Archive for the Open Access Category

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!

 

 

Thoughts on `Plan S’, `cOAlition S’ and Open Access Publishing

Posted in Open Access with tags , , , , , , on September 22, 2018 by telescoper

Those of you who have been following my recent updates on progress with The Open Journal of Astrophysics may be interested to hear about `Plan S’, which is a proposal by 11 European Nations to give the public free access to publicly funded science. The 11 countries involved in this initiative are: France, Italy, Austria, Ireland, Luxembourg, the Netherlands, Norway, Poland, Slovenia, Sweden, and the UK. Since the plan will not come into effect until 1st January 2020, which is after the UK leaves the EU it is by no means clear whether the UK will actually be involved in ERC initiatives after that. Norway is not in the EU but is associated to the ERC. It is unlikely that the UK will have a similar status after Brexit.

Anyway, these 11 countries have formed `cOAlition S’ – the `OA’ is for `Open Access’ – to carry out the plan, which can be found here.

Here is a summary:

You can read more about it here. I have not yet looked at the details of what will be regarded as `compliant’ in terms of Open Access but if the the Open Journal of Astrophysics is not fully compliant as it stands, I expect it can be made so (although we are a genuinely international journal not limited to the 11 countries involved in Plan S).

Anyway, although I support Plan S in general terms what I sincerely hope will not happen with this initiative is that researchers and their institutions get mugged into paying an extortionate `Gold’ Open Access Article Processing Charge (APC) which is simply a means for the academic publishing industry to maintain its inflated profit margins at the expense of actual research. The Open Journal of Astrophysics is Green rather than Gold. In fact the cost of maintaining and running the platform is about $1000 per annum, and the marginal cost for processing each paper is $10 or actually $11 if you count registering published articles with CrossRef (though we do not incur that cost if the article is rejected). In effect running the entire journal costs less than a typical APC for Gold Open Access for one physics paper. Those costs will be born by my institution, Maynooth University. The UK was conned into going down this route some years ago by the publishing lobby, and I hope the other cOAlition S partners do not fall for the same scam.

The Open Journal of Astrophysics – Call for Editors

Posted in Maynooth, Open Access with tags , , , on September 17, 2018 by telescoper

It’s nice to see that my recent post on the Open Journal of Astrophysics has been attracting some interest. The project is developing rather swiftly right now and it seems the main problems we have to deal with are administrative rather than technical. Fingers crossed anyway.

I thought I’d do a follow-up re-iterating a request in that recent post. As you will be aware, the Open Journal of Astrophysics is an arXiv overlay journal. We apply a simple criterion to decide whether a paper is on a suitable topic for publication, 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. This section of the arXiv, which is rather broad,is divided thuswise:

  1. astro-ph.GA – Astrophysics of Galaxies.
    Phenomena pertaining to galaxies or the Milky Way. Star clusters, HII regions and planetary nebulae, the interstellar medium, atomic and molecular clouds, dust. Stellar populations. Galactic structure, formation, dynamics. Galactic nuclei, bulges, disks, halo. Active Galactic Nuclei, supermassive black holes, quasars. Gravitational lens systems. The Milky Way and its contents
  2. astro-ph.CO – Cosmology and Nongalactic Astrophysics.
    Phenomenology of early universe, cosmic microwave background, cosmological parameters, primordial element abundances, extragalactic distance scale, large-scale structure of the universe. Groups, superclusters, voids, intergalactic medium. Particle astrophysics: dark energy, dark matter, baryogenesis, leptogenesis, inflationary models, reheating, monopoles, WIMPs, cosmic strings, primordial black holes, cosmological gravitational radiation
  3. astro-ph.EP – Earth and Planetary Astrophysics.
    Interplanetary medium, planetary physics, planetary astrobiology, extrasolar planets, comets, asteroids, meteorites. Structure and formation of the solar system
  4. astro-ph.HE – High Energy Astrophysical Phenomena.
    Cosmic ray production, acceleration, propagation, detection. Gamma ray astronomy and bursts, X-rays, charged particles, supernovae and other explosive phenomena, stellar remnants and accretion systems, jets, microquasars, neutron stars, pulsars, black holes
  5. astro-ph.IM – Instrumentation and Methods for Astrophysics.
    Detector and telescope design, experiment proposals. Laboratory Astrophysics. Methods for data analysis, statistical methods. Software, database design
  6. astro-ph.SR – Solar and Stellar Astrophysics.
    White dwarfs, brown dwarfs, cataclysmic variables. Star formation and protostellar systems, stellar astrobiology, binary and multiple systems of stars, stellar evolution and structure, coronas. Central stars of planetary nebulae. Helioseismology, solar neutrinos, production and detection of gravitational radiation from stellar systems.

The expertise of the current Editorial Board is concentrated in the area of (2), and a bit of (5), but we would really like to add some editors from different areas (i.e. 1, 3, 4 and 6).  We  would therefore really appreciate volunteers from other areas of astrophysics (especially stars/exoplanets, etc). If you’re interested please let me know. Please also circulate this call as widely as possible among your colleagues so we can recruit the necessary expertise. The journal is entirely free (both to publish in and to read) and we can’t afford to pay a fee, but there is of course the prestige of being in at the start of a publishing revolution of cosmic proportions!

If you join the Editorial Board we will invite you to an online training session to show you how the platform works.

