Nature Podcast 1 November 2007

This is a transcript of the 1st November edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (, which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to


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Adam Rutherford: This week, we introduce the Brainbow.

Jeff Lichtman: We were struck very early on in looking at the rainbow of colours we saw in the brain and so was not much effort to put those two ideas together.

Kerri Smith: And with forest fires currently in the news we take a look at how climate change is affecting the carbon balance of forest systems.

Tom Gower: With climate warming we have got increased fire frequency and severity of those fires that have basically caused the boreal system from becoming a weak carbon sink instead of a weak carbon source.

Kerri Smith: This is the Nature Podcast, I'm Kerri Smith.

Adam Rutherford: And I am, Adam Rutherford. It is the society from neuroscience conference in San Diego this week with around 25,000 scientists descending on the city to eat and sleep neuroscience. We have got a whole stack of brain food for you in this show including a diet try from Susan Greenfield on the problems of funding consciousness research. First up though, Mike Hopkin on how the brain prepares for the ear to hear.

Mike Hopkin: Interpreting the sounds you are hearing right now is a complex job for your brain, but even trickier is the task of setting up the auditory system at the very beginning of life, when the brain has never heard any sounds before. A study of newborn rats now shows how the developing auditory nerve is triggered without hearing any sounds preparing the brain to make sense of the real thing. Dwight Bergles of Johns Hopkins University explains the discovery. Nature 450, 50–55 (1 November 2007)

Dwight E. Bergles: So, we discovered was that a small group of non-nerve cells in the inner ear were responsible for initiating electrical activity in the developing auditory system. We found that the so-called supporting cells spontaneously release ATP, adenosine triphosphate, which is normally the energy currency of the cell, but it is also known to be a neurotransmitter, a chemical that is released by cells and can activate other cells. So, we found that these supporting cells spontaneously released ATP and that this ATP could spill over and activate receptors on the ear cells. These are the sensory cells that are normally involved in translating sound information into electrical activity. So, through a kind of Rube Goldberg device we found that this ATP caused the release of another chemical messenger from the ear cells, in this case glutamate and then glutamate acted on the auditory nerve cells that caused them to initiate bursts of electrical activity that was then conveyed to the brain.

Mike Hopkin: And this will happen without the rat hearing any sound, so why is that an important process?

Dwight E. Bergles: Yes, so we know that development of sensory systems there is a lot of electrical activity that occurs in these developing sensory systems before they are able to get information from the external world and that this electrical activity is important for laying down so-called sensory maps in the brain and so in order for this electrical activity to be present we need to have some mechanism for initiating it in the absence of an external stimulus and so all of the experiments that we did involved studies of animals during the pre hearing period, before they were capable of detecting sound.

Mike Hopkin: And why is this process important, what might happen to the brain and to the auditory system if this process did not happen before birth?

Dwight E. Bergles: Right, so for that we rely on some studies that have been done by other groups, which showed that if you removed the cochlea during this period, you get abnormal targeting or path finding of the nerve cells to their targets in the brain and also you have a situation where the survival of those target neurons is jeopardized and many of them just undergo programmed cell death if they do not receive input from the nerve cells upstream if you will and furthermore, we know that the target nerve cells undergo a very precise maturation process where they express different types of receptors and ion channels that give them a sort of an unique phenotype and if they do not receive this electrical activity, they do not undergo those appropriate changes, which are important for the proper encoding of sound.

Mike Hopkin: And, is this the process that also happens during human development and if so, what sort of age of embryonic development are we talking?

Dwight E. Bergles: Of course, much less is known about the development of the human auditory system. We suspect that similar processes are at play, but probably the major difference is that development of the human auditory system takes place in-utero, whereas development of other mammalian species like rats, which is the species that we used in this study, takes place after the animals are born in the first two weeks of life.

Kerri Smith: Dwight Bergles talking to Mike Hopkin. Now, it is hard to deny these days that human activity is dramatically altering the climate, but it can also indirectly set in motion changes in ecosystems that may worsen the problem. One of these is an increase in forest fires. Geoff Brumfiel reports.

