Building Blogs of Science

[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!

Synapse #fail, Science #win

Posted in Science by kubke on November 25, 2009

ResearchBlogging.orgThe endbulb or calyx of Held is a very large synapse found in the auditory system. It consists of a very large ‘calyceal’ ending, literally wrapping around the cell body of the postsynaptic neuron. It was first described by H Held in the late 1800’s and has since been shown to characteristically be present in neuronal circuits that require very high temporal precision. (It is, by the way, my favourite synapse.)

Because the synapse is so large, there are numerous sites of contact where the neurotransmitters are released, which will happen whenever an action potential reaches the synaptic terminal. Because of this, it has always been thought that these synapses never fail to produce a response (action potential) on its target (postsynaptic) neuron, that is, that it is a fail-safe synapse: every time that there is neurotransmitter release, the postsynaptic neuron produces an action potential.

Endbulb of Held

Barn owl endbulb of Held (by Kubke)

But is this true?

Jeannette Lorteije, Silviu Rusu, Christopher Kushmerick and Gerard Borst examined precisely this, and they did so in a series of really elegant experiments in mice. They examined whether the discrepancies in the data regarding the degree of reliability at the enbulb or calyx of Held could be attributed to different methodological approaches or differences in the interpretation of the raw data. To examine this they did a series of recordings from cells in the Medial Nucleus of the Trapezoid Body (MNTB), which is part of the mammalian auditory system. The authors conclude that that there is a significant incidence of failures of transmission at this level of the system.

This is in contrast with the results reported by Bernard Englitz, Santra Tolnai, Marey Typlt, Jürgen Jost and Rüdolf Rübsamen. Here the authors recorded the failure at the endbulb of Held in the auditory cochlear nucleus AVCN and the calyx of Held in the MNTB in mongolian gerbils. They report that although failures of transmission were often found in AVCN, this was not the case in MNTB.

Synaptic structures analogous to the endbulb or calyx of Held are found in neuronal circuits that require high temporal precision. In the auditory system high temporal resolution is necessary for the measurement of interaural time differences, which in mammals are used to localize low frequency sound in the horizontal plane. Benedikt Grothe has argued that low frequency hearing appeared later in mammalian evolution, and that anatomical differences in a nucleus that receives inputs from the MNTB and is involved in the detection of interaural time differences (MSO) reflect this evolution. He argues that although MSO may have evolved to detect ITDs in low frequency hearing mammals (such as gerbils), its function may be different in higher frequency hearing mammals. On therefore wonders whether the differences in the data between the two studies may be related to adaptations associated with different temporal processing requirements in mammals with different frequency hearing ranges.

What did Lorteije and collaborators do?

In order to decide whether there are times in which synaptic release fails to elicit an action potential on the target cell, one needs to simultaneously monitor the activity happening at the synapse as well as at the postsynaptic neuron. There are traditionally two ways of doing this: One is to record the currents near the synapse that are produced by the electrical activity of the synapse and the cell, and the endbulbs of Held are large enough to produce sufficient current that can be detected. The other is to actually record the activity simultaneously from the cell and the synaptic terminal, which is usually done in an ‘in vitro’ preparation.

Lorteije and colleagues produced a set of data that is simply amazing, and their findings explain many of the discrepancies that can be found in the literature. They answered some very straightforward questions:

  1. Are the extracellular recordings done in vivo representative of what is actually going at a single endbulb-neuron contact? (the answer is yes)
  2. Is there synaptic  release that fails to produce an action potential in the postsynaptic neuron? (the answer is also yes)
  3. Is the short term synaptic depression seen in vitro also seen in the whole animal (in vivo)? (Short term depression is a reduction in the effect of synaptic release on the postsynaptic cell.). (The answer is basically no)

The authors recorded from cells in the Medial Nucleus of the Trapezoid Body (MNTB), which receives inputs in the form of the large calyces of Held and is involved in auditory processing. They did this by recording the spontaneous and auditory-evoked activity extracellularly (as most people do) as well as directly from the cells with a patch pipette in anaesthetized mice. They then repeated these experiments in vitro, this time simultaneously recording extracellularly and in whole cell patch, which allowed them to confirm that the extracellular recordings in vivo did indeed represent the activities of the terminal and the cell and that it could also provide information as to the size of the synaptic potential. Their results have two important findings:

  1. in vivo there is no observable short term synaptic depression. The synaptic depression observed in vitro may be partly due to the concentration of Calcium in the bathing solution, but other factors may be involved.
  2. They also found that the release of neurotransmitter at the synapse often failed to produce an action potential in the postsynaptic cell. A similar rate of failure to that observed in vivo can be obtained in vitro by lowering the calcium concentration of the bathing solution.

