Nature Podcast

This is a transcript of the 27th June 2013 edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (www.nature.com/nature/podcast), which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to mailto:podcast@nature.com.

Thea Cunningham: Coming up, how elephants evolved from tree eaters to grass eaters.

Alan Lister: What you find is that it takes about three million years of grass eating before the trees start to actually change their morphology and adapt.

Charlotte Stoddart: And why we're so good at baseball.

Neil Roach: Even if you train an adult male chimpanzee to throw, they can only throw around 20 miles per hour which is, you know, a third of the speed of a young 12-year-old boy.

Charlotte Stoddart: We find out what sets us apart when it comes to throwing.

Thea Cunningham: Plus the oldest genome sequenced to date from an ancient horse bone. This is the Nature Podcast. I'm Thea Cunningham.

Charlotte Stoddart: And I'm Charlotte Stoddart.

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Thea Cunningham: Ancient DNA can tell us a lot about an organism's evolutionary past, but extracting ancient genomes is far from easy because DNA has a limited shelf life. Until now, the oldest genome to be sequenced belonged to a human that lived around 80,000 years ago. This week in Nature, there's a genome sequence nearly ten times older, dating back around 700,000 years. It comes from an ancient horse and it has been sequenced by Ludovic Orlando from the University of Copenhagen and his team. Geoff Marsh spoke to Ludovic about why his project did more than just flog a dead horse. Nature (2013)

Geoff Marsh: What is so useful about ancient DNA?

Ludovic Orlando: So, ancient DNA as you know is the survival of DNA molecules of older times or other evolutionary times, and actually these molecules, they can bring a lot of information about the past. For example, they could bring information about the ancient diseases that our populations have suffered from, they could also give information about the ancient ecosystems we were living in, also how many species have been influenced by the climactic changes, for example, and on top of that ancient DNA can also give information about the relationships between different extinct species. So, actually there's a full range of different topics that you could address using ancient DNA.

Geoff Marsh: Okay and in this paper, you found some horse DNA which is 700,000 years old or thereabout, that's sounds like an absolute game changer.

Ludovic Orlando: Exactly, actually so far the oldest genome that has been even characterized is dating back to something like 70,000 or 80,000 years ago. So 700,000 years ago is an order of magnitude older than the previous ones.

Geoff Marsh: Alright and just to get a sort of picture what you've found, it's a bone fragment it wasn't sort of a fully preserved horse mid-gallop.

Ludovic Orlando: So, it was a piece of about like 10 to 15 centimetres long of a metapodial, which is sort of a other bone from one of the limbs.

Geoff Marsh: And so how was the DNA, had it aged well?

Ludovic Orlando: You know what when we started the project it was really almost impossible to characterize the DNA that old, so we're expecting the DNA to be very much damaged and so it was. The DNA was pretty much fragmented, not only this is for DNA but what we've done in the study is characterizing as well a full set of proteins, actually the number is 73 of those proteins, that we were able to sequence from the extract, and again the basic components of the proteins are the amino acids and some of these amino acids also are extremely damaged such as glutamine for example.

Geoff Marsh: That sounds like a bad thing. What kind of bearing does that damage have on, you know, what we can do with the DNA?

Ludovic Orlando: First you can't manipulate it, like you would manipulate some really freshly extracted DNA. It would be very, very difficult to assemble back the pieces of information you could get access to, simply because they are so short so you would have to find the pieces of the puzzle to reconstruct the whole set of information present in the given genome. The third consequence that I can see is that because of the damage, some of the sequence of the individual has been modified sometime and actually after this, so the sequence has been kind of damaged and modified. So we have to find out a way to tweak that damage out in order to identify the genuine kind of information that we could rely on to do some evolutionary inference.

Geoff Marsh: So, this paper isn't just the result of a lucky find. It's neatly tied in with the advances in our ability to manipulate this old DNA.

Ludovic Orlando: Absolutely. You couldn't be more mistaken if you thought that it was just, you know, find the right sample, plug it in, in a sort of super fancy machine and then just wait for an easy genome to get assembled. Actually it was a very long story that took over something like three years where we had to develop some of the molecular tools that were available to make that adventure possible. One of the tools that we pioneered, the use of what we call the true single DNA molecule sequencing, which was a sequencing platform that are able to sequence DNA molecules without even to amplify them and you read through the sequences as they stand. So that means that you will have the higher sensitivity to get access to that pool of molecule and that will remove a few result biases in the downstream analysis on top of it.

