Nature Podcast 15 March 2007
Introduction
This is a transcript of the 15 March edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (http://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 podcast@nature.com
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Chris Smith: This week, how scientists have pieced back together the remnants of a collision that took place in the outer Solar System four billion years ago.
Michael Brown: It's very likely, in fact inevitable, that some of the comets that we have seen in our lives have been from this actual collision sometime in the past. Chunks of this very large object that broke apart in the outer Solar System have landed on the Earth and are somewhere around, somewhere.
Chris Smith: More from Mike Brown coming up shortly. Also, paaleontologists have uncovered fossil evidence of where we get our ears from.
Zhe-Xi Luo: What is unique about this fossil mammal is it has preserved an intermediate evolutionary condition of the middle ear structure and now we get a much better understanding of how the modern mammalian ear came to be the way it functions.
Chris Smith: And how scientists unearthed the roots of where flowering plants come from.
Sean Graham: It popped out in a place in the phylogenetic tree that just totally surprised us. Right near the very roots of a flowering-plant tree of life.
Chris Smith: Sean Graham will be grasping that nettle later in the programme. Hello, I'm Chris Smith and welcome to this week's Nature Podcast. First up this week, there was an icy collision that took place over four billion years ago in the Kuiper Belt, out beyond Pluto. Mike Brown has worked out what happened and tracked down the remnants of the smash. Nature 446, 294–296 (15 March 2007).
Michael Brown: This is one of those things that you stumble upon without having any idea that it's there. We found this very interesting object a couple of years ago. It's out in space beyond Neptune and it's bigger than Pluto in one dimension, but it's actually about half the size of Pluto in the other dimension. It's shaped sort of like an American football that has had some of the air let out of it and stepped on, and it spins end over end every four hours. And what we have recently found is that the object was smashed by something else that was maybe half the size of Pluto, maybe four billion years ago, and that's what led it to rotate, and the interesting thing that finally happens is that we found the other chunks that fell off of it after it got smashed.
Chris Smith: So, where have they gone? You would anticipate that something was smashed into by something the size of Pluto, the remnants, the shrapnel, would disappear?
Michael Brown: Right, so, two of the little pieces actually went into orbit around this object. The other six pieces that we found are not in orbit around the object, but they are in orbit around the sun. They got ejected from the object itself, but they didn't get ejected fast enough, so you can still see them in the vicinity of this object out there past Neptune.
Chris Smith: Frankly, as devil's advocate, how do you know, Mike, that those remnants are actually from that parent object that first got smashed into and not just other debris that's accumulated nearby?
Michael Brown: Yeah, that's a really good question. The only way that we realize that these were all chunks from the original body is that they are all made of exactly the same material and there is nothing else out there beyond Neptune that we found that looks like it's made of exactly the same material. So, that's the original thing we found —we thought, well, this is strange, there is this one big body that's rotating fast, shaped like a football, that's made out of this and then we started finding just a few more and we thought, what's going on, why are there all these objects — and then suddenly it dawned on us that these are all really right in the same place, in orbit around the sun. If you trace their orbits back, you can actually see essentially that they intersect.
Chris Smith: So, that's the outer Solar System, but does this give us any clue as to whether these are the configurations that you see closer in, nearer to Earth?
Michael Brown: The fast spinning implication for the inner Solar System is that this collision that happened probably four-and-a-half billion years ago, right at the beginning of the Solar System, this collision just by chance happened to occur in a region of the outer Solar System that is close to being unstable, that is, if you put something in orbit there, it won't stay in that orbit for a very long time, which means that all of these fragments from this massive collision have had the chance to become unstable, and when they become unstable they work their way into the inner Solar System and they become things that we call comets today. So it's very likely, in fact inevitable, that some of the comets that we have seen in our lives have been from this actual collision, and in fact it must also be that sometime in the past chunks of this very large object that broke apart in the outer Solar System have landed on the Earth and are somewhere around somewhere.
