Archive for Covid-19

The R in Ireland

Posted in Covid-19 with tags , , , on July 9, 2020 by telescoper

I was playing about with different ways of presenting the Covid-19 data I’ve been collecting here to make the trends clearer. This is what the daily confirmed cases and reported deaths look like if smoothed with a simple 7-day moving average and plotted on a log-linear scale:

This confirms something I’ve suspected over the last couple of weeks: that the number of confirmed cases has been edging upwards. This is not so clear in the raw counts, but is suggested: the smoothing makes this easier to see by reducing the noise and removing any weekend reporting artefacts:

This recent upward trend is consistent with the latest estimates of the basic reproduction number R that suggest it has crept up to around unity.

The number of cases per day remains low and confined to particular clusters. Hopefully contact tracing and isolation will prevent the increase getting out of hand.

It seems about two thirds (15 out of 23) of the new cases are associated with travel, though, so any loosening of restrictions on overseas travel would be very unwise.

The maximum age of any of the new cases reported yesterday is 44 and 77% are under 25. Perhaps its younger people who are less likely to observe social distancing.

I worry a bit that Ireland may be unlocking too quickly and people may be getting a bit complacent about the situation.

This is not over.

Open Contact Tracing

Posted in Covid-19 with tags , , , on July 9, 2020 by telescoper

I was interested to see in the news this week   that Ireland’s Covid-19 contact tracing app has been released and is now available for download. According to the HSE it has been downloaded over a million times in the last few days. I haven’t downloaded it myself (yet) but I probably will.

One of the interesting things about this app is that it cost €850,000 (which is about £760K at today’s exchange rate). The UK’s attempt to produce a similar bit of software has so far cost over £11M for an app that doesn’t exist. It seems a rather similar situation to the £50M paid for ferries that didn’t exist.

“Where has that money gone?”, I hear you ask. The answer is “I don’t know”, but it’s probably been pocketed by friends of Mr Cummings.

But UK residents needn’t fear. Not only is the Irish Covid-19 tracker app free to download and I’m told it also works on the other side of the Irish Sea. Not only that, but  the source code is also freely available on Github.

This app does of course raise genuine concerns about data protection, though perhaps not as great as it would if the data was being handed to friends of Mr Cummings. I was amused yesterday however to see usual conspiracy theorists expressing their fears about what would happen to their data if they downloaded the app on – of all places – Facebook.


Getting Back to Work

Posted in Covid-19, Maynooth with tags , , on July 7, 2020 by telescoper

It’s Consultation Day here in Maynooth, which is when students can get some feedback on the exam results released last week and also discuss what they may need to do in terms of repeating assessments next month.

A few minutes ago I took a short break from dealing with such things to make a cup of coffee and I thought I’d provide an update on the processes going on to allow people to return to work. Signs went up on the outside doors to the Science Building last week.

The furniture in the Foyer area has been rearranged to facilitate social distancing…

The Department of Theoretical Physics will be operating a two-way system, with people sticking to the left of the corridors. People came to yesterday to stick the signs on the floor.

Fortunately the corridors in the Department are just about wide enough to maintain social distancing. If people pass each other coming in different directions their encounter will only be transient anyway, which is of low risk.

The computer room (not shown) will have a one-way system so students and staff will enter through one door and leave through the other. We will also have to take half the machines out of use for social distancing purposes, but that should be manageable.

Elsewhere in the Science building in order to avoid people passing each other on the (rather narrow) stairs there is one set for up and another for down.

Social distancing is being enforced in the other facilities too…

That’ll do for now. Time to get back to work.

Excess Deaths due to Coronavirus: Compare and Contrast

Posted in Covid-19, Politics with tags , , on July 3, 2020 by telescoper

I saw an interesting news item this morning about excess deaths registered in Ireland between 11th March and 16th June, the period that brackets the peak of the Covid-19 pandemic.

According to the official numbers, 1709 deaths occurred during that time of people who had tested positive for the Coronavirus. During the same period, however,  about about 1100-1200 deaths were registered in excess of the average mortality figures.
One interpretation of this discrepancy is that many of those counted as Covid-19 cases actually died of other causes. Consistent with that interpretation is the fact that over 60% of those deaths were people in care homes, many of whom may have had chronic illness.

