Building Blogs of Science

Thinking about education

Posted in Science and Society by kubke on December 26, 2009

I have been putting more thought into education this year than I have in a long time. Part of it was stimulated by discussions held at kiwi foo camp, and part of it by some discussions held with my colleagues over courses we taught together. The common thread around both of them was how the material being taught fits within the student’s career choice (not always homogeneous in a class cohort) and how this, in turn, fits within the larger context of the contribution of the University to society as a whole.

Although the answer might be straightforward, implementing it is not so easy. As teachers we are constrained by the need to deliver a minimum of relevant information, limitations in the number of contact hours, and the ability to assess the students to make their degrees a meaningful measure of their professional capacities.

We can only provide students with the knowledge and training they need to develop their professional careers in today’s system. But we all know that the professional environment in which they will operate will continuously be changing. And it is the students that will be creating these changes, and we as teachers cannot know what those will be.

So, how do we, as teachers, pass down knowledge and training they need today, while making room for the changes of tomorrow?

As I prepare my lectures for next semester I am drawn back to “The Element” by Sir Ken Robinson. And from it I take his definition of creativity:

“the process of having original ideas that have value”

While Robinson talks a lot about encouraging student creativity, I am thinking more about my own creativity as a teacher. How do I teach an inhomogeneous cohort of students so that they will have the tools to create their own professional future?

While I think about this, I encourage you to be entertained by Sir Ken Robinson’s TED talk.

[Open] Science Sunday – 20.12.09

Posted in Environment and Ecology, Health and Medicine, Science, Science and Society by kubke on December 20, 2009

Great things to share this Sunday thanks to the magic of the internet and open access….

The good

There are some good news around Open Access:

First, last week Nat Torkington alerted me of this link. The first paragraph of the summary states

“With this notice, the Office of Science and Technology Policy (OSTP) within the Executive Office of the President, requests input from the community regarding enhancing public access to archived publications resulting from research funded by Federal science and technology agencies.”

Some commenting around this issue can be found in the Office of Science and Technology Policy Blog. (via @BoraZ on twitter). It is great to see the OSTP having started this discussion, and I will be interested to see where this leads to.

With the year coming to an end, nothing like summarizing what has been achieved, and here is a post summarizing how 2009 was a great year for Open Access (also via @BoraZ)

And it was great to hear about the new partnership between and PLoS. Nice!

The ‘How is this Reasonable?”

There is a post by Martin Fenner describing a talk on Open Access he gave at his University. I especially liked this extract:

“Reuse of a figure or table in an academic seminar usually falls under fair use, but many journals still require a (free) permission. And using the same figure in a medical conference can cost several hundred dollars, and it doesn’t really matter that you are one of the authors of the paper”

I did not know that use of my own figures at a conference did not fall under fair use. It’s just not right.

But this is even worse:

Who could oppose non-profit blind/disabled groups helping disabled people get access to written work?

You can find the answer in BoingBoing.

Back to the good: Cornell University

Cornell University Library partners with the Internet archive (heard through Open Access News). Absolutely priceless gems can be found here! There is nothing like dusting off the cobwebs of some old journal issues and reading the scientific discoveries as they were described originally by the scientists themselves. Cornell University has made this a lot easier.

Cornell University has a great series of videos on YouTube, including a really interesting one on bird’s songs. (By the way, wonderful description of feathers in Ed Yong’s Not Exactly Rocket Science blog.)

The Cornell lab of Ornithology also runs a great Citizen Science programme. (Dave Munger has a wonderful post about Citizen Science in Seed Magazine.)


OK, granted, I didn’t get this tweet from @sciencebase this week, but it is really so worth it! So, if you are not up to becoming a citizen scientist you might still be up for some quirky science party tricks. (If you like this video, there is more at Richard Wiseman’s Blog)

The ever-changing world of dendritic spines

Posted in Science by kubke on December 18, 2009

ResearchBlogging.orgSantiago Ramón y Cajal originally described spines in the dendrites of neurons in the cerebellum back in the late 19th century, but it wasn’t until the mid 1950’s with the development of the electron microscope that these structures were shown to be synaptic structures. Although it has been known that the number of dendritic spines changes during development and in association with learning, most studies have inferred the changes by looking at static time points rather than monitoring individual spines in the same animal over time, partly, due to the difficulty of tracking a single structure of about 0.1 micrometer in size (0.0001 mm). But new advances in imaging technology have allowed researchers to ‘follow’ individual spines over time both in vitro and in the whole animal.

Purkinje Cell by S Ramon y Cajal

Dendritic spines are no longer thought of as the static structures of Ramón y Cajal’s (or even my) generation, but rather dynamic structures that can be added and eliminated from individual dendrites. And because each spine is associated with a synaptic input, and because their structure and dynamic turnover is known to have a profound effect on neuronal signaling, one cannot but be tempted to propose that they are associated with specific aspects of memory formation.

Two developments have made it possible to monitor individual dendritic spines at different time points in the same animal: the ability to incorporate fluorescent molecules into transgenic mice that make the spines visible under fluorescent illumination, and the development of in vivo transcranial two photon imaging that allow researchers to go back to that individual dendrite and monitor how the dendritic spines change over time. Two papers published in Nature make use of these techniques to look at how dendritic spines change in the motor cortex of mice that have learned a motor task.

In one, Guang Yang, Feng Pan and Wen-Biao Gan looked at how spines changed when either young or adult mice were trained in to learn specific motor strategies. They observed that spines underwent significant turnover, but that learning the motor task increased the overall number of new spines and that a small proportion of them could persist for long periods of time. They calculated that although most of the newly formed spines only remained for about a day and a half, a smaller fractions of them could still persist for either a couple of months or a few years. Based on their data they suggest that about 0.04% of the newly formed spines could contribute to lifelong memory.

