The End of Extinction?

22 July 2014
Presented by Chris Smith, Kat Arney.

Will wooly mammoths roam the tundra once more? This week we ask whether improvements in genetic technologies mean extinction is no longer the end, as well as meeting moss that came back to life after 2000 years buried in permafrost, and the million-year-old microbes lurking in the ice of Antarctica. Plus, news that our genes control who we make friends with, how fossil sea urchins hold the key to finding your lost car keys, and what ancient tooth plaque is revealing about the diets of our ancestors...

In this episode

00:53 - Friendships down to your genes

Genes don't just control the way we look and what diseases we may develop: they also determine who we choose to make friends with...

Friendships down to your genes
with James Fowler, University of California

Shared interests and hobbies might bring people together, but new research hasFriends shown that we may be picking friends with similar genes to our own.

By comparing the genes of friends and strangers, James Fowler, from the University of California San Diego, has found that we share more than just our interests with our close allies, as he explained to Chris Smith...

James - Well we looked all across, the human genome at different markers and found that friends tend to share genes in common. In fact, the level of similarity between friends is so strong,  it's as if that friend who we don't share common ancestor with is our fourth cousin. Even more interesting than that, one of the things that we found was that those genes that we share in common with our friends are also the ones have been evolving the fastest. So as a result, these things together suggest that friendship has been turbo charging human evolution.

Chris - Wow! So why should people logically if they're friends with each other have more genes in common than you would expect by chance. Why should that happen?

James - Well, we know a wide variety of traits are similar between friends. In this case, we find that friends have some more genes is because they chose each other or they were drawn to similar environments where they met other people who were like them. So just for example, imagine that you have genes that make you really, really love coffee. Like a zombie, you're just drawn to the coffee house and you might find other people who are similarly drawn to the coffee house and that's where you tend to make friends.

Chris - And how did you actually discover this?

James - We took information from the Framingham Heart Study on about 2,000 people and looked at their genes and also looked at their friendships. We compared how similar how the genes were between friends to how similar the genes were between strangers drawn from the same group.

Chris - The thing is that if you look at who we tend to marry, have sex with and have children with, we're always being told that the human race is evolving to have the biggest genetic diversity. We go for the biggest differences. So, if you were to do your study on people who were choosing mates rather than choosing friends, would you see a different relationship?

James - So, it's interesting you should ask that question. Some colleagues of ours just recently published a paper that showed that spouses also tend to be genetically similar. But that hides some parts of the genome where we tend to be different.  nd so, one long standing result, when you look at spouses is that they tend to have opposite genotypes for the immune system. And the reason there is, you don't want your spouse to be susceptible to something that you're also susceptible to. You want them to be an extra line of defence against disease. We found actually the same thing in our friendship study. Your friends also tend to have genotypes that are opposite to you for the immune system. So, it's really interesting that we get these similar results both for spouses and for friends.

Chris - So, what are the implications of this then that literally, you could take my genes and you could make predictions from a bunch of people in my environment and say who I'm likely to get on with or not? Could you do that?

James - Yes, we could. This is one way to validate what we found. We take our model where we look at all the genes that were similar and all the genes that were different and with our friends. And we can use that then just to take the genes of people for whom we don't know whether or not they're friends and make a prediction. We can create what's called a friendship score. In going from a low value of this friendship score to a very high value on this friendship score actually increased by 24%, the probability that 2 people were friends. I was really surprised actually that it was this strong because we know that social environment is also really important for determining who's friends with whom. But here, it looks like genes are also playing an important role.

Chris - So, why do you think that evolution is opted to make us be drawn to people who have a similar genetic makeup? Do you think it is just as simple as, "I have a chemical preponderance to like coffee and so do you therefore, we've become friends"? Or do you think actually there are more subtle mechanisms at work here that make people who are genetically similar be drawn to each other?

James - I think that at least some of this is active choice and the reason why I think that is because another thing that we found in the study was that those genes that we share in common with our friends, those genes are actually evolving the fastest which suggested those are also the genes that are giving us a survival advantage. So, think about language for example. If you're the first person to get a mutation to speak language, is that going to do you any good whatsoever unless you are connected socially to other people who have that same mutation. This is a genetic variant that only gives you an advantage if someone else has it. And that's exactly what we'd expect to find across the whole genome if it was a case that we had this relationship between how much you share genes in common with friends and how quickly those genes are evolving. In other words, one of the things that it seems like we found is that this is a way that friendship might actually be increasing the speed of human evolution.

06:34 - Doing the Levy walk

Many animals across the world walk the same way to find food, and evidence of this hunting behaviour is even present in the fossil record...

Doing the Levy walk
with David Sims, University of Southampton

What's the best way to locate your next meal, if you can't see or smell it? Sea Urchin

Animals throughout the world, including some human tribes, all use a similar foraging technique called the 'Lévy walk', which seems to be the best way to find a randomly scattered resource.

But when did this evolve? Well, for the first time evidence of this Lévy walk has been found in the fossil record, showing this technique is at least 50 million years old.

David Sims at the University of Southampton told Kat Arney more about how various animals walk the walk...

