Posts Tagged Teaching

The great ideas of biology

The guardian has a series called “It’s a small world“, among which is a video called “Gregor Mendel and the genesis of genetics” where

Nobel laureate Sir Paul Nurse tells the story of another great idea in biology – genes as the basis of heredity – in a lecture at the Royal Institution in London. It all started with the gardening monk Gregor Mendel and his peas in the 19th century and reached a key milestone with the unravelling of the molecule of heredity, the DNA double helix, by James Watson and Francis Crick in 1953

The great ideas of biology covered are

  • the cell
  • the gene
  • natural selection
  • Life as chemistry
  • Biology as an organized system.

Similarly to “A Brief Introduction to GeneticsDavid Murawsky (as mentioned around here before, but hey, they repeat stuff on TV all the time, and not only the goodies) put another impressive clip out there: “18 Things You Should Know About Genetics“. Enjoy!

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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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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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deBugging Code


Just recently, I found this REAL bug sitting on the edge of my screen while coding – the (admittedly quite nerdy) irony of it is hard to miss. Rest assured, I ‘guided’ it away from ‘the system’ to the outside as gently as possible, resisting any impulse to to squash it using the keyboard on the spot. You know the rule, “Never touch a running system”, and unfortunately double-clicking and pressing <DEL> didn’t seem to work here.

A more funny (and nerdy) take on debugging code is this video by Atlassian called “Software Bugs” that made my morning:

“All bugs welcome! … create some buzz, … and when the spider gets here, I guess we can start talking web development”

Some more in-depth understanding of the issues involved is provided in this talk by Prof. Stephen Freund on “Stopping the Software Bug Epidemic” – he also touches on the halting problem, memory leaks and parallel code execution.

Although the talk is very informative throughout while presenting the basic issues in an entertaining way, I wonder why he didn’t mention the “Dining Philosophers Problem” – I guess it’s hard to trace deadlocks by automated checkers? In addition, he only refers to the (ancient) waterfall-modell of software engineering. Some comments on how more modern development philosophies (eXtreme programming, agile etc.) fit into the picture would have been nice. Anway, Happy deBugging!

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Molecular Interaction Exchange

The International Molecular Exchange Consortium IMEx is the latest effort of data-providers to integrate Protein-Interaction Data –

IMEx provides

  • A non-redundant set of protein-protein interaction data from a broad taxonomic range of organisms
  • the data in standards compliant download formats (MITAB or PSI-MI XML 2.5)
  • Expertly curated from direct submissions or peer-reviewed journals to a consistent high standard.
[ … aiming to … ]
  • Develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals
  • Make these interaction available in a single search interface on a common website
  • Make all IMEx records freely accessible under the Creative Commons Attribution License

If you’ve been looking for that one-stop shop for getting a representative dataset of Protein-Protein Interactions, this just looks like it. There is an overview available on youtube (see below)

… and a training course on “Networks and Pathways Bioinformatics for Biologists” will take place at EMBL-EBI in May.

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The Tail of the Elephant

There is this old story of the 3 wise blind guys who come to examine an elephant. They are lead up to it, and one of them gets to grab the ear, another the holds on to a tusk, and the third gets hold of the tail.
Later, they come to completely different opinions about the nature of the object under study – is it flat and flappy, thin and wriggly, or hard and pointy? And, obviously, later they spend a looong time arguing and beating each other up about their theories on what it really is like.

George Cham, creator of Ph.D. comics, refers to this in this beautiful animation on how current science might redefine our understanding of the universe – Enjoy!


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