Archive for open science

New Publication at the Open Journal of Astrophysics!

Posted in Open Access, The Universe and Stuff with tags , , , , , , , , , on March 20, 2019 by telescoper

It’s nice to be able to announce that the Open Journal of Astrophysics has just published another paper. Here it is!

It’s by Darsh Kodwani, David Alonso and Pedro Ferreira from a combination of Oxford University and Cardiff University.

You can find the accepted version on the arXiv here. This version was accepted after modifications requested by the referee and editor.

This is another one for the `Cosmology and Nongalactic Astrophysics’ folder. We would be happy to get more submissions from other areas of astrophysics. Hint! Hint!

P.S. A few people have asked why the Open Journal of Astrophysics is not listed in the Directory of Open Access Journals. The answer to that is simple: to qualify for listing a journal must publish a minimum of five papers in a year. Since OJA underwent a failure long hiatus after publishing its first batch of papers we don’t yet qualify. However, so far in 2019 we have published four papers and have several others in the pipeline. We will reach the qualifying level soon and when we do I will put in the application!

Advertisements

Splitting with Elsevier

Posted in Open Access with tags , , , , on March 7, 2019 by telescoper

Just time today to pass on a bit of Open Access news: the University of California has ended negotiations which academic publishing giant Elsevier and will no longer subscribe to Elsevier Journals. The negotiations broke down over two key points: a refusal by Elsevier to reduce its charges (currently $11M) and a failure to meet guarantees on Open Access. There’s another piece about this here.

The University of California should be congratulated on its firm position here, as should organizations in Sweden and Germany for their similar decisions last year.

I’ve made my views of the academic publishing racket very clear over a number of years so I won’t repeat that rant here. I’ll just remind readers of the staggering fact that the global revenues of the academic publishing industry amount to about, €22 billion per annum. This exceeds the global revenues of the recorded music industry. Profit margins for these publishers are much larger (up to 45%) than Apple, Google and BMW.

The research community is being fleeced, and the worst offenders are the `Big Four’: Elsevier, Springer, Wiley and Taylor & Francis. It’s taken a while but it seems many organizations are finally waking up to what is going on. I don’t think we need `for-profit’ publishers at all – there are far better and cheaper ways of disseminating scientific research in the digital era, such as the arXiv.

I’ll also make a small plea here. If there are any rich philanthropists out there who want to do something positive for science then let me suggest that instead of funding more prizes or awards they consider making a large donation to the arXiv? In my view that would do far more for science than throwing yet more money at a few eminent individuals!

Grave Wave Doubts?

Posted in Bad Statistics, The Universe and Stuff with tags , , , , on November 1, 2018 by telescoper

coverns

I noticed this morning that this week’s New Scientist cover feature (by Michael Brooks)is entitled Exclusive: Grave doubts over LIGO’s discovery of gravitational waves. The article is behind a paywall – and I’ve so far been unable to locate a hard copy in Maynooth so I haven’t read it yet but it is about the so-called `Danish paper’ that pointed out various unexplained features in LIGO data associated with the first detection of gravitational waves of a binary black hole merger.

I did know this piece was coming, however, as I spoke to the author on the phone some time ago to clarify some points I made in previous blog posts on this issue (e.g. this one and that one). I even ended up being quoted in the article:

Not everyone agrees the Danish choices were wrong. “I think their paper is a good one and it’s a shame that some of the LIGO team have been so churlish in response,” says Peter Coles, a cosmologist at Maynooth University in Ireland.

I stand by that comment, as I think certain members – though by no means all – of the LIGO team have been uncivil in their reaction to the Danish team, implying that they consider it somehow unreasonable that the LIGO results such be subject to independent scrutiny. I am not convinced that the unexplained features in the data released by LIGO really do cast doubt on the detection, but unexplained features there undoubtedly are. Surely it is the job of science to explain the unexplained?