The authors summarize their findings by saying:

“Due to its low release probability and large number of release sites, its average output can be kept constant, regardless of firing frequency. Its low quantal output thus allows it to be a tonic synapse, but the price it pays is an increase in jitter and synaptic latency and occasional postsynaptic failures.”

This is a carefully designed study, and despite my concerns as to whether their results are generalizable to other mammals, they do provide data that will be welcome by many auditory neurophysiologists. Their ability to record from a patch in vivo is no small feat, and the correlation between intracellular and extracellular data is extremely useful. Further, there is a cautionary tale around the way that data obtained from in vitro data can be interpreted.

And if you think this post is long, try reading the paper! (There are heaps more gems in there.)


Lorteije, J., Rusu, S., Kushmerick, C., & Borst, J. (2009). Reliability and Precision of the Mouse Calyx of Held Synapse Journal of Neuroscience, 29 (44), 13770-13784 DOI: 10.1523/JNEUROSCI.3285-09.2009
Englitz, B., Tolnai, S., Typlt, M., Jost, J., & Rübsamen, R. (2009). Reliability of Synaptic Transmission at the Synapses of Held In Vivo under Acoustic Stimulation PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007014
Grothe, B. (2000). The evolution of temporal processing in the medial superior olive, an auditory brainstem structure Progress in Neurobiology, 61 (6), 581-610 DOI: 10.1016/S0301-0082(99)00068-4

[Open] Science Sunday – 22-11-09

Posted in Health and Medicine, Science, Science and Society by kubke on November 22, 2009

Roaming through the web, I found great stuff this week that shows the value of an ‘Open’ attitude in science.

The Rutherford Medal, New Zealand’s top science prize, was awarded to Professor Peter Hunter from the Bioengineering Institute. Peter Hunter is also one of the minds behind the Physiome Project,

“…a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology.”

Peter Hunter is the Director of the Bioengineering Institute at the University of Auckland, a great model of what can be done in science in New Zealand when great thinkers are given the opportunity to build upon great ideas. You can read more about Peter Hunter’s award here and here.

A great article “Open Source Science: A revolution from within” written by Vivian Wagner was published in Linux Insider:

“Just as open source software allows programmers to access the code in order to create new and improved versions of software, open source science gives the scientific community open and easy access to fundamental experiments, methods and data in order to facilitate more research. The goal, ultimately, is better science.”

This type of approach to science is becoming a successful alternative and perhaps one that will be more successful in a world where scientific funding is continuously on the decline. (via @plos on twitter)

Ed Yong from Not Exactly Rocket Science has a wonderful post on the energetic problem that comes with having a large brain, and the genetic changes that may be a tell-tale of the evolution of brain size. And if you are at all interested in the evolution of brain size, Mark Changizi has started an incredibly interesting discussion on the topic. Both the post and the comments make for a great read. (I also like that he opened this discussion up and did not restrict it to academic circles.)

A great video from National Geographic shows the “supercrocs” in action:

“Paul Sereno, Paleontologist, University of Chicago: These stubby teeth didnt even touch each other to snare a fish, no, they were hook-like, strong cylinders to grab onto a dinosaurs limb or neck and pull it into the water. We began to understand this animal as a hidden predator of the dinosaurs.”

And related to this a great tweet from @carlzimmer linking to a dinosaur story on 60 minutes.

Ten summer fellowships were awarded to students to take part in the Tamaki Transformation project, and Wednesday marked the celebration of the beginning of what we hope will be a great collaboration between the University of Auckland and the community. I am part of  one of these teams with a project that will be led by Fraser Peat, a Med Student at the University of Auckland, wher we will be looking at issues surrounding science and health related education and literacy in the community. The results of the summer work will be shared with the community in March next year.

Not just a pretty face: The facial ruff of barn owls and sound localisation

Posted in Science by kubke on November 19, 2009

ResearchBlogging.orgThis post was chosen as an Editor's Selection for ResearchBlogging.orgBarn owls are the subject of many studies on auditory neuroscience because of their exquisite ability to localize sound. The auditory system is interesting from a neuronal computation point of view because the inner ear, where sounds are detected, relays no information to the brain as to the location of the sound source in space. It is then up to the neurons in the brain to extract other information transmitted from the ear to build an auditory space map which can be used for sound localization. The basic model is that the auditory system does this by comparing the differences in intensities of the sound at the two ears (interaural level differences) and the differences in the time of arrival of the sound to each of the ears (interaural time differences), and that this information is sufficient to sound localize.

