The Naked Scientists in New Zealand

26 August 2014
Presented by Chris Smith.

Dr Chris Smith

In this episode

00:53 - Problem solving lasers

Lasers are helping to create energy by using the suns rays.

Problem solving lasers
with Cather Simpson, Photon Factory, University of Auckland

Lasers are being used in lots of ways, now including harnessing the sun's rays to produce energy and detecting the gender of sperms. Cather Simpson spoke to Chris Smith and Simon Morton about how she's doing this... 

Cather  -   So a laser is a very special light source.  So, if you'll look at the lightsArgon-ion and He-Ne laser beams in the room, you'll see that they look white or maybe slightly blue.  That's because they're putting out light of all different colours in all different directions.  Lasers essentially pick out one colour and put it out in a very tightly focused - we call it a coherent beam.  So, I have three different lasers here.  One is very blue, one is very green, and one is very red.

Simon -   And Cather, these are like little Maglites, are they?  They're about the size of a sort of peg.  Do they actually burn?  Could you burn a hole on my head with any of those?

Cather -   Let's try it.

Simon -   Really?  Isn't it dangerous to try and laser someone's eyes?

Cather -   You should never shine laser at anyone's eyes.  Most laser pointers, I have two that are slightly bigger than the average laser pointer that you'd get in a $2 shop.  These are ones that we bought for my research lab.  so, we use these in experiments and that's why they've got duct tape on them because we take them apart and put them back together.  Never shine them at your eyes.

Simon -   What are you trying to discover then at the photon lab?

Cather -   So, what we're trying to discover at the Photon Factory is how molecules absorb light which is a kind of energy and turn it into a more useful form of energy.  And so, if you look for example - this is just tonic water - because we're scientists, I'll show you.  See, really tonic water - the Schweppes label.

Chris -   Where's the gin?

Cather -   That was you guys who were supposed to bring the gin.  So, tonic water has a chemical in it called quinine.  It's the stuff that makes it taste bitter and it's the stuff that cures malaria.  If I take my UV laser, my very purple one and I shine it at tonic water and all I've got - I've got two 2-litre bottles here and I've put some aluminium foil on one side to get a few more reflections.  What you can see - those of you who can see - and I'll hold it up.

Simon -   Wow!  It's amazing.  There's a very distinct beam there, going through the tonic water and it looks - I mean, that's sort of Han Solo sort of stuff, isn't it?

Cather -   It looks like a lightsaber, doesn't it?  So, for those of you who want to make a lightsaber, if you fill a tube with tonic water, you're right on...

Chris -   It would be quite heavy, wouldn't it?

Cather -   Yeah.  So, if you see this, it's a different colour, isn't it?  It's kind of a light blue colour, sort of white, compared to that purple colour.  And so, what the quinine molecule is doing is it's absorbing the light.  It's getting all excited and it's turning it into a different colour of light.  If I use my red laser, all you see is red.  If I use my green laser, all you see is green.  All you're seeing there are reflections.  The molecules aren't absorbing and converting it to anything.

Chris -   So in other words, the molecules of quinine in the bottle are exclusively and selectively responding to the purple light, but not the green and the red.

Cather -   Absolutely.  And so, what we study is the same light that's coming off of here or that you're getting out of these blacklights.  It's hitting the back of your eye and the reason that you're seeing something is because in a very, very short time, millions of a billionth of a second, the molecule in the back of your eye is converting it to molecular motion.  The molecules that are in plants that do photosynthesis are converting that light energy to a little battery.  The molecules that are in my finger when I take a green, even an intense green laser pointer, you can't see it at all, right?  the molecules that are in my finger are the hemes that make your blood red are absorbing that light and extremely rapidly sending it out as heat.  And so, we study how molecules and a lot of those are related to one another in structure, how molecules decide what they're going to do.

Chris -   What are the applications of this?  What sorts of things can we use our understanding of how lasers interact with materials, the way you've been showing us to do?

Cather -   So, in our lab, we do everything from that kind of fundamental research, looking at how these molecules change light into other forms of energy, and the students who are studying that are looking at things like how art pigments fade and how we might prevent them from fading, or how we might make better solar energy harvesting complexes.  But we also take our lasers and use the fact that they're dumping energy into a system to make them very practical.  So for example, Intel would love to be able to use one of our very short-pulsed lasers to dice chips for their semi-conductor industry.  Right now, the narrow pulses don't have quite enough energy in them, so it's too slow to be economical.  But we have a big grant from the government to try to use our physics knowledge to make them more efficient.  And that's very exciting.

Chris -   I was talking to a guy the other day who has actually found that you can put a lot of energy into something with a laser.  But if you were to put all of the energy in all at once, the temperature would be obviously very high because of the huge amount of energy going in.  but if you spread this as a series of little pulses over time, you can put enormous amounts of energy in but it's not going to get to a very high temperature and burn the thing.  But then you get the changes you've been showing us with light coming back out, you get that information coming out so you can interrogate materials and find out for instance what paints were used to paint a picture or tell if it's real or if it's a phony picture, or something someone knocked up in their back garden.

Cather -   You can certainly do that.  So, you can get the spectrum if you use a laser like you're describing, a pulse laser.  There's a really interesting thing that happens when you start taking a laser like this one which is coming out all the time.  this is continuous wave and you start taking the beam and you chop it into little pulses.  You don't get rid of light.  You essentially kind of - it's like if you had Playdoh and you made it into little hills, right?  At some point, you start making those pulses very dangerous because there's so much energy inside that you ablate the material - you remove it.  So, if I use one of the lasers in my lab, that is about a billionth of a second long then with a single shot - so, this is a nanosecond pulse - I could detach the retina from the back of your eye.  That's a little gruesome.  I wouldn't do that, I promise.

Chris -   I wouldn't love to work in your laboratory.

Cather -   But I could also drill through a piece of stainless steel.