Geoff Brumfiel: Boreal forests account for almost a third of the world's total forest area, but researches know little about their role in managing atmospheric carbon. In this week's Nature, a model of these forests shows that fire can turn them from a net carbon absorber to a carbon emitter. I called two of the authors to learn more. Nature 450, 89–92 (1 November 2007)

Tom Gower: My name is Tom Gower and I am a professor at the University of Wisconsin in Department of Forest Ecology and Management.

Ben Bond-Lamberty: My name is Ben Bond-Lamberty. I am a research associate in the University of Wisconsin, Madison. The basic question we were asking was what has been pushing in terms of a carbon sinker source, the boreal forest in the 20th century at least as much of the 20th century as we have good records for. The three big things we looked at, one was the rise of atmospheric carbon dioxide, one was the known increases in wildfire, which really shaped the northern boreal forest all around the world, and the third one was changes in climate.

Geoff Brumfiel: When you say pushing, what did you mean exactly there?

Ben Bond-Lamberty: I mean if you think conceptually, we put a big box around the forest and look at how much carbon finally is going in or out, we talk about that as a sinker or source, whether it is sequestering it or giving off carbon to the atmosphere basically and so we were curious, is there a single effect more than others that is affecting forest carbon balance that we can determine.

Geoff Brumfiel: So, Tom, what did you find was the dominant driver?

Tom Gower: Fire was clearly the dominant driver and if you look over the last sort of several decades, fire frequency has increased dramatically, it is such say in the 40s, 50s, and 60s they probably were anywhere from about 2 to 3 million hectares burning in North America each year. There had been several years and even a decadal average where it has gone up to 7 to 8 million hectares that have burned and to give you some perspective the fire that is burning in California right now is probably, I think, about 250,000. So, you know, these fires we are talking about are enormous in size collectively and what we found is that the low will last a couple of decades, with climate warming we have got increased fire frequency and severity of those fires that has basically caused the boreal system from becoming a weak carbon sink to sort of a weak carbon source.

Geoff Brumfiel: So, what you are basically saying is that these forests used to observe carbon primarily because the trees were growing and now they are emitting it, is that right?

Tom Gower: That is correct and what really determines that balance is you have got carbon uptake by the trees and carbon loss from the soil due to decomposition, the organic matter and so what happens is immediately after a disturbance you have no tress, so there is no carbon uptake, but yet the soil continues to decompose, in fact it even speeds up some because you have now got sunlight reaching the ground, maybe permafrost melting and warming up the soil even more and so the microbe activity speeds up and so, you get this large release of CO2 for several years, maybe up to as much as 5 to 10 years and then, the vegetation starts taking over again.

Geoff Brumfiel: Ben, how do you go about modelling a system like this?

Ben Bond-Lamberty: What distinguishes our approach why it is unusual first is that it sort of bridges the gap between a model that just runs it a little local point in space and time, say physiologically realistic model of a tree for instance and it is that in a sense applied over very large area, they cannot for instance afford to have continental or global scale effects. So, finally I guess getting in to answer your question is we used a physiologically very realistic plant model including with plant competition, which has really not been done before this scale and used a whole suite of input data over this million square kilometres.

Geoff Brumfiel: So, basically you are saying, I mean, to put it simply, I suppose that you modelled not just the forest, but the trees?

Ben Bond-Lamberty: Right and not just the trees, two kinds of trees and mosses, which in these high-latitude forests are really important and really have not been treated before.

Geoff Brumfiel: Tom, has there been good evidence for this in other systems or is yours really the first strongest swing from a carbon sink to a carbon source?

Tom Gower: I would say there is fairly compelling evidence for the Artic Tundra as well because they are even warming up more than the boreal forests. I would say those two probably really have provided probably the most compelling and the first evidence that we are now seeing the effects of climate change on sort of the overall function of two fairly important biomes simply because of either their size, which is the boreal forest which is the second largest forest biome in the world or the amount of carbon that they contain in them and the Arctic Tundra has the highest soak carbon concentration and boreal forest is the second. So, they both are really sort of key biomes in the global carbon cycle.