Geoff Marsh: As far as jigsaws go that sounds like an absolute mare. Nevertheless, you managed to eventually get useful information out, so did you make any significant revelations about horse evolution?

Ludovic Orlando: Definitely. So one of the main consequences of the work is that now that you have a date, 700,000 more or less for a given genome, then you could use the time difference you have and the number of mutations that you can identify compared to present day horses to calibrate a so called mutation rate and using that mutation rate now you could use it to date the time of origin of all the equids that are living today. The equids that are living today are the donkeys, the zebras, on top of the horses. So, now you could have the question when did it all start with them? What we found is that the story of the equids that are living today started somewhere around 4 to 4.5 million years ago and nowhere near the 2 million years ago that some palaeontologists thought were the actual date.

Thea Cunningham: That was Ludovic Orlando talking to Geoff Marsh.

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Thea Cunningham: Coming up soon in the research highlights, sound that can squeeze through tiny holes and how aerosols may have suppressed hurricanes over the Atlantic.

Charlotte Stoddart: Now I've never thought very much of my throwing ability. But according to a new study by scientists at Harvard University, I'm really good compared with other animals. I'll definitely beat a chimpanzee in a throwing contest. Darwin noted our aptitude for throwing in the 19th century, but since then the question of what makes us such good throwers has been rather tossed aside. So I caught up with new study leader, Neil Roach who took time out from field work in Kenya to find some phone reception and explain what sets us apart when it comes to our pitching prowess. Nature 498, 483–486 (27 June 2013)

Neil Roach: Humans are remarkably good throwers. We can throw both with incredible accuracy and incredible velocity. So a professional baseball pitcher can throw about 90 miles per hour and they can do that a hundred or more times in a single game, perhaps even more impressively if you go to any town in America, where there's a little league baseball game, you can find a, you know, 12-year-old kid throwing 60-70 miles per hour. You don't need to be adult sized, you don't need to be a professional athlete in order to produce these major throws.

Charlotte Stoddart: I'm guessing this ability to throw didn't evolve so we could play baseball or cricket in the UK.

Neil Roach: No certainly not, in fact, what we argued and the reason we're interested in the study is figuring out how far back this behaviour dates and we think it dates significantly further back than modern sports, in fact back about 2 million years ago. We came from a group of animals that do throw occasionally. They throw objects, including their faeces at each other when they're just playing, but they don't throw at the same power and the same accuracy that we see in humans. And I think really what happened around two million years ago is that as we began to be more reliant on a very different sort of life way we became reliant on hunting. The advantages of being a good thrower were really quite profound. The ability to injure an animal or successfully hunt or kill prey without having to be right next to that animal really did amazing things to our success as hunters and also our ability to survive in encounters with large animals.

Charlotte Stoddart: How can you tell that throwing evolved 2 million years ago? What kind of evidence is there?

Neil Roach: Well, what we did in our study was we took a look at the biomechanics, that's just the simple physics of the movement of some of them when they're throwing and that allowed us to look at the individual motions that were occurring at each joint in the body. And this type of approach combined with an approach in which we limited people's range of motion of their joints, we limited their ability to move, to mock up what a more primitive morphology would have looked like in primitive anatomy, in the anatomy of our ancestors. We figured out how much different joints contributed to the throwing motion and throwing performance and using that we were able to figure out how changes that has occurred in our evolutionary past has affected our ability to throw objects with incredible speed.

Charlotte Stoddart: Tell me more about the set up of the study. So you invited people into your lab, did you and they were throwing what?

Neil Roach: The people that came into our lab were all collegiate athletes and they threw baseballs at a target that we had set up and the data we collected came from little reflected markers that we put on their upper body. We used a 3D camera system to record how those markers were moving in space. These are the same type of camera systems that are used to make video games and animated characters in movies such as in Golem in The Lord of the Rings, we just don't have quite that many cameras because we're not Hollywood.

Charlotte Stoddart: What did you learn from that then about the biomechanics of throwing, and what makes us as humans so good at that?