Chris -   And just very briefly - I mentioned this at the beginning - you're also sorting sperm out with lasers.  How are you doing that?

Cather -   So, we sort sperm with lasers using the fact that the same kind of energy that we're talking about damaging stuff, you're essentially hitting materials.  And so, you're generating forces.  So, you can make a solar sail for example, put a big aluminium foil.

Chris -   And not the sperm though.

Cather -   No, but yes, we do with sperm.  So, one of the things that we do is we put them in a little channel.  These are bovine sperm for the dairy industry and they're disk-shaped.  And in fact, just like turning the sort of Frisbees.  So, we put them in a channel and we use the fact that these things generate pressure and that puts them all and oriented the same way, and they go down this channel and we say, "Ah!  There's a male sperm and a female sperm."

Chris -   How do you tell them apart?

Cather -   So, the male sperm has a Y chromosome which is a little bit smaller and so, when you use fluorescence, that means the males aren't quite as bright as the females.

Chris -   Just more aggressive and miserable and stroppy.

Cather -   No, it has nothing to do with aggression.  It has to do with brilliance.

Chris -   They refuse to ask directions.  The male sperm don't say which direction do I have to go.

Cather -   No, it's not about asking directions.  And then we use another laser pulse to take the ones that we've identified as female in this case and go boom, and we just move them over.

08:41 - Life on Mars

Did our closest planetary neighbour ever habour life? And how would we ever find it?

Life on Mars
with Steve Pointing, Institute for Applied Ecology at AUT

Classic David Bowie song or legitimate scientific question? Many believe Mars may have, at some point in time, harboured life, and one of those people searching is Steve Pointing, director of the Institute for Applied Ecology at AUT, who explained why we're looking for life on Mars. 

Steve -  Mars is our closest neighbour and to understand why it's worth looking Atmosphere of Mars taken from low orbitthere, it's more than just proximity and getting there easily.  It's also about understanding a concept.  That concept is known as the habitable zone.  So essentially for any star like our sun, there is a very small zone around that star that is able to support planets that can harbour life.  it's really a confluence of two functions.  Number one, the planet needs to be just the right distance from that star to allow water to exist as a liquid.  So, if it's too far away, the water is cold and frozen.  If it's too close, the water is evaporated and not available.  And the second thing is the planet has to have enough mass to retain an atmosphere, such that gases that are useful to life like carbon dioxide, like oxygen are retained, but heavier and more toxic gases are not retained.

Chris -   Do you know they were going to build a nightclub on Mars, but they said it was crap because there's no atmosphere?

Steve -   Great!  Parking would be an issue anyway.  Yeah, it's interesting.  Funny enough, going on from that though, there's actually a Dutch TV company who've been advertising for a bunch of individuals to take a one way trip up to Mars for a reality show.

Chris -   But they're all old people when they said old people only because they didn't want anyone who was going to come back.  They said, a.) it would affect the budget and b.) there was danger of radiation exposure because NASA did with the Curiosity rover that landed almost two years ago this weekend.  It's going to be 2 years of Curiosity rover that came down.

Steve -   It's 2 years this week, yes.

Chris -   They use the radiation sensor on Curiosity to measure the incident radiation exposure that it got during the - because over half a billion kilometres of travel to Mars, isn't it?

Steve -   That's right.  Six months in a cramped spaceship.

Chris -   Equated to basically an astronaut's entire working lifetime sort of radiation exposure just making that journey.

Steve -   Absolutely and that's largely because there is no atmosphere to block out those harmful incoming rays.  So yeah, it would be absolutely unimaginably large task to get people living up there permanently.  But you know, we have to aim big.  The simple truth is that when one considers our star, it has a finite lifespan and we're a single-planet species at the moment.  And so really, philosophically, we have to ask ourselves, do were really want to admit that once planet Earth becomes uninhabitable that we're going to die out.  So, that's really - from my mind - is the philosophy behind exploring Mars.

Chris -   What makes you think that Mars might have life on it at all?

Steve -   Well, it's a good question.  The sort of life we'd be looking for - let me be clear - is not little green men.  I don't think we're expecting.  We're not really looking at that.  the reason is this - I've got a bit of show and tell for the people listening.  I'm holding up a rock at the moment which has a rather smudgy green line just beneath the surface.  This is the surface of the rock here and this green line is about 20 mm below the surface and this is the sort of life that we expect to encounter on Mars.  This particular rock is actually from Antarctica but Antarctica is what we call a Mars analogue.  It's the closest thing on Earth that we have to Mars surface.  It's very cold, it's very dry, and it's relatively high radiation levels there because the atmosphere is thinner at the poles.  This sort of life, although it's green, it's not a green man or a green woman, it's actually cyanobacteria which are very, very primitive plants.  They're single-celled microbial plants essentially.  That's the sort of thing we're expecting to find.

Chris -   Just to be clear, they can actually thrive in the temperatures.  They're actually viable at the sorts of temperature you see in Antarctica.

Steve -   Well, they're not viable at surface temperature.  The temperature on Mars can be anything down to minus 110 degrees which biological reactions just won't occur there.  But these organisms are just below the surface.  The reason is that in Antarctica for example, they're exploiting very marginal gains in temperature and humidity that occur below the surface.  And so, the reason Curiosity for example has a drill on it is that NASA's aim is to drill into the rock and thereby, try to identify whether life is either present or has been present in the past which is probably our best bet.

Chris -   Have they found anything yet?

Steve -   No.  Curiosity doesn't have a primary aim to search for life.  Curiosity actually is looking for the chemical conditions that could've supported life.  So for example, how sustained was the presence of water on the surface. But in 2020, there is a sort of an amped up version of Curiosity going to be launched which will have a slightly adjusted payload and that will have a direct aim to search for life.  that is a good segue to our previous speaker because it's actually using lasers.  In this case, a Raman spectroscopy laser to try and identify compounds that are specific to life and in particular, these green life forms, the cyanobacteria.