Kerri Smith: Tom Gower and before him Ben Bond-Lamberty ending that report from Geoff Brumfiel.


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Adam Rutherford: This is the Nature Podcast and now is time for The Podium. This week, we invited Susan Greenfield, Director of the Royal Institution of Great Britain and Professor of Pharmacology at the University of Oxford to step up.

Susan Greenfield: The philosopher, John Searle once remarked that to study the brain without an interest in consciousness was like studying the stomach without being interested in digestion. Consciousness, that first-person experience of the world is surely far more interesting and mysterious than digestion. In July 2005, editors of that other journal 'science' selected the biological basis of consciousness as one of the top 25 questions for modern science. Whilst other leading questions such as, the origin of the cosmos, receives hundreds of millions of dollars and pounds and euros each year, the scientific study of consciousness has virtually no funding whatsoever. Perhaps, the basic problem is that consciousness is quintessentially subjective and subjectivity is an anathema to scientists ruthlessly bred on the impartial objective machinery of scientific method and yet consciousness can be studied scientifically. Just recently, Christof Koch and I have published a joint review of a debate on different approaches to consciousness by neuroscientists in Scientific American, but usually funding for such research has to be disguised under more traditional area such as mental health. The one exception is the Mind Science Foundation in Texas, which has funded work directly on consciousness from leading neuroscientists publishing in high-impact neuroscience journals. Sadly, however, they have only very small grounds. So, only strategic pilot investigations are possible and there are no large funding bodies like this foundation. My fear is that the unpopularity and queasiness of a consciousness research is not really due to a non scientific basis, but rather the question is just too hard, exciting, and downright conceptually formidable compared to sorting out the relative minutiae of subtypes of receptors, properties of ion channels, the latest relation of a phenotype to a genotype or indeed indulging in a modern phrenology with brain scans. The question of how the brain generates consciousness requires a novel hypothesis rather than merely prospecting around in the brain and as such research proposals maybe unpopular to the current risk-averse nature of peer review funding bodies of a dieting as they are prone to do on a gradgrind like obsession with facts of their own sake. The questions of how the brain develops consciousness require not just the hypothesis, but a conceptual framework for how different levels of brain organization be they genetic, anatomical, neuropharmacological, or electrophysiological might all work together, and here I fear people are shirking away from the true scientific enormity, but also the excitement of a task and there will be no coincidence that those have made their name in the field in the past, for example Gerald Edelman, Francis Crick, and Brian Josephson were all Nobel Prize winners. Not only might such a question attract the best and boldest brains, but perhaps only those who do not fear for their careers. How sad it was that the study of consciousness was once described as a CLM, a Career-Limiting Move.

Adam Rutherford: Susan Greenfield on The Podium and that review she mentioned is available on the Scientific American website that is

Kerri Smith: And now rather colourful piece of science and I think Baroness Greenfield would approve because it may well feed into research about consciousness along with a host of other topics. Jeff Lichtman and Jean Livet and their colleagues at Harvard University have devised a flashy new piece of kit for neuroscientists, which they are calling, the Brainbow. Brain researchers often use coloured dyes to track the pulse and connections of different neurons, but to date there have only been a few different colours available. Using these existing colours along with a clever piece of genetic jiggery-pokery the team have been able to stain hundreds of individual neurons each with a different hue. Here is Jeff Lichtman. Nature 450, 56–62 (1 November 2007)

Jeff W. Lichtman: The Golgi stain and subsequent techniques are basically like black and white movies, they are monochromatic i.e., all the nerve cells typically stain the same colour and our interest was to see how different nerve cells interact with each other in neuronal circuits and if they are all the same colour it is very easy to get confused i.e., you see a lot of little processes, but you cannot identify the neuron of origin of these processes. So, what we have done in essence is make a Technicolor Golgi, a stain just like the Golgi stain, although now using modern molecular biology to do this staining rather than silver staining and allowing us now to have many neurons, rather than just a few labelled, but rather than all of them labelled one colour, each cell being labelled a different colour.