Neil Roach: Well we found that the thing that really accounts for human's amazing performance is our ability to store energy in our shoulders. This is a rather odd concept but as if you can think of the shoulder acting almost like a sling shot. So what you're doing when you're throwing, you're actually moving your arm back, you rotate your arm back away from the target before you accelerate it forward at the target and as you rotate your arm back away from the target, the ligaments and the tendons and all of the muscles that are crossing your shoulder, they stretch and they store elastic energy just like if you would stretch an elastic band on sling shot, when you then release that energy, the ball, the projectile or whatever you're holding is rapidly accelerated at the target almost like a catapult. In professional baseball players, that motion can be up to about 9000 degrees per second which is an incredibly ridiculously fast speed and this is occurring over just a few milliseconds, so not a very small fraction of a second but this rotation that's enabled by this energy stored in our shoulders really treats the rest of the arm like a whip and rest of the arm is essentially along for a ride once that rotation happens.

Charlotte Stoddart: How do we compare with our closest living relatives, chimpanzees?

Neil Roach: Well, I think the remarkable thing about chimpanzees' throwing performance is that chimpanzees overall are incredibly athletic and very strong animals, yet even if you're training an adult male chimpanzee to throw they can only throw around 20 miles per hour which is, you know, a third of the speed of a young 12 year old boy. So, they're quite poor throwers in fact and that really is what sets us apart, the ability to throw things not only with accuracy but also with tremendous speed.

Charlotte Stoddart: That was Neil Roach who's recently moved from Harvard to the George Washington University in Washington DC.

Thea Cunningham: Now it's time for the research highlights read by Noah Baker.

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Noah Baker: Sound can squeeze through holes smaller than its wavelength in a specially made plastic wall. A few years ago, scientists transmitted light waves through seemingly impassable gaps. Naturally they wondered if they could do the same with sound. So, researchers at the Yangtze University in South Korea stretched pieces of plastic film across tiny holes in a thin metal plate. The incoming sound waves resonated with the film causing air to flow as if it were mass-less and funnel as much as 97% of the sound through the holes. The holes intensified the sound by a factor of nearly 6000. This could make the material useful in sensitive detectors. Find that paper in the Physical Review Letters. Nature 498, 411 (27 June 2013)Manmade aerosols may have suppressed a number of tropical storms over the Atlantic during the 20th century. Natural aerosols like dust particles are known to influence hurricane activity but the effects of anthropogenic aerosols aren't as clear. They simulated storms that either included or excluded changes in manmade aerosols. As the levels of these aerosols increased in the earlier part of the century, tropical storm activity dropped. When they declined at the end of the century, the number of storms went up. The team think it's down to the effects aerosols have on clouds. You can read that study in Nature Geoscience. Nature 498, 411 (27 June 2013)

Charlotte Stoddart: Soon to come, the news chat but first before Kerri went on a holiday she met some rather large teeth.

Kerri Smith: Which came first, the chicken or the egg? A sensible evolutionary question perhaps because it's not always clear what comes first in evolution. A Nature paper this week, tackles a giant question using some appropriately large case studies, not at all chickens and eggs, but elephants and their teeth. I'm here at the Natural History Museum in London with Adrian Lister, hello. Nature (2013)

Adrian Lister: Hi.

Kerri Smith: Adrian, we usually assume don't we that when a creature's environment changes its behaviour might change as well and physical characteristics it has might change.

Adrian Lister: Yes. I think mostly evolutionary biologists think about the environmental change and then they think about the adaptation. So you know, if you need to eat grass, you get the teeth. Natural selection will evolve your teeth to eat grass and so on. What I'm suggesting is that there is a missing step in that idea. We really have to think about the behaviour because many of the adaptations that animals have are useless unless they actually apply them to the environment using their behaviour, this is an idea that's been around for quite some time, but what we have lacked really are concrete examples of it in action.

Kerri Smith: Exactly and what we have here is, you have been testing this theory using the fossil record of elephants in Africa. So tell me a little bit about the samples you've been working with and in fact show me because you've got some here in this draw.

Adrian Lister: Yeah, well here are some specimens from the Natural History Museum collection. These are some molar teeth, these ones from Kenya, this specimen…

Kerri Smith: That's just one tooth? That's almost the size of a rugby ball!