Chris -   So, you've looked in rocks from Antarctica and then presupposed that if life does exist on Mars, it's probably going to be sort of similar or have similar chemistry to the life we see in extreme environments here on Earth that are sort of similar.  So, if we therefore go looking for those same sorts of chemical hallmarks on Mars, that's the best place to go looking.

Steve -   Yeah.  I mean, there are arguments for and against this strategy.  I mean, some people could argue why would life be DNA-based for example as all life on Earth is.  But the simple truth is that chemistry has arrived at the most parsimonious solution for life.  The simplest solutions were often the best.  And so, we know that there are certain compounds in life that are very good indicators and in particular, not necessarily DNA, but actually, compounds such as chlorophyll for example, a potentially very good indicator for life.

Simon -   So this habitable zone, Mars is basically the convenient option.

Steve -   It is a convenient option.

Simon -   Six months, I mean, that makes your trip through the violet pretty easy, isn't it?  You were whinging about that.

Chris -   What?  My trip down here?

Simon -   Yeah.

Steve -   Yeah.  I'm not sure what the land should be like.  But the great thing about Mars is looking at Mars' immediate past.  Probably as little as 5 million years ago, Mars very possibly was pretty much like maritime Antarctica is now.  It was much warm and much wetter and quite conceivably could've supported life.  and that's largely a result of the obliquity of the planet, having changed quite radically.

Chris -   Why do you think that's happened?  Why so recently?

Steve -   Well, this is down to astronomers, but quite simply, the angle of tilt for the planet Mars has changed from about 45 degrees to about 23 degrees which is more or less identical to Earth.  It's just in the last 5 million years.  Of course, the poles, with that much more exposed to the sun and most of the waters at the poles ergo there would've been much more water.  That's really the basic prerequisite for life.

Chris -   Because it's very recent, isn't it that it's undergone such a dramatic shift.

Steve -   Yeah, I mean, it is an estimate of course but those that know in the astronomy field stick by that.

Chris -   So, do we think then because life got started on Earth very quickly by 3.9 billion years ago and the planet is only 4.5 billion years old.  We've got evidence that there were little cells already here going about their business on Earth.  Do we think that probably the same thing was happening in parallel on Mars then?

Steve -   Well, a lot of people believe so.  I mean, life on Earth, there are traces for life on Earth pretty soon after the lunar cataclysm and life could've even conceivably originated before then, but being wiped out by the - as you may know, there was a very large impact of planet Theia that proto planet Theia that impacted early Earth.  The mess that resulted as ejected into space form our moon.  So, nothing really survived.  But very soon after as you say, life evolved.  But a lot of people believed that life could've evolved on Mars because Mars, although it's slightly outside the perfect habitable zone now was actually once in that zone, and will actually enter that zone again in the future.  So yeah, a lot of people believe life could've co-occurred on two planets.  Of course, that brings up some really amazing philosophical questions.

Chris -   Do you think that if there is life on Mars now, do you think that it could be in a sort of stasis, sitting, waiting, so that when the sun gets a bit warm and swells up a bit as it ages, that life could come back to life as it were?

Steve -   Yeah, it's quite possible.  I mean, one of the things about microbes that's really remarkable is their ability to essentially go dormant for very, very long periods.  We've retrieved bacteria from ice cores thousands of years old that are viable.  So, it's as quite conceivable.

17:21 - Love thy virus

Bacteria are getting more and more resistant to antibiotics like penicillin. A way around this might be to use viruses to attack bacteria.

Love thy virus
with Heather Hendrickson, Massey University

Antibiotics were first discovered in the 1920s.  They've since save millions of Bacteria pseudomonaslives, but within just a few years of them being introduced, resistant bacteria were already cropping up.  Now, we're at a stage where there are some infections afflicting humans here on Earth that we just can't treat.  But Heather Hendrickson who's lecturer in molecular biosciences at Massey University is exploring how we might be able to go back and use an older technology to solve this more modern day problem.

Heather -  The older idea that you're talking about in fact is, instead of thinking about using chemicals that bacteria and other microorganisms have been using against one another, let's just try using something like a microorganism.  And so, the idea here is that there are bacterial viruses.  So, viruses that exclusively infect bacteria and that if we can find targeted groups of bacteriophages which is the name for these viruses that only infect bacteria, then maybe we could come up with cocktails of bacteriophages that would be effective treatments.  We could actually take them as a therapeutic agent instead of taking something like an antibiotic.

Chris -   It's ironic to think that bacteria can catch a cold than humans.

Simon -   Yeah.

Heather -   It's much worse than a cold.

Chris -   So, what happens to it?

Heather -   Yeah, so what happens with a bacteriophage infecting a bacterial cell is that in fact, the bacteriophage will adhere to the bacterial cell and then many of them actually have this like, injector core tail.  So they're basically like - bacteriophages are just protein capsules and they have a little tail and they have like a little spider-like end often.  They kind of attach onto the cell and inject this core down into these cells and it just flood the cell with their copy of their DNA.  Usually, this is only like 50 genes, so pretty small.  But that 50 genes or so that's injected in allows the bacteriophage to take over the machinery of the bacterial cell, build hundreds, often, copies of itself and then ultimately, it explodes the bacterial cell, releasing hundreds of copies of itself.  So, it's a lot worse than a cold.

Simon -   Wow!  So, the tail, this injection thing is like the phages going in there and taking over the photocopier in the office, getting all the printer and just print all this weird stuff.

Heather -   Really very similar.  That's a great analogy, yeah.

Chris -   Photocopying your bottom.

Heather -   How did I not think of that before?

Chris -   Nice to hear about Radio New Zealand National office party.  So, when they do this, they get into the cell, they make hundreds of copies of the bacteriophage, burst the bacterial cell, and what those new copies, would then go off and track down and kill more of the same bacteria.

