Building Blogs of Science

[Open] Science Sunday – 28.2.10

Posted in Science, Science and Society by kubke on February 28, 2010

I am not sure why, but this week appeared to be filled with news about science to share. All of these are brought to you by the magic of Open Access or the efforts of people in the web to make science accesible to everyone.

I would normally not include articles published in Nature here, but this week David Winter from The Atavism pointed me to this one: “Complete Khoisan and Bantu genomes from southern Africa” by Stephan C. Schuster and a group of collaborators. The authors open their paper stating that

“The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity.”

The study has been published under a creative commons licence (http://creativecommons.org/licenses/by-nc-sa/3.0/) and the data has also been released here. I dont know whether Nature will ever move to a full Open Access format, but I think it is worth acknowledging that at least some of their material is made available withouth a subscription. To read a full review of the article, you can visit David Winter’s blog.

PLoS One (which yes is a  fully Open Access journal) published an article on the cognition behind spontaneous string pulling in New Caledonian Crows, by Alex Taylor, Felipe Medina, Jennifer Holzhaider, Lindsay Hearne, Gavin Hunt, and Russell D. Gray. New Caledonian crows are better known for their ability to manufacture tools both from materials that they would normally find in the environment as well as some they would not. New Caledonian crows can solve rather complex puzzles, and for the most part, it has been assumed that this reflected some ‘higher’ cognitive ability that require building a cognitive scenario and imagination. In this study, the authors subjected crows to a series of tests, and conclude that:

Our findings here raise the possibility that string pulling is based on operant conditioning mediated by a perceptual-motor feedback cycle rather than on ‘insight’ or causal knowledge of string ‘connectivity’.

As usual, things are not so black and white. You can read the details of the study on the PLoS One site, and Wired Science has a great review by Brandon Keim on the paper.

Research Blogging Awards 2010And, if you are looking for interesting blogs filled with science nerd content, then this is the best time to find them.

The finalists for best of Research Blogging are out and there is no shortage of interesting stuff to look into. Also out is the Open Laboratory 2009. This is a great collection of science blog posts that is really worth your money. So go on now, go get yourself a copy…

The Open Laboratory 2009

And if all that geekiness was still not enough, then you are in luck.

Next week will see Global Ignite Week: Ignite talks in 65 cities and 5 continents (and yes, there is one in Wellington on Tuesday). Ignites are a great presentation format (well, unless you are a speaker since they are really really hard to do well!).  If you have not heard one before, there are plenty on YouTube Ignite Channel.

If you cannot make it to Wellington, then Auckland will be having on Thursday another Late at the Museum, this time on innovate science. I know, I am now sounding like a tourist guide.

One more (an last). If you want to know everything there is to know about <ahem!> me :), thanks to the magic of Bora Zivkovic and The Blog Around the Clock, now you can. There should be a warning or disclaimer before I lead you to this link.

Full Disclaimer: I am an academic editor for PLoS One and I collaborate with the group behind the New Caledonian Crow Study

Congratulations Fellow Sciblings

Posted in Science by kubke on February 26, 2010

Congratulations to our fellow Sciblings who made it to the finals for the Research Blogging Awards 2010.
Research Blogging Awards 2010

  • Misc.ience (by Aimee Whitcroft) was nominated for best blog in Chemistry, Physics or Astronomy.
  • The Atavism (by David Winter) was nominated for best lay-level blog.

Congratulations to you both (and if I have failed in identifying a sciblogger, please let me know!

Getting up to speed with sound localisation

Posted in Science by kubke on February 25, 2010

ResearchBlogging.orgFunny how we are really good, for the most part, at knowing where sounds are coming from. And it is funny since the ear provides the brain with no direct information about the actual relationship in space of different sound sources. Instead, the brain makes use of what happens to the sound as it reaches both ears by virtue of, well, being a sound wave and that we have two ears separated in space.

