll be doing three first-year lectures and three second-year lectures from home using my famous blackboard. I explained this decision to my second-year class today and they were supportive.

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Worrying Times…

So here I am, trying to plan my teaching for next week and wondering what’s going to happen between now and the end of term. Here at Maynooth University lectures finish on 17th December, five weeks from now. I’m just about on schedule to cover everything I’m supposed to, so I’m not worried about that.

What I am worried about is that Covid-19 cases are continuing to climb. The latest 7-day rolling average of new cases is over 3900 per day and the increasing trend show no sign of slowing down. It will reach the 5000 mark in a week or two. Some daily figures have already passed that milestone. The death rate is still relatively low – 74 Covid-19 related deaths were recorded in the last week – but is edging up; over a hundred people with Covid-19 are being treated in ICU as of today.

The Irish Government seems to have no intention of introducing effective countermeasures and is instead just advising people to cut down the amount of socializing they do. I don’t think that will work. It seems very clear to me that the Government lost the room many weeks ago by frequently implying that the Covid-19 pandemic was over. They then caved in to the hospitality industry by allowing nightclubs to open. It is no doubt in such places that the virus is spreading. The Government keep stating that they are concerned but do nothing, blinking at the onrushing disaster like rabbits caught in the headlights of an approaching car.

Case numbers on campus at Maynooth remain fairly low, though the latest figure (69) is almost double last week’s figure (35). Students in my classes continue to wear face coverings and observe the other protocols and all the signs are that lecture halls and labs are pretty safe environments but we have no say in what happens off campus. As well as being concerned for the health of students and staff, I have particular worries about my Department. We’ve been short-staffed since the start of term and simply have no spare effort to provide cover for lectures or tutorials if anyone becomes sick.

The Irish Health Service is under extreme pressure and the delivery of booster shots is being rolled out very slowly. I had my second Pfizer dose in June so should get a third shot in December but it is not clear that I will. I’m not going anywhere at Christmas anyway so that’s not a big deal but I’m worried by the broader picture. A cartoon in a recent issue of Private Eye is very apt:

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Might we have to switch our lectures back online again before Christmas? Might our examinations be online again in January? Who knows. We’ll just have to wait and see but I think the blackboard in my study might be back in use very soon.

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A Year at Home

I was reminded this morning that it was a year ago yesterday that I received the keys to my house in Maynooth. I didn’t move in straight away as the house was empty and I had paid the rent on the flat I was living in until the end of August, so I moved my things gradually over the course of a week or so. Looking through all the paperwork this morning I found the pictures that the Estate Agent had used to advertise the property. Here are a few of them:

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You’ll see that the bookshelves in the sitting room were empty at the time. They mostly still are. I didn’t think this time last year that I’d still be waiting a year later for my belongings to arrive from Cardiff, but at least they are in transit now. Delivery is pencilled in for next week, as a matter of fact; doing the removal on the cheap as a return load meant waiting a few weeks. I am looking forward to filling the shelves with my books (20-odd boxes of them) and putting up my own artwork. I’ve had enough of bare walls.

This morning our weekly Faculty Executive meetings resumed, the main topic of discussion – as it was this time last year – being the plans to return to on-campus teaching next month. I thought it would be interesting to show a comparison between the Covid-19 figures in Ireland on August 25th 2020 and August 25th 2021:

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You will see that the daily case numbers in Ireland are currently about a factor 20 higher than they were this time last year: yesterday we had 2051 new Covid-19 cases in Ireland; a year ago there were 92. That is significant because the effect of vaccines in suppressing serious illness is at most 95%. Since the number of cases is up by a factor of 20, in some sense the risk level if everyone in the population were vaccinated would be about the same now as it was this time last year. And of course not everyone actually is vaccinated, and not everyone will be by the time teaching starts again on 20th September.

Last year the case numbers increased substantially between August and September meaning that we went back into lockdown in October. We don’t know whether or not case numbers will increase again this year, of course, but from the point of view of resuming teaching we’re really in no better shape now than we were at this time last year. Our optimism then was misplaced and that may well be true now too. This is why so many people in the University system are nervous about the edicts we have been given to return to full lecture theatres with no social distancing, no mandatory masks, and no vaccination certificates. This seems like asking for trouble.