David - We carried out some research a few years ago on living animals, sharks and penguins, and tunas and found that they move, they search for resources, in a very characteristic way. So, we're interested to know, where did this pattern arise? Could it have arisen many millions of years ago? I teamed up with a palaeontologist called Richard Twichett and together, we searched for fossils to investigate it and we found some in northern Spain.

Kat - So, how on Earth do you tell from fossils that are in the rocks how they were moving?

David - The fossils themselves obviously are just the fossilised trail that the animal moved through. So in our case, we were looking at worm-like animals and sea urchins from the Eocene era; about 50 million years ago. And so, what's preserved is their movement trail. As they displaced sediment, you get this sort of trail etched. And so in our lab, we study the movement ecology of marine predators. We use statistical methods to extract patterns from electronic tag data. And so, what we did was use that technique and analyse the trail that was fossilised from these extinct animals.

Kat - So, tell me about what you found.  How were these prehistoric extinct animals wiggling about through the sand?

David - Well, we found that the animals wiggled about as you put it in different ways. Some of the worm-like animals moved around with what's called a self-avoiding random walk. So, they avoid their own path and move into areas that could be good for feeding opportunities. What we found from the worm-like animals is that they tended to do spirals. But the interesting thing was that for the extinct sea urchins, they had patterns of movement that were clustered across 3 or 4 different scales. So imagine in the context of humans, we exhibit a search in our office, but then we don't find it so we then exhibit a search in our institution or our house. And if we don't find it then, we then do a search let's say, in our town. So, at each scale, the pattern looked the same. And so, that's why it's interesting because that is what's called theoretically at least a Lévy walk.

Kat - And that's what sea creatures today are doing when they're searching for food too.

David - That's right, yes. We've shown previously a few years ago in a few papers in Nature and proceedings in the National Academy that birds like wondering albatrosses, basking sharks, big eye tunas, and penguins, all have movement patterns that are very well approximated by this optimal model, this Lévy walk. And of course, Lévy walks are interesting because we showed that animals, living animals were using them. That's interesting because the Lévy walk is a theoretically optimal pattern of movement if you want to find resources that are sparsely distributed. So, imagine that you don't know where the resources are and you don't have a good mental map of where to find things, you don't know your environment that well. And so, this would be the best pattern in which to move. In fact, there are humans that have been shown to demonstrate this pattern of movement as well. So, just recently, there was a study on hunter gatherers in Northern Tanzania and they also adopt this Lévy walk pattern of movement. So, it seems that this is - when you don't know where things are, a Lévy walk is a very good approximation to what you should do to find the resources quickly.

Kat - The way that humans find food, the way that albatrosses and penguins find food, and the way that these tiny marine creatures millions and millions of years ago are all doing it in the same way. That tells us that this is a very old way of looking for stuff, doesn't it?

David - That's right. The evidence is pointing towards it being a very old pattern. I mean obviously, we only looked - I say 'only - we only looked at animals 50 million years old. But in fact, some of the patterns we saw, I mean, we had one fossil from the cretaceous which was 70, 80 to 140 million years ago. So, it's put it back a bit further. So, it could be that if this pattern of movement, if that has some sort of intrinsic pattern, one which is sort of innate to the animal, then of course, that could mean that it has a very long origin.

Kat - So, if I'm looking for chocolates or my lost keys, I can thank hundreds of millions of years of evolution for helping me.

David - That's right, exactly. It's the best way of searching for something and we imagine that this is a problem that was solved many, many tens of millions, if not, hundreds of millions of years ago.

12:01 - Supermoon

Many people will have noticed the moon looking especially big and bright recently. This is because of a phenomenon known as the supermoon.

Supermoon

The_moonA supermoon occurs when a full moon coincides with the closest point to theEarth that the Moon travels to. They happen about once a year.

The moon's orbit is not circular but elliptical, meaning its distance from the earth can vary between 357,000 km and 406,000 km.

When the Moon is at its closest point, known as 'perigee', it appears up to 14% larger and 30% brighter than at its farthest point, known as the apogee.

An optical illusion means that the moon always looks bigger when it is on the horizon, so when it is rising, it will look particularly impressive.

The moon creates tides on earth, because its gravity pulls harder on the side of the earth which is closest to it. The resultant tides are seen both in the sea and in the rock which moves up and down by up to half a metre.

The fact that the moon is closer at the moment will have an effect on tides - all be it a small one. Tides may be an inch higher, at most, but the difference is likely not to be noticeable for us humans.

The next supermoon will be seen on August 10th, with its closest pass at 7pm GMT. This will be the closest the earth comes to the moon all year, so is worth looking outfor.

13:57 - Alzheimer's risk factors

Up to a third of cases of Alzheimer's disease could be preventable by being fitter and healthier, new research suggests...

Alzheimer's risk factors
with Carol Brayne, Cambridge Institute for Public Health

Alzheimer's disease affects around half a million of us in the UK alone, and this Alzheimers Senile Plaquesnumber is predicted to increase as the population gets older.

However, this week a team at the University of Cambridge suggested that up to a third of cases could be preventable just by changing the way that we live. They identified several risk factors that could increase the likelihood of developing the disease, some of which simply came down to lifestyle choices.

Ginny Smith spoke to Carol Brayne, to find out just what these risky behaviours were...