Taking 1150 as an estimate of the excess deaths caused by Covid-19 the mortality per million in Ireland drops from 352 to about 237. It must be noted that this figure is still much higher than similar-sized countries such as Denmark and Norway.

The contrast with the United Kingdom is stark. A recent analysis of excess deaths there suggests about 69,000 people have lost their lives directly or indirectly due to Covid-19, which is about 57% higher than the official figure of around 44,000. Taking 69,000 instead of 44,000, the United Kingdom’s mortality rate increases from 647 per million to over a thousand.

I haven’t really been following the reporting in the United Kingdom very closely, because I don’t live there anymore, but the data on new cases found by testing is hopelessly confusing. This, together, with the apparent under-reporting of deaths, may be the reason behind the lax adherence to public health measures over the other side of the Irish Sea.

There is also the fact that daily Covid-19 briefings here in Ireland are led by medical experts, with the politicians taking a back seat (and often not involved at all). These are much more likely to be trusted than politicians, especially those involved in the current Tory government.

And so to Phase Three..

Posted in Biographical, Covid-19, Education with tags , , , , on June 29, 2020 by telescoper

Well, Phase Three of the Great Reopening happened has started on schedule. As I walked to campus this morning I saw long queues in the street outside every barber’s shop in Maynooth. I decided to wait a few days before trying to get my long overdue haircut. It’s been over three months now.

Maynooth has quite a lot of barber’s shops for a town of its size. It also has quite a lot of nice restaurants. I noticed this evening that quite a few will be opening this week for sit-down meals rather than takeaway. I wish them well, but I think I’ll be sticking with the takeaways for a while longer.

When I got into the office to start work on the risk assessment I’m supposed to complete so staff can return to work, there was quite a lot of activity in the Science Building, including signs of various kinds being put up.

Some of the signs are bisexual bilingual:

All this reminded me of some lines from the Leonard Cohen song Anthem:

We asked for signs. The signs were sent


Signs for all to see.

The arrows will be put on the floor at regular intervals to enforce a one-way system around the building to allow people to circulate without bumping into each other.

I’m also expecting to be issued with tape to be used to mark some of the machines in our computer laboratory out of use, to keep users from sitting too close. I was going to remove the chairs but I don’t have anywhere to out them and we’ll probably – hopefully – need them back sometime!

I started work on the risk assessment but didn’t get it finished. I should be able to complete it tomorrow. Then it needs to be approved. Only after that will staff be able to begin routinely working in the Department. Until then, working from home continues.

Before Phase Three..

Posted in Biographical, Covid-19, Maynooth with tags , , on June 28, 2020 by telescoper

Tomorrow (on Monday 29th June) Ireland will enter Phase Three of its (accelerated) Roadmap for Reopening after the Covid-19 restrictions.

The Coronavirus situation here remains relatively stable, with new cases steady at a low level:

This is not the case for the rest of the world, however. Yesterday two grim milestones were passed: 10,000,000 confirmed cases of Covid-19 worldwide and 500,000 deaths:

Much of the recent numerical growth of the pandemic is associated with North and South America. Brazil is particularly badly affected as are some of the United States. I don’t need to comment on the quality of the political leadership involved.

I am very nervous about the situation in the United Kingdom too, where I feel the reopening is being rushed. Poor leadership is partly responsible for the continuing high levels of infection there too.

Anyway, back to Phase Three in Ireland. Yesterday I bought a copy of the Irish Times and found this booklet inside:

The emphasis is on the fact that despite the low levels in Ireland Covid-19 has not gone away and we all have to be prepared to take special precautions for the foreseeable future. I would be amazed if there wasn’t another flare-up here at some point, actually, it’s just a question of when. And those optimistic about the delivery of a vaccine in the near future, I’ll remind you that there isn’t yet a vaccine for any form of Coronavirus let alone the novel form responsible for Covid-19 (SARS-CoV-2).

Anyway, on Friday I attended a virtual Question and Answer session with the President of Maynooth University, Professor Philip Nolan, about the plans for reopening campus over the Summer and into the new academic year. It is clear that lots will have to be done before staff can return fully and even then it won’t be anything like “normal”.