Chris Smith: Mike Brown from the California Institute of Technology piecing back together what happened four billion years ago to the Kuiper Belt object 2003 EL61. Well, not quite that far back, in fact about 100 million years ago, our mammalian ancestors were busy evolving the middle-ear structures that we rely on to be able to hear today. But unlike us, in the first mammals the bones in the middle ear were fused to the jawbone, and it was only later that they separated, well no one knows exactly when or how they did it. That is, until now, because Zhe-Xi Luo from the Carnegie Museum in Pittsburgh has found a beautifully preserved shrew-like early mammal called a triconodont, and what it shows is a jaw partially disconnected from ear structures, which paves the way for the anatomy that we see today. Nature 446, 288–293 (15 March 2007).
Zhe-Xi Luo: We have discovered a 125-million-years-old fossil mammal. What is unique about this fossil mammal is it has preserved the intermediate evolutionary condition of the middle-ear structure and now we get a much better understanding, how the modern mammalian ear came to be the way it functions.
Chris Smith: What sort of mammal was this when it was running around?
Zhe-Xi Luo: This is a triconodont mammal and triconodonts are characterised by their teeth with three cusps and these mammals are all fairly small, and the best they were at were to eat worms and the small insects. By general habitat, they are terrestrial mammals and possibly they could also dig into tunnels and were living underground.
Chris Smith: And how long after mammals first appeared on Earth would these animals have been running around?
Zhe-Xi Luo: The first mammals appeared on Earth about 220 million years ago and this animal that we are studying now that are represented by this new triconodont mammal is about 125 to 65 million years and so this new mammal is about a 100 million years after the first mammal appeared on Earth.
Chris Smith: So, given that mammals had already been around for 100 million years or so when this animal first appeared, what changes have happened in its ears in that time and why are these so useful, these clues to understanding how we got our own ears?
Zhe-Xi Luo: Modern mammals have this very elaborate hearing function because its ear structure is separated from the jaw, but we also know from the fossils of even more ancient time, in the mammalian precursors that middle ear are actually connected to the jaw and so how did this disconnection between ear and the jaw take place and this has been an important question that palaeontologists have been searching for fossil evidence to address; and what we have now in this new discovery is the ear structure of this new mammal is already fairly like some of the modern mammals, but it's still partially connected to the mandible, and this gave us for the first time a structure of intermediate evolutionary stage and that's why we are so excited about the discovery of this particular fossil.
Chris Smith: Zhe-Xi Luo with a 125-million-year-old fossilised mammal that was unearthed in northeastern China and now is helping to point the way to how modern mammals' ears evolved.JingleNature's podcast, bringing the world of nature to life.End Jingle
Chris Smith: On the way, how researchers are shaking up the field of seismology and how genetics has helped to unearth the plant and the root of the flowering plant phylogenetic tree. First though, to the founding father of phylogenetics and taxonomy and that's Carl Linnaeus. Here's Kerri Smith.
Kerri Smith: I'm here at the Natural History Museum in Central London standing in front of a prime example of an animal called Procyon lotor. Its name, and those of every other animal found here, have a legacy of one man, Carl Linnaeus, known today as the father of taxonomy. This year is the 300th anniversary of his birth. His great contribution was to survey and classify all the known plants and animals of this world, giving them a two-part name and a place in the tree of life. These names were adopted by the scientific community and are still used today. Nature is running a special package of features this week to celebrate. I'm here with two of the authors, Henry Nicholls and John Whitfield, who have been looking at the man and his legacy. Linnaeus is a scientist matched by his passion for his work and Procyon lotor is a creature particularly dear to his cause. Henry, if I could turn to you first, what's the connection between this animal and the taxonomist? Nature 446, 255–256 (15 March 2007).