Kerri Smith: And you have come up with quite an apt name for this.

Jeff W. Lichtman: Yeah! Brainbow! I think we were struck very early on in looking at our images at the rainbow of colours we saw in the brain and so, it was not much effort just to put those two ideas together.

Kerri Smith: Well, we here as well have been really struck by the images and they are really beautiful. I will refer people to the website at the end of the interview for those. Jean turning to you, your article this week demonstrates in quite breathtaking Technicolor that it is possible to paint neurons in hundreds of different colours using these fluorescent proteins that already exist, what is the theory behind your technique?

Jean Livet: Basically, the idea is to sort of, take the existing elements of the tool box that the molecular biologists have today, which include genes coating fluorescent proteins of different colours and also other elements such as promoters or sites for recombination and sort of assembled them into a construct and here it would be equivalent to a little molecular gambling machine so that each cell would sort of play this machine and pick randomly a different colour.

Kerri Smith: So, you have used standard genetic recombination techniques to get basically loads of different colours by mixing these fluorescent proteins that we already have?

Jean Livet: Exactly! So, basically each cell sort of makes a choice between different colours. Let us say cyan, yellow or red and by repeating that choice several times because there is in fact multiple copies of the construct in a cell, then the colours get combined together. So, you get combinations of the colours and so that actually allows you to have basically many, many different colours in the same way that the computer screen would un-code the colour space by mixing the three primary channels, red, blue, and green.

Kerri Smith: And you have got some results, then what happened when you used this process to look at the cerebellum, what were you able to tell that you could not tell before about the organization of the cerebellum?

Jean Livet: What could be done before actually was to trace, one or few neurons within nervous tissue and what we could do here with the Brainbow was to access the anatomy of not only one or few cells, but many of them and what we could see then was we could see axons labelled in different colours and by virtue of the different colours we could tell they are coming from different cells and that allowed us to investigate the connectivity in the cerebellum and investigate what is the convergence of the actions over cells within the cerebellum.

Kerri Smith: How do you see this new technique being used?

Jeff W. Lichtman: Well, I think there are three or more, but I cannot think of three right off the bat, places where these kinds of tools might be useful. The first is that there was a whole range of diseases of the nervous system about which we know very little, perhaps because these diseases are ones that in some way have caused a defect in the wiring of the nervous system, the connections between nerve cells and we think these kinds of staining approaches may be useful in animal models of such diseases. A Second area is in the normal development of the nervous system we are aware in mammals and certainly in humans, the nervous system undergoes rather impressive changes in its wiring in early life, but we have very few tools that allow us to see how those changes take place and lastly and maybe most interestingly because one does not really know how this will turn out, the wiring of our nervous system of our brain has a lot to do with who we are as human beings. We have very little insight, I think, into this most complex of our organs, the brain and just seeing that wiring may give us some insights into how the brain works, how cognition works, where memories are stored and other fundamental questions about the way the brain works.

Kerri Smith: Harvard's Jeff Lichtman and Jean Livet, who have high hopes for their Technicolor technique, Brainbow, those stunning images are available at

Adam Rutherford: And you can hear more from the Brainbow authors in the second edition of Neuropod, Nature's brain research podcast.

Kerri Smith: That is right. In our special society for neuroscience episode, I will be looking at how to switch mice on and off using a trick of the light and hush realities we ask psychiatrists about the links between cannabis and psychosis. That is live on the 1st November is the address.

Adam Rutherford: That is it for this week, write to us. The address is As usual we are playing out with a sound of science, the Gene2Music program developed by Rie Takahashi and Jeffrey Miller at UCLA translates gene sequences into melodies. We have converted FOXP2, a gene involved in speech and language and incidentally Kerri's favourite gene into this delightful tune. I am Adam Rutherford.

Kerri Smith: And I am Kerri Smith. Thanks for listening.

[Sound of science – music]


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