Carol - So, the risk factors, they work across a life course. So, there's education, physical inactivity, smoking, there's midlife hypertension, midlife obesity, diabetes, and then depression. Individually, these have all been shown in studies to be associated with increased risk. Now, if you put them together and don't think about the relationship between them you might think that we could prevent one in two cases of Alzheimer's disease. But in fact of course, they're all clearly linked and they all work across a life course.  o that when you put them altogether, it's about 1 in 3.

Ginny - Do we know what it is about things like this? Why is physical activity so important? Why are those other risk factors, why are they risk factors?

Carol - There's an enormous amount of research going on into these risk factors at the moment. We try to tease out why this protection might be there. And there are all sorts of reasons why it might occur. It might occur because the cells of our bodies work in different ways if we're very physically active and well, but it could also work in terms of the way that the neurons fire and communicate with each other, and the vessels that supply our brain with blood and with oxygenated blood, they might be working in better ways they may be more effective. So, it's about health in the whole body if you like, including the brain.

Ginny - Now, some of these risk factors you've talked about are very obviously under people's control - doing more exercise, stopping smoking, that sort of thing,  but you mentioned depression as well. To me, that doesn't seem like something that is a kind of lifestyle factor. You don't choose to get depression so why is that in the same sort of category?

Carol - It's in this analysis because in the original work that was done, it was identified as being a risk factor that had been shown again and again to be associated with dementia. There is a sense that it is possible to do things about depression in societies. There are situations in which people are more likely to depressed, but also, there are effective treatments for depression. So, we don't know whether treating people with depression does overt dementia later on because that's a different type of study. But we do know that depression is associated with dementia later and that there are effective treatments for depression and there are certain social conditions which enhance depression.

Ginny - So, the fact that you say that 1 in 3 cases could be prevented, that means that someone could do all the right things, do all the exercise, not smoke, and still, get Alzheimer's. is that all down to genetics or are there other factors we maybe don't understand yet?

Carol -  For the population, age is the biggest risk factor and clearly, there are some groups in the population where genetics plays an important part. And for those folk, it may be that there are drug therapies or in particular, interventions that might work in the future. But for the bulk of the population, it will be age. And so, it's difficult to say that we would prevent a third. I think it's more straightforward to say we will reduce our risk at a given age. And so, we do have some evidence from the UK that we may have reduced our risk for dementia at particular ages. It's not so much about preventing a case or that if you do these things, then you will not develop dementia. It's more about us, reducing our risk at a particular age because the things that are in these risk profiles, if we do engage as a society in more physical activity and have less diabetes and so on, then of course, we'll all live longer. And that means that we become older therefore, we're at a great risk. It's just that if we reach 65 healthy, we have a much greater chance of having a healthier old age and a shorter period of decline before we die.

17:57 - Ancient tooth plaque

Why was a population of ancient humans munching on a rather foul tasting weed, even after the dawn of agriculture?

Ancient tooth plaque
with Karen Hardy, University of Barcelona

Diet has always been an important factor throughout human history. But, looking
Human toothback through time it becomes harder and harder to know what our ancestors were eating, especially before the dawn of agriculture.

One clue, however, may lie in the plaque on the teeth of ancient skeletons. Graihagh Jackson talked to Karen Hardy of the University of Barcelona, to find out more about what these gnashers can tell us...

Karen - The samples that we're looking at come from Central Sudan. It's an archaeological site that covers a timespan of around 9,000 years from before agriculture through the development and the introduction of agriculture right through to the late Neolithic period which ended at the beginning of the modern era. I was contacted by the excavators and they asked me if I would take a look at samples of dental calculus to see if we could degrade these and determine what people had been eating.

Graihagh - And when you say calculus, you mean tooth decay, tooth rot.

Karen - No, it's not tooth rot. It's actually dental plaque. If you don't clean your teeth, you get a sort of sticky film and when you go to the dentist, this is what they have to scrape off. So, within about a space of about 2 weeks, the dental plaque, if it's not cleaned off, calcifies and becomes hard. And then it keeps evidence of what has been ingested within the dental calculus.

Graihagh - So, what exactly did you find? What was in this plaque?

Karen - So, for example in this case, there was a very, very clear indication for something called rotundine, which exists in purple nutsedge. It's a plant that is very abundant in subtropical zones and in fact, is considered a real nuisance because it spreads very rapidly and is difficult to get rid of. Today, it's used as animal fodder. However, historically, it's known to have been used as a source of food, as a source of medicine. It was used as a perfume and also in water purification.

Graihagh - You're looking over quite a large timescale, all the way from the hunter gatherers, all the way through to the farmers and they continue to eat this purple nutsedge throughout. Normally, when you see a transition from hunter gatherers to farmers, you normally see a transition in what they're eating. So, why do you think they continue to eat this purple nutsedge?

Karen - This plant does have antibacterial properties as well. It is possible that they recognised and knew about the antibacterial qualities and may have made use of those. However, of course, we cannot say that. We have no idea why they ate it, but I'm sure that the primary reason for eating it would've been as a source of carbohydrates.

Graihagh - These antibacterial properties you're talking about, does that mean that their teeth were better than perhaps they would've normally been?

Karen - There have been some studies by plant biologists that suggest this plant can inhibit Streptococcus mutans. However, to make the leap from that to saying that their teeth in the agricultural periods were better, we can't actually do that  It's a possibility.