Henry Nicholls: Procyon lotor is a raccoon and Linnaeus had a pet one. Now he is of course most famous for his botany, but he was also an avid and keen zoologist and, at the botanical gardens in Uppsala over the years there as director, he had a small menagerie that included various kinds of parrots, cassowaries, cockatoo, an orangutan and a raccoon called Sjupp. It had been given to him, we think, in 1746 or 1747 by the Swedish royal couple, the crown prince Adolf Frederik http://www2.nrm.se/fbo/hist/linnaeus/galleri.html.en#kungen and his wife, Louisa Ulrika, both of whom collected huge amounts of natural history specimens, and he sort of kept it as a pet for probably about a year. In 1747, there is this wonderful paper that he delivered to the Swedish Royal Academy of Sciences to his colleagues — unusual for a large chunk of it being devoted to his personal interaction with this raccoon that reveals a side of the man we rarely see and it's quite a charming account in fact.
Kerri Smith: So, he delighted in having this raccoon as a pet, but that wasn't the only function for it?
Henry Nicholls: So, he described, in the first half of this article he described what it ate and what it likes to do and the stuff it got up to in the botanical gardens, and then tragically one day it hopped over a wall and was mauled by a dog. A couple of days later they found its body, and Linnaeus, the naturalist, refused to forgo this opportunity to sort of explore the natural world and put it up on the dissecting table and took his scalpel. So, the second half of this paper is an organ-by-organ account of the raccoon for the first time this animal was ever described.
Kerri Smith: And so did that help him to fit raccoons into his classification system, given that it had made this posthumous contribution?
Henry Nicholls: It did, some thought when he wrote he gave her the name Ursus cauda elongata, elongata because of the long tail, of a bear. So, he thought it was allied to the bear and that was before he came up with this binomial nomenclature that he devised a few years later in 1753. So, by the time he came to the 10th edition of his Systema Naturae, he then revised its name and it had become Procyon lotor, which means 'the washing bear'. It liked to wash its food in water before it ate it and it's current name then came into use after Linnaeus's death; and then people have subsequently allied it with pandas, and today we are still even grappling with raccoon taxonomy — exactly where it lies and of course exactly how many different species there are. So in the early 20th century, there was this enormous excitement and everyone was splitting the species up— the common northern raccoon into almost 20 different subspecies, now current taxonomists have kind of collapsed that down again using a combination of traditional morphological approaches and molecular biology to something much more manageable.
Kerri Smith: It's clear from that that most of the foundation that Linnaeus laid has stayed with us to this day and we hope some of his passion has also remained for modern-day taxonomists, who will know the name he gave to his beloved subspecies has been replaced, but recent advances in science have meant that taxonomy has changed rapidly in the last 90 years. John, you have been looking at the practices that modern-day Linnaean use to put species in the right places on the evolutionary tree. What is the field of systematics now based on? Nature 446, 247–249 (15 March 2007).
John Whitfield: Well, as you say, since Linnaeus was around what happened is we have discovered evolution and natural selection: Darwin's theory was actually unveiled in the Linnaean society in the summer of 1858, which is just a mile or so east of here on Piccadilly, and so, following that, the Linnaean project if you like becomes not just to give things names and describe them, but to also work out how they are related to each other, given a place in the tree of life, and to reconstruct the history of evolution and what's really revolutionised that particular project in the past 30 years is DNA sequencing. The sequencing of genes and genomes, increasingly, that has given us a whole new window on the tree of life.
Kerri Smith: Assuming that the data gained from genes and genomes seems to be much more definitive than simply looking at, say, the physical characteristics of a, say, animal or plant, are we pretty much there with taxonomy that we have got now?
John Whitfield: What's great about DNA is that everybody has got it. So, for example if you are trying to work out how a fly and a worm and a raccoon are related, what you would have had to do in the past was look at their anatomy and to try and find features that linked one species to another or that could be used to divide the species. Obviously for species that are similar, that is very hard, but like I say they have all got DNA. So, if you look at their DNA sequences that gives you a universal ground for comparison and so that's a tremendous help, obviously, but it's not yet cut-and-dried, there's lots of controversies still in the field and uncertainty, partly because it's terribly, terribly difficult to work these things out. So, for example let's say there is the three of us, me, you, and Henry. If you are trying to work out how we are related to each other, there's three possibilities: either I could be more related to Henry, I could be more closely related to you, or you and Henry could be more closely related and I would be on the outside. So, you could sequence the DNA and then you could test that against the various possibilities and you would get to an answer quite quickly. But if you have 10 species or groups, people, whatever, there are actually 34 million different possibilities to choose from. So, as you add more groups to that, the number rises astronomically and so, even though DNA data can be very good mathematically and computationally, it's still very, very difficult to decide between all the possible answers you might have to question in trying to answer.
