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Internet birdfest Fabiana Kubke Jun 01

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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.

For fireflies, getting the girl requires team work Fabiana Kubke Jul 10

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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

[Open] Science Sunday — 13.12.09 Fabiana Kubke Dec 13

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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.

Not just a pretty face: The facial ruff of barn owls and sound localisation Fabiana Kubke Nov 19

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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

Google, Waves and Fireflies Fabiana Kubke Nov 06

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Photinus pyralis Firefly glowing.jpg  Firefly (photinus pyralis) glowing

glowing Photinus pyralis by Artfarmer (Creative Commons Share Alike 2.0)

I just learned through ’The Complete Guide to GoogleWave’ (HT @BoraZ) that Google Wave takes its name after the way that characters in the TV series Firefly/Serenity communicated with each other through ‘waves’. Which reminded me of the fireflies in Elkmont in the Smoky Mountains National Park.

When I was a post-doc in the US, I would get on my car once a year to become a bit of a field hand but mostly a nuisance in a research project led by Andy Moiseff and Jon Copeland in the Smoky Mountains in Tennessee. (You can find one of the first news coverage of the story here).

Jon had been studying synchrony in the flashing of fireflies in Malaysia, because it was thought that it was only there where synchrony occurred. But a local from the Smokys (Lynn Faust) alerted him to a similar behaviour up in the park (and much closer to Jon’s hometown in Georgia).

Fireflies communicate using their light flashes, and in the Smokey’s they show synchronicity.

Photinus carolinus by Andy Moiseff

Photinus carolinus, by Andy Moiseff

A single male will produce a series of flashes in a sequence. When a male starts flashing, other males around it will start their own flashing sequence, in synchrony with the leader. The males around the second set of males then start doing the same, and so on, and what you see (if you are paying enough attention) is a sort of Mexican wave of fireflies flashing in synchrony. It is one of the most amazing light shows that nature has put together, and if you are ever in the area in the summer, I recommend visiting the park visitor centre and asking for a good viewing spot.

When I hear people use the word Firefly I immediately think of the Smoky Mountains (which usually brings me a couple of notches down the geek scale, since they mostly mean the TV show). I am sure I will be reminded of the summers in the Smokey’s every time I go into Google Wave.

How do birds sense the Earth’s magnetic field? Fabiana Kubke Nov 03

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ResearchBlogging.orgIf there is a physical property in the world that provides useful information, chances are that at least some animals will have evolved a sensory system to exploit it. The Earth’s magnetic field is no exception: it provides useful and reliable information to navigate the globe. There has been extensive research into whether and how animals may use the magnetic field for navigation, and although most agree that it is being used, the nature of how this information is processed can still be a matter of heated debate.

Thorup and Holland in a recent commentary on animal navigation in Journal of Experimental Biology state that:

[…] there are more reviews published on the subject than there are experiments providing evidence for the hypothesis at present

One more study by Zapka and collaborators has now been added to the mix, published in Nature last week. Here, they looked at the neural basis of the magnetic-based orienting behaviour in migratory European robins.

For birds, there are two theories of how magnetic information may be detected (magnetoreception), and data in favour and against each are not scant.

One theory proposes that there are specialized structures in the upper bill of the bird that can detect magnetic information, which is then carried to the brain through a branch of the trigeminal nerve. The other theory says that magnetic information is sensed through specialized molecules in the back of the eye, and that the information is processed by the visual system.

Several lines of evidence support the first theory. First, you can find magnetite in the upper bill of pigeons, in structures that appear to be contacted by the trigeminal nerve. Second, cutting the trigeminal nerve prevents pigeons from learning to behaviourally discriminate between the presence or absence of a magnetic anomaly.

The second theory proposes that light sensitive molecules known as cryptochromes in the eye are sensitive to magnetic fields. A molecular transformation sensitive to magnetic fields is then transmitted to a specialized visual area in the forebrain called Cluster N.

