Archive for the Covid-19 Category

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Staff Shortages

Posted in Biographical, Covid-19, Education, Maynooth on January 5, 2022 by telescoper

After two weeks of festive cooking for myself – something I was quite happy to do- this evening I thought I would mark Twelfth Night by getting a takeaway from my favourite local Thai restaurant. Sadly, however, this turned out to be impossible because they’re closed. The reason? Staff shortages caused by staff having to self-isolate due to Covid-19.

It’s not a big deal to have to make alternative arrangements for dinner, of course, but it got me thinking about all the other areas of life that are currently having the same problems. Many train services in and out of Dublin have been cancelled because of the lack of available train crew, for example. Ireland’s schools are supposed to reopen tomorrow after the Christmas break and it is likely that many teaching staff will be unavailable.

The timing of the academic term for staff Maynooth University is doing us some favours. On Friday 7th we start the examination period. Across the University, 95% of the assessments taking place are online. In my Department that is 100%, so neither students nor staff have to travel onto campus. Teaching does not start again until 31st January so we have over three weeks to see how the situation develops. Some other third-level institutions in Ireland had exams before Christmas so go straight back to teaching right now and I wonder how staff in those feelings are feeling about the prospect.

My biggest source of stress as Head of the Department of Theoretical Physics this academic year has been the fact that we have been short-staffed since the start of the year, half our teaching staff being temporary lecturers, and student numbers are well up on last year. If just one member of teaching staff were to become ill we would have serious difficulty covering the shortfall. Asymptomatic staff just having to self-isolate could teach online, of course, but someone who is ill can’t be expected to do that.

A specific worry I have for next Semester is the Computational Physics module I will be teaching. Last year we did this entirely online, which went satisfactorily; the subject lends itself fairly well to online teaching. This year however we are expected to be back in the lab. We have more than twice as many students in that class than we had last year so we’ll have to work out how to fit them safely into the relatively small teaching space we have available. We’ll certainly have to do two sessions per week but I may offer students the option of following along at home via Teams if they wish. I’ll decide that after the exams are over.

It is of course possible that the situation deteriorates very badly and we have to go fully online again. Possible, that is, but I think not likely. The Government seems determined not to countenance a return to remote working and probably won’t unless things get very much worse. As things stand, the omicron variant is running through the population like wildfire in terms of infections, but this has not led to ICU admissions or deaths on the same scale as last year.

All these issues are as nothing compared to the stress that must be felt right now by workers in the Health Services. After two years of exhausting work many health care workers are having to cover for staff absences in addition to dealing with an average of 20,000 new Covid-19 cases per day.

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Not My New Year’s Resolutions Again

Posted in Biographical, Covid-19, Education on January 1, 2022 by telescoper

What we call the beginning is often the end. And to make an end is to make a beginning. The end is where we start from.

from Four Quartets, ‘Little Gidding’ by T. S. Eliot.

Two years ago, in January 2020, I shared a list of things I planned to do in the (then) New Year. Here they are again for completeness.

  1. Go to more live concerts. Although I enjoy the radio and recordings, I far prefer to listen to live music at concerts. Attending such events helps also support the venues and musicians as without an audience both would die. I’m ashamed to say I haven’t heard any live jazz in Ireland!
  2. See more of Ireland. I moved to Maynooth two years ago but, apart from one visit to Galway and one to Armagh, I still haven’t travelled much beyond the Dublin area. I must get around more, especially to the South.
  3. No more working weekends. I’ve been in the office for at least one day every weekend since I started at Maynooth. I did the same when I was at Sussex too, and seem to have relapsed. I have always had problems managing my own work/life balance but I realize it’s not setting a good example to younger folk to be getting it so obviously wrong. I’ll add not reading work emails at weekends to this.
  4. Be a better colleague. This is something I think one should always strive to be, but I have particular need to improve. I know that over the last four years or so things weighed very heavily on me behind the scenes and I ended up letting people down on too many occasions. I apologize for that and will try to do better in future.
  5. Read more books. I used to be a voracious reader of all kinds of books, both fiction and non-fiction, but I somehow got out of the habit. I now have a stack of unread works that I must try to read before the year is out!
  6. Finish more things! Not unrelated to No. 4 above, I have been very poor over the last few years at completing projects and writing papers. I need to clear the backlog and get on with some new things.
  7. Do more to promote Open Access publishing. I’m not surprised that the status quo in academic publishing is proving hard to dislodge, but I believe that change can be achieved if researchers take the initiative. I’m proud of what we have achieved so far at the Open Journal of Astrophysics but there’s much more to be done.