Kerri Smith: So, there are some huge computational problems with this, but genetics is making a huge contribution to taxonomy and evolutionary biology. Is there a symbiosis? Is there any two-way talk?
John Whitfield: Yes and no. Obviously, when these techniques first came along, the traditional taxonomists who used descriptive anatomical tools, there was some hostility between the two camps and later people thought that the traditional taxonomists were firstly stamp collectors and the traditional taxonomists felt that these upstarts were coming in to tell on their job. So, that has been reconciled now. Everyone knows that you need that molecular dichotomy, it can do a lot for you and you need to also understand the biology of the animal for descriptive taxonomic studies. Where there are still issues where people aren't talking to each other as well as they might is that genomic researchers still often don't understand evolution as well as they might. For example, when the human genome was published, one of the findings that was trumpeted as the most important of that project was that about between 100 and 200 of the genes in people seemed to have come from bacteria. Peopled looked at genetic databases and they found genes in humans and in bacteria, but not in any other species that are sequenced. So, what the genome researchers suggested was that genes have come across by something called horizontal gene transfer. Basically, bacteria had passed their genes over. It's a kind of interspecies sex if you like, where genetic material gets transferred between two related organisms. This flabbergasted evolutionary biologists and they hurried to perform more evolutionary analysis of these sequences, and they found if you actually look at what we know as the tree of life, it's much more plausible that the common ancestor of humans and bacteria shared these genes that we now share, but that have actually been lost in the other species that they are absent from down the way and not having come across the bizarre genetic fusion at all. So that was an embarrassment for the genome sequences. On the other side, on the taxonomist side, now what we are finding is that some people with molecular backgrounds are wanting to turn taxonomy itself into a molecular project. So, you use DNA sequences to identify and define species instead of the kind of characters that have been used ever since Linnaeus found it and that is also causing a lot of argument and friction.
Kerri Smith: Thanks, John. So, molecular evidence is clearly pivoted to modern-day systematics, but at its heart it is the same principle to which Linnaeus adhered to to name all species and put them in their rightful places. It was no small task, but one of which Linnaeus felt himself more than capable. Later in his life, he claimed "that no man has ever transformed science in the way that I have". He might just have been right.
Chris Smith: Kerri Smith looking at the legacy of Carl Linnaeus at London's Natural History Museum. Now, from the person that shook up the world of taxonomy to someone who is trying to shake up the world of seismology and that's Greg Beroza. He has been trying to get to the bottom of what causes tremors at some faults. These are weak, very slow movements that can go on for extremely long periods of time, even up to weeks or months. No one knew what caused them though, but now an earthquake in Japan has provided Greg with a vital clue. Nature 446, 305–307 (15 March 2007).
Gregory Beroza: We have been trying to understand a recently discovered phenomenon called non-volcanic tremor; and this tremor is a weak shaking of the Earth that was discovered only about five years ago in Japan. It's different from ordinary earthquakes. So, rather than happening impulsively and being done as quickly as earthquakes are, this tremor shakes the Earth for hours, sometimes even days or weeks at a time, and we have fundamentally have not understood what causes it.
Chris Smith: And these rather bizarre earthquakes —are they occurring everywhere on the Earth surface as far as we know, Greg, or are they occurring just in fairly restricted areas?
Gregory Beroza: The tremor has been seen in fairly restricted areas, in Japan, also in the Pacific northwest of the US and deep underneath the San Andreas Fault. In part, this may be due to the fact that we don't have monitoring equipment capable of seeing it in large parts of the world.
Chris Smith: Well, if it is occurring in a very restricted place or places, then there must be something special about the faults in those areas, presumably that triggers this, and can they give you clues as to what's going on?