Adrian Lister: This is not even complete. This specimen would have been about 50% longer, it's slightly broken. So these are huge molars you've got. The original tooth that would have been about 30 centimetres long and weighing several pounds in life, of course they're heavier now because its fossilized but the animal was carrying these massive molars around because if you're as big as an elephant you'd do a lot of chewing. You're eating fairly low quality vegetation food and you have to eat a lot of it, so you need a lot of chewing power.

Kerri Smith: And in terms of the evolution of elephants and perhaps the environment that they were living in at that time, take us back as far as 10 million years to Africa. What kinds of changes were underway?

Adrian Lister: Well, we know from evidence on the environment that before about 10 million years ago, woodland was very widespread, woodland and forests and most of the mammals that we have were adapted to woodland life. In other words, those were herbivores were eating the leaves of trees and shrubs and those kinds of leaves, if you're a plant eating mammal are relatively soft, but starting from about 10 million years ago, the climate changed, it got drier and grasslands started to spread, this was a gradual process over millions of years but there was an opportunity there for mammal species to adapt to a different kind of environment, new species evolved, ones that became adapted to grass eating. Now if you're a herbivore and you're eating grass, you get a lot more wear on your teeth because first of all grasses are tougher kind of a leaf than tree leaves. Secondly you need to eat more of it because it's lower quality and thirdly if you're feeding close to the ground, you pick up more grit from the soil with your food and that also tends to wear down your teeth.

Kerri Smith: So this tooth here that you've got in your hand, this kind of rugby ball sized and it's lobed, it's almost like the bottom of a really strong walking shoe.

Adrian Lister: Yeah that's right, it's got the ridges but they're quite shallow. So the problem from an animal like this is if it's eating very abrasive food like grass and you're doing that if you're a elephant for may be 15-20 hours a day, the teeth gradually wear down and if the enamel of the teeth wears right down to the root, the animal can't feed anymore and it'll die. So there's the pressure of natural selection if you like to increase the height of the tooth crown so that it got longer to wear down before the animal expires and if you're eating a coarser food like grass, you need the high-crowned teeth.

Kerri Smith: So that sample you were showing us there, that's only one of a number of samples similar to this you have looked at. And what do they tell you about the relationship between the elephant's environment, this change from soft leaves, to harder, harsher grass.

Adrian Lister: So, the idea that the tooth crown increased in height, sort of broadly known about that but what we can do now, which is interesting is we can have a direct hand on what the animal is eating and the way that we can do that is by taking a small sample of the tooth enamel and actually analyzing it chemically and by looking in particularly at the isotopes of carbon we can tell which kind of food that animal was eating.

Kerri Smith: Presumably you found in this case that the elephant's climate or its environment changed then its behaviour somehow changed and then its teeth began to change.

Adrian Lister: That's exactly the three-step process that we got in the study. We start off with the environmental change, we've got the spread of the grasses, and we can see that about eight million years ago a lot of these different species of elephants and there were quite a few different lineages, a lot of them switched quite rapidly from browsing, which is eating tree leaves, to grazing, which is eating grass about eight million years ago, but they still got the leaf-eating adapted teeth. That's what is so interesting about it, and what you find is that it takes about three million years of grass eating before the teeth starts to actually change their morphology and adapt. That may be is the surprise of the study.

Kerri Smith: So, perhaps lessons for climate change these days and how readily species can adapt to changes in their environment.

Adrian Lister: Yes. I think, I mean, there's a plus and a minus there. It shows that animals are quite flexible behaviourally and can up to a point adapt behaviourally to a changed environment. Generally an evolutionary biologist will tell you the rates environment is changing now due to manmade factors is really too fast for what we normally consider to be the evolutionary process to keep up with it. This model here may be suggests it's not quite as bad as that, in that they can adapt behaviourally with their existing morphology and perhaps those that are there for survival, changes that are going on are those that are more flexible in their adaptations and their behaviour.

Kerri Smith: Well, you know, I feel like I've really sunk my teeth into that and thank you for helping me.

Adrian Lister: A pleasure. Thanks very much.

Charlotte Stoddart: That was Adrian Lister at the Natural History Museum in London and he was talking to Kerri.