Graihagh - What strikes me about these studies that previously, lots of people have looked at protein, but not really so much about vegetables and other elements of their diet. How have these techniques changed how we might look at our ancestors?

Karen - There is a big gap in our knowledge of hunter gatherer diets because the evidence is not there. Evidence for plants tends to disintegrate very quickly and it's very rare. I think that this type of study is certainly opening a window to gain access to a broader perspective on pre-agricultural, that is hunter gatherer diet in the past.

21:58 - Bringing back the woolly mammoth

Could a resurrection of an ancient species, as seen in Jurassic Park, ever actually be possible?

Bringing back the woolly mammoth
with George Church, Harvard University

In 1993 the blockbuster Jurassic Park burst onto cinema screens, grossing nearly a billion Dollars and capturing the imaginations of millions.

But could a resurrection of an ancient species like this ever actually be possible?

In 2003 the last surviving member of a wild goat species called the Bucardo was successfully cloned after it had passed away, making the species the first ever example of 'deExtinction'.

The success was short lived, as the clone died after only a few minutes, but the idea of bringing animals back from the history books has captured the Wooly mammothsimagination of many scientists.

George Church from Harvard University is one such scientist, looking to make our Jurassic Park dreams a reality, by bringing back, not dangerous dinosaurs but the gentle giants - woolly mammoths as he explained to Kat Arney.

George - So, we're really interested in reaching modern ecosystems that might be advantageous to human survival and reducing the cost of adaptation of survival of various species in those modern ecosystems. It turns we have reason to believe that mammoths might be very well adapted to the extreme cold that ironically still exists in global warming in Siberia and Canada.

Kat - So, you want to see mammoths roaming free across the Siberian tundra?

George - Or at least cold-resistant elephants.

Kat - What sort of creature are we talking about? Are we talking about 100% mammoths or some kind of hybrid in between?

George - Almost every animal species, it is hybridised with adjacent species. And so, there is really a mythology of purity here. But I think the important thing is, modern ecosystems require modern solutions and we want to use whatever we can be inspired by recently extinct species help us maintain modern ones so for example, the Asian elephant is in great trouble because it's so surrounded by humans. And so the mammoths are very closely related Asian elephants. And so, if you could get some of them sequestered where there are very few humans, it might be a plus for them and a plus for the tundra as well.

Kat - So, give us a little - a quick parted history of the mammoth. When did mammoths die out and how can you get their DNA to kind of recreate them?

George - So, they died out about 10,000, 5,000 years ago. An increasing number of them were becoming available as the tundra melts. So, their DNA is still in terrible shape because of cosmic radiation if nothing else over those 10,000 years or even 40,000 years for some of the specimens. But we can recover this DNA that's broken into sort of flattened based fragments and sequence it with determinist chemical structure with a new set of technologies that my lab and others have developed recently.

Kat - How do you turn this DNA sequence, the DNA that you've dug out of frozen mammoths?  How do you turn that into a living, breathing woolly mammoth?

George - So, another set of technologies, and this should mean read the ancient DNA that we now synthesise and insert any DNA we want into mammals with a new method called CRISPR. It's about a year and a half old, mainly developed for gene therapy but also useful for agricultural species and now, these wild species.  And it simply made the cut into the DNA very precisely at one place - needle in a haystack - sort of location in one end and then we'll swap out the new DNA for the old DNA in an elephant's stem cell, and that stem cell is capable of producing an entire baby eventually.

Kat - So, you basically chopped and changed the DNA so you've got some mammoth DNA, some elephant DNA. Presumably then you have to have an elephant surrogate mother. I mean, how good are elephants at being surrogates?

George - I mean, this would look at very much like a normal baby elephant except for the extra hair and even the hair could be delayed until they're fairly mature.

Kat - I have this idea of like a female elephant go, "What? What's that! It looks nothing like me."

George - Yeah, I think they're predisposed to cherish - you know, you've heard the expression, 'a face only a mother could love'.

Kat - A mammoth only a mother could love. So, I mean, how far away is this? I have wonderful visions of flocks of mammoths roaming free. How long do you think it will be before this becomes a reality?

George - So, it's hard to put an exact date on it, but the technology is moving very quickly. It's a sort of exponential improvement due to the excitement over healthcare benefits to humans. It kind of drives across down, so the fastest we could possibly go if it's a small number of changes need to make a cold resistant elephant to get it started, it could be in the order of a couple of years and then it takes 22 months for the baby to be born. So, that's the absolute fastest it could go and then probably much more than that.

Kat - So, it's going to be a while. But you know, with elephants and mammoths, it's very easy to see that there's kind of a relationship there. Are there other species you have your eye on? Are you kind of going to go Spielberg on us?

George - Well, I can speak for myself, that's the only one on my laboratory agenda. I'm trying to avoid carnivores for example, Revive and Restore has a large community that's looking into other species that are on the brink of extinction. We're bringing in ancient DNA to help increase their diversity, including other animals that are very recently extinct like the heath hen that was on the east coast of America.

Kat - And so, if we can get mammoths, bring the mammoths back to life, very briefly, how do you see they would enrich the diversity of the tundra and these kind of places? What good would they do?