Heather -   Right and I think that one thing to remember is that they don't actually - this is a real problem actually with online videos of these things.  They often look like they're kind of swimming.  They're out seeking for their next lunch or their next parasitism candidate.  But actually, they're completely inert.  So, they're just these protein shells with a little bit of DNA inside and there's like very lethal-looking tail, little spidery bit.  But they are completely inert.  They don't have any ability to generate ATP.  They don't have any energy source or anything.  So, they just kind of bump into the next cell.  It's really about the particular molecular identity of the bacterial cell and the bacteriophage that allows them to be specific.  Actually, it's that specificity that's one of the things that make them really interesting in terms of therapeutic agents in the future.

Chris -   You mean as in, that they can only get into bacterial cells.

Heather -   Well, only bacterial cells and all of the bacteriophage that we've ever found have very specific bacterial targets.  And so, if I find a bacteriophage that's really good at infecting some kind of pseudomonas, it's not very likely that that's going to be able to infect some kind of mycobacterium or some kind of E. coli.  The reason that that's really cool, especially when we compare it to this antibiotics.  And the things that we're going through in terms of antibiotics is that antibiotics are often very like broad spectrum which means that you dump antibiotics into your system, you've got lots of really good for you kinds of bacteria in your system, and that antibiotic almost goes off like a small nuclear bomb, right?  And so, it just kills tons of these bacteria, tons of bacteria that are really good for you.  The thing about a bacteriophage is because it's so targeted, if you can figure out what's making you ill and you can take a cocktail of these bacteriophages that are making you ill, then they'll only kill the bacteria that are making you ill.  And that's really powerful actually, compared to what we've been dealing with.

Simon -   So, why haven't we got them today?  What's going on?

Heather -   What's that?  What had happened?

Simon -   Why haven't we got them in action today?  What's stopping you?

Heather -   So actually, I should say that there was a time in Russia and in Russian Georgia where phage therapy was the 'done' thing.  And so, phage therapy has been used for human therapeutics in the past, but it's not currently approved right now.  And so, one of the things that I'm doing at Massey University is, I have a class of undergraduates and we're trying to find new bacteriophages.

Chris -   And you're using them as victims.

Heather -   I'm using them as scientists.

Chris -   Just checking.

Heather -   I have a group of undergraduates and they go out and they bring us soil samples and then they take the soil samples and they search for bacteriophages.  So far, we've found about a half-dozen bacteriophages.  We've sequenced 3 and what the students are able to do is find their very own bacteriophage, completely unique, it's never been seen before.  They're able to name them and then we sequenced the genome of each of these bacteriophages.  And so, the students actually get the opportunity to look at the DNA of a completely novel organism and using the kinds of bioinformatic tools that we have access to today.  Figure out where the genes are and what the genes are in this completely new entity.  The undergraduates in my class are going to be publishing a paper with me on this.

Chris -   Will they be potentially therapeutic, any of these?  Will they attack human infecting bacteria or are they just infecting soil bacteria?

Heather -   So, it's all about the target organism that you use and we happen to be using a pseudomonad.  So, this is a safe pseudomonas.

Chris -   It's another kind of bacteria, isn't it - pseudomonas?

Heather -   Yes.  So this is a pseudomonas that's like really beneficial to plants, but it's very closely related to Pseudomonas originosa which is the really problematic agent in cystic fibrosis.  It's also very closely related to Pseudomonas Syringae actinidiae which is the kiwifruit pathogen.  And so, we're hoping that in the future, we can find bacteriophages that you would be able to - for example, if you had a big load of pollen that was headed on into the kiwifruit industry here in New Zealand.  you could spread these bacteriophages onto...

Chris -   Because you import pollen to fertilise crops, don't you?

Heather -   Yeah.  It's a really important part of the way the kiwifruit industry works here because of the male female bias in the orchards for example.

Chris -   So of course, if you brought in pollen that was contaminated with a pathogen, obviously, New Zealand may have very good buyer security at the airport but if you've got some microscopic freeloader in your pollen then you could infect your crops here and this would be devastating.  But you're saying, you could have a bacteriophage, a virus that would attack any bacteria that are in the pollen and wipe them out.

Heather -   And it would be very specific.  The other nice thing about bacteriophage is if you have those kinds of entities then they of course degrade.  They're made out of protein in DNA and they're delicious to lots of organisms.  So you sprayed them on the pollen.  They infect anything that's there and then they're basically going to be recycled.

25:20 - Video game therapy

New ideas in treating mental illness such as depression could mean that video games replace the iconic psychiatrist chair.

Video game therapy
with Sally Merry, University of Aukland

Traditionally, counselling sessions have involved fact to face meetings between patients and doctors or therapists but they didn't suit everybody and it wasn't always convenient to go and sit down for an hour to meet somebody.  But now, Sally Merry who is at the University of Auckland has developed an online solution to the problem using an eTherapy video game that she calls Sparx. She explains why they came up with this idea...

Sally  It does seem obvious although I think that there are a number of steps along the way.  So, I have been met with a great deal of scepticism by therapists who say, "How on Earth can you replace face to face therapy?" A computer mouse

Chris -   Do you think they might have a vested interest?

Sally -   They could, possibly.  But I think they also do make a good point in that, interactions between two people are quite complex and there are a lot of subtleties within that.  And how do you actually get a computer which is basically metal and plastic and so on, and get an interaction that somewhat mimics what you might actually do in that therapy session.  I think what we'd actually done in Sparx is, we've actually taken both afantasy game format  but also, some of the eLearning theories where you actually think about how do people interact with computers and what are the things that make it compelling.  What keep people in there and how might you actually - what we're actually trying to do here is change habitual ways of thinking and deliver basically a cognitive behavioural therapy through the medium of an interaction online.

Chris -   Or if you link it to 888 Poker or online bingo you'd be sorted, wouldn't you?

Sally -   Yes, I think that might be some slightly some for interaction of course.

Chris -   But I mean, what sorts of conditions could you treat with this?

