Archive for May, 2021

Open Science and Open Software

Posted in Open Access, Science Politics, The Universe and Stuff with tags , , , , on May 22, 2021 by telescoper

As the regular readers of this blog – both of them – will know, I’ve been banging on from time to time about Open Access to scientific publications. After posting a video featuring Volker Springel and the GADGET-4 code I thought I’d return to an issue that came up briefly in my recent talk about Open Access and the Open Journal of Astrophysics here which is the question whether open access to scientific results enough, or do we have to go a lot further?

An important aspect of the way science works is that when a given individual or group publishes a result, it should be possible for others to reproduce it (or not as the case may be). Traditional journal publications don’t always allow this. In my own field of astrophysics/cosmology, for example, results in scientific papers are often based on very complicated analyses of large data sets. This is increasingly the case in other fields too. A basic problem obviously arises when data are not made public. Fortunately in astrophysics these days researchers are pretty good at sharing their data, although this hasn’t always been the case.

However, even allowing open access to data doesn’t always solve the reproducibility problem. Often extensive numerical codes are needed to process the measurements and extract meaningful output. Without access to these pipeline codes it is impossible for a third party to check the path from input to output without writing their own version assuming that there is sufficient information to do that in the first place. That researchers should publish their software as well as their results is quite a controversial suggestion, but I think it’s the best practice for science. There isn’t a uniform policy in astrophysics and cosmology, but I sense that quite a few people out there agree with me. Cosmological numerical simulations, for example, can be performed by anyone with a sufficiently big computer using GADGET the source codes of which are freely available. Likewise, for CMB analysis, there is the excellent CAMB code, which can be downloaded at will; this is in a long tradition of openly available numerical codes, including CMBFAST and HealPix. Researchers in these and other areas do tend to share their software on open-access repositories, especially GitHub.

I suspect some researchers might be reluctant to share the codes they have written because they feel they won’t get sufficient credit for work done using them. I don’t think this is true, as researchers are generally very appreciative of such openness and publications describing the corresponding codes are generously cited. In any case I don’t think it’s appropriate to withhold such programs from the wider community, which prevents them being either scrutinized or extended as well as being used to further scientific research. In other words excessively proprietorial attitudes to data analysis software are detrimental to the spirit of open science.

Anyway, my views are by no means guaranteed to be representative of the community, so I’d like to ask for a quick show of hands via a poll that I started about 8 years ago.

You are of course welcome to comment via the usual box, as long as you respect my comments policy…

Marking Blues

Posted in Covid-19, Education, Maynooth with tags , , , on May 21, 2021 by telescoper

“May is a pious fraud of the almanac.” – James R. Lowell

The rainy weather we’ve been having for the last few days has at least deprived me of distractions from the job at hand: the marking of examinations and other assessments. Examinations started here in Maynooth last Friday (14th May) , a week ago today, and as I write this morning another one has just started. That’s the third in the past week. Yesterday I managed to finish all the assessments for one Module, just in time for today’s batch to arrive. It’s not only examination marking of course, I’ve also had computational physics projects to assess and feedback to write. Suffice to say that it’s a busy time of year.

When I was getting this morning’s examination online timed assessment ready it suddenly struck me that some of the students taking it belong the year group that entered the University in September 2018, and are the first students I will have seen all the way through the degree as they are taking their last set of exams now and will graduate this summer.

Of course when I say “will have seen” I’m not really being honest. I’ve hardly seen any of them since last March. Although I have spoken to them via Teams I haven’t even seen them virtually, as students virtually always have their video on mute during online teaching sessions.

Because of the Covid-19 restrictions, the students on three-year programmes have had most of their teaching online since last Spring, and by the time they finish the current set of examinations half their assessment will have been online.

You’ll have to ask students whether the lack of face-to face interactions has impacted their learning, but speaking for myself as a lecturer it has made life very difficult. Lecturing to a camera is not easy, and the absence of visual cues from the audience makes it difficult to know whether what you’re saying is sinking in. I guess we’ll find out when we look at the examination grades.

Thinking about the group of students who will form the graduating class for this year, though, the saddest thing is that they will shortly finish their exams and complete their degrees. We the staff won’t have the chance to congratulate them properly, nor will they the students be able to celebrate properly with each other (as they are scattered all over the country).

Although we’ve worked very hard to do what we can over the past year and a bit, I can’t rid my mind of the feeling that this group in particular has been let down very badly. I know the circumstances are beyond our control and all that, but they just haven’t had the educational experience they expected and deserve. At least – we hope – other groups can look forward to something like normality, possibly from next year, but for this group that’s it for their third level education. It’s really not fair.

