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!

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 avatarGowers'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…

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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.

 

 

 

Sinister Moves by Elsevier

Posted in Open Access with tags , , , , on May 18, 2016 by telescoper

I’ve been away at yet another Awayday today so only have time for a brief post before I go home and vegetate. I felt obliged, however, to draw the attention of my readership to the fact that there’s something sinister afoot in the world of academic publishing. It seems that the notoriously exploitative academic publishing company Elsevier has acquired the Social Science Research Network (SSRN), which is  the leading social science and humanities repository and online community. The SSRN currently allows readers free access more than 500,000 academic papers for free but that is highly likely to change under Elsevier whose previous practice has always been to squeeze the academic community for every penny it can get. In particular, Elsevier has a reputation for cracking down on academic papers for which it owns licences, so these recent acquisitions look like very bad news.

The Chairman of SSRN is  trying to present this as a positive move:

SSRN announced today that it has changed ownership. SSRN is joining Mendeley and Elsevier to coordinate our development and delivery of new products and services, and we look forward to our new access to data, products, and additional resources that this change facilitates.

Like SSRN, Mendeley and Elsevier are focused on creating tools that enhance researcher workflow and productivity. SSRN has been at the forefront of on-line sharing of working papers. We are committed to continue our innovation and this change will enable that to happen more quickly. SSRN will benefit from access to the vast new data and resources available, including Mendeley’s reference management and personal library management tools, their new researcher profile capabilities, and social networking features. Importantly, we will also have new access for SSRN members to authoritative performance measurement tools such as those powered by Scopus and Newsflo (a global media tracking tool). In addition, SSRN, Mendeley and Elsevier together can cooperatively build bridges to close the divide between the previously separate worlds and workflows of working papers and published papers.

We realize that this change may create some concerns about the intentions of a legacy publisher acquiring an open-access working paper repository. I shared this concern. But after much discussion about this matter and others in determining if Mendeley and Elsevier would be a good home for SSRN, I am convinced that they would be good stewards of our mission. And our copyright policies are not in conflict — our policy has always been to host only papers that do not infringe on copyrights. I expect we will have some conflicts as we align our interests, but I believe those will be surmountable.

Until recently I was convinced that the SSRN community was best served being a stand-alone entity. But in evaluating our future in the evolving landscape, I came to believe that SSRN would benefit from being more interconnected and with the resources available from a larger organization. For example, there is scale in systems administration and security, and SSRN can provide more value to users with access to more data and resources.

On a personal note, it has been an honor to be involved over the past 25 years in the founding and growth of the SSRN website and the incredible community of authors, researchers and institutions that has made this all possible. I consider it one of my great accomplishments in life. The community would not have been successful without the commitment of so many of you who have contributed in so many ways. I am proud of the community we have created, and I invite you to continue your involvement and support in this effort.

The staff at SSRN are all staying (including Gregg Gordon, CEO and myself), the Rochester office is still in place, it will still be free to upload and download papers, and we remain committed to “Tomorrow’s Research Today”. I look forward to and am committed to a successful transition and to another great 25 years for the SSRN community that rivals the first.

Michael C. Jensen
Founder & Chairman, SSRN

It sounds like they made him an offer he couldn’t refuse…

I don’t think Elsevier’s involvement in this is likely to prove beneficial to anything other than their own profits. Elsevier is one of the biggest problems in academic publishing and can  never be part of the solution.

My main concern, however,  is  that some day Elsevier might launch a hostile takeover bid for the arXiv, which would be a major setback to the physics community’s efforts to promote the free exchange of scientific papers. That must be resisted at all costs. How did the academic community allow its publishing culture to be hijacked by such companies?

 

 

 

 

Discrete Analysis launched

Posted in Open Access on March 1, 2016 by telescoper

I’m reblogging this to congratulate Tim Gowers on the launch of his new arXiv overlay journal, Discrete Mathematics. I wish this venture every success!

The Open Journal of Astrophysics won’t be far behind, and hopefully this will be the start of a real change to “the absurdly expensive and anachronistic system of academic publishing” that Tim Gowers describes in his post!

gowers's avatarGowers's Weblog

As you may remember from an earlier post on this blog, Discrete Analysis is a new mathematics journal that runs just like any other journal except in one respect: the articles we publish live on the arXiv. This is supposed to highlight the fact that in the internet age, and in particular in an age when it is becoming routine for mathematicians to deposit their articles on the arXiv before they submit them to journals, the only important function left for journals is organizing peer review. Since this is done through the voluntary work of academics, it should in principle be possible to run a journal for almost nothing. The legacy publishers (as they are sometimes called) frequently call people naive for suggesting this, so it is important to have actual examples to prove it, and Discrete Analysis is set up to be one such example. Its website goes…

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The Open Journal of Astrophysics: Update

Posted in Open Access with tags on February 25, 2016 by telescoper

Just a quick post to update you all on the Open Journal of Astrophysics project. The journal was opened to submissions just before Christmas 2015 and we’ve been putting papers through our editorial processes since then. We did plan to go live in January, but we have not yet done so because we haven’t had enough publishable articles. It has taken a bit longer than we expected partly because of the relatively low numbers of papers submitted – presumably because authors are understandably nervous about submitting to a new journal – but also because editors and referees are still learning how to use the system, which has slowed us down a bit. However the submissions we have had have allowed us to test the platform and do a bit of tinkering behind the scenes. We also fixed a bug that caused a problem when the site was viewed using Safari (rather than a proper browser).

