Archive for open science

The Zel’dovich Universe – Day 4 Summary

Posted in History, The Universe and Stuff with tags , , , , , , , on June 27, 2014 by telescoper

And on the fourth day of this meeting about “The Zel’dovich Universe”  we were back to a full schedule (9am until 7.30pm) concentrating on further studies of the Cosmic Web. We started off with a discussion of the properties of large-scale structure at high redshift. As someone who’s old enough to remember the days when “high redshift” meant about z~0.1 the idea that we can now map the galaxy distribution at redshifts z~2. There are other measures of structure on these huge scales, such as the Lyman alpha forest, and we heard a bit about some of them too.

The second session was about “reconstructing” the Cosmic Web, although a more correct word have been “deconstructing”. The point about this session is that cosmology is basically a backwards subject. In other branches of experimental science we set the initial conditions for a system and then examine how it evolves. In cosmology we have to infer the initial conditions of the Universe from what we observe around us now. In other words, cosmology is an inverse problem on a grand scale.  In the context of the cosmic web, we want to infer the pattern of initial density and velocity fluctuations that gave rise to the present network of clusters, filaments and voids. Several talks about this emphasized how proper Bayesian methods have led to enormous progress in this field over the last few years.

All this progress has been accompanied by huge improvements in graphical visualisation techniques. Thirty years ago the state of the art in this field was represented by simple contour plots, such as this (usually called the Cosmic Chicken):

chicken

You can see how crude this representation is by comparing it with a similar plot from the modern era of precision cosmology:

chicken

Even better examples are provided by the following snapshot:

IMG-20140626-00352

It’s nice to see a better, though still imperfect,  version of the chicken at the top right, though I found the graphic at the bottom right rather implausible; it must be difficult to skate at all with those things around your legs.

Here’s another picture I liked, despite the lack of chickens:

IMG-20140626-00353

Incidentally, it’s the back of Alar Toomre‘s head you can see on the far right in this picture.

The afternoon was largely devoted to discussions of how the properties of individual galaxies are influenced by their local environment within the Cosmic Web. I usually think of galaxies as test particles (i.e. point masses) but they are interesting in their own right (to some people anyway). However, the World Cup intervened during the evening session and I skipped a couple of talks to watch Germany beat the USA in their final group match.

That’s all for now. Tonight we’ll have the conference dinner, which is apparently being held in the “House of Blackheads” on “Pikk Street”. Sounds like an interesting spot!

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The Zel’dovich Universe – Day 3 Summary

Posted in History, The Universe and Stuff with tags , , , , , , on June 26, 2014 by telescoper

Day Three of this meeting about “The Zel’dovich Universe” was slightly shorter than the previous two, in that it finished just after 17.00 rather than the usual 19.00 or later. That meant that we got out in time to settle down for a beer in time the World Cup football. I watched an excellent game between Nigeria and Argentina, which ended 3-2 to Argentina but could have been 7-7. I’ll use that as an excuse for writing a slightly shorter summary.

Anyway we began with a session on the Primordial Universe and Primordial Signatures led off by Alexei Starobinsky (although there is some controversy whether his name should end -y or -i). Starobinsky outlined the theory of cosmological perturbations from inflation with an emphasis on how it relates to some of Zel’dovich’s ideas on the subject. There was then a talk from Bruce Partridge about some of the results from Planck. I’ve mentioned already that this isn’t a typical cosmology conference, and this talk provided another unusual aspect in that there’s hardly been any discussion of the BICEP2 results here. When asked about at the end of his talk, Bruce replied (very sensibly) that we should all just be patient.

Next session after coffee was about cosmic voids, kicked off by Rien van de Weygaert with a talk entitled “Much Ado About Nothing”, which reminded me of the following quote from the play of the same name:

“He hath indeed better bettered expectation than you must expect of me to tell you how”

The existence of voids in the galaxy distribution is not unexpected given the presence of clusters and superclusters, but they are interesting in their own right as they display particular dynamical evolution and have important consequences on observations. In 1984, Vincent Icke proved the so-called “Bubble Theorem” which showed that an isolated underdensity tends to evolve to a spherical shape.Most cosmologists, including myself, therefore expected big voids to be round, which turns out to be wrong; the interaction of the perimeter of the void with its surroundings always plays an important role in determining the geometry. Another thing that sprang into my mind was a classic paper by Simon White (1979) with the abstract:

We derive and display relations which can be used to express many quantitative measures of clustering in terms of the hierarchy of correlation functions. The convergence rate and asymptotic behaviour of the integral series which usually result is explored as far as possible using the observed low-order galaxy correlation functions. On scales less than the expected nearest neighbour distance most clustering measures are influenced only by the lowest order correlation functions. On all larger scales their behaviour, in general, depends significantly on correlations of high order and cannot be approximated using the low-order functions. Bhavsar’s observed relation between density enhancement and the fraction of galaxies included in clusters is modelled and is shown to be only weakly dependent on high-order correlations over most of its range. The probability that a randomly placed region of given volume be empty is discussed as a particularly simple and appealing example of a statistic which is strongly influenced by correlations of all orders, and it is shown that this probability may obey a scaling law which will allow a test of the small-scale form of high-order correlations.

The emphasis is mine. It’s fascinating and somewhat paradoxical that we can learn a lot about the statistics of where the galaxies are fom the regions where galaxies are not.

Another thing worth mentioning was Paul Sutter’s discussion of a project on cosmic voids which is a fine example of open science. Check out the CosmicVoids website where you will find void catalogues, identification algorithms and a host of other stuff all freely available to anyone who wants to use them. This is the way forward.

After lunch we had a session on Cosmic Flows, with a variety of talks about using galaxy peculiar velocities to understand the dynamics of large-scale structure. This field was booming about twenty years ago but which has been to some extent been overtaken by other cosmological probes that offer greater precision; the biggest difficulty has been getting a sufficient number of sufficiently accurate direct (redshift-independent) distance measurements to do good statistics. It remains a difficult but important field, because it’s important to test our models with as many independent methods as possible.

I’ll end with a word about the first speaker of this session, the Gruber prize winner Marc Davis. He suffered a stroke a few years ago which has left him partly paralysed (down his right side). He has battled back from this with great courage, and even turned it to his advantage during his talk when he complained about how faint the laser pointer was and used his walking stick instead.

IMG-20140625-00351

BICEP2, Social Media and Open Science

Posted in Open Access, The Universe and Stuff with tags , , , on March 20, 2014 by telescoper

I’ve been finding it a bit difficult to keep up with all the BICEP2 excitement in between all the other things I’ve had to do this week but at least the blog has been generating some interest and there’s no sign of that abating yet.  In fact, according to the wordpress elves, today is the busiest day I’ve ever had on In the Dark – and it’s not even 6pm yet!

I realize that I’ve posted several items on B-modes without ever showing a picture of what they look like, so here you go, an image of the B-mode polarization seen by the BICEP2 experiment:

b_over_b_rect_BICEP2

When the BICEP2 team announced that  a “major astrophysics discovery” would be announced this Monday I have to admit that I was quite a bit uncomfortable about the way things were being done. I’ve never been keen on “Science by Press Release” and when it became clear that the press conference would be announcing results that hadn’t yet been peer-reviewed my concerns deepened.

However, the BICEP2 team immediately made available not only the “discovery” paper but also the data products, so people with sufficient expertise (and time) could try to unpick the content. This is fully in the spirit of open science and I applaud them for it. Indeed one could argue that putting everything out in the open the way they have is ensuring that that their work is being peer-reviewed in the open by the entire cosmological community not secretly and by one or two anonymous individuals. The more I think about it the more convinced I am becoming that this is a better way of doing peer review than the traditional method, although before I decide that for sure I’d like to know whether the BICEP2 actually does stand up!

One of the particularly interesting developments in this case is the role social media are playing in the BICEP2 story. A Facebook Group was set up in advance of Monday’s announcement and live discussion started immediately the press conference started. The group now has well over 700 members, including many eminent cosmologists. And me. There’s a very healthy scientific discussion going on there which may well prove to be a model of how such things happen in the future. Is this a sign of a major change in the way science is done, the use of digital technology allowing science to break free from the shackles placed on it by traditional publication processes? Maybe.

Anyway, no time to write any more. I just remembered I have to participate in a seminar on Open Access publishing and I have to start thinking about what I’m going to say!

P.S. The Vernal Equinox happened at 16.:57 GMT today, so welcome to Spring!

Science 2.0 and all that

Posted in Open Access, Science Politics with tags , , , on July 9, 2012 by telescoper

I cam across this on Twitter today and thought I’d share it. Although I have written at various times about open access and the virtues of sharing scientific data, I hadn’t realised that such things came under the umbrella of “Science 2.0“, a term which is quite new to me. This post contains some very interesting ideas and information on the subject.