I achieved very few of these in 2020 or 2021. The pandemic made the first two impossible. Number 3 changed when we had to start working from home, which made it difficult to get away from work at all but since I moved into my house in August 2020 I at least have a study on which I can close the door. I haven’t improved much on the 4th one either, although the reasons for the past two years are different. Likewise with 5 and 6. I have done as much as I possibly can on 7 but there is a lot to do.

It is true however that I haven’t coped with the stress and isolation of being a Head of Department during the Covid-19 era as well as I should. I don’t know whether it is the high levels of anxiety that have sapped my energy or whether I’m just feeling the effects of age.

Anyway, there’s no improvement in sight in terms of workload so I suppose I’ll just cut and paste this old set of non-resolutions into this year and hope that 2020 v3 turns out better than the first two! More immediately I think I will take the opportunity to do a thorough clean-up of the house before the examinations start (a week today).

Finally, today Irish becomes an official language of the European Union so let me take the opportunity to say athbhliain faoi shéan is faoi mhaise daoibh!

P.S. I note with disappointment that once again I have been denied the opportunity to turn down an award in the New Year’s “Honours”.

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Another Covid New Year

Posted in Biographical, Covid-19 on December 30, 2021 by telescoper

I’ve had a very quiet Christmas break. Apart from regular trips into the garden to feed the birds, and putting out and bringing in the bins yesterday, until this afternoon I hadn’t left the house since Christmas Eve. I ran out of bread and milk, though, so had to venture forth to do a bit of shopping. I didn’t pick a good time for it: it was pouring with rain.

I’m doing my bit to slow down the spread of the Omicron variant through sheer inertia. Although this strategy is perfectly fine by me, it does leave me short of new things to blog about. I therefore had a look at what I posted on December 30th last year.

On December 30th 2020 the Taoiseach announced that Ireland would go into Level 5 restrictions following a surge in Covid-19 cases. This was the state of play then together with today’s figure:

Notice that the y-axis on the right is ten times the scale of that on the left. The increase at the end of 2020 was to continue into the new year to produce a huge spike in cases (and, sadly a great number of deaths) that peaked around January 10th, after the Level 5 restrictions were imposed. A similar trajectory seems likely in early 2022.

At the time I was very angry about the Irish Government’s decision to relax restrictions before Christmas, which I still think was culpable. This time round there was a similar increase in cases following a relaxation in November to reopen nightclubs and other hospitality venues (which I also think was wrong). It wouldn’t be fair to blame the recent surge in cases on that, however. The timescale of increase of the omicron variant is so short that the wave would probably only have been delayed by a week or two.

The latest 7-day average of new cases is 12582.0 per day and it is likely that we’re at least a week away from the peak. These figures are almost certainly serious underestimates, as testing capacity has been reached. What I wrote on December 30th 2020 also applies today:

Unfortunately the Christmas wave hasn’t really hit these figures yet so I think thinks are going to get a lot worse before they get better. 

Fortunately this year we have the vaccines and these have had a clear effect on the death rate. Let’s hope this line of defence holds but, even if it does, the Health Service will be under severe strain in January. Although the vaccines reduce the rate of serious illness and death per case to about 10% of that experienced last year, we have more than ten times as many infections.

I didn’t imagine things would look even grimmer at the end of 2021 than they did at the end of 2020, but there we go. We’ll just have to wait and see how it pans out. One thing I can be sure about is that I won’t be going out on New Year’s Eve!

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Reasons to be cheerful?

Posted in Biographical, Covid-19 on December 24, 2021 by telescoper

We’ve all been bracing for the arrival of the omicron storm here in Ireland. I has been like waiting for a tsunami know is coming and praying that the flood defences are strong enough to hold.

