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.

Science lessons from 8 year old children

Posted in Science, Science and Society by kubke on December 22, 2010

[Cross posted from Talking Teaching]

Ed Yong in Not Exactly Rocket science alerted me to an article published in Biological Letters Biology Letters from the Royal Society. I will not discuss the content of the article, Ed Yong has (as usual) done a wonderful job. I would like instead to share the ‘concept’ of the article.

The article reports on some research that shows that bumble-bees use both colour and spatial relationship in their foraging behaviour. But enough about that. What is unique about this article is that the research was conducted by a group of school children. It is also unique in that it is written by a group of school children (in their language). And the icing on the cake are the figures: pencil coloured; no fancy graphic software.

This is, in my opinion, authentic teaching at its best. And authentic learning. And while we are at it, authentic publishing.

So what have I learned from this group of children? That, as they say, science is fun. And that teaching science, whatever the student age group, can be made fun and authentic and can get children motivated.

The background reads:

Although the historical context of any study is of course important, including references in this instance would be disingenuous for two reasons. First, given the way scientific data are naturally reported, the relevant information is simply inaccessible to the literate ability of 8- to 10-year-old children, and second, the true motivation for any scientific study (at least one of integrity) is one’s own curiosity, which for the children was not inspired by the scientific literature, but their own observations of the world.

I could not agree more. I love biology because I ‘played’ with biology as a child. I was fortunate enough to have a father who never answered my question with ‘I don’t know’ without following that up with ‘but lets try to find out’. As a child my father valued my questions and my curiosity, more so about things he didn’t have an answer for. And I will always be grateful to him for that. For my teachers, well, that was a different issue: rather annoying having a pupil in the class that just refused to overcome the ‘why?’ stage.

And these children have been given a great gift by being it let known that their thoughts and ideas have value. And that, once that barriers that have to do with the specific language of the scientific literature are withdrawn, their ideas and thoughts can bring about new knowledge.

These children will also grow up having learned a few fundamental things about science: How an idea is brought into shape, how scientific questions are narrowed, and the hard work and discipline that is needed to see an experiment through. Oh yes, and that no matter how good an idea may be, reviewers may still reject your grant.

None of this they could have learned from a science textbook.

The editors of the Royal Society should also be commended for not requiring that the manuscript adjust to the traditional publishing formats and allowing the authentic voice of the children to come through. This paper should become obligatory reading in science classes. If nothing else, children will recognise their own voices and curiosity in the reading, and, who knows, other groups of children with innovative teachers may teach us (adult scientists) another thing or two.

P. S. Blackawton, S. Airzee, A. Allen, S. Baker, A. Berrow, C. Blair, M. Churchill, J. Coles, R. F.-J. Cumming, L. Fraquelli, C. Hackford, A. Hinton Mellor1, M. Hutchcroft, B. Ireland, D. Jewsbury, A. Littlejohns, G. M. Littlejohns, M. Lotto, J. McKeown, A. O’Toole, H. Richards, L. Robbins-Davey, S. Roblyn, H. Rodwell-Lynn, D. Schenck, J. Springer, A. Wishy, T. Rodwell-Lynn, D. Strudwick and R. B. Lotto (2010) Blackawton bees. Biology Letters DOI:10.1098/rsbl.2010.1056

#SciFoo lightning talk [Reloaded] – Part 3

Posted in Science by kubke on August 25, 2010

(Slides 6,7)

I have always been fascinated by the series of studies in electrophysiology that led to our current understanding of how electrical signalling takes place in neurons. And no collection of classical electrophysiology is complete without the 1952 article by AL Hodgkin and AF Huxley on the sodium and potassium currents in the giant axon of the squid.

Saying that Hodgkin and Huxley were brilliant minds would be an understatement. But I was always fascinated by the following phrase in this paper:

‘These results support the view that depolarization leads to a rapid increase in permeability which allows sodium ions to move in either direction through the membrane.’

