Archive for the Open Access Category

LIGO, Leaks and NGC 4993

Posted in Open Access, The Universe and Stuff with tags , , , , on August 23, 2017 by telescoper

No matter what the official policy may be, the more people there are in a collaboration the more likely it is that someone will let their excitement get to their head and start leaking news and starting rumours either directly or indirectly via social media. And so it came to pass last Friday that the following tweet appeared:

I didn’t comment on the time as I thought it might be unreliable – as it indeed it still may be – but now New Scientist has amplified the signal I feel I can’t really be blamed for mentioning it here.

The rumours going round identify the optical counterpart as being in the galaxy NGC 4993 , a red band image of which, from the Second Digitized Sky Survey (DSS2) is shown below:

NGC 4993 is the fuzzy blob slightly above and to the left of the centre of the image. It’s a fairly nondescript lenticular galaxy in a group that can be found in the constellation of Hydra. It lies in the constellation of Hydra, was actually first discovered by William Herschel and it is about 10 arcmin across on the sky. It’s quite nearby, as these things go, with a distance of about 124 million light years (i.e. 40 Mpc or so) and is about 14th magnitude.

If there is an optical counterpart to a gravitational wave event coming from this galaxy then that suggests it may be a coalescence of neutron stars. The black hole mergers that appear to be responsible to the three existing gravitational wave signals that are claimed to have been detected are not expected to release optical light. Confirmation of this interpretation can be found by where the Hubble Space Telescope was pointed yesterday:

Look familiar? HST was, in fact, observing a `BNS-Merger’ (which is short for `Binary Neutron Star’)…

BNS

If this rumour is true then it’s obviously exciting, but there are questions to be asked. Chief among these is how sure is the identification of the counterpart? A transient optical source in NGC4993 may have been observed at the same time as a gravitational wave signal was detected,  but the ability of LIGO to resolve positions on the sky is very poor. On the other hand, the European VIRGO experiment joined Advanced LIGO for the ongoing `O2′ observing run (which ends in a couple of days). Although VIRGO is less sensitive than LIGO having a third detector does improve the localization of the source – assuming, of course, that it detects a signal. Even in that case it certainly won’t be possible to pinpoint the GW source to within 10 arc minutes, which is the precision needed to place it definitely within NGC 4993.

Anyway, we wait and see what, if anything, has been found. If it is a claimed detection then I hope that LIGO and VIRGO will release sufficient data to enable the analysis to be checked and verified. That’s what most of the respondents to my poll seem to hope too!

Advertisements

LIGO and Open Science

Posted in Open Access, Science Politics, The Universe and Stuff with tags , , , , on August 8, 2017 by telescoper

I’ve just come from another meeting here at the Niels Bohr Institute between some members of the LIGO Scientific Collaboration and the authors of the `Danish Paper‘. As with the other one I attended last week it was both interesting and informative. I’m not going to divulge any of the details of the discussion, but I anticipate further developments that will put some of them into the public domain fairly soon and will comment on them as and when that happens.

I think 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. Particle physicists, by contrast, generally treat all their data as proprietary.

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.

Now, if you are interested in trying to reproduce the analysis of data from the first detection of gravitational waves by LIGO, you can go here, where you can not only download the data but also find a helpful tutorial on how to analyse it.

This seems at first sight to be fully in the spirit of open science, but if you visit that page you will find this disclaimer:

 

In other words, one can’t check the LIGO data analysis because not all the data and tools necessary to do that are not publicly available.  I know for a fact that this is the case because of the meetings going on here at NBI!

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.

I know I’m an extremist when it comes to open science, and there are probably many who disagree with me, so I thought I’d do a mini-poll on this issue:

Any other comments welcome through the box below!

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.

Time for Elsexit?

Posted in Open Access on November 29, 2016 by telescoper

I, for one, agree very strongly that we should ditch Elsevier completely. Tim Gowers gives the lowdown on the scandalous situation.

