Nature Podcast

This is a transcript of the 24th December edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (, which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to

Kerri Smith: This week on the final Nature podcast of 2009, the velocity of climate change.

Scott R. Loarie: We are really interested in how fast is climate sweeping across the Earth's surface and how fast the plants and animals have to keep up.

Adam Rutherford: And geek tidying filling in the gaps left open up by genome scientists.

Jonathan A. Eisen: Yeah, it is in essence scientific spring-cleaning and I view this as sort of my community service project.

Kerri Smith: Plus it has been a whopper. We review the year in science. I am Kerri Smith.

Adam Rutherford: And I am Adam Rutherford. Another week, another genome, except this time it is not just one but 56 and thousands more to follow. With the advent of genome sequencing last century certain decisions were taken about which organisms to prioritize in joining the genome club. When it came to Bacteria and Archaea, many of those selected were chosen according to interesting individual characteristics such as extreme habitats or tendency to cause disease, what has resulted is a peculiar bias that ignores evolutionary relationships and d iversity. Well, it is an oversight that Jonathan Eisen and the legions of the Joint Genome Institute in California have begun to correct. Nature 462, 1056–1060 (24 December 2009)

Jonathan A. Eisen: Bacterial genomes and archaeal genomes are much smaller than most animal and plant genomes and so they are cheaper and easier to sequence and they are also very important for a variety of reasons, pathogens, environmental organisms, they do all sorts of interesting things and so right now there are about a thousand complete genomes of Bacteria and Archaea available and some two or three thousand in progress.

Adam Rutherford: So the animals that were chosen for having their genome sequenced there were various criteria in order to prioritize them as humans and mice and rats and things like that, what has been the method by which we choose which bacteria to sequence, given that there are hundreds of thousands of them?

Jonathan A. Eisen: So initially when people were sequencing genomes, there was an effort to try and cover the phylogenetic diversity of bacteria of archaea. And then after those sort of first few genomes were done, there was, I am not so sure with the conscious decision but a general decision by everybody in the community that now they can focus on the biology and so most of the genomes were selected either because the organism was a pathogen of humans or animals or plants or the organism was economically or agriculturally important, or the organism carried out some important environmental function.

Adam Rutherford: And so has that resulted in a kind of genomic bacterial bias in a total diversity of all the bacteria and archaea that exists?

Jonathan A. Eisen: Yeah, so we noticed this quite a few years ago in about 2000 there were some 30 years or so officially described phyla of bacteria and almost all of the genomes came from three of those 30 phyla.

Adam Rutherford: And so what are you doing about that?

Jonathan A. Eisen: So, what we have done is to test whether or not it would be beneficial to fill in the other groups to fill in the dark matter of the bacterial and archaeal phylogeny that did not yet have genome sequences, and in essence copy the efforts that were being done in animals where the people interested in the human genome agreed a few years ago that it would be useful to have a sampling from across animal diversity and they went through and sequenced a marsupial, and a frog, and a fish, and a reptile and bird and other major branches in the animal tree and they justified this as being beneficial to other aspects of genomics, that is the individual reptile was not particularly important but having a reptile genome would be. And so we basically did the same thing for bacteria and archaea, we went through the phylogenetic tree of bacteria and archaea, identified branches in the tree for which there were no genomes available but for which there was an organism that we could grow in the laboratory and get its DNA and we grew them and sequenced the genomes of, as of now about 150 of those, our paper focuses on the first 56.

Adam Rutherford: So why has it taken so long to get the project off the ground?

Jonathan A. Eisen: One of the reasons that this had not been done previously in bacteria and archaea is because there seems to be a pervasive belief among many people in the community that phylogeny is meaningless for bacteria and archaea and that is because many people think that lateral gene transfer, the swapping of genes between different organisms has completely wiped out any record of the history of bacteria and archaea. And that was probably the reason why this type of project had not been done previously on this scale in bacteria and archaea.

Adam Rutherford: Had there been any great surprises in what you found so far?

Jonathan A. Eisen: Yes, so when we took this set of genomes we analyzed them in a couple of ways partly to just test whether or not it would be beneficial to have this diversity of genomes but also to look for sort of nuggets of brilliance, things that would convince people that this was a really worthwhile thing to do and I can give you a couple of examples of those. We found a bacteria that encodes a homologue of actin, so this is a protein previously only found in eukaryotes and there is a bacterial protein that is sort of like actin but not very closely related called MreB and now we have a bacteria that has a true eukaryotic actin protein and actin is important in the cytoskeleton of eukaryotes. We do not know what this bacterial protein does but it basically highlights that these rules that we have come up with for where genes should be found across the diversity of life are not based upon a good sampling of the diversity of life.