Sally -   Well, I think we're just at the start of exploring what might be done here.  So, what we've actually done is, this is actually targeted to depression in young people and the cognitive behavioural therapy model that we've actually used is one that's being proven in fact to face therapy.  I think one of the things that makes it one of the easier things to perhaps put online is that we've actually got quite a clear theory behind it where the whole idea that your feelings just happen to you is not actually true.  What you actually think about things and what you actually do impact on your feelings.  You don't just have to be passive recipient.  We can extend that very easily to anxiety disorders and there are effective eTherapies for anxiety disorders as well.  We're thinking about where can we go next.  So, might we use it to help substance use disorders or can we help parenting, and can we teach people social skills, and should we and can we be using some of the social media to create therapeutic communities online and so on.  So, I think there's a huge number of things that we can do.  There's quite a lot of things where we could perhaps link into some of the biology.  So, if you're stressed, your heart rate variability goes down.  Generally speaking, your heart rate fluctuates and if you're not stressed out then there's quite a big fluctuation with how you breathe.  If you are stressed out then your heart rate variability goes down because your heart rate is at a higher level.  You can actually measure this obviously using pulse things and there are actually some games as - there's a lovely game called "Journey to the Wild Divine" and it's played with clips on people's fingertips.  You clip in and then you just do it with your mind.  So, you can go into this game and you can spin wheels, you can shoot arrows, you can balance rocks, and you have to do it, just with how you're thinking.

Chris -   So, if you think yourself into a calm mental demeanour thinking, you make a programme so that the success in the programme is linked to somebody adopting the right sort of physiology, the right level of calmness.  And this, without them even realising it, their thinking themselves into a calm place.  And so, your sort of app would approach this in the same sort of way?

Sally -   Sparx doesn't do this.  This is actually looking to where we might be going.  Sparx is actually very active.  So here, when we were developing it, a lot of people have taken cognitive behavioural therapy, they put onto box and then putting it onto lines.  Lots of people have put, what I think about as manuals online.  So, there's lots of writing and this stuff that tells you what you can be doing.  And we tried some of this approach with young people some of our early iterations.  The nice thing about working with young people is they do give you very honest feedback.  They say, "This is really boring.  It sucks.  We don't want to do this.  We don't want to read anything.  We want to do stuff."  Particularly, the boys wanted to shoot stuff.  This is a game or an intervention for depression so we didn't want anybody to die.  So, we had to think about what we're going to do.  So, we created a story in every bit of cognitive behavioural therapy that we could think of, we tried to think about, what could you do in a fantasy game format?  So, one of the things that we actually did was, we had to deal with a shooting issue.  So, in the game the idea is that the world has been infested with nets which are gloomy negative automatic thoughts.  And so, we decided that's actually quite a good thing that you could shoot.  So, we shoot this.

Chris -   On a swat?

Sally -   Yeah.

Chris -   Splat with a swatter.

Sally -   That's right, but you also want to convert them and think about how you can actually change things.  People are prone to depression, tend to take a bit of a negative view on life and then interpret the world in a negative way.  How can you actually change that and how can you transform that?  So, we have swamp province which is infested with nets and the nets come flying at you and they say awful things like, "You're a loser" and then you have to work out, "What kind of a net is this?"  If you can classify it correctly, you get nice little Sparx.  The Sparx sends with smart, positive, active, realistic X-factor thoughts.  So, if you can classify your net properly then out comes the spark that tells you, "You're not a loser at all.  You're just giving it a good go and you need to think about yourself in a different way."  So, it's actually changing things and trying to help, that's called cognitive restructuring people to do that.

Simon -   Does it actually work?  Have you been able to measure its success and how effective this is versus face to face because...?

Chris -   I thought you're going to say versus Facebook.

Sally -   There's a whole another story.  Yeah, it does work.  We've done a big trial in New Zealand.  We tested it with 187 young people in New Zealand.  We randomised them to have their treatment as usual which is mostly face to face counselling with mostly very good counsellors and Sparx was as good as the face to face therapy.

Chris -   I think it also is popular or effective because people do it on their terms when they want to do it whereas if you say to someone, "You've got to turn up to this appointment at this time."  if someone is not in the mood for whatever reason for going and engaging in that appointment at that time, it's not going to work as well.

Sally -   Absolutely and in fact, I'm a child and adolescent psychiatrist.  I don't find that young people are necessarily beating their way to my door.  So yes, this means that people can do it anywhere anytime in privacy.  Mental illness still carries quite a stigma to it.  But the other thing is, we don't have enough therapists.  Depressive disorder is one of the most common and most expensive illnesses in the world.  About three quarters of young people with depressive disorder will never get any help for it.

33:06 - Outbreak Origins

How did Ebola and HIV first infect humans? Analysing viral DNA holds the answers to their evolutionary history.

Outbreak Origins
with Alexei Drummond, Department of Computer Science University of Auckland

Analysing the DNA of viruses like Ebola or HIV can tell us a lot about how theyEbola virus are evolving, and also about how they first started affecting humans. Alexei Drummond, Professor of Computational Biology at the University of Aukland explained how understanding DNA can tell us a lot about outbreaks...

Alexei -   Specifically, we do research ourselves on viruses, HIV, hepatitis C, influenza.  And those viruses are particularly interesting because they're examples of what we call measurably evolving populations.  I mean, influenza 2 years ago to today, there's been about 1% evolution.  So, the genomes are 1% different now than they were just 2 years ago.  Now, that's about the same difference as between humans and chimpanzees and it's happened in 2 years.  So, we're talking about a million times faster than things like us are evolving.  And so, that creates a huge problem and one of the reasons we don't have any vaccine for influenza yet, we get a flu jab which each year, which is designed for that season, it actually doesn't work very well because it's already moved on a bit from when we designed that flu jab.  And so, this is a major issue obviously and one that our software tries to track and help.