I’m always delighted when I see something like this on the daily arXiv listing:

OJ_planet

That and several other papers are already in the system but we could do with a few more to join the first batch of half-a-dozen or so we intend to publish soon. For that reason I’m appending below some information I’ve already circulated about the philosophy of the project and the practicalities of how to submit a paper.

–0–

We no longer need traditional academics journals to disseminate research in astrophysics and cosmology. We all post our research to the arXiv and read other papers there too. It’s been years since I last accessed a paper in a journal.  The only useful function that journals provide is peer review, and we in the research community do that (usually for free) anyway.  We only need journals for peer review, although we also like the prestige that is associated with them. But traditional journals have an unnecessarily slow and expensive editorial process, along with a nasty habit of placing the articles they publish behind a paywall.

The Open Journal does things differently, because we are not a publisher in the traditional sense. Instead, we are a peer-review platform, piggybacking on the arXiv for all the “publishing.” The Open Journal provides peer review for arXiv articles, making the process as fast and easy as we can. Once peer review for a particular article is successfully completed, we mark that article as accepted and send that information to the arXiv. Accepted articles will receive a DOI, and citations to them will get picked up through the CrossRef system just as they would in any other journal — but in a fraction of the time, and at a fraction of the cost. In fact, the service is provided free of charge both for authors and readers. There is no Article Processing Charge, no submission fee and no subscription is payable. The Open Journal is a service to the academic community, not a profit-making venture.

Moreover, articles published by the Open Journal are open, in that all articles  are released under a Creative Commons Attribution license. The infrastructure is open too – the code running the Open Journal is available under an MIT license. The reviewer comments can be made open too, with the agreement of both the authors and reviewer(s).  In the long run I hope  that the community will embrace the spirit of open reviewing so anonymous confidential reviews will become the exception rather than the rule, but we’ll see how that goes just for now.

Any paper that’s suitable for the astro-ph section of the arXiv can be subvmitted to the Open Journal of Astrophysics. We will consider any “traditional” papers as well as others which may find it difficult to get into other journals, such as papers on astrophysics education or outreach or technical papers relating to instrumentation, mission proposals, and other documents.

Now, to business. The best way to get an idea of how the Open Journal works is by watching the following video (which was made using a beta version of the site, but nothing much has changed except for a few layout issues being changed):

Note that the site is currently just called the Open Journal, which is so that it can be used with minimal modification to create similar journals in other fields.

If you don’t want to watch the whole thing here’s a quick summary of the steps you have to take to submit to the Open Journal.

  1.  If you don’t have one already, get an ORCID ID!
  2. Write your paper. There is latex style file you can use here, although it is not compulsory to use this and we will allow anything that produces a PDF that can be viewed easily using our mark-up tool. Single-column is strongly preferred.
  3. Submit your paper to the arXiv. You have to be registered in order to do this. Note also that you have to be prepared to submit your paper to the arXiv before it is reviewed. There is an enormous advantage in doing this, actually, as you may get more comments and suggestions than our refereeing system will generate.
  4. Log on to the Open Journal website
  5. Go to the submit tab on the left hand side of the screen.
  6. Type in the arXiv reference of your paper (you can do this in various ways)
  7. Our software will assign the paper to an editor, who will then select referee(s). Each referee makes comments by marking “issues” on the PDF, each of which needs a reply from the author. When all issues are resolved the paper is accepted. If revision is required a new version can be submitted to the arXiv which will be picked up by the software.
  8. When it us ready our software will automatically assign a DOI and write it to the appropriate field in the arXiv.
  9. That’s it! The paper is published and can be accessed either directly on the arXiv or through the Open Journal website.
  10. Go and have a beer.

One other thing is worth mentioning. Because this service is provided free we do not have the effort required to undertake extensive copy-editing or rewriting of papers that are very poorly written. If the editor or referee deems a paper to be unfit for review then we will refer the author to a professional writing and editing service who will charge a fee depending on the length and complexity of the task.

As well as submissions we are also looking for new editors. At the moment our Editorial Board is dominated by cosmologists but as word gets round we will probably need expertise in other areas of astrophysics. If you’d like to volunteer please send me an email or use the comment box below.

Well, that’s about it. I just remains for me to thank all the people without whom this project would never have got off the ground, chiefly Chris Lintott, Arfon Smith and Adam Becker, developers Stuart Lynn and Marc Rohloff, and of course the good folk of the wonderful arXiv!