George - A few papers have been written by ecologists such as Sergey Zimov describing how the mammoths could decrease the average temperature by poking through the snow and allowing the spring grass to come up through the dead winter grass and pushing aside trees so the grass can grow. And so, overall, resulting in a stabilisation of the tundra which is melting and releasing greenhouse gases like carbon dioxide and methane which total - and this is an amazing number - they total about 2 to 3 times the total carbon in all the forests of the world. So, if we let that escape from the tundra by melting, it would be like we burned all the forests of the world. And so, even if we don't believe in other sources of greenhouse gases, that's one we really need to be concerned with.

Chris - George, do you think it will be possible to do a full mammoth genome one day? So, rather than have to make a sort of mixture of the right bits of elephant with some mammoth genes, do you think we'll be in a position where we could get the entire mammoth genome back and see real mammoths?

George - I think if we see progress in doing the cold resistant elephants and it seem to be the cost plummets as I think it is. We have the ability. We know the basic method of doing it. It's just really a matter of bringing the price down to a point where it's exploring the feasibility from the environmental standpoint. But yes, I think it is quite feasible to do based on what we know today.

29:07 - Is de-extinction a conservation plan B?

With the planet in the middle of its 6th mass extinction event, does de-extinction hold any hope for the species we are losing?

Is de-extinction a conservation plan B?
with Kate Jones, UCL and the Zoological Society of London

Mammoths went extinct over 4,000 years ago, but what about the countless
Tiger cub at London Zoospecies that we're losing today, due to climate change, habitat loss and hunting? Could DeExtinction be an effective "plan B"? Georgia Mills went to London Zoo to find out...

Georgia - With all this talk of bringing mammoths back to life, I wanted to find out how conservationists would react to the potential end of extinction. Zoos are currently one of the key players working to conserve our planet's wildlife, so I headed down to London Zoo to see some of their newest arrivals - 3 Sumatran tiger cubs. With only 300 Sumatran tigers left in the wild, these cubs will have a key role in the fight to save the species from extinction.  Rebecca Blanchard of London Zoo told me more.

Rebecca - These cubs are going to play a huge role in the future of Sumatran tigers. Not only for helping us raise funds from people coming in to see them here at the zoo, but raising awareness for the conservation work that we're doing and the conservation status of these animals and helping us just talk about how important they are. Tigers have been a key focus for us for the past few years. Really developing our conservation projects in Indonesia which is all based around veterinary work and working to reduce habitat loss and the anti-poaching patrol is out there. So, there's a huge variety of work that we're doing.

Georgia - With so few Sumatran tigers left in the wild, conservationists are working hard to keep them from going the same way as their close relative, the Balinese tiger which disappeared in the last century. But with recent claims that animals can be brought back from extinction, what does this mean for our fight to save the planet's current diversity? I met Professor Kate Jones of London Zoo and University College London.

Kate - There's been a lot of hype recently that perhaps extinction isn't as forever as we originally thought it was. There's been a huge development in synthetic biology techniques over the last few years, so using more refined techniques to manipulate genomes, either stitching genomes back together from ancient DNA or implanting DNA into a cell so that you're manipulating the DNA in that cell and creating something else. So, it's kind of making new organisms by manipulating the genomes.

Georgia - So, there are some claims that people can bring back species such as maybe the woolly mammoth or the thylacine. Do you think these claims are realistic?

Kate - I don't know what's going to happen in the future, but those are pretty far off at the moment. If you imagine the woolly mammoth genome, you get some ancient DNA from a woolly mammoth and you get a bit of DNA and you sequence it. Imagine having a library of books and you shred that into tiny, tiny pieces and throw it up in the air. What you're picking is those bits of DNA. So somehow, you've got to recreate a whole library from those bits on the floor. So, that's where we are with the mammoth DNA. So, there are sequencing efforts, but in the end, you'll get a piece of DNA back and then it's a huge deal to go from a piece of DNA into creating a cell to having a mammoth. So, those steps are quite vast and it's going to take a very long time to do that if we can ever do that.

Georgia - I imagine this technique will be very expensive. Do you feel that this would divert funds that are much needed in places like London Zoo to conserve the species we still have

Kate - I think it's easy to jump on the bandwagon and react in a very negative way to de-extinction. So, I think conservation biologists have said this is not worth it, this is a waste of money. But I think the synthetic biology community is here to stay and whether we like it or not, efforts will go into thinking about how to use this for industry and they're going to be doing it anyway. So, I think a more smart approach would be to think about how to best use these techniques to aid conservation instead of a blanket, "this is bad, this is a waste of money," it might be more clever to work with these guys and think about how we can use it best for conservation. So for example, the Sumatran tigers are critically endangered and maybe efforts would be better made to use the synthetic biology techniques to help their conservation breeding programme in a better way of restoring some of the genetic diversity from extinct specimens. Thinking about de-extinction, it is really cool. There is a kind of wow factor in de-extinction.  It would be a shame to lose that. I would travel the world to see a mammoth. So perhaps one way to capture the attention of the media and the public would be to de-extinct some subspecies that is extinct. So, for the tigers, maybe that would be the Balinese subpopulation you could put efforts into helping recreate that. And that would add in to the genetic diversity of the entire species. So, I'm not advocating that, but I'm just saying that's an example of how we could be a bit more smart and less reactive against these ideas which are coming up.