I have said so before on this blog that I think any student who wishes to should be able to repeat the last year at university free of charge in recognition that they have been severely short-changed. It seems to me that would be the right thing to do, which is why I don’t think the Government will allow it.

Now, it’s still raining so I’ll try to get some more marking done while the exam goes on.

Emails to be wary of..

Posted in Uncategorized on May 20, 2021 by telescoper

Although it’s been an issue ever since I started writing a blog over a decade ago I’ve noticed a recent increase in phony comments, some of them using domains like that above to generate plausible email addresses. I’ve blocked all comments from people using such email addresses, including those from above. I had a lot of trouble a few years ago from someone sending nasty anonymous emails which has left me ill-disposed towards people using addresses like these.

Anyway, I thought I’d remind potential commenters of what it says on the front page of this blog:

 Feel free to comment on any of the posts on this blog but comments may be moderated; anonymous comments and any considered by me to be abusive will not be accepted. 

I don’t block comments that disagree with my opinions, but I write the posts and I’m not anonymous so I don’t see why commenters should be allowed to be.

For you information, since I started this blog in 2008, a total of 37,062 comments have been published (including those by me). A total of 2,730,621 have been blocked.

A Legacy of Spies

Posted in Literature with tags , on May 19, 2021 by telescoper

When the writer John Le Carré passed away in December 2020, I ended my little tribute to him with the following:

The last John le Carré book I bought was A Legacy of Spies (2017), which I haven’t yet got around to reading. I’ll put that on the list of Christmas reading, and drink a toast to an author who has given me so much to enjoy and to think about over so many years.

I didn’t actually get around to reading the book at Christmas. I did however notice it the other day still among my (substantial) pile of as-yet-unread books while I was looking for a distraction from examination marking, and decided to read it now, which I have. It’s very good, and also brought back a lot of memories of the entire Smiley sequence, so I heartily recommend it.

I watched the two TV series based on books by John le Carré – Tinker Tailor Soldier Spy and Smiley’s People – when they were broadcast so decided to read those books, and after those read all the others he had written by that time.

Not all his early books were great, but The Spy who came in from the Cold is excellent as are Tinker Tailor Soldier Spy, The Honourable Schoolboy and Smiley’s People – the so-called Karla trilogy. A Legacy of Spies is based on many of the characters to be found in these other novels. The central character, Peter Guillam, appears in the Karla Trilogy and the plot itself revolves around the failed operation described in The Spy who came in from the Cold that resulted in the death of Elizabeth Gold and Alec Leamas at the Berlin Wall. There are even short appearances by Jim Prideaux (the British agent captured during Operation Testify in Tinker Tailor) and right at the very end by George Smiley himself.

Smiley’s remarks at the end, looking back over his career as a spy, with all the cruelty and death and amorality that entailed, are apposite:

‘So was it all for England, then?’ he resumed. ‘There was a time, of course there was. But whose England? Which England? England all alone, a citizen of nowhere? I’m a European, Peter.

No prizes for guessing where that phrase came from!

A Legacy of Spies has an unusual narrative structure, the story told in part through flashbacks and documents. Guillam, in retirement in Brittany in his old age, is dragged into an investigation into alleged wrongdoings by the Circus and has to prepare some sort of defence but lots of important evidence is missing. He has to rely on his own memory but there are things he must withhold to protect himself and others. It’s a gripping read and made me want to read the entire sequence again right from the beginning.

Job in Theoretical Physics at Maynooth!

Posted in Maynooth with tags , on May 19, 2021 by telescoper

Just a short post passing on the information that we have a fixed-term job available in the Department of Theoretical Physics at Maynooth University. You can find the details here.

The position is for one calendar year starting in September 2021. I know it is a short appointment, but it seems to me that it would provide a good opportunity for an early-career academic to gain some teaching experience while carrying on their research in a lively and collegiate Department.

The deadline for applications is 23.30 on Tuesday 8th June 2021 and you should apply through the Maynooth jobs portal here.

If you’d like to know any more please feel free to contact me privately.

Oh, and please pass this on to anyone you think might be interested!

Cosmology Talks: Volker Springel on GADGET-4

Posted in The Universe and Stuff with tags , , , , , , , on May 18, 2021 by telescoper

It’s time I shared another one of those interesting cosmology talks on the Youtube channel curated by Shaun Hotchkiss. This channel features technical talks rather than popular expositions so it won’t be everyone’s cup of tea but for those seriously interested in cosmology at a research level they should prove interesting.