Imagine a sound coming from the front, the sound will arrive to the two ears at the same time. But if it is coming from the right it will arrive to the right ear first, and to the left ear a wee later. This ‘time difference‘ will depend on the speed of sound in air and how far apart our ears are. Even more, as the sound source moves from the far right to the front of the head those time differences will become smaller and smaller, until they are zero at the front. If one could put one microphone in each ear, one could reliably predict where the sound comes from by measuring that time difference. And this is exactly what a group of neurons in the brain does.

Easy enough? Not quite.

The way the brain works is that things on the left side of our body are mapped on the right side of our brains, and things on the right side of our bodies are mapped on the left side of our brains. So the ‘time comparison’ neurons on the right side of the brain deal mainly with sound from coming from the left (and neurons dealing with the sound from the right are on the left side of the brain). But to do the time comparison these neurons need to get the information from both ears, not just from only one side!

Figure 1 (by Kubke CC-BY)

This raises this conundrum: the neural path that the information from the left ear needs to travel to get to the same (left) side of the brain will inevitably be shorter than the path travelled by information coming from the other side of the head. So how does the brain overcome this mis-match?

And here is where having paid attention at school during the  “two trains travelling at the same speed leave two different stations blah blah blah” math problem finally pays off. When a sound comes from the front, the information arrives to each of the ears at the same time. The information also arrives to the first station in the brain (nucleus magnocellularis) at the same time. But time comparison neurons need information from both ears, and the path that the information needs to travel from the right side to the time comparison neurons in nucleus laminaris on the left side (red arrow in figure 1) is longer than the path from the same side (blue arrow in figure 1).

However, when you look into an actual brain, things are not so straight-forward (sorry for the pun). The axons from nucleus magnocellularis that go to the time comparison neurons on the same side of the brain take a rather roundabout route (as in figure 2). And for long we assumed that such roundabout way was enough to make signals from the left and right sides to arrive at about the same time.

Figure 2 (by Kubke CC-BY)

Easy enough? Not quite

When Seidl, Rubel and Harris actually measured the length of the axons (red and blue) they found that there was no way that the information could arrive at about the same time and that the system could not work in the biological range. But this problem could be overcome (back to the old school problem) by having the two trains (action potentials rather) travel at different speeds. And this is something that neurons in the brain can relatively easily do in two ways: One is to change the girth or diameter of the axon. The other is to regulate how they are myelinated. Myelin forms a discontinuous insulating wrap around the axon, which is interrupted at what is called the Nodes of Ranvier. The closer the Nodes of Ranvier are, the slower the action potential travels down the axon.

What the group found was that both axon diameter and myelination pattern were different in the direct (blue) and crossed (red) axons. When they now calculated how long it would take for the action potential from both sides to reach the time comparison neurons in nucleus laminaris, adjusting speed for the differences in the two axons, they found that yup, that pretty much solved the problem.

Easy enough? Quite

Like the authors say:

The regulation of these axonal parameters within individual axons seems quite remarkable from a cell biological point of view, but it is not unprecedented.

But remarkable indeed, considering that this regulation needs to adjust to a very high degree of temporal precision. I have always used the train analogy when I lecture about sound localisation, and always assumed equal speed on both sides. Seidl, Rubel and Harris’ work means I will have to redo my slides to incorporate differences in speed. Hope my students don’t end up hating me!


Seidl, A., Rubel, E., & Harris, D. (2010). Mechanisms for Adjusting Interaural Time Differences to Achieve Binaural Coincidence Detection Journal of Neuroscience, 30 (1), 70-80 DOI: 10.1523/JNEUROSCI.3464-09.2010

[Open] Science Sunday – 21.2.10

Posted in Science and Society by kubke on February 21, 2010

Long, long, long time ago in a faraway kingdom called the Society for Neuroscience Meeting (if my memory does not fail me), I was approached by a woman carrying a business card from the Public Library of Science. She described to me that they were trying to set up a publishing format whereby all articles would be accessible to anyone for free through the internet. I laughed: “I find it hard to imagine how you will make this happen”, said I. Fast forward to 2010: I am now a proud academic editor for PLoS One, one of the journals from the Public Library of Science. I am honoured to be part of the team, and hope that I will do a good job. And role models for how to go about the job are not lacking: Here is a great example by Björn Brembs.(via Bora Zivkovic). I have to say, that is scientific review awesomeness.