Chris -   What sorts of things are you able to wind the genetic clock back on to sort of work out when they come from?  If I asked you for example where you think HIV - the virus that causes AIDS, came from and how long ago, could you apply your sort of technology to the virus to work out how fast it's evolving and then wind its genetic clock back?

Alexei -   Absolutely.  I mean, that's one of the first of major applications of the software that we've developed.  It's now fairly well established that the HIV strains that are circulating in humans today had about 4 or 5 origins, all from Africa around 100 years ago.  And it didn't come into - for instance the Americas until about '60s or '70s based on genetic evidence.  But that was still 10 or 15 years before we recognise that there was such a thing as HIV and that was the cause of AIDS.  Part of the reason for that is because you don't die from the HIV virus.  You die from pneumonia or something else, because it destroys your immune system and it takes 10 or 15 years for that to happen.  So, a lot of people would've had HIV in the '60s and the '70s in the US and were undiagnosed and probably died undiagnosed.

Chris -   But 100 years ago is not very long for a virus of the sort of impact that HIV has had to have occurred.  So, where it come from then 100 years ago to pop up out of existence?

Alexei -   So, HIV is related to the simian amminodeficiency viruses.  SIVs which are found in many different species of monkeys and apes in Africa.  And so, there's like I said, at least 4 major introductions into humans and probably, hundreds actually that got into one human, but never continued to spread within humans.  And so, this is constantly happening.  We're having cross species transmissions.  What the genetics tells us is, what time that the ones that have been successfully able to spread have come from.

Simon -   We're talking romantic interludes here?  I'm sorry to ask the dumb question, but...

Alexei -   Well, one of the major things happening in Africa right now is there's an increase in bushmeat trade and bushmeat trade is people going in to find food from wild sources within the jungle and what you get is contact between blood essentially most of the time - blood contact, eating wild game that is infected is one of the ways that you can get HIV.  It's also the way that probably Ebola sometimes has been getting into...

Chris -   I was going to ask about this.  This is a very modern kind of current threat with Ebola, the worst outbreak we've ever seen this year, currently occurring in Africa, of Ebola.  So, what does your research reveal about where that may have come from and how old that is?

Alexei -   So, the Ebola that's currently spreading in Guinea and a few other countries is genetically related to Ebola Zaire which was first - the first identified human outbreak was in 1976.  So, we've known about this genetic strain for almost 40 years now and the outbreaks have been occurring small outbreaks of a few hundred cases every 5 or 10 years since then.  To put that in perspective, Ebola is a fairly typical RNA virus.  It evolves maybe 10 times slower than HIV or influenza.  Its evolution rate is say, 1% change in 10 or 15 years.  It's got the same as measles.  The other thing to put in perspective is although maybe a couple of thousand people in that 40 years have died from Ebola.  Influenza kills half a million a year.  AIDS related illness takes 1.4 million people per year.

Simon -   Is there an idea that Ebola though could speed up?  So, could Ebola become incredibly virulent?

Alexei -   Typically actually, when a virus comes into a new species, the pattern is for virulence to decrease, not increase.  But in terms of the evolutionary rate, this is really determined by fundamental features of how the virus translates and how it's spread and the way it copies its genome.  These things done change over time.  So, we know a lot about filoviridae - the group of viruses that Ebola comes from.  That pattern of 1% for 10 or 15 years.  We now have data from '76, from the '80s, the '90s, 2002, 2006 and the latest outbreak.  It's very clear what the pattern of the evolution of that virus is.  I think probably, the only reason we don't have a vaccine for it because in the scale of things, it hasn't been a major disease compared to many of these other ones.

Chris -   Where did it come from in the first place?

Alexei -   It's not naturally a human virus.  It's a virus that has some sort of wild animal reservoir.  You can find Ebola in monkeys and chimpanzees, gorillas, but they also get disease.  So, it's probably not their natural reservoir either.  They get very bad disease.  It's most likely they come from fruit bats.  A number of different species of fruit bats have been found to have Ebola virus within them at high prevalence and they're asymptomatic.  So, it very much looks like the virus has adapted to them.  It's not very good for a virus to kill off its host.  It makes it hard for it to spread well.  The Ebola doesn't spread well in humans because it's got such a high rate of lethality.

Simon -   Really briefly, are you going to be able to predict in the future what's happening?  It sounds like you're now looking back.  What about the future in under 30 seconds?

Alexei -   So, I think influenza is the main one that we want to predict and it comes every season to New Zealand a new from the airways, landing in Auckland to Christchurch.  So, we also know a huge amount about the molecular structure of that virus and the proteins, how they fold.  So, I think in those cases, we've got huge amounts of data and we know a lot about how the virus actually functions to infect the cells.  We do have chances to predict these things.

40:03 - Mutual Microbes

You scratch my back, I'll scratch yours. A motto you may not expect in the microbial world, but evidence has been found of mutual microbes..

Mutual Microbes
with Mat Goddard, School of Biological Sciences, Auckland University

Mat Goddard, senior lecturer at the School of Biological Sciences at Auckland University, has just discovered evidence of mutualism in microbes. He starts bMutualismy explaining just what mutualism is...

Mat -   Most organisms interact with other organisms in some way.  Sometimes that's not very good.  Parasites for example interact with other organisms to the detriment of the other.  Sometimes however, both organisms benefit from that interaction.  Both gain and that is simply a mutualism.  So, think about insects pollinating plants, the insect gains, it might get nectar, and the plant gains because it gets pollinated - mutualism.

Chris -   That sounds pretty straightforward.  What are you actually trying to find out then?

Mat -   Well, whilst we've known about mutualisms for a long time, the way that they might become established in the first place is unknown.  There's not general rule to help us understand how two organisms might come together for the benefit of each other.

Chris -   So, like yeast and human - beer, we drink it.

Mat -   Yeah, that's a special kind of mutualism.