Barn owl, by Stevie B cc-by-2.0

But the sound that reaches the tympanum is not an exact replica of the sound emanating from the source, to a great extent due to the way that sound interacts with and is modified by the animal’s own head structures (for example, the external ear or pinna). These changes in the structure of the sound are described in the Head Related Transfer Function (HRTF). Because we are not identical clones of each other, each one of us has a slightly different head related transfer function.

In a recent study published in PLoS One, Laura Hausmann, Mark von Campenhausen, Frank Endler, Martin Singheiser, and Hermann Wagner examined whether the contribution of the facial ruff to the barn owl’s HRTF affected the owl’s ability to sound localize. They recorded the HRTF of each of the owls in the study, as well as the HRTF of a barn owl in which the facial ruff had been cut off. They used these functions to build a virtual auditory stimulus that simulated the presence or absence of the ruff, and assessed the ability of the barn owls to sound localize. (They can do this behaviourally, because barn owls turn their heads to the source of the stimulus with great precision.)

Their results show that the facial ruff contributes to the cues used for sound localization by increasing the effective interaural time difference range that barn owls use to localise sound in the horizon and by contributing to the differences in interaural level differences that barn owls use to localize sound in elevation. But they also showed that there were no differences in the localization ability when when barn owls used  interaural time differences whether the virtual acoustic stimulus was built with their own HRTF or one of another owl. This was not true when the owls were using interaural level differences, where the owls did not localize equally to the different  HRTFs. Removal of the ruff had, as expected, several effects on sound localisation, one being that they lost the ability to discriminate between sounds coming from the front or from the back.

Baby barn owl (Tyto alba)

Barn owls learn how to associate interaural time and level differences with the location of the sound source during their first two months of life, when their head is growing and the facial ruff develops. They do this by instructive signals derived from the visual system, by which they attribute specific combinations of interaural time and level differences to particular sound source locations, and that leads to the development of a ‘space map’ that is custom built for each particular owl.

  • Disclaimer: Hermann Wagner is a former collaborator of mine.

Hausmann, L., von Campenhausen, M., Endler, F., Singheiser, M., & Wagner, H. (2009). Improvements of Sound Localization Abilities by the Facial Ruff of the Barn Owl (Tyto alba) as Demonstrated by VirtualRuff Removal PLoS ONE, 4 (11) DOI: 10.1371/journal.pone.0007721

Open Science Sunday – 15.11.09

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

ResearchBlogging.orgAn article entitled University Public-Access Mandates are Good for Science by David Shulenburger was published in PLoS Biology this week. It is a great read, and a topic I feel passionate about. As the article states:

“Not many taxpayers know what university faculty are doing. In fact, not many university administrators or even other faculty know what research their colleagues are performing. This veil over faculty research may contribute to the 20-year trend of declining real per-student subsidy from states to their institutions of higher education.”

This is partly because many of us scientists are not good communicators to begin with, but also because we publish our data in specialist journals that are not readily and freely accessible to the general public. But what would happen when we do put it out in the open?

“Suddenly the invisible campus becomes a place populated by individuals researching topics relevant to the average citizen. Legislators who complain about faculty productivity would find their arguments more difficult to sustain. Donors and potential donors might even alter their gift-giving based on such searches.”

This is the key, especially considering that both my (and my colleague’s) salary and research expenses are paid for by taxpayers and individual donors. Accountability and transparency should be expected of academic researchers as much as it is expected from other branches of public service. Do taxpayers, after all, not have the right to have access to the information that is generated from their investment, or are they to accept a version that is filtered through the lenses of PR offices and newspapers? Importantly, among the public with limited access are the policy makers and local GPs.

There are other consequences to access to scientific literature that impact on the research itself:

“Surveying 2,157 US scientists in 2007, Stephen Hansen of the American Association for the Advancement of Science found that 29% of respondents said that their own research had been affected by difficulties in gaining access to or disseminating copyrighted scientific literature.”

And later on the article:

“The only solution that gives science the maximum chance for advancement is one that ensures that all science findings are available to all researchers.”

Public access mandates have now been adopted by funding agencies such as the National Institutes of Health of the USA, the Wellcome Trust, among others. However, New Zealand funding agencies have not yet taken the step to adopt similar mandates to ensure that the science generated in New Zealand and funded by New Zealanders be made publicly accessible.

Much has been said and continues to be said about Open Access, and this article is another one to add to the reading list. I would argue that aside from the issues that centre on the accessibility of data there are issues arising from the copyright agreements with many scientific journals that limit the dissemination of science (even one’s own) and have potential legal implications. But that is a topic for another post.
David Shulenburger (2009). University Public-Access Mandates Are Good for Science PLoS Biology, 7 (11) e1000237