The reason it fascinates me is that this phrase would not look out-of-place in any modern neurophysiology textbook. But the state of knowledge at the time about how cell membranes were organised was quite different to that of today. Back at that time, cell membranes were thought to be formed by a layer of lipids ‘sandwiched’ between 2 layers of proteins. That meant that for ions to move in and out of the membrane they would have to break through the protein layers and move through the non-aqueous  fatty acid layer (something that would be thermodynamically hard for ions to do). Or, something had to ‘open up’ in the membrane to create an aqueous path for the ions to move.

The idea of pores was not foreign to cell biologists at the time, but the demands of Hodgkin and Huxley’s model of ionic movement in neurons could not be easily reconciled with the (then) current model of the cell membrane structure. Hodgkin and Huxley knew ions had to move rapidly and selectively and that the properties of the membrane changed dynamically for this to happen.

Singer and Nicolson, 1972

In 1972 Singer and Nicolson published a classic model of the cell membrane. In it they propose that rather than ‘sandwiching’ the lipids, proteins are found in the membranes in two forms: as partially embedded proteins, or as intrinsic proteins that traverse the entirety of the cell membrane. It would not take long to see how these intrinsic proteins could form aqueous channels that would allow ions to move from one side to the other of the membrane. That proteins were able to change their shape had already been shown, and so similar mechanisms could be envisioned for the gating of ion channels.

Neurophysiology would never be the same. By 1976 Neher and  Sackmann had published their patch clamp method which allowed them to record currents from single channels (and later won them the Nobel Prize),  and only two years later Bertil Hille had written and extensive review on ion channels.

It has never been clear to me (or my friends) how much thought Hodgkin and Huxley put into the structure of the cell membrane and how their work fit into the models of the time. But I like to think that they did and chose to trust and follow their data, regardless of the conflicts and lack of sleep that may have raised for cell biologists.


#SciFoo lightning talk [reloaded]

For fireflies, getting the girl requires team work

Posted in Science by kubke on July 10, 2010

ResearchBlogging.orgImagine you drive into a motel in Gatlinburg TN, and see behind an open room door 2 guys setting up cameras pointing at the beds while two young women peek from the parking lot. Well, if it was in the mid ’90’s it might have been Drs Moiseff and Copeland setting up the equipment before venturing into Elkmont in the Smoky Mountains to study the local fireflies. (And one of the two women would have been me.)

Andy Moiseff and Jon Copeland started studying the population of fireflies in the Smoky Mountains National Park after learning from Lynn Faust, who had grown up in the area, that they produced their flashes in a synchronous pattern.

Image courtesy of Andy Moiseff

In the species they are studying (Photinus carolinus) the males produce a series or bursts of rhythmic flashes that are followed by a ‘quiet period’. But what is particularly interesting about this species is that nearby males do this in synchrony with each other. If you stand in the dark forest, what you see is groups of lightning bugs beating their lights together in the dark night pumping light into the forest in one of nature’s most beautiful displays.

Females flash in a slightly different manner and, as far as I know, they don’t do it synchronously either with other females nor with the males. One interesting thing in Elkmont is that there are several species of fireflies, and you can pretty much tell them apart by their flashing patterns. But as useful as this is for us biologists (since it avoids having to go through extensive testing for species determination), the question still remained of whether the flashing patterns played a biological role.

And this is what Moiseff and Copeland addressed in their latest study published in Science. They put females in a room where LEDs controlled by a computer simulated individual male fireflies. The LEDs were made to flash with different degrees of synchronisation and they looked at the responses of the females. They found that while the females responded to synchronous flashes of the LEDs, they really didn’t seem to respond when the flashes were not synchronous. Even more, they responded better to many LEDs but not much to a single one. What this means, is that if you are a male of Photinus carolinus, you better play nice with your mates if you want to get the girl.

What *I* want to know is how this behaviour is wired in the brain. At first hand, this seems like a rather complex behaviour, but in essence all that it seems to require is a series of if/then computations, which should not be too hard to build (at least not from an ‘electronic circuit’ point of view). But Bjoern Brembs reminded me of a basic concept in neuroscience: brains are evolved circuits, not engineered circuits. So, Andy and Jon, how *do* they do it?

Original article: Moiseff, A., & Copeland, J. (2010). Firefly Synchrony: A Behavioral Strategy to Minimize Visual Clutter Science, 329 (5988), 181-181 DOI: 10.1126/science.1190421

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.