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:

Lyrebird

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.

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[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 ResearchBlogging.org 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.)

Finally,

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)

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.

Citation:

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