Chris -   It's very special in my case, yeah.  Some very special mutualism going on in the pub last night between me and Simon.  And so, what you're saying is, that there's got to be a special sort of evolutionary niche there where there's a gap made and something can fall into it to help something else and one scratches the other's back.

Mat -   Yes, hard to imagine how that would become immediately established, how both partners can immediately benefit.  It's hard to imagine how those things can suddenly come to be.

Chris -   But why because I would think that there's lots of opportunities in nature for many rolls of the dice and it's just chance that this thing happens to have something the other thing wants and vice versa, and they get together?

Mat -   Yes, that's right.  But at the moment, we have no general rule to describe that.  the only general rule that we have is that both partners must leave more descendants by interacting with one another.  But there's no general rule to understand how that would become established in the first place.

Chris - Isn't the first sort of really fancy example of this, that if we go right back to the sort of the history of the beginning of life on Earth, where you see the cells we're all made of coming into being in the sense that you get bacterial type organisms snuggling up with more advanced cells like ours, the two then establish a relationship and we still this sort of bacterial cells living in every single one of our cells now in the form of these things we call mitochondria.

Mat -   Indeed and that's a stunning mutualism.  You could take any other of the myriad of mutualisms in the biological world, and individually, you could explain how that came to be.  But the question is, is there a general rule that allows you to explain how mutualisms comes to be.

Chris -   So, do you think there is a rule?

Mat -   We set about trying to test one of these rules.  And so, there's another central theme in evolution and ecology which is called niche constructional ecosystem engineering and this simply says that organisms, by their own actions modify their environment to some extent, from simply consuming food and making waste to more elaborate ideas like beavers constructing dams.  And so, this suggests that maybe an organism has a hand on its own evolutionary trajectory because if an organism is modifying its own environment and it's modifying the environment to which it's exposed to and thus, its selection pressures.

Simon -   Wow!  So, the scenario there is, I've got a cat.  I put a cat flap in at home.  Now for me, that's a modification of my environment.  I get a bit of a draft and the cat flap, it's a bit of a hassle.  But the cat can come and go.  They can have a crack at the local mice.  I'm living in a rodent-free environment.  When the plague comes, I'm going to survive.

Mat -   I take your point, yes.

Simon -   I modified a niche though.

Chris -   Also, is it not fair enough to say there's another kind of mutualism going on between cat and your kid's sandpit?

Simon -   True and that modification is something that I really don't enjoy especially when you scrape it off.  But your discovery is specifically looking at microbes.  That's been the niche modification.

Mat -   So, we put together both of these ideas.  This idea of the evolutionary mutualisms and this ecosystem engineering and asked the question whether this ability of organisms to modify their environment, whether that could be a general instigator for the evolution of mutualisms.  So, another thing that yeast kick out and there's a bunch of volatile compounds.  So, these are the things that make beer on wine taste and smell nice to us.  But clearly, yeast didn't make these compounds for us.  There must be a biological reason that yeast kick out these volatiles and that was unknown.  So, one idea is that they in fact kick out these volatiles as chemical lures for insects.  Imagine a funny little microbe sitting on a bunch of grapes, it can't move.  When that bunch of grapes is eaten or fall to the ground in rots, that microbe dies with it.  So, the only way this microbe is going to persist in evolutionary and ecological time is, if it escapes.  How is it going to escape if it can't move?  Well, maybe attract something to move it for it.  Maybe attracts a vector.  Maybe it lures in something that it can get stuck to and then gets moved through the environment.  So, the idea is that these volatiles that yeast kick out during fermentation are there to attract insects.  And so, we tested this directly in the lab.  we found that to be the case.  We found that fruit flies are differentially attracted to different types of yeast.  And that those yeast that are more attractive, in fact get dispersed more in the environment, both in the lab.  and then we went to the vineyard and did the same thing.

 

45:34 - Plight of the bumblebee

Honeybees are used worldwide as pollinators, but as numbers dwindle their price is increasing. Could bumblebees hold the answer?

Plight of the bumblebee
with David Pattemore, Plant & Food Research's Ruakura site

In the news we often hear about the demise of honey bees and bumble bees. Dr David Pattemore, a pollination scientist at Plant and Food Research's Raukura site spoke to Chris Smith and Simon Morton about how he's trying to help the future of pollination... Bumblebee - Bombus terrestris

David -   So, what we're trying to do is actually develop alternative pollination systems for growers in New Zealand.  And that's largely because of the threats that are facing honeybees.  The biggest problem for growers is it means that honeybees get more expensive.  So, they have to pay hundreds of dollars per each hive to put it in their crop.  They want 8 hives per hectare, that's a lot of money.  So, what we're trying to do is we're trying to develop alternative systems.  One of the big things that we're doing is trying to turn bumblebees into a system that growers can manage in their orchards.  So currently, if you want bumblebees in an orchard, you have to pay over a hundred bucks for a cardboard box like this.  I'll just open this absolutely carefully.  In here, there's probably about 100 bumblebees in a small colony.  I'll turn the microphone on and you can hear it.  If I whack it, they'll start coming out.

Chris -   Don't do that.

David -   So, this is what growers have.  Often they have at the moment if they want bumblebees.  But this really a design for glasshouse tomato pollination.

Chris -   When you say a hundred - because if that were a box of that size of honeybees and you'd have a 100,000 in something that size.  Do bumblebees live in smaller groups than honeybees then?

David -   They definitely live in small groups.  That's one of the big limitations.  If you're just wanting numbers of bees, get yourself a honeybee hive with 60,000 bees.  This is only maybe 100 to 200.  This works well in glasshouses for tomato pollination, but when you put it out in the field, they often really struggle to figure out how to get outside the box to start with and that they're actually meant to forage.  It's just simply too expensive.  If you only got a couple hundred bees and a box like this, one will just buy a honeybee hive.

Chris -   So, we need to learn to think outside the box is what you're saying?

David -   There were go.  