Open Science Data:

I love it when I come across new stuff: It shows that I am still learning. And this week, I found this site: The Panton Principles: Principles for Open Data in Science. (Via Glyn Moody on Open…).

“For science to effectively function, and for society to reap the full benefits from scientific endeavours, it is crucial that science data be made open.

Many clicks later, I found these very cool sites that will surely be great sources of information and ideas. As I get around digesting their content I am sure you will hear more about them here:

Open Education

For those of you in Auckland, the olpc team is back with their (our?) tester meetings. From the mission statement, the aim of the project is:

“To create educational opportunities for the world’s poorest children by providing each child with a rugged, low-cost, low-power, connected laptop with content and software designed for collaborative, joyful, self-empowered learning.

To learn more about the olpc project and the New Zealand testers, visit the olpcnz webpage. If you are interested in joining the group, you can find information here too.

  • Auckland meets are fortnightly, and are taking place at 144 Parnell Road (at the Windsor Castle).
  • Wellington meets weekly on Saturdays at 10:30 am at Southern Cross, 35 Abel Smith Street
  • Christchurch meets Sun: 2pm-7pm Wed: 7pm-11pm, at http://chchspace.nztech.org/

Open [Science] Sunday – 14.2.10

Posted in Science and Society by kubke on February 14, 2010

What happens when you put around 200 motivated people in a room and let them decide what to talk about? Well, if that happens in Warkworth, New Zealand, then it is Kiwi Foo Camp. Structured as an unconference, the group introduces itself to each other start talking and, one by one, session themes are proposed which slowly populate the empty schedule board on the wall. By the end of the first night, the slots are taken, and the conference schedule is set.

And so it is that Kiwi Foo happens. (Well, actually, Nat Torkington, Jenine Abarbanel and Russell Brown make this awesomeness possible in the first place). With invited attendees coming from very different backgrounds (software developers, politicians, media, artists, scientists, etc.) the discussions that emerge develop multiple and sometimes unexpected dimensions. And they don’t disappoint: they are energizing, inspiring and as awesome as the people that participate in them, and I have spent most of the afternoon trying to formalize some ideas that were developed there.

In a previous post, I had described that as result of my first experience at Kiwi Foo I had found my lap: things started falling on it, and I started paying attention to them.  (This blog is one of them.) The underlying themes of my Kiwi Foo experience last year were Education and Communities. This year, they were Openness, Data Sharing, Education, Communities and Science.

I have been thinking a lot about data sharing, in particular after participating in SciBarCamp in Palo Alto last year. As many of us, I struggle less with the question of if and more with the question of how. Data comes in different shapes and forms: we may need to develop different solutions to different data problems, and that will take time. And this is true beyond science. Bar camps and Foo Camps are a great place to discuss these issues and to start finding solutions. The good news is that policies for making data from scientifically published results are already there, like for example

(Led to them by Bora Zivkovic and Cameron Neylon).

As for me, I have taken the first step. I now have a page (albeit very primitive)on OpenWetware.org. As I try to populate it I come across this question: what do I own? Many of the protocols/data of my lab have been built through collaboration and contributions from many of my collaborators. Do I have the right to publish that without consultation, and is attribution enough? Where does my data end and my collaborator’s begin? What if they are not comfortable with me making that available? Finding a solution to this problem is the cahllenge I set for myself for 2010.

In his book “The Element”, Sir Ken Robinson discusses the power of finding one’s “tribe”:

“Finding your tribe can have transformative effects on your sense of identity and purpose. This is because of three powerful tribal dynamics: validation, inspiration, and […]  the ‘alchemy of synergy’.

As for Kiwi Foo, I have been inspired, made to critically look into my world, encouraged to identify my strengths and weaknesses. successes and failures. I cannot wait to see what will develop in 2010. I just got a wonderful glimpse of what is possible; the work starts now.