It is 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). In normal-sized laboratory physics it suffices to explain the experimental set-up in the published paper in sufficient detail for another individual or group to build an equivalent replica experiment if they want to check the results. In `Big Science’, e.g. with LIGO or the Large Hadron Collider, it is not practically possible for other groups to build their own copy, so the best that can be done is to release the data coming from the experiment. A basic problem with reproducibility obviously arises when this does not happen.

In astrophysics and cosmology, results in scientific papers are often based on very complicated analyses of large data sets. This is also the case for gravitational wave experiments. Fortunately, in astrophysics these days, researchers are generally pretty good at sharing their data, but there are a few exceptions in that field.

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. In any case there are often intermediate stages between `raw’ data and scientific results, as well as ancillary data products of various kinds. I think these should all be made public. Doing that could well entail a great deal of effort, but I think in the long run that it is worth it.

I’m not saying that scientific collaborations should not have a proprietary period, just that this period should end when a result is announced, and that any such announcement should be accompanied by a release of the data products and software needed to subject the analysis to independent verification.

Given that the detection of gravitational waves is one of the most important breakthroughs ever made in physics, I think this is a matter of considerable regret. I also find it difficult to understand the reasoning that led the LIGO consortium to think it was a good plan only to go part of the way towards open science, by releasing only part of the information needed to reproduce the processing of the LIGO signals and their subsequent statistical analysis. There may be good reasons that I know nothing about, but at the moment it seems to me to me to represent a wasted opportunity.

CLARIFICATION: The LIGO Consortium released data from the first observing run (O1) – you can find it here – early in 2018, but this data set was not available publicly at the time of publication of the first detection, nor when the team from Denmark did their analysis.

I know I’m an extremist when it comes to open science, and there are probably many who disagree with me, so here’s a poll I’ve been running for a year or so on this issue:

Any other comments welcome through the box below!

UPDATE: There is a (brief) response from LIGO (& VIRGO) here.

The Open Journal of Astrophysics Blog

Posted in Open Access with tags , , , on October 5, 2018 by telescoper

Since I’ve recently been boring all my readers with a stream of stuff about the Open Journal of Astrophysics, I thought I might as well continue by pointing out that this journal also has a blog feature, on which we will include commentaries on some of the papers published and on wider issues in astrophysics. To illustrate this feature I’ve written a short post about the background to the Open Journal project, which you can find here. The text is as below.

I first proposed this idea several years ago and it has taken a while to make it happen, but here we are at last.

Astrophysics has taken the lead for many years in opening up access to scientific publications – all publications of any merit are available for free on the internet via the arXiv and, in my opinion, the traditional journals are already more-or-less redundant even without considering their “astronomical” cost. The one thing that seems a consistent objection to dispensing with journals altogether is the element of peer review.

My suggestion was that we set up a quick-and-easy system to circumvent the traditional (ruinously expensive) publishing route. The basic idea is that authors who submit papers to the arXiv can have their papers refereed by the community, outside the usual system of traditional journals. I was intially thinking of a website on which authors would simply have to post their arXiv ID and a request for peer review. Once accepted, the author would be allowed to mark the arXiv posting as “refereed” and an electronic version would be made available for free on the website. What we have now is a little more involved than that, but the basic idea remains the same.

Whether or not this idea is a success really depends partly on the willingness of the community to submit high-quality papers here, and partly on the performance of those of us involved on the Editorial Board at providing the community with what I hope will prove to be an effective resource.

 

The Open Journal of Astrophysics – Update

Posted in Maynooth, Open Access, The Universe and Stuff with tags , , , on October 4, 2018 by telescoper

Well, it was a bit fiddly importing the legacy papers from the earlier version of the Open Journal of Astrophysics website to the new platform, but I managed to do it this afternoon as planned. The result looks rather nice, I think,

The only things left to do now are (a) to train the members of the Editorial Board on how to handle the workflow through the journal site and (b) to open up for submission of new papers. Both these steps should be trivial so we’re definitely entering the final stages of this project. There is  an event at Maynooth University Library next Tuesday afternoon at which I am doing a talk about Open Science. This will represent the official launch of the Open Journal of Astrophysics.