Adam Rutherford: Now Jonathan, with a project of this scale to effectively filling in some really really important major gaps in our understanding of genomes, does it ever feel a bit to you like sort of scientific spring cleaning?

Jonathan A. Eisen: Yeah, it is in essence scientific spring-cleaning and I view this as sort of my community service project. This is a project that is for everyone in the microbial community. It is not really just for us, so the data has been released immediately for anybody to use, the data will continue to be released immediately and this is really the Joint Genome Institute effort to correct this bias that exist previously and hopefully that will benefit everybody and anybody who makes use of microbial genome data.

Adam Rutherford: Jonathan Eisen from UC Davis. As with all our genome papers that is available free to all users on our website.

Kerri Smith: Coming up later in the show we will be chomping on the plump ham that was the science year, juicy, meaty and Oh! So nourishing!

Adam Rutherford: Yumm! But before that sumptuous feast, and with the chaotic kerfuffle that was COP15 fresh in our Minds, here is Natasha Gilbert working out the velocity of climate change.

Natasha Gilbert: Plant and animal species will have to migrate to new habitats to respond to climate change but how far and how fast will they have to move to survive. Scott Loarie at Stanford University in California and his colleagues combined several climate change models and emission scenarios to answer these questions for species living in different habitats across the globe. Scott's analysis found that the velocity of climate change is low as a mountainous ecosystem such as temperate coniferous forests. Here species only have to move short distances to find a habitable climate, but species living in deserts or the Amazon will have to move large distances to survive. I called Scott to find out more. Nature 462, 1052–1055 (24 December 2009)

Scott R. Loarie: We are really interested in trying to understand how fast climate is changing and the way we thought about this is we tried to answer two questions. First, what is the rate that temperature change across the world in units of degrees per year, but the second is if I am standing in a landscape, how far do I have to travel in order to change my temperature and that is in units of degrees per kilometre. So if we combine those numbers we get a velocity which is how fast is climate sweeping across the Earth's surface and how fast will plants and animals have to keep up.

Natasha Gilbert: What were your findings then once you would crunch the numbers?

Scott R. Loarie: Well, we have increasingly realized is that heterogeneous complex mountainous landscapes really have the ability to buffer climate impacts because the plants and animals do not have to move very far to change their temperatures. The flipside of that is in many parts of the globe that we have overlooked such as tropical basins like the Amazon, plants and animals will have to move very very far in order to change just a degree or two.

Natasha Gilbert: So how did you work this out?

Scott R. Loarie: To work this out, we combined these two estimates into one number which is this velocity of climate change. The first is the rate of temperature change, so this comes from a climate model. So we combined these estimates from 16 different models and three different emission scenarios which is how much emissions will humans emit into the atmosphere in the next 100 years. The second part of this statistics is how far do animals and plants have to move in order to change their climate and to get this number we combined data sets from climate weather stations across the globe and what is interesting about it is, it really summarizes both of our strategies for combating climate change. In the numerator you have, how fast is the Earth warming in time and to combat that we reduce emissions, we do mitigation strategies but in the denominator is how intact is the landscape, how far do plants and animals have to go to find new climates to track their climate and in order to do that those are adaptation strategies that we need to work on, we need to make sure our landscape is connected, make sure our preserves are heterogeneous. So you could think of some of these mitigations strategies as win-win situations where we could reduce the amount of climate change but we could also increase the ability for plants and animals to adapt to change in climates.

Natasha Gilbert: So how fast is the climate changing?

Scott R. Loarie: What is interesting is that coming out of the last Ice Age, trees were perhaps able to recolonise Europe as fast as one kilometre per year is likely much slower than that. We project that across the landscape across large parts of the globe, about 30% of the globe, plants and animals will have to move much faster than this.

Natasha Gilbert: And is that faster than we thought they would have to move?

Scott R. Loarie: In places it is slower, in places because of the heterogeneous nature of landscape, there will be opportunities for plants and animals not to have to move that fast. Imagine yourself in a mountain range, you might only have to move up slope about a kilometre and you could change a temperature of degree Celsius but in much of the globe, in parts of the globe that we really overlooked like the Amazon basin, the plants and animals might have to move as much as 10 times faster. If you are in a sort of a flat desert you might have to move a 100 kilometres in order to change a degree. The second thing is that when we compare these speeds with historical speeds we imagine that these animals and plants are moving across the landscape with no human barriers, no roads, no deforestation, no forest fragments, so today if we think of the size of our protected areas what we realize is that climates are sweeping outside of all the 8% of the globe's protected areas in the next 100 years.

Natasha Gilbert: So that means we are not protecting enough reserves in order to conserve the animal species will have to move because of climate change?