Dendritic spine by Tmhoogland

Another study by Tonghui Xu, Xinzhu Yu, Andrew J. Perlik, Willie F. Tobin, Jonathan A. Zweig, Kelly Tennant, Theresa Jones and Yi Zuo did a similar experiment, but using a different motor training task. Like the Yang group, they also saw that training leads to both the formation and elimination of spines. Although newly formed spines are initially unstable, a few of them can become stabilized and persist longer term. Further, training made newly formed spines more stable and preexisting spines less stable. The authors interpret their results as an indication that during learning there is indeed a ‘rewiring’ of the network and not just addition of new synapses.

The two papers were reviewed by Noam E. Ziv & Ehud Ahissar in the News and Views section. Here they raise the issue that, if such a small number of spines are to account for the formation of stable memories, then what are the consequences of the loss of a somewhat larger number of spines on the neuronal network?

For someone like me that more than once as an undergraduate used a microscope fitted with a concave mirror to use the sunlight to illuminate the specimen, the ability to monitor individual synaptic structures over time in a living organism can only be described as awesome. But, as pointed out by Ziv and Ahissar,

“[…] although it remains to be shown conclusively that these forms of spine remodeling are essential components of long-term learning and not merely distant echoes of other, yet to be discovered processes, these exciting studies make a convincing case for a structural basis to skill learning and reopen the field for new theories of memory formation.”

Yang, G., Pan, F., & Gan, W. (2009). Stably maintained dendritic spines are associated with lifelong memories Nature, 462 (7275), 920-924 DOI: 10.1038/nature08577
Xu, T., Yu, X., Perlik, A., Tobin, W., Zweig, J., Tennant, K., Jones, T., & Zuo, Y. (2009). Rapid formation and selective stabilization of synapses for enduring motor memories Nature, 462 (7275), 915-919 DOI: 10.1038/nature08389
Ziv, N., & Ahissar, E. (2009). Neuroscience: New tricks and old spines Nature, 462 (7275), 859-861 DOI: 10.1038/462859a

The Hippocratic Oath and its younger relatives

Posted in Science, Science and Society by kubke on December 15, 2009

I came across this blog post by Alex Madrigal on Wired Science the other day: ‘Should earth scientists take a Hippocratic Oath’? In his post he argues that such an oath would

“[…] provide a set of agreed-upon ethical norms for geoscientists, at a time when they are increasingly being called upon to pass judgment on massive human alterations to the Earth’s carbon, nitrogen, and water systems.

Many of you may not know that the University of Buenos Aires in Argentina requires all graduates of all professions to take an Oath that is appropriate for their degree, without which a degree will not be conferred.

The Faculty of Exact and Natural Sciences from which I graduated has currently 4 different formulae, which primarily differ on whether the oath is made in the name of god, the scriptures, the country, or your honour. The common text in all 4 formulae is

“[…] to put to the service of society and your equals the art and the science of your profession”

The new text for the oath in the science faculty

I entered the University when Argentina was still under dictatorship, and witnessed the discussion, soul searching and changes that accompanied the transition to democracy. In 1988 (the year I graduated) a new optional text (which is non-legally binding) was introduced to the graduating oath as the result of a symposium on “Scientists, Peace and Disarmament”.

I had the honour to be among the first graduates that had the option to make this oath. I opted in.

Loosely translated, this is the text:

Being conscious that science and its results can cause harm to society and to human beings when ethical controls are not in place,

Do you swear that the scientific research and technology that you will develop will be in the benefit of humanity and in favor of peace, that you are firmly committed in your scientific capacity to never serve aims that will harm human dignity, guided by your professional convictions and beliefs, seated in an authentic knowledge of the circumstances that surround you and of the possible consequences of the outcomes that can result from your work, and not to put remuneration or prestige first, nor subordinate yourself to the interests of your employers or political leadership?

If you weren’t to do so, let your conscience be your judge.

If you can read Spanish, the original texts can be found here.

[Open] Science Sunday – 13.12.09

Posted in Science by kubke on December 13, 2009

More Sunday sharing thanks to the people in the internet and Open Access

ASCILITE is over, but it left me with a lot of work to do because of the great sessions in the conference. You can get a lot of the information covered there thanks to Grainne Conole on Cloudworks. I also posted some interesting resources on my FriendFeed page.

We’ve come a long way baby

The Wikipedia entry for Brain-Computer Interfaces, describes a prototype done in 1978. It was successful in having a man blinded as an adult perceive the sensation of light. But (continue reading), its operation required being “hooked up to a two-ton mainframe”. Well, things have changed, and a recent article by Frank H. Guenther, Jonathan S. Brumberg, E. Joseph Wright, Alfonso Nieto-Castanon, Jason A. Tourville, Mikhail Panko, Robert Law, Steven A. Siebert, Jess L. Bartels, Dinal S. Andreasen, Princewill Ehirim, Hui Mao, Philip R. Kennedy published in PLoS One talks about a wireless brain-machine interface that could be used to produce synthetic speech for individuals with speech impairments. You can read the article here, and Brandon Keim has a great take on it on Wired Science.

Great stories online

My favourite tweet has to be one by @Mark_Changizi read Ed Yong’s post and you will know why it made me laugh so much!

Oh, and congratulations to NeuroDojo for being named “blog of note

Tweeting my own horn

I was contacted by Jose Barbosa from 95bFM’s Sunday Breakfast, and we got to chatting about brains. You can find the recording of the radio segment here. And thanks to Jose, who found the link to Jeremy Corfield’s thesis on the kiwi brain.