Building Blogs of Science

Internet birdfest

Posted in Environment and Ecology, Science, Science and Society by kubke on June 1, 2013

A few days ago I got an email from a colleague of mine pointing me to a video about birds of paradise. I am happy I went and looked at it because it is quite amazing. There is no question why this group of birds stand apart from others – they are not beautiful to watch, but their behaviour, too, is quite amazing. Watch:

There are other birds that I find absolutely amazing. The Lyrebird for example, incorporates into its song sounds that it hears as it goes about life. There are two types of song learning birds (songbirds). Some will learn to imitate a song from an adult tutor as they are growing up, and pretty much sing that song as adults. Others can continue to incorporate elements to their song as adults. The lyrebird falls into this last group. But what I find amazing about the lyrebird is not that it incorporates new song elements, but that some of those sounds are not “natural” sounds. Watch:


Another amazing bird is the New Caledonian crow. A while back Gavin Hunt (now at the University of Auckland) came to find out that these birds were able to manufacture tools in the wild. They modify leaves and twigs from local plants to make different types of tools which they then use to get food. This finding spurred a large body of work on bird intelligence. Watch:

And if you are interested of where these wonderful animals all came from, there is a fantastic blog by Ed Yong over at national Geographic. Read:

The changing science of just-about-birds and not-quite-birds
(HT @BjornBrembs)

I am sure there is a screenplay somewhere in there, inspired by Tron and involving cats chasing birds in cyberspace. But I shall leave that for someone more creative than me.

[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 ( 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

[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.

Getting the timing right for song control

Posted in Science by kubke on December 11, 2009

ResearchBlogging.orgSongbirds have evolved special areas in the brain that are used for song learning and song production. Two types of output connections from a cortical area known as HVC (proper name) each go to two ‘separate’ pathways. Some HVC neurons connect directly with neurons in a brain area called RA (robust nucleus of the archopallium), which in turn connects with the motoneurons that control the muscles in the vocal control organ (syrinx). Another set of HVC neurons connect through what is called the anterior forebrain pathway, a collection of cortical, thalamic and basal ganglia nuclei that are important for birds to learn their song. The two pathways talk to each other through a nucleus called LMAN that sends a direct input to RA.

Vocal circuit, by Kubke

The anterior forebrain pathway sends an error signal through the connections from LMAN to RA to ultimately control the motoneurons in nXIIts to produce the desired song structure. What is puzzling about the circuit is how the precise timing for this to operate efficiently is achieved. Because it takes time for the action potential to travel down the axon, and because it takes time for information to travel through synapses, the anterior forebrain pathway roundabout way (HVC-to-X-to-DLM-to-LMAN-to-RA) should be much slower than the speed of travel of information from HVC to RA. And this is precisely what Arthur Leblois, Agnes Bodor, Abigail Person and David Perkel examined.

To determine this, they electrically stimulated HVC and recorded from area X, DLM and LMAN, and were able to explore the mechanisms by which information travels around the anterior forebrain pathway as well as how long it takes to get from one point to another (latency).

How is transmission routed along the anterior forebrain pathway?

What they found is that low intensity stimulation from HVC produces excitation of area X neurons, but that higher intensity stimulation also produces a rapid inhibitory input from local area X circuits. One of the effects of this early inhibition is a lengthening of the time interval between consecutive action potentials in the neurons in area X that project to DLM (pallidal neurons).

DLM is normally inhibited by pallidal neurons in area X. But if the time interval between action potentials in the pallidal neurons is increased, it releases the ‘veto’ signal on DLM neurons which can then fire action potentials (either in response to other excitatory inputs or as a result of ‘post inhibitory rebound’). Based on the results, DLM neurons will therefore become activated (and in turn activate LMAN) when the local inhibition in area X (in this case triggered by HVC stimulation at high intensity) lengthens the time period between action potentials in the pallidal neurons. This is consistent with the observation that responses in LMAN could only be elicited by high levels of stimulation in HVC.

Zebra Finch (male) by Peripitus (GNU documentation licence v1.2)

In this way, an input from HVC sufficient to elicit fast inhibition in area X, removes the veto signal on neurons in DLM, which are then able to discharge and excite LMAN, which can then send the appropriate signals to RA.

Does the timing work?

The short answer is yes. First, the authors showed that although the path-length between HVC-Area X and that of Area X-DLM, are similar the conduction times are much smaller in the latter. This, they suggest, is achieved both by an increase in diameter of the axons projecting from AreaX to DLM, axons which are myelinated even within DLM. The population latency in DLM and LMAN following HVC stimulation is very similar, but the authors argue that perhaps the population of DLM neurons that have the shortest latencies that are the ones that are playing the key role.

The specialisations in axonal morphology and myelination of the pallidal neurons may be an evolutionary adaptation that contributes to a short latency pathway that can modulate fine temporal features of song production.


Leblois, A., Bodor, A., Person, A., & Perkel, D. (2009). Millisecond Timescale Disinhibition Mediates Fast Information Transmission through an Avian Basal Ganglia Loop Journal of Neuroscience, 29 (49), 15420-15433 DOI: 10.1523/JNEUROSCI.3060-09.2009

[Open] Science Sunday-29.11.09

Posted in Science by kubke on November 29, 2009

Cool science on the web made availabe by people who like to share….

About the language of open access

I am a big supporter of open access. But as I ponder on its virtues, I also ponder about its reach. As we move towards making our work available to the public through open access publishing, I wonder whether the language in which we write our work will continue to represent a barrier for true public reach. It is a difficult one, most of the jargon we use is required to express ourselves with precision and without ambiguity.

Then this week I came across this PLoS One article by David M. Lambert, Lara D. Shepherd, Leon Huynen, Gabrielle Beans-Picón, Gimme H. Walter, and Craig D. Millar that I think has bridged this gap. The article describes some genetic studies they did on museum specimens of the extinct huia, and although I would normally give a short summary of the article, this one is worth a read by scientists and non-scientists alike.

Great finds on the web:

  • Ed Yong from ‘Not exactly Rocket Science’ has a great blog on an article that looked at vision in hammerhead sharks
  • Brandon Keim has a great article on Wired Science on “paleoart’, the creation of 3D representations that bring our ancestors to life
  • Dr Zen from ‘NeuroDojo’ has a great blog on hummingbirds, their song and their tail sound (and how it all evolved)
  • And if you aren’t yet convinced about the beauty of science, check out these beautiful pictures of fluid dynamics from New Scientist.

Become a citizen scientist

As a biologist I often get asked a lot of questions about biology, most of them of the form

“I heard that <insert favourite rumour here>. Is that true?”

Most of the time, I don’t have the answer, and more often than not, the answer is not there. These are the ‘rumours’ of science that prompted Matt Halstead, John Montgomery and I to actually try to seek the answer. For that reason, we opened a webpage at where the data can be posted and, hopefully, rumours be put to rest (one way or another).

We launched the website with a very simple rumour about Tuis, and we are hoping that New Zealanders of all ages (but especially the younger ones) will tell us when and where they spot these fantastic birds.

In the future, we hope that schools will take advantage of the site to gather data for science projects, or communities will gather data that they need to put forward to their local councils, and so forth. It is, in itself an experiment, one that we think could be a lot of fun. So visit the site, and if you spot a tui please let us know here!

And my favourite tweet has to be this by @MsBehaviour, the first data point in the Tui project. Thanks Helen!