Scott R. Loarie: Well, if you want species to be able to move fast, they will likely to be able to do so better and faster in connected, continuous stretches of habitat and because our protected areas are generally quite small these climates are literally sweeping outside of these reserves in the next 100 years.

Natasha Gilbert: So what do we need to do? How do we need to change our strategies to conserve protected areas and animals at risk?

Scott R. Loarie: We need to start thinking about our protected areas as being a portfolio of different climates, because if we protect heterogeneous landscapes in our preserves that offers suites of different climates, it is much more likely that the plants and animals will be able to keep pace with changing climate, protected areas will need to be big and will need to be connected and they will need to have different climates represented within them.

Natasha Gilbert: Would it be possible to develop area specific conservation strategies?

Scott R. Loarie: In the past, much of the work of climate scientists has been sort of raise the flag that we really need to slow climate change, we really need to stop emissions but what we are increasingly able to do now is, is start making adaptation strategies to use our science in order to better adapt, better plan for how to reduce the impacts on biodiversity from climate change.

Natasha Gilbert: And have you been in discussions with government bodies or conservation organizations to put these ideas in the science forward.

Scott R. Loarie: We have been working around the San Francisco Bay Area in California, we have been working with state agencies to really try to plan how to best manage for climate change by connecting reserves together, we are still in quite early stages.

Kerri Smith: That was Scott Loarie talking to Natasha.

Adam Rutherford: On climate change we sent our filmmaker and chief Charlotte Stoddart and climate change editor, Olive Heffernan to Copenhagen to file daily reports on what turned out to be a right old mess?

Olive Heffernan: Well, over the past two weeks more than 45,000 people have arrived in Copenhagen hoping to witness the birth of stalled global climate deal. Many of those who have turned up have been left disappointed before the final curtain was even drawn on the deal as overcrowding left the most in the chaos. But for those of us lucky enough to get in side the Bella Center we have watched eagerly as nations have engaged in an ethic struggle to solve what is arguably the world's most complex problem.

Adam Rutherford: Find out from Olive what it was like to be on the ground as the gathered world leaders struggle towards a toothless agreement. Those videos, we think the first content in Nature to feature two presidents and the rock guard are on our YouTube channel,

Kerri Smith: And now for the best stuff elsewhere in Nature. Here are the headlines.

Adam Rutherford: Scientists have made a transistor from a single molecule of benzene; transistors are like electronic valves controlling how much charge passes through a material. They are usually made from chunks of silicon but if these chunks could be made smaller then electronic circuits could be made much more powerful. Now in a carefully measured series of experiments, a team lead by Takhee Lee in South Korea have seen a benzene molecule trapped between two ends of a gold wire acting like a transistor, to get the tiny transistor to work they use an external voltage to manipulate the overdose of the molecule, the shells that electrons occupy. Nature 462, 1039–1043 (24 December 2009)

Kerri Smith: Tidal forces on the Earth could be causing tremors and mini-earthquakes in some parts of the world, finds a team studying the patterns of tremors near the town of Parkfield, California. This town is the centre of a long running earthquake monitoring program and the team was able to catalogue nearly 2000 non-volcanic tremors over an 8-year period. These tremors correlate with stresses caused by tidal forces dragging on the San Andreas fault which lies very near the town. The team led by Amanda Thomas at UC Berkeley suggests that very high fluid pressures in the rock and the stresses already present combine to cause these quakes. Nature 462, 1048–1051 (24 December 2009)

Adam Rutherford: A New type of cancer drug could help reduce the growth of tumours by tackling multiple types of mutations. Uncontrollable cell division caused by mutated proteins can result in lung cancer tumours. When secondary mutations occur in these proteins, the tumour can become drug resistant with one mutation T790M responsible for around half of all drug resistance in patients. A team from Harvard Medical School use mouse models to screen a range of inhibitors that suppress that mutation. Pasi Jänne and colleagues found a special inhibitor was capable of tackling both the mutant receptor and the drug-resistant mutant paving the way for new treatments. Nature 462, 1070–1074 (24 December 2009)

Kerri Smith: Three new papers round off an industrious year for cancer genome projects. About 25-years ago scientists found the first mutation link to cancer in a gene called HRAS, thousands more have been found since. Last week in Nature, the full sequences of two individual cancer samples from two patients were published. Here's Mike Stratton of the Sanger Institute in Cambridge, UK who led the team behind the papers. Nature 458, 719–724 (9 April 2009) ; Nature advance online publication 16 December 2009; Nature advance online publication 15 December 2009

Michael R. Stratton: What we have now with these two papers is for the first time, two individual cancer samples from two patients, one with a melanoma and one with a small-cell lung cancer in which we have essentially the complete set of somatic mutations that are present in each of the two genomes, the genomes of the melanoma and the genomes of the lung cancer. So what one means by that is that all the somatic mutations whether they are base substitutions or they are small insertions and deletions or whether they are rearrangements or whether they are copy number changes, the complete comprehensive list is there down to sequence level resolution and one can just list them on an excel sheet. In the melanoma it turns out there are about 33 thousand somatic mutations present in that cancer genome and in the small-cell lung cancer there are about 25 thousand.