Incidentally the issue of face masks came up and there was some discussion about their effectiveness. Not being a medical expert I don’t really know about that, but I think one of the important things about masks in a work environment is that their visibility means that they work as a signal to remind people to be aware of Covid-19. I have discarded my home-made face masks and bought a box of proper ones and I intend to wear them whenever I am in a work setting in which anyone else is present.

On Friday evening I finally received (relatively) detailed instructions on how the return to work process will work. The Department of Theoretical Physics at Maynooth University is still basically in Phase 1 while the university working group has been assembling this guidance. It will probably be several more weeks before we can get people back to work because there are many things still to be done: including the installation of hand sanitizers, one-way systems, screens, and new signage.

Another thing that came up during the President’s Q&A was the question of vacations for staff. Fortunately I had muted both my audio and video feeds for this as I laughed out loud. What with organising the return to work, overseeing repeat exams, recruiting a sabbatical replacement, planning teaching for next year, rewriting my own lectures for the “new normal”, etc etc, and (hopefully) moving into a new house, I can’t see any prospect of any summer holiday this year at all!

Scrambled Phases

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

A couple of weeks ago I posted about the imminent start of Phase 2 of the Irish Government’s Roadmap for Reopening after the closures enforced because of the Covid-19 pandemic.

Since then the Irish Government has decided that there will only be four phases instead of five, and many elements of the programme will be moved forward. For example, all travel restrictions within the Republic will be lifted from next Monday (29th June), which is when Phase 3 is due to commence. It has also been announced that hairdressers, barbers, nail and brow salons, beauty salons, spas, make-up application services, tanning, tattooing and piercing services will re-open. I find that surprising, as I find it hard to see how such services can be provided at low risk of transmitting Covid-19.

In fact I find the whole idea of accelerating the Roadmap rather worrying. I hope I’m proved wrong, but it seems to me that the Government is rushing this. There are worrying signs in Germany that the R-number is increasing significantly and undue haste in opening business may lead to a similar rise. It must be stressed that the number of cases involved in Germany  is rather small and most are confined in local outbreaks that can be contained. Nevertheless, this remains a concern.

At the moment the situation looks stable, with new cases at a very low level:

I do worry however that, since only a very small fraction of the population (at most a few percent) have been infected with Covid-19, there will be very little resistance if Covid-19 starts to spread again.

As for my own work situation here at Maynooth University, what happens in Phases Three and Four is all a bit hypothetical, because we’re still stuck in Phase One! The University management is being extremely cautious about allowing anyone back to work at all until various protocols are agreed, risk assessments carried out, and staff training delivered. It seems likely therefore that we will reach Monday’s scheduled start of Phase 3 before we are even ready for Phase 2. In practice, therefore, the various phases of the Roadmap are no longer relevant in this particular setting. I think I’ll remain the only person coming in to the Department for quite some time!

I fully understand and support the careful approach adopted  by the University, of course, and the delay doesn’t matter that much as our teaching semester is now finished and, being theorists, we can all work from  home reasonably effectively. It must be more of a challenge for laboratory-based researchers. My main concern is  I’d be very surprised if all the other organizations and businesses due to open next Monday are as cautious. The last thing we need for people to cut corners and send us all back to square one.


Psychological Time

Posted in Biographical, Covid-19, Education with tags , , , on June 21, 2020 by telescoper

So, the Summer Solstice for 2020 is now in the past. It’s all downhill from here!

As the Solstice approached last night I was thinking back to the Vernal Equinox which had happened this year on March 20th, exactly three months before. That was at the end of Study Week in the Spring Semester but the students did not return the following week and we switched to remote teaching. I find it astonishing to think that was just three months ago. It seems like ancient history. Not only that but several major events took place during that period that I find it hard place in chronological order without looking at written records (including this blog).

I am not an expert on such matters but it seems to me that the isolation, disruption of social interaction, and the loss of familiar routines imposed by work are among the things responsible distorting perception of the passage of time. I have tried to impose a regular pattern on my day during this time but only with limited success. I suspect it’s not only me who has felt like this over the past weeks and months!

It’s not just the disruption to routine of course. There was also a genuine fear of becoming infected. My last in-person lecture was on 12th March, the Thursday before Study Week. From time to time I wondered if I would ever see those students again. I also made arrangements to write a will. For a time it looked likely that intensive care facilities in Ireland might be overwhelmed so I felt it important to make contingencies of that sort. Fortunately they weren’t needed. As far as I know the Coronavirus hasn’t reached me. I certainly haven’t had any symptoms, though I haven’t actually been tested.