Science 2.0 study

We’re approaching the final stage of our study. So far, we have  opened up our bibliography on our Mendeley group here; our notes through this very blog; our model for open science; and our draft policy recommendations for EU. And we’ve benefited from your comments and insight.

Now, we need your help to improve the evidence about the importance of Science 2.0, if we want policy-makers to take it seriously.

Therefore, we share the final presentation that we have presented to the European Commission, DG RTD here.

Help us improving it, by gathering more data and evidence, showing that Science 2.0 is important and disruptive, and that it’s happening already. In particular, we ask to share evidence and data on the take-up of Science 2.0: how many scientist are adopting it? With what benefits?

We ask all people interested in Science 2.0 to share the evidence at hand, by adding

View original post 15 more words

If it ain’t open, it ain’t science

Posted in Open Access, Science Politics, The Universe and Stuff with tags , , , , , , on May 16, 2011 by telescoper

Last Friday (13th March) the Royal Society launched a study into “openness in science”, as part of which they are inviting submisions from individuals and organizations. According to the Royal Society website

Science has always been about open debate. But incidents such as the UEA email leaks have prompted the Royal Society to look at how open science really is.  With the advent of the Internet, the public now expect a greater degree of transparency. The impact of science on people’s lives, and the implications of scientific assessments for society and the economy are now so great that  people won’t just believe scientists when they say “trust me, I’m an expert.” It is not just scientists who want to be able to see inside scientific datasets, to see how robust they are and ask difficult questions about their implications. Science has to adapt.”

I think this is a timely and important study which at the very least will reveal how different the attitude to this issue is between different science disciplines. On one extreme we have fields like astronomy, where the practice of making all data publically available is increasingly common and where most scientific publications are available free of charge through the arXiv. On the other there are fields where experimental data are generally regarded as the private property of the scientists involved in collecting the measurements or doing the experiments.

I have quite a simple view on this, which is that the default should be that  data resulting from publically funded research should be in the public domain. I accept that this will not always be possible owing to  ethical issues, such as when human subjects are involved, but that should be the default position.I have two reasons for thinking this way. One is that it’s public money that funds us, so we have a moral responsibility to be as open as possible with the public. The other is that the scientific method only works when analyses can be fully scrutinized and, if necessary, replicated by other researchers. In other words, to seek to prevent one’s data becoming freely available is profoundly unscientific.

I’m actually both surprised and depressed at the reluctance of some scientists to make their data available for scrutiny by other scientists, let alone members of the general public. I can give an example of  my own experience of an encounter with a brick wall when trying to find out more about the statistics behind a study in the field of neuroscience. Other branches of physics are also way behind astronomy and cosmology in opening up their research.

If scientists are reluctant to share their data with other scientists it’s very difficult to believe they will be happy to put it all in the public domain. But I think they should. And I don’t mean just chucking terabytes of complicated unsorted data onto a website in such a way that it’s impossible in practice to make use of. I mean fully documented, carefully maintained databases with both raw data, analysis tools and data products. An exemplar is the excellent LAMBDA site which is a repository for data arising for research into the Cosmic Microwave Background.

I’ve ranted before (and will no doubt do so again) about the extremely negative effect the academic publishing industry has on the dissemination of results. At out latest Board of Studies meeting, the prospect of further cuts to our library budget was raised and the suggestion made that we might have to cancel some of our journal subscriptions. I, and most of my astronomy colleagues, frankly don’t really care if we cancel astronomy journals. All our relevant papers can be found on the arXiv and/or via the NASA/ADS system. My physics colleagues, on the other hand, are still in hock to the old-fashioned and ruinously expensive academic journal racket.

One of the questions the Royal Society study will ask is:

How do we make information more accessible and who will pay to do it?

I’m willing to hazard a guess that if we worked out how much universities and research laboratories are spending on pointless journal subscriptions, then we’d find that it’s more than enough to pay for the construction and maintenance of  sufficient  open access repositories.  The current system of publishing could easily be scrapped, and replaced by something radically different, but it won’t be easy to change to a new approach more suited to the era of the internet.  For example, at present  we are forced to  publish in “proper journals” for the purposes of research assessments, so that academic publishers wield immense power over university researchers. These vested interests will be difficult to overthrow, but I think there’s a growing realization that they are actively preventing science adjusting properly to the digital age.

Anyway, whether or not you agree with me, I hope you’ll agree that the Royal Society study is an important one so please take a look and contribute if you can.

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