Georgia - So, do you think if they brought back something like the Balinese tiger, would it be more of a gimmick than an actual scientific endeavour?

Kate - You have to think very carefully about what you're doing the de-extinction for. Is it to re-release the thing back into its natural environment, which means you've got to have a natural environment to release it back into. The Yangtze River dolphin is thought to have gone extinct in the last few years. There wouldn't really be any point in bringing that back even if you could because there's nowhere to put it. So, are you just bringing it back to have a little zoo specimen that people could come to? I'm sure it would increase revenue, but is that really conservation? But perhaps if you did that but with an associated conservation re-introduction programme or putting that money generated from that increased interest might help other species which are critically endangered. So, like a coupling of maybe the wow-factor with some pragmatic help for some of the species conservation programmes might be the way forward. The other really interesting thing is using synthetic biology to help conservation in other ways. So, there's been a massive decline in bats in North America for this white nose fungus disease. Perhaps if we could think about manipulating the genomes so that they're resistant to these species would be really cool or manipulating a tree so that it scrubs more pollution out of our atmosphere from where I work in Central London would be awesome.

Georgia - A lot of people listening will think, bringing something back once it's dead is playing God. Do you think there's any reason why we shouldn't do it just because they've gone, they've had their chance, we should just let things lie.

Kate - I think these are really interesting questions which I don't have the answers to. You could also argue on the opposite side that we made them extinct in the first place. If they went extinct naturally, then fair enough. The Balinese tigers subpopulation went instinct because we hunted it to extinction. That's the same with the thylacine, that's why it went extinct. What kind of legacy have we left and what kind of responsibility do we have? I think those are very interesting ethical questions.

36:36 - Two thousand year old moss in permafrost

Moss recovered frozen from Antarctica and dating back 2000 years began to grow when it thawed out...

Two thousand year old moss in permafrost
with Peter Convey, British Antarctic Survey

While scientists are working on bringing extinct species like mammoths back to life, some things that we thought had gone for good may not be quite as dead as we had imagined. Peter Convey and his colleagues at the British Antarctic Survey examine ancient moss to study climate change, but were in for a surprise when, just like the film Gremlins, they simply added wate, as he explained to Kat Arney and Chris Smith...

Peter - Mosses give quite a good climate record and in parts of the Antarctic mosses have been growing in one place for several thousand years, up to 5,000 years is the oldest moss bank we know. And they're unusual in that mosses grow at the surface. They're green on top and each year they put on a few more millimetres of green growth. But the stem stays behind underneath them if you like. And ultimately, in the Antarctica, you'll get up to 2 or 3 meters thickness of moss and 20 centimetres down in this, it goes into permafrost because the Antarctic is very cold environment. And once it's in the permafrost, it's effective in stasis. We status cores from this moss banks because they tell us things about what the climate was like when the moss was actively growing hundreds or thousands of years ago, like that's our primary interest. But we looked at these moss cores and they actually looked very well preserved. The stems looked pretty well preserved, the leaves looked pretty well preserved, even if you go down to cellular level, the cell walls are intact. They don't look very damaged at all. So, we simply thought, how far down a moss core might it be possible for the moss to recover? We started out with, figuring the literature on the subject suggests a small number of decades. That's the sort of the time span the people have managed to get mosses to regrow from. But we got a core out that covered about 1600 years and we divided it into sections and put it in a plant growth incubator very simply. As you said, just added water and gave it some light. And lo and behold! We did get some shoots growing right through the depth of the core.

Kat - That must've been staggering when you sort of opened the lid, like crikey, it's gone green! How do you know that that's definitely those very, very old 1600 years for a plant to come back to life? How did you know it's definitely them?

Peter - It was surprising and pleasing, I must say. You have a feeling that's something is going to happen and it's nice when it does for once. If you looked in great detail, if you stick the core surface under the microscope and you look at the old shoots that were there, then the new shoot is growing, very definitely emerged from the older shoots. They were very firmly attached to them which wouldn't be the case if you got a sort of polluting spore in or a plant fragment in while we were drilling the core out. So, I think we're actually pretty confident that the new growth we're getting is from that depth, that age in the core. We're confident of the age. It's within radio carbon dating range. We're confident of the age because we've got plenty of very well preserved carbon based core material to get dates from.

Kat - So, these are mosses that were last green and leafy, around about the time of the end of the Roman Empire. It's fascinating that you can make them grow again, but is this little more than just, "Ooh! That's kind of cool!" What can it tell us?

Peter - To be fair, it was a blue sky question to start with, how long can things stay alive for? But having to discover they can stay alive, it tells us that if for instance you have an area of ground, an area of moss that's covered by ice, ice expands and contracts over century or millennial timescales. Then you have potential for surviving in the place where they are rather than being - we always used to think as ice comes forward, everything underneath it is wiped out. If that's not the case then biology survives or biodiversity survives where it is. The next time the ice retreats, you have potential for recolonizing the area so understanding the biodiversity of the area in a different way.

Kat - You mentioned that these mosses, they're 1600 years old and you said, "We thought they might be decades old." How does that compare to some of the other animals that we know that can kind of go into stasis and then be rehabilitated?

