Archive for category Science & Society

Weekend Science Videos: Views from and into the (night) sky above us

A message from space to our blue marble:

And here is the executive summary: “Our Story in 1 Minute” (somewhat reminiscent of the BigBangTheory Intro Sequence) by melodysheep

The following footage taken from the International Space Station left me speechless anyway: “View from the ISS at Night” by  (fullscreen view is a must)

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Happy birthday Richard !

Not that he won’t mind it was already yesterday. Since there are a couple of posts related to him on this site there is probably no need re-iterate how inspirational he was and even over 2 decades after his death still is. Just a welcome occasion to point out richard-feynman.net which has a great collection of videos, a photo gallery and quotes like this one on the ignorance of experts:

Science alone of all the subjects contains within itself the lesson of the danger of belief in the infallibility of the greatest teachers in the preceding generation … Learn from science that you must doubt the experts. As a matter of fact, I can also define science another way: Science is the belief in the ignorance of experts…

Let me refer you to this post with a bit more physics in it while leaving you with this scene from the movie “Infinity”, showing Feynman at the tender age of 6 learning a few things about science from his father.

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Engineering Connections in an Invisible World – a Crash Course

For several years I’ve been a big fan of  Top Gear – the guys have been entertaining my inner child. Seen rationally, the petrol-based internal combustion engine is a dead end,  but getting from A to B is hardly the point, or is it? I like the irreverent, playful and fun approach to how things actually work – by taking them apart, blowing them up or whatever else seems suitable – they have an immense imagination in that department. You know, what distinguishes the men from the boys is the size of their toys. In this regard, the top gear presenters are the real grown-ups, thinking big and out of the box. Some of their projects on science and engineering are among my all-time favourites, so I am happy to see Richard “Hamster” Hammond back on the screen again.

First, there’s the recently launched “Crash Course” :  

And then I have to mention his series “Engineering Connections” on the National Geographic Channel where Hammond

looks at how engineers and designers use historic inventions and clues from the natural world in ingenious ways to develop new buildings and machines.

And if you still can take some more, there is some really stunning footage in the “Invisible worlds” –  series (2010). Definitely something to go into my DVD collection, here’s a teaser:

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Play more …


The Federation of American Scientists (FAS) Learning Technologies Program (pre-)launched the Science Game Centerto demonstrate to teachers, scientists, museums, and parents the myriad ways games can be used to improve education in math and science“. Next to Phylo and Fold.it (which I mentioned around here before) are several entries listed I haven’t seen yet. It may be due to the movie “Fantastic Voyage” that made a lasting impression on me as a kid that “Immune attack” immediately caught my attention. After all, I’d rather kick some pathogenic butt than blowing up poor aliens in space. Good hunting!

P.S.: Reminds me of this quote by 137th Gebirg on battlestarforum.com

“I may appear unoccupied to you, but at the molecular level, I’m really quite busy.”

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Free Ivy-League Education

 After I mentioned theScienceNetwork in the previous post and you might already be aware of sites such as SciVee.tv, labtube.tv and iTunes U it’s time to share some recent links in the area of online-courses:

First, with a biological focus, there is iBioSeminars accompanied by iBioMagazine – let me just highlight this talk by David Baltimore.

On the computational side, there is udacity which was started by former Stanford professor and Google fellow Sebastian Thrun. He developed a vision for “University 2.0” under the motto of “democratizing higher education”. After having experienced that he could reach out to more people in a better way by a single online course than he could have by traditional teaching (even in huuuge overcrowded lecture halls) during the next couple of years he just couldn’t go back to the olden ways. He really has a point in dumping his professorship I heartily agree with, and that’s an understatement. I highly recommend to check out his talk at DLD (hosted by the gorgeous Maria Furtwängler), here is a teaser-trailer for the CS101-class “Building a Search Engine”:

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(You might want to check out this previous post on the online courses at Stanford)


To round things up, at the moment there is a free introductory course on Machine Learning “Learning from Data” ongoing at Caltech by Professor Yaser Abu-Mostafa covering basic theory, algorithms, and applications. Registration is still possible, the previous lectures are available here.

Video et studio, ergo sum.

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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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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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