Archive for open science

Gruber Prize 2020: Volker Springel & Lars Hernquist

Posted in Open Access, The Universe and Stuff with tags , , , , , on May 8, 2020 by telescoper

I’m delighted to be able to pass on the news released yesterday that the 2020 Gruber Prize for Cosmology has been awarded to Lars Hernquist (left) and Volker Springel (right) for their work on numerical simulations.

The citation reads:

The Gruber Foundation is pleased to present the 2020 Cosmology Prize to Lars Hernquist and Volker Springel for their transformative work on structure formation in the universe, and development of numerical algorithms and community codes further used by many other researchers to significantly advance the field. The contributions of Hernquist and Springel have led to profound insights spanning billions of years of cosmic evolution, including simulations of the growth of early density fluctuations through to present-day galaxies, the influence of galaxy mergers on star formation, and the close coevolution of supermassive black holes with their host galaxies.

I’ll just add that as well as being enormously influential in purely scientific terms both these scientists have contributed to the culture of open science through making codes (such as GADGET) freely available to the community.

Heartiest congratulations to Volker Springel and Lars Hernquist on their very well deserved award.

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.

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , on December 11, 2019 by telescoper

We seem to be having an end-of-year rush and have published yet another new paper at The Open Journal of Astrophysics!

Here is a grab of the overlay:

The authors are Aditi Krishak (IISER Bhopal) and Shantanu Desai (IIT Hyderabad), both in India.

You can find the accepted version on the arXiv here. This is another one for the `Cosmology and Nongalactic Astrophysics’ section with a cross-listing in `Instrumentation and Methods for Astrophysics’, both of which are proving rather popular.

We would be very happy to get more submissions from other areas, especially Stellar and Planetary astrophysics. Hint! Hint!

P.S. Just a reminder that we now have an Open Journal of Astrophysics Facebook page where you can follow updates from the Journal should you so wish..

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , on December 9, 2019 by telescoper

We have published yet another new paper at The Open Journal of Astrophysics!

Here is a grab of the overlay:

The authors are Emilio Bellini (Oxford, UK), Ludovic van Waerbeke (University of British Columbia, Canada), Shahab Joudaki (Oxford) and David Alonso (Cardiff)

You can find the accepted version on the arXiv here. This is another one for the `Cosmology and Nongalactic Astrophysics’ section, which is proving rather popular.

We would be very happy to get more submissions from other areas, especially Stellar and Planetary astrophysics. Hint! Hint!

P.S. Just a reminder that we now have an Open Journal of Astrophysics Facebook page where you can follow updates from the Journal should you so wish..

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , , , on December 2, 2019 by telescoper

We have published another new paper at The Open Journal of Astrophysics. We actually published this one last week but (presumably because of the Thanksgiving holiday) it has taken longer than usual to register the DOI with Crossref and I held off mentioning this paper here until everything was sorted.

Here is a grab of the overlay:

The authors are Farhad Feroz and Mike Hobson of the Cavendish Laboratory at the University of Cambridge (UK), Ewan Cameron (now at Oxford, UK) and Anthony N. Pettitt of Queensland University of Technology in Australia.

You can find the accepted version on the arXiv here. This version was accepted after modifications requested by the referee and editor. Because this is an overlay journal the authors have to submit the accepted version to the arXiv (which we then check against the copy submitted to us) before publishing; version 3 on the arXiv is the accepted version (which contains a link to updated software).

It is worth mentioning a couple of points about this paper.

The first is that it is mainly a statistical methods paper rather than astrophysics per se but it does contain applications to astrophysics and cosmology and, more relevantly, was posted on the `Instrumentation and Methods for Astrophysics’ section on the arXiv. The Editorial Board felt that we should consider it for publication because our rule for whether a paper can be considered for publication in the Open Journal of Astrophysics is stated clearly on our instructions for authors:

We apply a simple criterion to decide whether a paper is on a suitable topic for this journal, namely that if it it is suitable for the astro-ph section of the arXiv then it is suitable for The Open Journal of Astrophysics.

So far our publication list is dominated by papers in `Cosmology and Nongalactic Astrophysics’ and `Instrumentation and Methods for Astrophysics’ (which is not surprising given its origin) but we would be very happy to get more submissions from other areas, especially Stellar and Planetary astrophysics. Hint! Hint!

The other point to make is that this paper actually appeared on the arXiv over six years ago and has been widely cited as a preprint but it has never previously been published by a journal. The Editorial Board felt that we should consider it for publication in order to ensure that it is properly curated and citations properly assigned, but we treated it as a new submission and sent it out for review just like any other paper. The review led to some changes and, most importantly, a few updates to the software which you can find here. The editorial process has been quite lengthy for this paper but I think we have done a valuable service to the community in reviewing and publishing this paper.

P.S. Just a reminder that we now have an Open Journal of Astrophysics Facebook page where you can follow updates from the Journal should you so wish..

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , on November 24, 2019 by telescoper

Yesterday we published another new paper at The Open Journal of Astrophysics. Here is a grab of the overlay:

The authors are Katarina MarKovic (now of JPL in California), Benjamin Bose (of the University of Geneva) and Alkistis Pourtsidou (Queen Mary, University of London).

You can find the accepted version on the arXiv here. This version was accepted after modifications requested by the referee and editor. Because this is an overlay journal the authors have to submit the accepted version to the arXiv (which we then check against the copy submitted to us) before publishing; version 2 on the arXiv is the accepted version.

I’d like to apologize to the authors for a delay in publishing this paper. It was ready to go a couple of weeks ago, but we had some trouble with an extension to the platform provided by Scholastica which was intended to register Digital Object Identifiers automatically and thus speed up the process. Unfortunately we found some bugs in, and other problems with, the new software and in the end have given up and reverted to the old manual registration process. Hopefully Scholastica will be able to offer a working system for DOI registration before too long.

Anyway, you will see that this is one for the `Cosmology and Nongalactic Astrophysics’ folder. We would be happy to get more submissions from other areas, especially Stellar and Planetary astrophysics. Hint! Hint!

P.S. Just a reminder that we now have an Open Journal of Astrophysics Facebook page where you can follow updates from the Journal should you so wish..

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , , , on September 24, 2019 by telescoper

Yesterday we published another new paper at The Open Journal of Astrophysics, but I didn’t get time to write a post about because of teaching and other start-of-term business so I’m correcting that omission now.

 

The authors are Selim Can Hotinli  of Imperial College London (UK), Marc Kamionkowski of Johns Hopkins University, Baltimore (USA) and Andrew Jaffe, also of Imperial College.

You can find the accepted version on the arXiv here. This version was accepted after modifications requested by the referee and editor. Because this is an overlay journal the authors have to submit the accepted version to the arXiv (which we then check against the copy submitted to us) before publishing; version 2 on the arXiv is the accepted version.

You will see that this is  one for the `Cosmology and Nongalactic Astrophysics’ folder. We would be happy to get more submissions from other areas, especially Stellar and Planetary astrophysics. Hint! Hint!

P.S. Just a reminder that we now have an Open Journal of Astrophysics Facebook page where you can follow updates from the Journal should you wish..