All we will need then is for people to submit some papers!

 

 

A Python Toolkit for Cosmology

Posted in The Universe and Stuff with tags , , , , on December 14, 2017 by telescoper

The programming language Python has established itself as the industry standard for researchers in physics and astronomy (as well as the many other fields, including most of those covered by the Data Innovation Research Institute which employs me part-time). It has also become the standard vehicle for teaching coding skills to undergraduates in many disciplines. In fact it looks like the first module I will be teaching in Maynooth next term is in Computational Physics, and that will be delivered using Python too. It’s been a while since I last did any significant hands-on programming, so this will provide me with a good refresher. The best way to learn something well is to have to teach it to others!

But I digress. This morning I noticed a paper by Benedikt Diemer on the arXiv with the title COLOSSUS: A python toolkit for cosmology, large-scale structure, and dark matter halos. Here is the abstract:

This paper introduces Colossus, a public, open-source python package for calculations related to cosmology, the large-scale structure of matter in the universe, and the properties of dark matter halos. The code is designed to be fast and easy to use, with a coherent, well-documented user interface. The cosmology module implements FLRW cosmologies including curvature, relativistic species, and different dark energy equations of state, and provides fast computations of the linear matter power spectrum, variance, and correlation function. The large-scale structure module is concerned with the properties of peaks in Gaussian random fields and halos in a statistical sense, including their peak height, peak curvature, halo bias, and mass function. The halo module deals with spherical overdensity radii and masses, density profiles, concentration, and the splashback radius. To facilitate the rapid exploration of these quantities, Colossus implements about 40 different fitting functions from the literature. I discuss the core routines in detail, with a particular emphasis on their accuracy. Colossus is available at bitbucket.org/bdiemer/colossus.

The software can be downloaded here. It looks a very useful package that includes code to calculate many of the bits and pieces used by cosmologists working on the theory of large-scale structure and galaxy evolution. It is also, I hope, an example of a trend towards greater use of open-source software, for which I congratulate the author! I think this is an important part of the campaign to create truly open science, as I blogged about here.

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). At present, this can’t always be done. In my own field of astrophysics/cosmology, for example, results in traditional 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.

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 aren’t guaranteed to be representative of the community, so I’d like to ask for a quick show of hands via a poll…

…and you are of course welcome to comment via the usual box.

Science for the Citizen

Posted in Education, Open Access, The Universe and Stuff with tags , , , , , , on March 20, 2017 by telescoper

I spent all day on Friday on business connected with my role in the Data Innovation Research Institute, attending an event to launch the new Data Justice Lab at Cardiff University. It was a fascinating day of discussions about all kinds of ethical, legal and political issues surrounding the “datafication” of society:

Our financial transactions, communications, movements, relationships, and interactions with government and corporations all increasingly generate data that are used to profile and sort groups and individuals. These processes can affect both individuals as well as entire communities that may be denied services and access to opportunities, or wrongfully targeted and exploited. In short, they impact on our ability to participate in society. The emergence of this data paradigm therefore introduces a particular set of power dynamics requiring investigation and critique.

As a scientist whose research is in an area (cosmology) which is extremely data-intensive, I have a fairly clear interpretation of the phrase “Big Data” and recognize the need for innovative methods to handle the scale and complexity of the data we use. This clarity comes largely from the fact that we are asking very well-defined questions which can be framed in quantitative terms within the framework of well-specified theoretical models. In this case, sophisticated algorithms can be constructed that extract meaningful information even when individual measurements are dominated by noise.

The use of “Big Data” in civic society is much more problematic because the questions being asked are often ill-posed and there is rarely any compelling underlying theory. A naive belief exists in some quarters that harvesting more and more data necessarily leads to an increase in relevant information. Instead there is a danger that algorithms simply encode false assumptions and produce unintended consequences, often with disastrous results for individuals. We heard plenty of examples of this on Friday.

