Posts Tagged Science

The Network that (likes to think it) runs the World


Scientists at the ETH Zurich analysed the international ownership network of multi-national companies. If you had a look at the intrinsic properties of real-world and biological networks, the 80-20 rule comes as no surprise: in biological networks, usually over 80% of the edges are covered by less than 20% of the nodes. A related phenomenon is called the Pareto Principle in economics. The core of this network contained 1318 companies, which

… represented 20 per cent of global operating revenues, the 1318 appeared to collectively own through their shares the majority of the world’s large blue chip and manufacturing firms – the “real” economy – representing a further 60 per cent of global revenues …

“Reality is so complex, we must move away from dogma, whether it’s conspiracy theories or free-market,” says James Glattfelder.

It took me some time to find the original paper on PLoS, which isn’t linked from this article on the NewScientist – probably because it wasn’t out yet at the time:

Reference: The Network of Global Corporate Control by Stefania Vitali, James B. Glattfelder, Stefano Battiston (2011) PLoS ONE 6(10): e25995. doi:10.1371/journal.pone.0025995

How these findings relate to the error and attack tolerance of scale-free networks in the context of the current economic situation is further food for thought. But I urge caution to naïvely transfer insights from one domain to another, there are no simple (mono-causal) answers to complex problems. Especially when dealing with the emergent properties of networks, there is only one constant: they tend to work out quite differently from what we initially thought.

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Biophilia

Biophilia is an extraordinary and innovative multimedia exploration of music, nature and technology by the musician Björk. Comprising a suite of original music and interactive, educational artworks and musical artifacts, Biophilia is released as ten in-app experiences that are accessed as you fly through a three-dimensional galaxy

I still haven’t downloaded and checked out the app myself in detail, the price-tag is a bit hefty for my taste. So far I have never spend over 10 bucks on a single app, and personally find it very hard to digest more than 2 Björk-songs in a row. OK, my ears aren’t bleeding, and in this case my eyes are very much tempted by the visuals. Biophilia contains several subsections (in-apps), so one could argue it’s more than just a single app, comparable to an entire (concept?-)album. On the app-store reviews there’s some criticism of the pricing-policy, however content-wise one reviewer goes as far as claiming that “we will eventually see Biophilia as the Sergeant Peppers of music apps“. A steep claim indeed to liken it to the fab four… but even though the music is not exactly my cup of tea, I am thrilled by the unique combination of contemporary art, science and technology.

As for the scientific content, the spring 2012 issue of the quarterly newsletter published by the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB for short) features a snapshot of the video for Björk’s title “hollow”:

To accompany the song “Hollow,” Björk’s meditation on biological ancestry, [Biomedical animator Drew] Berry
created a lush landscape for DNA to replicate (and sparkle) to the music. Molecular
machines work at real-time speed, culminating in the appearance of Björk as a complex
protein structure. Many of the molecular shapes, illustrated with great depth and rich
color, were created with the help of crystal structure data from the PDB.

More of these stunning, educational and award-winning 3D animations by Drew Berry and his colleagues are available on WEHI.TV at the Walter+Elisabeth Hall Institute of Medical Research. Enjoy!

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Democratization of Science

If anything, then it’s the MultipleSequenceAlignment (MSA) problem (in combination with the folding problem) which defines the core of bioinformatics. At least from my perspective, since that’s from where I started out my adventures in the field. Already fold.it successfully demonstrated for protein folding that it is possible to tackle hard problems by crowd-sourcing, a.k.a. Citizen Science. After all, the pattern recognition software installed on the wetware between your ears is highly evolved and can complement pure in-silico calculations. With Phylo researchers from McGill university have taken this approach to the sequence level:

Phylo is a challenging flash game in which every puzzle completed contributes to mapping diseases within human DNA.

Although the call for CitizenScience is not entirely new, it is boosted by such developments over the internet significantly. Who said that science and fun do not go together and can only be done while wearing a labcoat and operating extremely expensive machinery (?) – quite the opposite!

Biochemist Erwin Chargaff advocated a return to science by nature-loving amateurs in the tradition of Descartes, Newton, Leibniz, Buffon, and Darwin — science dominated by “amateurship instead of money-biased technical bureaucrats”.

Now that’s some company to be proud of. And I can’t say I completely disagree, albeit I’d like to think the two are not necessarily mutually exclusive (for-the-love-of-it vs. for-profit). If you’d like to get started, check out the tutorial video below and have fun aligning!

Reference: “Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment” by Alexander Kawrykow, Gary Roumanis, Alfred Kam, Daniel Kwak, Clarence Leung, Chu Wu, Eleyine Zarour, Phylo players, Luis Sarmenta, Mathieu Blanchette and Jérôme Waldispühl (2012) PLoS ONE 7(3): e31362. doi:10.1371/journal.pone.0031362

P.S.: For recent developments on the algorithmic frontier see this one by the Söding group (@LMU Munich, http://toolkit.genzentrum.lmu.de/hhblits/)

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment” by Michael Remmert, Andreas Biegert, Andreas Hauser & Johannes Söding (Nature Methods 9, 173–175 (2012) doi:10.1038/nmeth.1818)
“HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.”  

The entire suite of programs is available for all major OSs.

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Ars Electronica


(not to be confused with ars technica) … Next time I make it to Austria, I’ll have to visit this exhibition (in Linz), maybe even the festival. Awesome, definitely.

New cultural techniques are emerging in the ever more tightly-knit global networks of digital technologies.

Read the rest of this entry »

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HapPi π-day!


March the 14th (3/14) is Pi Day – a holiday commemorating the mathematical constant π (pi).

There are a number of matching accessories for geeks and nerds around, for example on the official Pi-Day page or in this collection on mashable.com.

It’s also happens to be Albert Einstein‘s birthday. Plenty of reasons to celebrate – for example by watching the video below and eating some (round) pies. Have fun!

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Making Data Work

Just a couple of days ago the O’Reilly STRATA Conference took place, the youtube-playlist of the presentations can be found here. Among them is this excellent talk by …

Ben Goldacre, the physician and  biostatistician behind the always-excellent Bad Science column in the Guardian, gave a barnburner of a talk at Strata 2012 yesterday, “The Information Architecture of Medicine is Broken“. For anyone not aware of the problems caused by publication bias in clinical trials (for example, ineffective drugs with a wide variety of side-effects coming to market), his talk is a must-watch.

(Shared by İbrahim Mutlay via LinkedIn, see also this blog-entry on the topic)

The line “Everybody should have a cousin who is a better Python programmer than oneself” made my day. Enjoy!

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Europe’s science cloud: Helix Nebula

… a consortium of leading IT providers and three of Europe’s biggest research centres (CERNEMBL and ESA) announced a partnership to launch a European cloud computing platform. ‘Helix Nebula ‐ the Science Cloud’, will support the massive IT requirements of European scientists, and become available to governmental organisations and industry after an initial pilot phase.
The partnership is working to establish a sustainable European cloud computing infrastructure, supported by industrial partners, which will provide stable computing capacities and services that elastically meet demand.

Building an efficient scientific cloud infrastructure in europe is a good thing, considering the onslaught of data from genomics, high-energy physics and sattelites. But I somewhat can’t shake off the uneasy feeling that the big-science flag-ship projects don’t leave any room for grassroots developments anymore, i.e. movements like the WWW when it took off in the mid-nineties. Along these lines, I’d rather (or at least equivalently) see the LinkedOpenData (as advocated by Tim Berners-Lee for several years) agressively being pushed forward and funded appropriately, the pay-offs are hard to (over-)estimate. But anyway, here are some links to make up your own mind:

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