The wave now seems to be here, with 11,182 new cases reported today. That is by far the highest figure reported during the entire pandemic so far and it has dragged the 7-day average up to 6776.4 from yesterday’s figure of 5697.3.

I think it’s probably true to say the worst is yet to come. So far, though, the number of hospitalizations and deaths has not increased hugely; the former has, if anything been falling, and the latter is only rising slowly:

The number of Covid-19 related deaths reported in the last week was 55, which is an average of about 7.9 per day. We won’t know until the New Year whether the latest surge will drive these curves up.

There is some good news in that the omicron variant may be less likely to lead to severe illness than the delta variant. This is non-trivial to assess because one has to allow for factors other than the infecting variant (such as age, underlying health and vaccination status)  before one can see the true effect of this one variable. Comparing sickness and mortality rates now with earlier stages of the pandemic is virtually impossible for this reason. However, because the UK has allowed very large case numbers of both delta and omicron to occur for several weeks, there is enough data to see some difference between omicron and delta in hospitalization rates.

It also seems that while a booster seems to be needed to prevent infection by omicron, a standard two-dose vaccination still seems to be effective at preventing serious illness.

There are grounds for optimism, then. The problem as I see it is that if the number of people infected with omicron goes through the roof then there will still be lots of very sick people around, some of whom will die. Say a combination of vaccination and less severe variant reduces the mortality rate per case to 10% of what it was last January, which seems reasonable. If there are ten times as many cases, the number of deaths will be similar to last January so we’re still in for a terrible New Year.

We’ll just have to wait and see. I recommend staying as drunk as possible over the next week or ten days so as to avoid thinking about it.

 

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End of Term Blog

Posted in Biographical, Covid-19, Education, Maynooth with tags , , , , , on December 18, 2021 by telescoper

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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Boosted!

Posted in Biographical, Covid-19 with tags , , on December 15, 2021 by telescoper

This morning I duly made my way for the third time this year to City West vaccination Centre to get a booster shot of the Moderna vaccine. Given reports of lengthy queues I was prepared for a long wait but that wasn’t the case. I was in and out in 40 minutes including the mandatory 15 minutes after the jab. It was busy, but good organisation kept us all moving steadily. Once again huge thanks are due to the HSE staff and volunteers (including the piano player) for all their efforts!

It could have been even quicker but the computer system had mistakenly registered that I have a history of anaphylaxis (which I don’t) so I had to answer a longer set of questions and wait for my record to be corrected. I guess someone ticked the wrong box the last time I was there!

I didn’t have any serious side effects with my other doses but I am working from home anyway, and don’t have anything scheduled this afternoon, so I can crash out if needs be. In the meantime I’ll get on with some work…

P. S. There seemed to me to be much less nervousness among the people in the queue this time. Everyone was quite chatty. I guess we’re all getting used to this rigmarole now!

Update: 10.20pm. No particularly serious side effects but I’m feeling very tired and achey so am having an early night!

Update: 9.30am the following day. The third dose (booster) has given me a far stronger reaction than the previous two. In particular my left arm (where I had the jab) is so numb as to be virtually useless and all my joints are aching. I’m glad I can stay at home today!

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The Coronavirus Vaccine Effect

Posted in Covid-19, mathematics with tags , , , , , , on December 12, 2021 by telescoper

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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Last Week Ahead

Posted in Biographical, Covid-19, Education, Maynooth on December 12, 2021 by telescoper

We’re approaching the end of term here at Maynooth University; the forthcoming week is the last week of teaching, after which we have the luxury of a full week without lectures or tutorials before Christmas itself. Apart from eating and drinking I think I’ll spend most of the holiday sleeping. The first official duty I will have in the new year is on Saturday 8th January when one of my online examinations is due to take place. After that it will be all marking papers and after that it will be preparing teaching for Semester 2…

At this start of this academic year I was quite confident that Semester 2 would find us more-or-less back to normal but that now seems very unlikely. I think that we’re going to be starting Semester 2 at the end of January 2022 exactly the same way that we started Semester 2 in January 2021, i.e. with everything fully online.