Although it is clearly the case that personal data can be – and indeed is – deliberately used for nefarious purposes, I think there’s a parallel danger that we increasingly tend to believe that just because something is based on numerical calculations it somehow must be “scientific”. In reality, any attempt to extract information from quantitative data relies on assumptions. if those assumptions are wrong, then you get garbage out no matter what you put in. Some applications of “data science” – those that don’t recognize these limitations – are in fact extremely unscientific.

I mentioned in discussions on Friday that there is a considerable push in astrophysics and cosmology for open science, by which I mean that not only are the published results openly accessible, but all the data and analysis algorithms are published too. Not all branches of science work this way, and we’re very far indeed from a society that applies such standards to the use of personal data.

Anyway, after the day’s discussion we adjourned to the School of Journalism, Media and Cultural Studies for a set of more formal presentations. The Head of School, Professor Stuart Allan introduced this session with some quotes from a book called Science for the Citizen, written by Lancelot Hogben in 1938. I haven’t read the book, but it looks fascinating and prescient. I have just ordered it and look forward to reading it. You can get the full-text free online here.

Here is the first paragraph of Chapter 1:

A MUCH abused writer of the nineteenth century said: up to the present philosophers have only interpreted the world, it is also necessary to change it. No statement more fittingly distinguishes the standpoint of humanistic philosophy from the scientific outlook. Science is organized workmanship. Its history is co-extensive with that of civilized living. It emerges so soon as the secret lore of the craftsman overflows the dam of oral tradition, demanding a permanent record of its own. It expands as the record becomes accessible to a widening personnel, gathering into itself and coordinating the fruits of new crafts. It languishes when the social incentive to new productive accomplishment is lacking, and when its custodians lose the will to share it with others. Its history, which is the history of the constructive achievements of mankind, is also the history of the democratization of positive knowledge. This book is written to tell the story of its growth as a record of human achievement, a story of the satisfaction of the common needs of mankind, disclosing as it unfolds new horizons of human wellbeing which lie before us, if we plan our new resources intelligently.

The phrase that struck me with particular force is “the democratization of positive knowledge”. That is what I believe science should do, but the closed culture of many fields of modern science makes it difficult to argue that’s what it actually does. Instead, there is an increasing tendency for scientific knowledge in many domains to be concentrated in a small number of people with access to the literature and the expertise needed to make sense of it.

In an increasingly technologically-driven society, the gap between the few in and the many out of the know poses a grave threat to our existence as an open and inclusive democracy. The public needs to be better informed about science (as well as a great many other things). Two areas need attention.

In fields such as my own there’s a widespread culture of working very hard at outreach. This overarching term includes trying to get people interested in science and encouraging more kids to take it seriously at school and college, but also engaging directly with members of the public and institutions that represent them. Not all scientists take the same attitude, though, and we must try harder. Moves are being made to give more recognition to public engagement, but a drastic improvement is necessary if our aim is to make our society genuinely democratic.

But the biggest issue we have to confront is education. The quality of science education must improve, especially in state schools where pupils sometimes don’t have appropriately qualified teachers and so are unable to learn, e.g. physics, properly. The less wealthy are becoming systematically disenfranchised through their lack of access to the education they need to understand the complex issues relating to life in an advanced technological society.

If we improve school education, we may well get more graduates in STEM areas too although this government’s cuts to Higher Education make that unlikely. More science graduates would be good for many reasons, but I don’t think the greatest problem facing the UK is the lack of qualified scientists – it’s that too few ordinary citizens have even a vague understanding of what science is and how it works. They are therefore unable to participate in an informed way in discussions of some of the most important issues facing us in the 21st century.

We can’t expect everyone to be a science expert, but we do need higher levels of basic scientific literacy throughout our society. Unless this happens we will be increasingly vulnerable to manipulation by the dark forces of global capitalism via the media they control. You can see it happening already.