To distinguish between these two alternatives, Zapka and the group studied how the European robins performed a compass orientation behaviour when either the trigeminal or the visual ‘magnetic’ pathway (Cluster N) was destroyed. What they found was quite straightforward. Cutting the connections of the trigeminal nerve between the beak and the brain, did not have any effect in the behaviour. But when they destroyed Cluster N, then the birds were no longer able to show magnetic compass orientation. This rules out the need to use the trigeminal pathway for this orienting behaviour, and instead suggests that the responsibility of the neural processing is on the visual pathway. (Although it would be nice to see some electrophysiology to rule out this is not just a result of the lesion itself that may not be specific to cluster N).

So how can this be reconciled with the trigeminal data?

It comes down to what question the experiment is actually asking. This particular study looks at a very simple question: do the birds use one or the other system to do ’compass orientation’. The studies in pigeons asked ’is the trigeminal system necessary to learn a magnetic discrimination task’. They are not incompatible results (even less when you think they are different types of birds).

As Witschko and Wistschko state:

The magnetic vector provides a compass; magnetic intensity and/or inclination play a role as a component of the navigational map.

The question that still remains to be answered is whether pigeons use the trigeminal system to navigate. Although pigeons follow magnetic contours as they home, cutting the trigeminal nerve does not prevent them from homing. This means that the trigeminal system may not be necessary for that aspect of navigation per se, and perhaps (as the Mora and collaborator’s paper suggests) it may be involved in some aspect of learning associated with magnetic fields. Hopefully, more funding will be available to these groups so they can sort this one out.

Zapka M, Heyers D, Hein CM, Engels S, Schneider NL, Hans J, Weiler S, Dreyer D, Kishkinev D, Wild JM, & Mouritsen H (2009). Visual but not trigeminal mediation of magnetic compass information in a migratory bird. Nature, 461 (7268), 1274-7 PMID: 19865170doi:10.1038/nature08528.

Other references

  • Wolfgang Wiltschko and Roswitha Wiltschko. Magnetorececption in birds: two receptors for two different tasks. Journal of Ornithilogy 148:S61-S76 (2007)
  • Cordula V Mora, Michael Davison, J Martin Wild and Michael M Walker. Magnetoreception and its trigeminal mediation in the homing pigeon. Nature 432, 508-511 (25 November 2004)
  • A Gagliardo, P Ioale, M Savini and JM Wild. Having the nerve to home: trigeminal magnetoreceptor versus olfactory mediation of homing in pigeons. The Journal of Experimental Biology 209, 2888-2892 (2006)
  • Miriam Liedvogel, Kiinori Maeda, Erik Schleicher, Thomas Simon, Christiane R Timmel, PJ Hore and Henrik Mouritsen. Chemical magnetoreception: Bird Crytochorome 1a is excited by blue light and forms long-lived radical-pairs. PLoS One 2(10) e1106 [Open Access]
  • Dominik Heyers, Martina Manns, Harald Luksch, Onur Gunturkin, Henrik Mouritsen. A visual pathway links brain structures active during magnetic compass orientation in migratory birds. PLoS One 2(9) e937.[Open Access]
  • Kasper Thorup and Richard A. Holland. The bird GPS — long-range navigation in migrants Journal of Experimental Biology 212, 3597-3604 (2009) doi: 10.1242/jeb.021238

Disclaimer: Martin Wild, an author on the recent Nature study is my collaborator and my Head of Department. Some of his work on this area was funded by the Marsden Fund.

Marsden 2009-I: An eye on the birds and the bees Fabiana Kubke Oct 08

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The projects funded by the Marsden Fund of the Royal Society are out, and there are many interesting neuroscience projects that were funded this year, which I will tell you about over the next few days. Here are the first three.

Ben Thompson, from the University of Auckland will try to teach an old brain new tricks.

Ben Thompson works in amblyopia or ’lazy eye’, which affects about 3% of the population. During early development information coming from the two eyes fight for real estate in the visual cortex, and if you have normal vision in the two eyes, the visual cortex receives information from each of the eyes in alternating patches called ocular dominance columns. But if both eyes are providing unequal images then the dominant eye will displace the connections from the weaker eye in the visual cortex.