Peter - Well, it's sort of an open question. The ability to survive in these conditions is known as cryptobiosis, so the ability to survive long term freezing or long term drying out. And when you have an animal or a plant or even a microbial cell in that state, you or I can look at it and we can't do anything that tells us it's alive. We've sort of got to put it back in normal conditions and see if it gets up and walks away so to speak.

Now, there are a number of invertebrate animal groups best known are tardigrades and nematodes, but also some mites, some springtails, even some insects that can survive similar sorts of periods to what we thought mosses could survive, so 10, 20, 30 years, that sort of order. One thing we haven't done as yet with any of these cores is look to see whether there are any contained animals or any way that we can actually revive any contained animals within them. It's actually perfectly viable question. It's just we haven't had the chance to do it.

Kat - Jurassic Park for ants.

Peter - Yes, so much smaller. There's no dinosaurs in there.

Kat - This is fascinating. We talked on the show last week about taking humans to the Moon. If you could take maybe some plants in a dried static form, that would be quite useful if we were going to go and terraform or colonise other planets.

Peter - Well certainly, it's a way of carrying things in a sort of much lighter and much easier to maintain condition. I mean, it's sort of it's science fiction at the moment I guess. But we do know for instance that lichens, which are another sort of - they aren't plants. They're a symbiosis between algae and fungi, but they're very common in polar regions and extreme environments as well. We know that you can take either whole lichens or spores from lichens up onto the space station and they can survive space conditions. So yeah, potentially, these groups could play a role in, we would call it terraforming or at least providing oxygen into a space capsule environment.

Kat - Just very briefly, what would happen to the mosses that you've brought back to life if you then just planted them outside? Would they just be okay?

Peter - Basically, yes. I mean, they are polar species, so they are reasonably well-adapted to cold environments. But one of the species that we can do this or that we have in the Antarctic is actually a species that occurs up in the Arctic, it occurs in mountains in Scotland. I think a very close relative even occurs in Thetford Forest. So, in principle, you could actually sort of put it at least not in bright sunshine, but somewhere with reasonably cool, moist conditions and it would be quite happy here.

Kat - So, maybe one day, we might have George Church's woolly mammoths eating your rehabilitated moss.

Peter - We'd have to grow an awful lot of them, but yes.

Chris - Peter, have you done any genetic analysis on the moss to see if the stuff right at the bottom is similar to the stuff 1600 years younger right at the top?

Peter - The straight answer is no, but it is a question we're looking at. I mean, it's actually very interesting to see whether there have been any genetic or even physiological biochemical changes over that time because if the conditions were different 1600 years ago. You might expect different gene expression or different physiological adaptation to be there.

Chris - We interviewed a lady, quite a while ago now, but she found in an archaeological site some date pips that have been spat out by someone several thousand years ago in what's now Israel. And she was able to germinate them, and she got dates back from them, but she said the plants do look subtly different than the plants that grow now. And so it strikes me, your moss may have evolved as it's grown up its stem over those 2,000 years.

Peter - It's quite possible. It's a very fair approach to take. It's something we would like to - we are trying to do it.

43:56 - Million year-old microbes in ice

When bacteria or viruses become extinct this is usually a cause for celebration, but can we ever be sure that they are gone?

Million year-old microbes in ice
with John Priscu, Montana State University

When bacteria or viruses, like Smallpox, become extinct this is usually a cause for Icebergcelebration, but can we ever be sure that they are gone? Entire communities of bacteria have recently been discovered to be hiding beneath antarctic ice from up to a million years ago.

Chris Smith spoke to John Priscu of Montana State University who told him about how they found these microbial communities.

John - A few years ago, the deepest sample we drilled was 800 meters. It took about 3 days and we used a special drill that melted snow and then heated the snow up to about 95 degrees centigrade and shot it out a jet, we lowered that down through the ice and it made about a 50-cm diameter hole which stayed open about 2 days. So, we'd sampled around the clock to gather water underneath the ice sheet and bring it to the surface to do our experiment.

Chris - When something is 800 meters deep, how far back in time is that?

John - That ice near the bottom of the ice sheet can be up to a million years old. This is in Antarctica and about the oldest ice is about a million years old so it's some of the oldest and the most pristine water on our planet.

Chris - And you're specifically interested in what's living in that ice.

John - Exactly. Up until now, the Antarctic continent, it's been sort of depicted as a non-living part of our planet and one thing we're trying to do is change that conception. We're trying to show that there are ecosystems that exist in and underneath the ice.

Chris - These are microbiological communities, tiny microbes.

John - Exactly. Under the ice and in the ice, it's a pretty harsh environment. There's no solar energy to drive photosynthesis. So, there's really no plant-life down there. So, the organisms have to exist by obtaining energy. I always like to call it, 'they're eating the rocks'. So, they're actually mining the rocks for energy.  The temperatures down there, they're sub-zero. They're about minus 0.5 to minus 2 centigrade and they're under quite a bit of pressure. So, that's not really a good house to live in.

Chris - Are these organisms actually living or are they in a state of sort of suspended animation?