On a personal note, I am pleased to report that the mild symptoms I mentioned on Monday have completely disappeared and, to no surprise at all, my PCR test came back negative. It may or may not be relevant that the weather has improved greatly over the last two or three days. I have now come to the conclusion that what I had was some form of seasonal allergy, possibly connected with crop harvesting in the area spreading pollen or fungal spores. The latter are more prevalent in damp or humid weather, which might be the reason for reduction in effect now. Or it could just be that a nearby farmer has stopped doing whatever he was doing. I don’t know enough about field theory to be certain.

Anyway, all of this means I can now stop self-isolating and start returning to campus again. To be honest, though, it was rather nice self-isolating at home as I spent most of the time working in the garden…

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Vaccination for Lectures?

The full guidelines on the return to on-campus teaching in September that I referred to on Monday have now been distributed to all staff, not without comment.

Basically the new advice is that in-person teaching will return in September (in fact a month from today in Maynooth) for all forms of class except lectures containing over 250 people, which will be online. Lecture halls and labs will be at full capacity, i.e. with no social distancing requirement. Students will be “asked” to wear face coverings, but we are told not to attempt to enforce this. Importantly, there will be no requirement for students to have been vaccinated in order to attend lectures.

In Ireland there is a vaccination passport system so that those who wish to dine indoors at a bar or restaurant have to show vaccination status. Perhaps someone can explain to me how it makes sense for this to be a requirement in a restaurant while it is not a requirement for a student having to sit for an hour in close proximity to up to 249 others with no social distancing and no mandatory face coverings.

This conundrum is taken to another level of absurdity when you consider that a student wishing to get lunch indoors on campus will presumably have to show their vaccine passport?

There is an article here that argues that a safe return in the presence of the delta-variant requires 90% of the student population to have been vaccinated.

A more acceptable plan would have students show their vaccination status when enrolling on the course. Those who are unvaccinated but willing to have a vaccination shot could be vaccinated there and then and be allowed to attend lectures when the vaccine takes effect. Or I should say “could have been” because the facilities required to do on-campus vaccinations have not been set up and now there probably isn’t time. Those that refuse to have a vaccine should attend lectures online on a permanent basis.

(How such a scheme would be policed is a difficult question: we don’t usually have people on the doors of lecture theatres checking student IDs or anything and there is a far greater rate of traffic at the start of a lecture than you would have at a restaurant…)

There will of course be some students who are at very high risk and should not be attending lectures anyway even if vaccinated. For them we should be providing lecture recordings. Unfortunately I don’t think we have good enough facilities to record live lectures from theatres as there has been inadequate investment in cameras etc. If we’re told we have to provide lecture recordings, for many of us that means doing the lectures twice. And so our workload increases.

On the other hand it seems increasingly likely to me that all this will be irrelevant. New case numbers are running at about 1800 per day, a level that the HSE admits to being “unsustainable”. When the first colleges return in September, a substantial surge can be expected and everything will be back online anyway.

It’s like déjà vu all over again…

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The vaccine effect

I saw this nifty graphic from the Financial Times floating around on social media and thought I would share it here. It’s a nice demonstration of the way the use of vaccines has impacted mortality rates from Covid-19. Basically the vaccines reduce the probability of a death by a factor greater than 10 (i.e. are more than 90% effective in doing this). On the logarithmic plot this appears as a downward shift in the “risk of death” that is more or less independent of age.

This behaviour is generally consistent with the observation that while infections in the UK are quite high the mortality rate is still rather low. Low is not zero, however, and there will still be some deaths if infection levels are high: a small fraction of a large number can still be significant.

Incidentally, about 70% of the adult population of Ireland has now been vaccinated with about 80% having received partial vaccination. The fraction of the total population fully vaccinated is about 54%. On this measure Spain has just overtaken the UK in vaccinations; Ireland is well above average for the EU. The USA and Israel have both flattened out considerably.

When I got back from my break I tried my best to update the statistics relating to Ireland here. Doing so reminded me that when I first decided to plot the data on a log y-axis I got a slew of comments on Twitter complaining that I was “manipulating the data”! The backlash against anything even simple mathematics is quite extraordinary sometimes.

Anyway, the latest logarithmic plot looks like this:

The death figures are unreliable because of the lingering effects on the ransomware attack on the Health Service Executive IT system but do seem to be much lower relative to infections than they were at earlier stages of the pandemic, even allowing for the fact that the first peak in the case curve should be higher as testing was not so extensive at this early stage. The 7-day average of new cases is currently around 1200-1300 per day.

It still fascinates me how the case numbers managed to stay roughly constant for such a long time at such a high level earlier this year…

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