Thea Cunningham: Finally this week, the news chat. You may remember in a news chat in April we talked about HeLa cells, the cell line famously derived from young cancer victim, Henrietta Lacks. When she died in 1951, her cells were taken by scientists and grown in labs for research. The cells became invaluable to medical science but their use is controversial because they were taken without her or her family's permission. In a news feature this week, we hear about a similarly important cell line but one that's no less controversial. WI-38 was created by biologist Leonard Hayflick using a piece of tissue from an aborted foetus. Meredith Wadman has written about the cells and she joins me on the line. Meredith when Leonard created WI-38, the HeLa cell line was already being used by scientists, but these cells were different, weren't they?

Meredith Wadman: Yes they were. The HeLa cell was an overtly cancerous cell, whereas these cells were normal. They had the normal human complement of 46 chromosomes, they were not cancerous, and they were a first in that regard.

Thea Cunningham: And since then they've proved enormously useful to scientists wanting to study vaccines. In fact, hundreds of millions of people have been immunized by vaccines made using these cells.

Meredith Wadman: Yes that's true. They became quickly useful in vaccine research where up till that time cells like monkey kidney cells had been used that required killing lots of monkeys and were expensive and had problems with being infected with monkey viruses. So, having a human cell line that was virus free was really valuable and quickly many vaccines were created using these cells.

Thea Cunningham: Now the cells were derived from an aborted piece of tissue. In this particular case, the abortion was entirely lawful, but we don't know for sure whether the mother gave consent and this has raised a whole set of questions.

Meredith Wadman: Yes, I should say that at the time it did not particularly raise a set of questions but the abortion that occurred to give rise to these cells was conducted in Sweden in 1962, where abortion was legal at that time and using leftover surgical tissue or including aborted foetal tissue was a routine thing. It was done too quickly without donor consent and so it was kind of standard practice. As we've evolved through the decades there's been a heightening of ethical awareness around it, issues about tissue consent and donor consent in general. So this is a more prickly issue today, although it should be stressed that even in the United States today, leftover surgical tissue including tissue from aborted foetus may be used without consent, provided that it's stripped off identifiers.

Thea Cunningham: And then there's this separate issue of compensation. Roughly how much money is being made by vaccine makers that use these cells?

Meredith Wadman: It's very difficult to quantify that. At best what you can come up with is an order of magnitude which would be billions of dollars with a B.

Thea Cunningham: So, as you say these cells are incredibly valuable, now compensation is perhaps one of the biggest concerns for Leonard and I called him to ask who he thought the cells belonged to and what his opinion was on that. Let's have a little listen to what he had to say.

Leonard Hayflick: Well, the tissue belongs first of all to the foetus from which it was taken. The foetus was not alive in the sense that it would survive and thrive, so that the owner of the tissue in a legal sense is the estate of the foetus.

Thea Cunningham: And by that you mean the family?

Leonard Hayflick: Yes, the surviving family.

Thea Cunningham: And in your mind, should the estate be offered compensation for those cells?

Leonard Hayflick: Well, if the cells that you're referring to are WI-38 which was derived from the lung of that foetus, then there are four stakeholders - the estate of the foetus, the scientist who gave value to those cells, the institution in which the work was done and finally any organization that may have supported the work. To the best of my knowledge, no compensation has ever been made and I think that's wrong.

Thea Cunningham: Meredith that's Leonard's view. What do other people have to say?

Meredith Wadman: I think 50 years after the fact legal experts feel it'll be very difficult to establish a financial claim to either the WI-38 cell strain or any product that was derived using it simply because the amount of time that has gone by, is itself a formidable barrier, but at the same time that doesn't mitigate against a sort of a moral claim to some recognisance of this family's contribution and as Len argued possibly of the scientists who gave it value.

Thea Cunningham: Does the US have plans to change the way it regulates tissue donation?

Meredith Wadman: Not so much donations that consent around them. The department of Health and Human Services has proposed changing current rules so that if I as a scientists or a company go to a bio-bank and get some de-indentified surgical material including possibly material from an aborted foetus, the donor of that tissue needs to have signed a written consent saying yes it's okay, even though at the point of picking up that tissue, the bio-bank, the researcher or the company scientist, has no idea who it came from.

Thea Cunningham: Okay, thanks Meredith. Remember you can read Meredith's feature and more news stories for free at http://www.nature.com/news.

Charlotte Stoddart: That's it for this week. Join us again next time to find out how to build a human heart. I'm Charlotte Stoddart.

Thea Cunningham: And I'm Thea Cunningham.

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