John - This is a question we've been addressing a long time. As we go down through the ice and take cores and look at the organisms in there, we can actually melt the ice and the organisms will come back to life. It's quite amazing. The oldest we've done it on is maybe half a million years and the organisms within a minute or 2 minutes are back doing metabolism. So, I think the organisms in the solid ice sheet are probably somewhat dormant. They're kind of organisms waiting for liquid water whereas when we go underneath the ice sheet and hit a liquid water pocket, those organisms do have the elixir of life, if you want it and that's liquid water. So, the work we recently did with sampling the water underneath the ice and we brought it to the surface, and those organisms were alive and living down beneath the ice sheet.

Chris - Tell us a bit about the organisms that you're discovering down there? What are they and why do they survive this incredible environment for potentially tens to hundreds of thousands of years?

John - These organisms are all single-celled bacteria. We see an ecosystem down there where organisms use minerals for the energy. We see another group of bacteria that actually can feed on them. That's what I mean by an ecosystem.  We're seeing organisms that complement each other here. These single-celled organisms are very good at being able to survive freezing and thawing. If I stuck my finger in a refrigerator and froze it and thawed a few times, that wouldn't be a good thing. It would all bleb up and turn black, and probably fall off. But a microorganism, you can freeze and thaw, and freeze and thaw a number of times, and they're good to go.

Chris - Do you think that they could be potential pathogens that are threats to humans locked away and when we melt the ice or if the ice is melted by global warming for example, that they could come out and could pose a threat?

John - We've clearly thought about the ramifications of these organisms being pathogens and released to the surface. So, to be pathogens of course, we have to have an immunity to these pathogens to survive. Now, if an organism has been out of contact with human population for a long time, humans can lose that immunity. So, we're going to have to look at the balance to see if the humans have lost our immunity to let's say, a smallpox well that would be a virus, but if we saw an anthrax bacterium in the ice or some other pathogenic organism, if we still retain the immunity to that organism, we should be okay. But if something comes out that we've lost immunity to, we would have to worry.

We thought about sending ice samples to the Centre for Disease Control and getting them screened, but we're looking at only a million years in history which is a pretty small window of evolution for organisms. The fact that we've now cultured a lot of these organisms and looked at their sequenced data, we're not seeing anything exactly really bizarre or any kind of really pathogenic strain. However, if we look at the ice sheet itself - now, I'm talking about what's at the bottom, but if we look at the ice sheet itself, we have an ice - sort of a history of our planet that goes back up to a million years. So, the material at the surface is young. As we get deeper, it gets older and older, and older. So, when we go back up to a million years and we're just starting to do this kind of science. But if we can sequence the DNA in these organisms, we may be able to trace anthrax epidemics and organisms that caused the plague in Europe, and things of that nature. We hope in the next 5 or 10 years to be able to do it as our sequencing methodologies get better and better.

What DNA is needed to bring a species back?

George Church (Harvard University) - Well, the simple answer is, we don't know. But we think that if the goal is to bring back part of the genome and adapt it for new environments, the old genome needs to be changed in any case. The critical thing is, how close a genome do you have and in the case of mammoths, they're very, very close to Asian elephants. They're both close to each other than they are to the African. So, I think that's a best case scenario relatively small number of changes might be needed to adapt them to the cold.

Can we clone any extinct species?

George Church (Harvard University) - Cloning is very unlikely in most cases because they weren't properly stored. If they're not properly stored, their DNA is fragmented and they won't be viable the way that the mosses that we were talking about earlier and bacteria are viable. If they're not viable, then you have to read them into a computer and then reprint them out into some living species and change that living species into an ancient one.

Chris Smith - Peter, what do you think about the same question as applies to plants? Can we get anything back to think plant-wise based on what you found?

Peter Convey (British Antarctic Survey) - The same problem exists in that if something is properly dead then the DNA fragments gradually over time. So, the older your material is, the less likely it is that you got much material to clone from. So, with the sort of what we've been talking about, the potential is that you have a very long preserved but viable i.e. undamaged DNA sequence. If that's the case then we do have the ability to bring things back.

How much of our body do we need to survive?

Georgia - Over to Elena Teh, Cambridge University medical student, lending us a hand to find the answer.

Elena - Lots of people live having had lots of bits like kidneys and livers taken out. And the answer is more complicated these days where we have very clever machines that can pump blood around our body just like our hearts can and they put oxygen in our blood just like our lungs do, and they can clean our blood like our kidneys can.

Georgia - But without these machines, what are the bits of our bodies we just can't do without?

Elena - Firstly, we need our brains and spinal cord to work. They control our breathing and heart rates. It's mostly the bottom of our brains that do these things. So, in theory, we could take out the frontal lobes which control our personality and still be fine. We also need our hearts to pump blood which carries oxygen and other nutrients to the rest of our body. Then we need our lungs or rather, 'a lung'. We really only need one good lung to live, but it's nice to have two just in case. We also need a liver to process all the drugs and toxins that enter our bodies, but only a chunk of it, as it's a clever little thing that grows as much as we need it to. We also need a kidney, but just one will do and a gut, but we only need a meter and a half of small bowel, and there's no need for our large bowels if we really don't want it. We also need some skin to keep the bad bugs out and the water in so that we don't get too dehydrated. Everything else like our limbs, our eyes, our ears, nose, teeth, hair, appendix, reproductive organs, pancreas, spleen, oesophagus, belly buttons, these really are just a luxury. It's definitely very nice to have them all, but we are able to stay alive without them.

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