Building Blogs of Science

[Open] Science Sunday 27.06.10

Posted in Health and Medicine, Science, Science and Society by kubke on June 27, 2010

It’s been a while since I wrote one of these posts, and a lot has been happening which is really great. But, as usual, exam marking took priority, or should I say, took over my life.

And the SPARC goes to….

First of all, I would love to congratulate the authors of the Panton Principles for receiving the SPARC innnovation award. Who is SPARC? According to their website

“SPARC has become a catalyst for change. Its pragmatic focus is to stimulate the emergence of new scholarly communication models that expand the dissemination of scholarly research and reduce financial pressures on libraries.”

According to the press release of June 22nd, the authors of the Panton Principles (Peter Murray-Rust, Cameron Neylon, Rufus Pollock and John Willbanks) were given this award because:

“The authors advocate making data freely available on the Internet for anyone to download, copy, analyze, reprocess, pass to software or use for any purpose without financial, legal or technical barriers. Through the Principles, the group aimed to develop clear language that explicitly defines how a scientist’s rights to his own data could be structured so others can freely reuse or build on it.”

There is a great article on the award and the history of the Panton Principles here. It is definitely worth a read.

(HT Jonathan Gray)

Open Science Summit

The “First Ever Open Science Summit” will be taking place in Berkeley California on July 29-31. It promises to be a great event not only because I am sure it will bring a lot of energy from the people attending a “First” but also because the session schedule just made me drool. From a retrospective of the human genome, to Open Access publishing, to Citizen Science, this looks like it will be a couple of days to remember by those able to attend.

(HT @JasonHoyt on Twitter)

Licencing Open Data

The Panton Principles address some of the issues surrounding how data should be share. Last week Glynn Moody on twitter pointed to this site: the Open Data Commons, a project ran by the Open Knowledge Foundation. This site provides 3 types of licences for data. I found the FAQ section quite informative, especially the linked section that discusses why these licences are put into place as opposed to the Creative Commons licences. (HT @glynmoody on twitter)

Related to this, there is a really interesting article on the Open Knowledge Foundation site that discusses the differences in non-commercial (NC) and share-alike (SA) licences, which addresses why the licences offered by the Open Data Commons are the way they are.

“This interoperability is absolutely key to realizing the main practical benefits of “openness” which is the ease of use and reuse — which, in turn, mean more and better stuff getting created and used.

[…]The aim is to ensure that any license which complies with the definition will be interoperable with any other such license meaning that data or content under the one license can be combined with data or content under the other license.

[…]Non-commercial provisions are not permitted because they fundamentally break the commons, not only through being incompatible with other licenses but because they overtly discriminate against particular types of users.”

Already the Panton Principles had suggested that licences other than CCZero of the Creative Commons should be discouraged. The Open Data Commons provides licencing formats for data and databases that should facilitate the way that data can be shared.

And that is a good thing.

How to build a [water] brain

Posted in Science by kubke on June 18, 2010

Whenever I try to teach some aspects of neuronal integration in class, I run into trouble, since most of the neuronal properties are defined by mathematical formulae that describe the electrical properties of neurons that are sometimes difficult for the students to grasp. Without a basic knowledge of electricity, it is hard to build a conceptual image of what neurons are doing.

Or is it?

I was invited to talk about the brain to a group of 9-11 year old pupils in a primary school in the North Shore yesterday, when I thought it might be fun to try to build neurons and discover how they worked. So, here is my water neuron:

The water neuron

It turns out, this little water neuron (which can be built with pretty much household items) has a lot to show about the passive properties of neurons.

Synaptic currents:

The pipette dropper was used to inject [current] water into the different dendrites. Because of the properties of the dropper, there is a limit to the amount of current that can be injected at a given time, and the injection of current is not instantaneous but has a time course that is analogout to the time course of the synaptic potential.

Spatial and temporal integration:

Current can be injected in one or more dendrites with different time patterns. Injecting into all dendrites at the same time, or into one or more dendrites at different time intervals provides a good idea of how the output of the neuron is shaped by spatial and temporal integration.


By tilting the ‘soma’ to different degrees the amount of current needed to be injected into the dendrites to allow for an output of the axon will increase. Therefore, one can build neurons with different thresholds and see how that affects the output of the neuron.

Leak currents:

One can poke tiny holes into the soma so that some of the current injected into the neuron leaks out. Combining this with changing threshold and the temporal patterns of injection into the dendrites is a good way of showing how temporal and spatial integration work in different ways to produce an output through the axon.  One can also put some leaks into the axon, and ‘myelinate’ it with saran wrap to show the insulating  properties of the myelin sheath.

Although this ‘water neuron model’ cannot illustrate the active properties of the neurons, it does contribute to an intuitive construct of how currents may be acting in individual neurons. The different neurons can be connected to form a circuit, and then one could examine how the output of the circuit is affected by changing things likethreshold, leak and number of inputs into individual neurons.

Well, it was fun. I may give this a go in my next neuro class at Uni.

About Paulo Freire

Posted in Science and Society by kubke on June 8, 2010

[Cross posted from Talking Teaching]

As part of the Postgraduate Certificate where I am a student, I was to give a 10 minute lecture on one theory of teaching. A list of ‘candidate’ theories were provided, and to my surprise Paulo Freire‘s ‘Pedagogy of the Opressed’ was in the list.

Well, that was quite a surprise.

I had first come across Paulo Freire’s orginal book about over twenty years ago, when I read it in the context of literacy programmes in Latin America. I would not have, then and now, predicted that his ideas would ever make it to a rather mainstream reading list. So, of course, I thought it would be fun to read him once again.

I don’t think I was aware how much I had internalised Freire, and how much of the way that I think about teaching is inspired by that original reading. It was indeed an interesting excercise. Especially because this time around I read his book while thinking how (or if) his ideas could be put in place in tertiary education given the real life limitations of the current tertiary system (like the large size of the classes).

In any case, this lecture also gave me the opportunity to give Prezi a go. First time user, but I love what can be done with it.

Freire’s philosophy is perhaps better defined for what it is not (it is not what he calls banking education). What it is, to me, is what is in this presentation. This presentation also has some thoughts about how I think his ideas could be applied to the current educational system.

It may make for a nice debate, so I thought why let all the work go to waste, right?

Well, here it is:

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