In this talk from a couple of months ago  Volker Springel discusses Gadget-4 which is a parallel computational code that combines cosmological N-body and SPH code and is intended for simulations of cosmic structure formation and calculations relevant for galaxy evolution and galactic dynamics.

The predecessor of GADGET-2 is probably the most used computational code in cosmology; this talk discusses what new ideas are implemented in GADGET-4 to improve on the earlier version and what new features it has.  Volker also explains what happened to GADGET-3!

The paper describing Gadget-4 can be found here.

 

International Day against Homophobia, Biphobia and Transphobia

Posted in LGBTQ+ on May 17, 2021 by telescoper

Today is May 17th which means that it is International Day Against Homophobia Transphobia and Biphobia.

If you need reasons why such a day is still necessary then you can look here.

Normal services will be resumed as soon as possible…

Posted in Biographical, Covid-19 with tags , , , on May 16, 2021 by telescoper

After posting updates about Ireland’s Covid-19 situation every single day since the end of March 2020 – a total of 441 entries so far – I’ve been forced to pause. The reason is that a “significant ransomware attack” has crippled many of the computer systems of the Health Service Executive and while it is being dealt with, no data on Covid-19 (including vaccinations) are being published. As far as I understand it, testing and vaccination are going on as before, but we will have to wait until systems are restored before announcements will resume and backdated data is published.

When the dust settles on this I’m pretty sure the inevitable investigation will reveal that the HSE has been using outdated IT hardware and software that made it much easier for the cybercriminals than it should have been.  The disruption is of course extremely annoying but there is a real possibility that the cancellation of urgent medical procedures may lead to loss of life. I sincerely hope the perpetrators are caught and subjected to the full force of the law.

Meanwhile, out of interest, here is my latest summary plot (dated 14th May) which shows new cases steady at the (uncomfortably) high level of around 430 per day (7-day average) but deaths falling:

It is reasonable to infer that the combination of falling mortality figures and constant infection rates is attributable to the vaccination most people in the groups most at risk.

Last Monday (10th May) saw various relaxations of the current restrictions around Covid-19 and tomorrow there will be further loosening. In particular all remaining “non-essential” shops will open. This won’t make much difference to me personally as I shall be locked down marking examinations for at least the next fortnight.

I don’t think the cyber attack will affect the timing of my second vaccine dose, which is due in early June, but that remains to be seen.

I’m Old Fashioned – Curtis Fuller

Posted in Jazz with tags , , , , on May 15, 2021 by telescoper

Saddened to hear of the death last week of the great Jazz trombonist Curtis Fuller I’ve been thinking of an appropriate track to play. Fuller had a long and distinguished career alongside many great artists which makes it difficult to pick just one track as a tribute, but as so often is the case I found myself gravitating back to the late 1950s which I think is probably my favourite period in Jazz history.

Thus I settled on a track from the studio album Blue Train recorded in 1957 by a sextet led by John Coltrane and featuring Curtis Fuller (trombone) and Lee Morgan (trumpet) with Kenny Drew on piano, Paul Chambers (bass) and Philly Joe Jones on drums. It’s a superb album which is a must-have for any serious collector of this music. I thought I had already posted a track from this album on here, actually, but apparently I haven’t.

John Coltrane is now an established as one of the leading figures in the development of modern Jazz but this record is a reminder that he achieved recognition somewhat later in his life than many other soloists. At 31, he wasn’t exactly old when this album was recorded in 1957 but he was certainly no newcomer either. Obviously it took him a while to find his voice. By contrast the trumpeter Lee Morgan was, astonishingly, only 19 when this record was made; Curtis Fuller was in his mid-twenties.

Everyone plays beautifully on all the tracks on this album, and the blend of trumpet tenor sax and trombone in the ensemble gives this band a very distinctive sound, but I’ve picked a track on which Curtis Fuller really excels as a soloist. The rest of the tunes being based on the blues, this is actually the only ballad on the album, written by Jerome Kern and Johnny Mercer, and called I’m Old Fashioned

R.I.P. Curtis Fuller (1932-2021)

Analysis of Diverse Perversities

Posted in Art with tags , , on May 14, 2021 by telescoper

by Paul Klee (1879-1940), painted in 1922, 24cm x 31cm, pen and watercolour on paper.