As of today, the recent rapid growth in Covid-19 infections seems to have slowed (and cases have been decreasing for a few days) but a Christmas surge seems inevitable and with many people having low protection against the omicron variant and very high case numbers even before the festive period, the period from January to March may be very difficult indeed. I stand to be proved wrong, though, and the trajectory of the pandemic is highly uncertain. We’ll just have to wait and see how things turn out. Fingers crossed.

I have explained before on this blog that I am going to be working from home next week, delivering my last lectures from my study and via recordings. I have better facilities for doing online lectures at home, because the University has failed to invest in decent recording equipment in its lecture theatres.

In any case I only have one full lecture to give in my first-year module (due tomorrow); the other two will be revision classes. I have finished the lectures for my second-year module so was just planning to do a revision class in the Tuesday slot. I did have some other (virtual) meetings in my calendar for next week but most of these have all been cancelled for one reason or another.

The one remaining task is to get all the online exams ready to go in January. We haven’t got the special Moodle spaces set up yet, but I imagine that will happen sometime next week.

By the way, when I responded to the close contact alert I received on Friday I was told I’d be sent an antigen test kit from the HSE. I haven’t got it yet but I suppose it may arrive next week. I still don’t have any symptoms though, and am effectively self-isolating anyway, so I’m not concerned. I just hope I get my booster on Wednesday without having to queue for too long…

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Irony Alert!

Posted in Biographical, Covid-19 with tags , on December 10, 2021 by telescoper

Having just started working from home yesterday, this afternoon I received the above message, via the Covid-19 tracker app, saying that I have been a close contact of someone who has tested positive for Covid-19. I don’t have symptoms so don’t have to do anything drastic, just restrict my movements for 5 days. I was going to do the latter anyway, so the timing is somewhat ironic!

Oh and they’re going to send me an “antigen kit”, presumably to keep me occupied for the next few days. It should be fun because I’ve never made an antigen before.

Incidentally the message isn’t very clearly worded. I think I was a close contact on 6th December of someone who subsequently tested positive. That may account for why I have only got this message on 10th!

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A Date for a Boost!

Posted in Biographical, Covid-19, Education with tags , , , , on December 9, 2021 by telescoper

After expressing concern about the prospects of getting a timely booster jab last night I received an SMS message offering me an appointment next Wednesday for a shot. The text was sent on 8th December, six months to the day since my second jab (8th June). I will once again have to travel to City West in order to receive it, so will have take some time off work but that’s a small price to pay.

I had inferred (incorrectly) that it would take much longer to get a date for booster because most of the people I know in their sixties haven’t had theirs yet and they are higher priority than me. I now realise that may be because they had the AstraZeneca vaccine, which had a longer interval between first and second doses than the 4 weeks for the Pfizer vaccine I had, so had a later second dose than mine.

My third vaccine dose will be of the Moderna vaccine; the previous two were Pfizer/BioNTech. It seems everyone who is getting a shot this month will be getting the Moderna version as Ireland has a large stock of this vaccine due to expire next month. Although its efficacy against the omicron variant is unknown, I will of course attend the appointment.

Yesterday, before I received the text message announcing my booster shot, I emailed the students in my classes to say the remaining lectures of the term will be online-only because of the high levels of Covid-19 in circulation and my waning immunity. Next week’s booster doesn’t change that as next week is the last week of teaching. My plan is to do the lectures live as webcasts and make the recordings available afterwards, which is how I’ve done them the entire term, except I’ll be doing them from home with no in-person audience. Apart, that is, from next Wednesday, when I’ll only be able to offer a pre-recorded lecture as I’ll be at City West when the lecture is scheduled. That will be my last lecture of the Semester, as most of my teaching is concentrated in the early part of the week.

Owing to a combination of Covid-19, Storm Barra and no doubt sheer exhaustion, student attendance at lectures and tutorials on campus has fallen sharply, though attendance at my second-year class has remained quite high. On Tuesday the campus was virtually deserted but about 70% of my class for Vector Calculus & Fourier Series were there. Somehiw, though, I don’t think they’ll mind too much watching the remaining couple of lectures from the comfort of their homes!

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