Thank you in advance for your interest in this project, and I look forward to hearing from you.

 

 

 

The Open Journal of Astrophysics – Update

Posted in Maynooth, Open Access with tags , , , on September 13, 2018 by telescoper

The observant among you will have noticed that the website for the Open Journal of Astrophysics is currently offline. This emphatically does not mean that this project is dead so

In fact we’re in the process of moving the journal to a new platform (at the same web address) and the new site will be up and running as soon as we have completed the transfer, have tested the new configuration and done a few administrative things. All papers already published on the old site will be transferred to the new one and their DOI will remain unchanged. In fact the old site is still available, but at a secret location.

I’ll be blogging in a bit more detail about the new-look Open Journal of Astrophysics in due course, but in the mean time I’ll just make a few points.

First and foremost, if you don’t know what this project is about it is an idea I first floated over five years ago, shortly before I moved to Sussex. Although we got a website together and published a few papers, for one reason or another I didn’t have time to iron out some remaining bugs and the project stalled. However, after my move to Maynooth University I’ve been delighted to receive the support of the Maynooth University Library team and we’re now moving ahead. I know there have been a few false dawns on this project – for which I apologize – so I won’t announce the full re-opening until I’m absolutely sure everything works.

Second, and actually most importantly, the Editorial Board for the Open Journal of Astrophysics is looking for new members. We already have several distinguished editors, but the expertise we currently have is concentrated (not surprisingly) in cosmology, and we would really appreciate volunteers from other areas of astrophysics (especially stars/exoplanets, etc). If you’re interested please let me know.

Third, although the platform will look a little different (i.e. better) the overall philosophy of the Open Journal will remain as it always was, a fully `Green’ Open Access Journal, as defined by the following points:

  • There will be no charge for accessing or downloading OJA papers (i.e. no subscription fee).
  • There will be no charge for submitting, reviewing or publishing OJA papers (i.e. no `article processing charge’).
  • The OJA is a peer-reviewed journal; all papers accepted for publication will be assigned a DOI and registered with Crossref for citation tracking purposes.
  • The OJA is an arXiv overlay journal, so paper submitted to it must first be submitted to the arXiv.

Finally, I will mention that I was motivated to post this update by a piece by George Monbiot in todays’s Guardian. I don’t agree with everything Monbiot says, but he is dead right about this:

In the great majority of cases, the research reported has been funded by taxpayers. Most of the work involved in writing the papers, reviewing and editing them is carried out at public expense by people at universities. Yet this public asset has been captured, packaged and sold back to us for phenomenal fees. Those who pay most are publicly funded libraries. Taxpayers must shell out twice: first for the research, then to see the work they have sponsored. There might be legal justifications for this practice. There are no ethical justifications.

I’ve said as much myself on this blog. My point is that the academic publishing industry is not going to change of its own volition. If the Academic Journal Racket is to be rumbled, it is we (by which I mean academics and our institutions) who have to take control. Sitting on our hands while we get systematically fleeced is not an option. One way to do this is for institutions and organizations to themselves become Open Access publishers, which is precisely what my current institution is doing: Maynooth University will be the official publisher of the Open Journal of Astrophysics (and hopefully many more similar journals in the future).

Citation Analysis of Scientific Categories

Posted in Open Access, Science Politics with tags , on May 18, 2018 by telescoper

I stumbled across an interesting paper the other day with the title Citation Analysis of Scientific Categories. The title isn’t really accurate because not all the 231 categories covered by the analysis are `scientific’: they include many topics in the arts and humanities too. Anyway, the abstract is here:

Databases catalogue the corpus of research literature into scientific categories and report classes of bibliometric data such as the number of citations to articles, the number of authors, journals, funding agencies, institutes, references, etc. The number of articles and citations in a category are gauges of productivity and scientific impact but a quantitative basis to compare researchers between categories is limited. Here, we compile a list of bibliometric indicators for 236 science categories and citation rates of the 500 most cited articles of each category. The number of citations per paper vary by several orders of magnitude and are highest in multidisciplinary sciences, general internal medicine, and biochemistry and lowest in literature, poetry, and dance. A regression model demonstrates that citation rates to the top articles in each category increase with the square root of the number of articles in a category and decrease proportionately with the age of the references: articles in categories that cite recent research are also cited more frequently. The citation rate correlates positively with the number of funding agencies that finance the research. The category h-index correlates with the average number of cites to the top 500 ranked articles of each category (R2 = 0.997). Furthermore, only a few journals publish the top 500 cited articles in each category: four journals publish 60% (σ = ±20%) of these and ten publish 81% (σ = ±15%).

The paper is open access (I think) and you can find the whole thing here.

I had a discussion over lunch today with a couple of colleagues here in Maynooth about using citations. I think we agreed that citation analysis does convey some information about the impact of a person’s research but that information is rather limited. One of the difficulties is that publication rates and citation activity are very discipline-dependent so one can’t easily compare individuals in different areas. The paper here is interesting because it presents an interesting table showing how various statistical citation measures vary across fields and sub-fields;  physics is broken down into a number of distinct areas (e.g. Astronomy & Astrophysics, Particle Physics, Condensed Matter and Nuclear Physics) across which there is considerable variation. How to best to use this information is still not clear..

 

 

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…

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)