Overall I found the lockdown very difficult at first but I think adjusted reasonably well despite (or perhaps because of?) having very peculiar dreams.

Now that the Covid-19 restrictions are gradually being wound down hopefully some measure of routine will resume and the sense of disorientation will fade. Time will tell.

Marking Time

Posted in Covid-19, Education, Maynooth with tags , , on June 12, 2020 by telescoper

In among all the other things I have to do I’ve just finished marking my portion of examinations and other assessments in time for next week’s Examination Boards. I have to attend two (virtually), one for Theoretical Physics and one for Engineering Mathematics. You may recall that, this year, along with many other universities, we switched from the usual examination format to online timed assessments.

Obviously I can’t talk about any actual results here but I can relay a few general points.

First, there were remarkably few hitches in the examination process. I would like to say that I was totally confident that the new system would work, but I’m afraid I was very nervous during the examination period. I’m glad that I was proved wrong. That’s not only due to very hard work by the teaching staff in getting everything together to go online and the technical support staff for ensuring the submission portals could handle the load, but also due to the students who coped admirably well with the new assessment style.

That said, I think if we are going to have such assessments again in the future there are things we could improve.In particular the mathematical nature of our work means that students have to do their working, diagrams etc by hand and sometimes the quality of scanning made the resulting submissions very difficult to read. If we had had time we could have offered more training to the students on how to scan their work more legibly, so next time we will probably do that too. Indeed we will probably be doing most of the coursework that way next term so they will probably get more practice anyway.

Printing the work out usually made the legibility problem worse, so I generally marked as much as I could on the screen. We don’t have very good software for doing this in bulk so it was painfully slow. I estimate it took me about three times as long to mark an examination script this way than doing it on paper. I’d be very interesting to hear via the comments box of any suggestions or recommendations of software to help this process!

The main purpose of this post however is to say a very public thank you to all the teaching staff in the Department of Theoretical Physics and to our admirable Departmental Administrator Suzie  for working so hard in difficult circumstances to get everything done in time!





Time for Phase 2 in Ireland

Posted in Covid-19, Maynooth with tags , , on June 7, 2020 by telescoper

Tomorrow (June 8th) sees the start of Phase 2 of Ireland’s Roadmap for Reopening. You can see that, as of yesterday, the number of confirmed cases per day is small and stable after three weeks of Phase 1, which has justified proceeding to Phase 2.

Incidentally, since the Covid-19 outbreak took hold in Ireland there have been daily press briefings by the Department of Health. Yesterday’s was the last of these: from now on the updates will be twice a week, on Mondays and Thursdays. Data will still be released every day but there won’t be a press conference every time. I’ve been following these every day for three months so this will be quite a change to the routine!

Moving to Phase 2 means that most shops will be able to reopen (subject to social distancing measures being in place), people will be able to travel much further (anywhere within your own county and 20 km into another) and there will be a limited return to work (subject to the completion of various protocols, risk assessments, etc).

For us at Maynooth University there won’t be a sudden change. Staff who can will continue to work from home (which is basically everyone in the Department of Theoretical Physics) but labs will gradually reopen for research when the necessary arrangements are in place. Other than that Phase 2 will be very similar to Phase 1.

On Friday, however, the Taioseach announced that the Roadmap would be accelerated so that Phase 4, starting 20th July will, if all goes well, be the last, though measures will be in place for some time after that.

That’s good news of course but it’s all dependent on there being no second wave. As a cautionary tale, take a look at the numbers for Covid-19 Iran:

Iran has been experiencing a second wave of new cases for some time now, and this looks set to produce more cases than the first, but this has only recently resulted in an increase in daily mortality figures:

Note the lowest number of new cases per day in Iran was just under 1000. That’s far fewer than the United Kingdom, which has chosen to undo its restrictions far more rapidly in Ireland. The number of confirmed new cases in Ireland reported yesterday was just 24; in the United Kingdom the figure was 1557. In my opinion there is a strong possibility that the UK will follow a similar trajectory to Iran…