Gowers's Weblog

This post is principally addressed to academics in the UK, though some of it may apply to people in other countries too. The current deal that the universities have with Elsevier expires at the end of this year, and a new one has been negotiated between Elsevier and Jisc Collections, the body tasked with representing the UK universities. If you want, you can read a thoroughly misleading statement about it on Elsevier’s website. On Jisc’s website is a brief news item with a link to further details that tells you almost nothing and then contains a further link entitled “Read the full description here”, which appears to be broken. On the page with that link can be found the statement

The ScienceDirect agreement provides access to around 1,850 full text scientific, technical and medical (STM) journals – managed by renowned editors, written by respected authors and read by researchers from…

View original post 3,447 more words

Autumn Dreams

Posted in Open Access, Poetry, Uncategorized with tags , , on October 2, 2016 by telescoper

I know the year is dying,
Soon the summer will be dead.
I can trace it in the flying
Of the black crows overhead;
I can hear it in the rustle
Of the dead leaves as I pass,
And the south wind’s plaintive sighing
Through the dry and withered grass.

Ah, ’tis then I love to wander,
Wander idly and alone,
Listening to the solemn music
Of sweet nature’s undertone;
Wrapt in thoughts I cannot utter,
Dreams my tongue cannot express,
Dreams that match the autumn’s sadness
In their longing tenderness.

by Mortimer Crane Brown (1857-1907)

Open Science in the European Union

Posted in Open Access, Science Politics with tags , on May 29, 2016 by telescoper

A few days ago I noticed a remarkable announcement about a meeting of European Ministers in Brussels relating to Open Access Publishing.This has subsequently been picked up by the Grauniad and has been creating quite a stir.

To summarise the report coming out of the meeting, here is a quotation from the draft communique, which states that they

…welcome open access to scientific publications as the option by default for publishing the results of publicly-funded research..

They also plan to

To remove financial and legal barriers, and to take the necessary steps for successful implementation in all scientific domains.

In a nutshell, the proposal is a move to abandon the traditional journal subscription model and embrace freely-available scientific research by 2020.

This is definitely a very good move. My only worry is that those involved seem not to have been able to make a decision on whether to go for the Green or Gold Open Access Model. The latter route has, in my opinion, been grossly abused by profiteering academic publishers who charge eye-watering “processing fees” for open access. I hope this initiative by the EU is not hijacked by vested interests as was the case with the UK’s Finch Report.

There’s clearly a lot more to be done before this proposal can be implemented, but it’s a very positive development the EU which will benefit science, both in the UK and across the continent, hugely. The European Union’s enthusiastic embrace of the principles of open access to scientific research is just one more to add to the list of reasons to remain.

 

 

 

Yes, academic publishers are greedy (and dishonest)

Posted in Open Access, Uncategorized with tags , , , on May 22, 2016 by telescoper

I saw a blatant piece of propaganda in the Guardian the other day, written by the Chief Executive of the Publishers Association.The piece argues that the academic publishing industry benefits the academic community through “innovation and development” and by doing so “adds value” to the raw material supplied by researchers. This is nonsense. The academic publishing industry does not add any value to anything. It just adds cost. And by so doing generates huge profits for itself.

I was annoyed by several other things relating to this item:

  1. It’s written by a vested interest but is presented without a balancing opinion, which makes one wonder why the Guardian is allowing itself to be used as a mouthpiece by these profiteers;
  2. It has been tweeted and retweeed by the Publishers Association several times, as if it were a piece of reporting instead of what it actually is, essentially a commercial;
  3. Some of the claims made in the piece are so risible that they’re insulting.

However, the most annoying thing for me is that I’ve been too busy marking examinations to let off steam by writing a riposte.

I should have worried however, because scrolling down to the comments on the article you can easily find out what academics really think. Moreover, there’s an excellent rebuttal by Mike Taylor here, which I shall reblog.