There is a critical period (which in humans is thought to end between the ages of 5-7 years old) over which treatment of lazy eye can be efficient in restoring normal projections from both eyes to cortex, and it has been traditionally thought that after that there is not enough plasticity in cortex to treat the effects of lazy eye. Some experiments in mice, however, suggested that Prozac could restore some of this plasticity, and this is what Ben wants to investigate. The idea is that if Prozac can restore pre-critical periods of plasticity in the adult brain, then therapies that are effective in children should now also become useful in adults.

The visual cortex has been one of the most intensively studied systems for plasticity in cortex, and if these experiments are successful, then Ben plans to see whether they can be extrapolated to other parts of cortex. For example, inducing plasticity in motor cortex could have a profound impact on the recovery of motor function following stroke.

Gavin Hunt and Russell Gray from the University of Auckland received funding to study tool manufacture and the brains of New Caledonian crows.

That New Caledonian crows were able to use tools had been known for a very long time, but it was Gavin Hunt who first saw these birds manufacture tools while he was doing his PhD in New Caledonia studying the endangered Kagu. He then contacted Russell Gray, and they started what was to become a very fruitful collaboration studying this behaviour.

This time, Gavin and Russell are asking a very interesting question: Did New Caledonian crows evolve a more complex brain associated with tool manufacture?  They plan to investigate the cognitive abilities of different types of crows and to try to identify what is different about the New Caledonian crow brains that makes this behaviour possible. The group has a great webpage where you can see the New Caledonian crow behaviour and two videos where Russell Gray provides a great description of their line of work.

And last but not least,

Alison Mercer from the University of Otago has received funding to study memory formation in bees.

Invertebrates have historically been a fantastic model in which to study fundamental aspects of neuroscience. Despite their small size the brains of bees (and other insects) are quite complex and bees have amazing learning abilities. Alison will look at two types of learning. Aversive learning is that where the bee learns to associate a stimulus with a negative reward. Apetitive learning is that where the bee learns to associate a stimulus with a  positive reward.

There are some differences between these two types of learning. First, apetitive learning develops earlier than aversive learning. Second, aversive learning (but not appetitive learning) can be blocked by a queen bee pheromone. From work in the fruit fly, it is known that these two types of learning are happening on the same population of neurons found in a specialized brain area known as the mushroom body. Since both types of learning are mediated by different neurotransmitters, and since only one type of learning is blocked by the queen’s pheromone, Alison will be able to investigate how a single neuron can create ‘functional’ compartments that allows it to store these two seemingly opposite types of information.

(Disclaimer: Fabiana Kubke is currently funded by the Marsden Fund, is a named investigator  in the New Caledonian project, and personally knows all of the researchers named in this post)

On electric fish, molecules and behaviour Fabiana Kubke Oct 01

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If you are an electric fish swimming through the murky waters of South America or Africa, vision will not be of much use to navigate. To circumvent this problem electric fish evolved an ‘electric’ sense which they use for navigation and communication. These fish produce electrical discharges through specialized cells in their electric organs. Because the electric field the fish generates becomes distorted by objects within the field, the fish can use these distortions to ‘see’ their environment. 

A group from Harold Zakon’s lab at the University of Texas has now shown that electric fish can change the amplitude of their discharge during different levels of activity by literally changing the amount of ion channels that are put into the membranes of cells in the electric organ during day/night cycles. When the fish are more active, they load the cells with sodium channels, which makes the amplitude of the discharge larger, allowing them to detect signals at longer distances.

The concept that proteins can be trafficked in the cell around circadian rhythms, and social cues is pretty cool. You can read the original work by Markham, McAnelly, Stoddard and Zakon that was published in PLoS Biology 7(9): e1000203 thanks to the magic of Open Access. (Or you can read the briefer commentary by Fortune and Chacron here).

If you are wondering what the electric discharge of these fish looks like, you can watch this amazing video from the Hopkins Lab at Cornell University. They connected electrodes to the fish tank to capture the electrical signal that can be viewed in the oscilloscope, or heard through a speaker. Ok, granted, not as pleasant as a canary, but if you have a spare oscilloscope at home they make really cool (albeit geeky) pets.

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