Gregory Beroza: Yes, it has been thought fluids moving around may be the source of this tremor, as it is for volcanic tremor, which happens in the plumbing system of volcanoes. In the study though, we have figured out that it's actually not fluid movement, but it's actually the same mechanism that generates ordinary earthquakes — that is, its slip on faults.
Chris Smith: So, why does it happen so much more gently and over such a long period of time in these sites, rather than in the rather catastrophic way that we normally associate with earthquakes?
Gregory Beroza: That's an excellent question. We don't really understand why these faults seem to slip slowly where they do, only that they do, and so that the next challenge, now that we have established this connection, is to figure out physically why these earthquakes seem to be happening so slowly.
Chris Smith: So, how were you actually watching them, given that they are presumably very difficult to watch and to observe because they are going on for extended periods and they are so small?
Gregory Beroza: Yeah, because they are so different from ordinary earthquakes, you know, a particular challenge for us to work with, we have the benefit of yet another discovery that came out of Japan: that is, there are episodes within this tremor, where it is slightly more impulsive, more earthquake-like, and these are called low-frequency earthquakes, and what we have been able to show is that the wiggles that the tremor makes on the seismographs matches exactly the wiggles of these recently discovered low-frequency earthquakes. These are little earthquakes— magnitude-one-to-two sized events and they occur slowly compared to ordinary earthquakes. What we found is that the deep tremor can be thought of as a swarm of hundreds of thousands of these tiny little slow earthquakes happening over a period of weeks.
Chris Smith: So, in other words, these are the individual movements, like the contour of an earthquake, and when added together that you get a big earthquake.
Gregory Beroza: Yes, that's exactly right. You can think of them as sort of quantum slow earthquakes so that the big earthquake that they add up to and the slow slip that accompanies them is on the order of a magnitude 6–7 earthquake, but it happens so slowly over a period of weeks that these things weren't even discovered until very recently.
Chris Smith: Stanford University's Greg Beroza. He has found that non-volcanic tremors are not done to fluids flowing around as we first thought, but instead miniature versions or quanta of the same slip events that cause catastrophic earthquakes.JingleEnd Jingle
Chris Smith: This is the Nature Podcast with me, Chris Smith. In a moment, where flowering plants came from, but first to a new way to measure quantum information in photons. Michel Brune has created an optical cavity to track photons and you can read the information they contain of a stream of passing atoms. Nature 446, 297–300 (15 March 2007).
Michel Brune: Two things: we store the photon in order so it does not escape before measurement — for this, we enclose it in a photon box and then, in order to detect it, we send atoms one by one, which get information about the photon number inside the cavity, and then we detect the atoms one by one, and by this we get information about the photon number and indeed we measure the photons.
Chris Smith: So, how do you know that when you put the atom to interact with the photon that the photon doesn't end up being changed by the action of the atom?
Michel Brune: Indeed, we notice in many ways. First, we arranged the interaction so that absorption of photon is forbidden, which is different from what we get for a neutron from detection. So, usual photodetector like photo diode is obtained by just absorbing the photon when they detect it; in our case, the single atom does not absorb the photon but feels in some sense the presence of a photon by chance. We can measure with a very high accuracy at the level of single atom.
Chris Smith: And now you have got this tool, what's it telling you?
Michel Brune: We can observe an intrinsic quantum feature, which is the fact that photon number experiences quantum jumps. So, these quantum jumps can only be observed if you are able to observe the photon without disturbing them.
Chris Smith: What are the sorts of quantum conundra, quantum questions that are outstanding at the moment, do you think you could try and tackle using this approach?
Michel Brune: So indeed the issue of these experiments are twofold. In one direction, it is extremely interesting to investigate the behaviour of quantum object and especially what happened to quantum measurement in a very controlled situation and the situation of interest, which has to do with the future development of this experiment is the generalisation to measurement of fields containing more than one photon and indeed now we are investigating this field by performing measurement not simply under vacuum or one photon field, but of a field containing up to about six or seven photons and so we enter a kind of domain where we quantum mechanically manipulate mesoscopic objects and then we go into the direction of investigation of the transition between quantum behaviour of the small systems to the classical behaviour of bigger ones.