Chris -   So, it's a problem of scale.  If you've only got 200 bees and you've got 200,000 plants, and you had 200,000 honeybees, they would have no problem - one bee per plant on average.  So, the bumblebees, why can't you just have more bumblebees then?

David -   Well actually, bumblebees have one thing in their advantage.  So, some of the studies, especially with kiwi fruit, I found that one of these bumblebee workers does the job of 50 honeybee workers.  So, that starts to even out a little bit more, but you still need a whole lot of these and these are simply too expensive.  So, what we're trying to do is develop ways that growers can harness the power of wild bumblebees because there's bumblebees out there in the environment anyway.  The key thing for the grower is that they like to count things.  If they can't actually count and say, "I have 10 colonies of bumblebees," they won't change their management at all.  They'll just bring in the same amount of honeybees.  So, we want to give them away to find out how many bumblebee colonies they have in their orchards and then give them tools to manage those colonies.  So, what we've developed up on your screen there is the picture of our bumblebee bunker.  And that's mark 2.0.  It looks kind of like a popcorn - not popcorn, the rice crispy slice.

Chris -   It looks like a Breeze Block.

David -   Yeah, Breeze Block, something like that.

Simon -   Have you got a designer onboard or is that...?

David -   I think we haven't got a designer onboard and that's part of the problem.  This is actually like a flat pack construction style because we've expanded to a massive trial.  We've got a thousand of these nest boxes going all throughout the country.  We've got 5 regions in New Zealand ranging from coastal avocado orchards to high country red clover stations in Marlborough.  And we're putting these in the ground and the idea is that we want to build the best nest box that attracts queen bumblebees.  So bumblebees, rather than honeybees, they continue year-round.  Bumblebees have an annual cycle and only the queen survives over winter.  So, those queens hibernate in the ground and they come out in spring and they're looking for a new nest site.  So, we want to build something that to them is just perfect.  This is where they want to set up a new colony.  So, we've been trialling it for two years now.  We've had great success which enables us to expand to this new trial.

Chris -   So, this is like the bee ideal home exhibition, isn't it?

David -   Absolutely, yeah.

Chris -   So, how do you decide that whether the bees like the home you've made for them or not?  What do you measure?

David -   We measure whether they turn up for a start.  So, it's interesting.  The simplest measure that most people around the world use is occupancy.  Did you ever see a bumblebee or a sign of a bumblebee or think that there may have been a bumblebee inside this box?  Globally around the world, when they do these trials, you get about 3% success rate.  You're going to have to put out 300 of these to get just a few colonies in your orchard which really doesn't work.  New Zealand has this reputation for doing really well with these artificial nests.  And so far, overall with our trial, we get about 30% occupancy.  Some orhcards, it's up to 60% occupancy.  That's pretty damn good.

Chris -   Could you boost that by putting some kind of smell or chemical in there that might lure the queen in?

David -   Yeah, we've tried that.  A lot of the lures have been sort of based on floral scents.  They're not looking for flowers when they're looking for nest sites.  So, that doesn't really work, but we're trying to sort of distil an essence of disturbed Earth.

Simon -   It might be like cavalier bremworth I'm thinking.

David -   ... a little kitchen sink, yeah.  Well, we actually have used carpet underlay and that's works pretty well, but that's a fibre.  So, the thing is, bees actually find it really easy to find their nest sites.  And that the key thing for us is understanding what is that trigger that when a bee comes into our nest site, what makes it think, "Ah!  This is the place I want to stay" rather than just going back out again.  So, one of the other things that we've been doing especially because there's one bumblebee species, we've had a lot of difficulty getting is that we're putting little radio transmitters and there's another picture here.  On the back of this bumblebee queens - so, we're actually able to track them as they're searching for their nest sites.  And we actually get at very early stage, we get a picture of where these bees are choosing to nest.  We've got a masters student from Massey University who's doing the study.  She was up in the Netherlands and she's just come back to New Zealand.  she's doing it again in New Zealand.  actually, chasing these bees across the landscape.

Chris -   Does she use G - B - S?

David -   No.

Simon -   Is that ethically - I mean, that's not fair.  I mean, that's like me having a rats tail 9 metres long.

Chris -   What we're seeing here is a bumblebee with a tail.  I presume that's the antenna, that thing stringing off the back.

David -   And you can see the little package.

Chris -   And it's about three times longer than the bee is.  Does that impair the bee when it flies around?

David -   Occasionally, it gets caught in the flowers, but it doesn't seem to bother them too much.  More of the problem is it gets caught and then it gets ripped off, and then we lose the bee.

Simon -   What about the weight of the little transmitter thing though?

David -   So, the weight is about a quarter of the body weight.

Simon -   Wow!

David -   That, you've got to take in account...

Chris -   It's the size of a grain of rice, the little thing you've got stuck on there.

David -   These bees will easily carry their own body weight in pollen and nectar.  So, I brought along a backpack that's a quarter of my body weight.  But that's very difficult to carry, but for the bees, they're used to carrying these sort of weights.  The interesting, when we first put a transmitter on the bee, I was quite nervous about this method.  It was blowing 30 knots at our research centre.  I thought, "Well, I can't release the bee into the wild."  I took it up to our orchard.  We have sort of good protection from the wind. I got there and I released this queen as she goes straight up over the top of the projection, into the wind and disappears.  Never saw her again.  So, they certainly have no problem flying with this.  We do need to make sure they're in good condition, that you get it good feed and active before you release them, but they fly with no problem.

Chris -  And is it working?  Do you think this is going to be a viable strategy?

David -  It certainly is.  It gives us a level of information that we're not able to achieve in any other way.  So, you can find colonies at the late end of the season when there's lots of work that's coming in and out, but it's almost impossible to find these early stage nests.  So, by putting these - when they first go to a nest, we can actually build up a picture of what is that nest site when those queens first say, "This is where I want to set up a colony."  We can figure it out and we can take those elements, build them into our bumblebee bunker design and hopefully improve the success rate.

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