Chris Smith: Michel Brune from Paris's Ecole Normale Superieure, with a novel way to watch the birth and death of photons trapped in an optical cavity. Now, finally this week, to the origins of the flowering plants and an unlikely player seems to have walked into the field. Here's Sean Graham. Nature 446, 312–315 (15 March 2007).
Sean Graham: We have been studying a question that Charles Darwin called "his abominable mystery." This served two parts to that mystery. One of the parts is that we don't have a really clear idea of which group of seed plants, or plants with seeds, are the closest relatives of the flowering plants. My research is really focusing on the other aspect of that question, which is looking at the very earliest branches within the flowering plants and trying to figure out how they branched off in relation to each other; and what we stumbled across today is a pretty extraordinary finding of one of the groups of flowering plants that we thought was related to grasses actually belongs very close to the roots of the flowering-plant tree of life.
Chris Smith: So, a flowering plant is not the earliest plants we had on Earth? Something else came first.
Sean Graham: Yeah. Flowering plants are real late-comers on the scene. Plants have been on the land for maybe 450 million years, something like that. Flowering plants appeared on the scene probably around 140 million years ago, their main variation occurred. So, they are real late-comers.
Chris Smith: So, how did you manage to get to the bottom of where they came from?
Sean Graham: We use genetic evidence, so we look at the genomes, the DNA, really we're predicting back in time what the relationships were, using evidence today.
Chris Smith: And when you do this, what specifically have you included in this study and what's it told you?
Sean Graham: The students who were involved in this were looking at the relationships of one of the two major groups of flowering plants called the monocots, and we were interested in a subset of these plants called the grasses and relatives, and a student was doing this phylogenetic survey looking at the DNA of all of these different families and we were very excited to include this one family in our study because it has long been known to be a bit of an oddball, so we couldn't wait until we ran our analysis to see where it popped out and it popped out in a place in a phylogenetic tree that just totally surprised us. Right near the very roots of the flowering-plant tree of life, close to another family called the water lilies.
Chris Smith: How do you actually know that it is so close a relative of that tree?
Sean Graham: We know because we have multiple lines of evidence from lots of different genes from several genomes of these plants. Plants actually have three genomes. They have a nuclear genome, a chloroplast genome, and a mitochondrial genome, and we have evidence from two of those genomes you can see in multiple genes and we have also backed this up by very carefully reconsidering the structural features of the plants. So, you can look at those similarities and differences too and use all of these different lines of evidence to ask the question what are the relationships of these different groups of plants, and when you do that, each of those lines of evidence give you the same answer.
Chris Smith: So, what's it going to take to wrap this up, because people usually say when you find a missing link what you do is create two smaller holes either side of it, so what are you going to take to plug those gaps?
Sean Graham: Well, I would like to have a time machine that I could go back several hundred million years and pluck out some of the long-extinct fossil plants, both angiosperms and other groups, and look at their genomes. So, we don't have that, but what we do have is lots of fossil evidence. We can look at the morphology and try and piece this together with the genetic evidence, and we can also explore and just increase the amount of evidence that we have from different plants so we can look at more genes, more genomes, and more species, and this is a very active area of research that people are doing right now to try and get at this and other questions.
Chris Smith: Sean Graham from the University of British Columbia probing the origins of flowering plants about 140 million years ago. Well, that's it for this week and thanks for listening. Next time, I will be finding out how predators control the emergence of new species. I hope you can join me. In the interim, if you would like to send us any feedback on the Nature Podcast, the address to write to is podcast@nature.com and if you are online you can catch up with any of the reports we featured this week because they are all in our website at http://www.nature.com/nature. For more audio science in the meantime, this week's Naked Scientist podcast takes a look at how contaminated fuel can damage engines, looks at a new way to put the brakes on car accidents, and explains how to make the invisible become visible. That's the Naked Scientist podcast and it is freely available from our brand-spanking-new website, which has to be seen to be believed, and that's http://www.nakedscientist.com. This week's programme was produced and presented by me, Chris Smith, and until next week, goodbye.
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