Kerri Smith: Incidentally Stratton says, according to his team's calculations one pack of cigarettes causes an average of one mutation enough to put anyone of. But Stratton and his colleague do not stop there, this week in Nature, the team published another paper using their next generation sequencing technique this time on breast cancer. Nature 462, 1005–1010 (24 December 2009)

Michael R. Stratton: So I went through moment ago the various types of mutation, you can find a base substitution, one base going to another base, you can have a small deletion or insertion of a number of bases and then you can have a rearrangement, basically a chromosome breaking, a double-strand break and then joining on to another double-strand break to make a chimeric chromosome or a rearranged piece of DNA. We have understood hardly anything about the process which generates these rearrangements in solid tumour genomes or what they are doing to the genes. What we did in this paper was to analyze 24 breast cancers specifically for rearrangements and what we found was remarkable diversity of these rearrangements.

Kerri Smith: Remarkable diversity means that in one cancer there might be 200 rearrangements and then in the next there may be hardly any. This, Stratton thinks, suggests a mutation phenotype in which some cancers have a defect in DNA repair and are more prone to rearrangements, some genes too seem more easily rearrange than others. The findings from Stratton and his team are only three papers of many published this year on cancer genomics. I asked him about some trends in the field.

Michael R. Stratton: Well, I think that large-scale systematic screens of cancer genomes are essentially coming of age. We have seen a couple of other cancer genome sequence not quite to the extent of coverage or analysis of the two that were published last week but some AML genomes or breast cancer genome and what these are beginning to tell us about is the patterns genomes wider mutations in those cancers and in the case of the breast cancer that was published in Nature a few weeks ago, it tells us how metastasis can differ from the primary cancer from which it is originated. We have also seen screens which are extensive but are not whole genome, but what they do is they take in more cancers.

Kerri Smith: Research teams around the world are getting in on the genomic act. A group based as of the US National Institutes of Health, The Cancer Genome Atlas published their pilot project just over a year ago. They looked at 600 genes in a hundred different brain cancer samples called glioblastomas and Mike Stratton has picked out their paper as a recent highlight in the field.

Michael R. Stratton: The interesting thing that really emerges from that paper is that we can begin by looking at those data to start to tot up the number of operative cancer genes that are working in individual cancers and the virtue of that TCGA paper was that it did in addition to exploring genes which were not known to be cancer genes it also went over all the genes that were known to be cancer genes and so this was a systematic look in about a 100 glioblastomas of all the known cancer genes were known to be involved in glioblastomas.

Kerri Smith: The team found that glioblastomas on average have about 5 active cancer genes from this pool of 600 that they looked at.

Michael R. Stratton: And this is really important because this, the number of cancer genes that mutated in an individual cancer sample is really a key fundament of our understanding of the evolution of cancer clones, a fundament of our knowledge about cancer and undoubtedly what would be influential in terms of understanding response to therapy.

Kerri Smith: The Cancer Genome Atlas is not the only large scale collaboration in cancer genomics, these experiments are so big and so expensive that it is common for labs worldwide to work together. Stratton's institution, the Sanger Centre is part of the International Cancer Genome Consortium. There are already 12 projects running under the auspices of the ICGC and funded to the tune of 20 million US dollars, each aims to take 500 cases of a particular cancer type and produce full sequences.

Michael R. Stratton: What essentially International Cancer Genome Consortium was set up to coordinate cancer genomics across the world, so it is a grand vision of how cancer genomics will look in the future.

Kerri Smith: That was Mike Stratton. Finally this week we are joined in the studio by reporters Dan Cressey and Geoff Brumfiel to talk us through what has been a whopper of a science news year 2009. Hi Dan.

Daniel Cressey: Hi Kerri.

Kerri Smith: And Hi Geoff.

Geoff Brumfiel: Hello!

Kerri Smith: Hello! Now fairly early in the year we were a bit scared by the threat of swine flu.

Daniel Cressey: That is right. This is probably the biggest science story of 2009 in my view. Around about March the first cases of what we now know is H1N1 started cropping up in Mexico and by the time we hit June, the WHO had declared a full-blown influenza pandemic which is the first influenza pandemic in 40 years.

Kerri Smith: Now there have been, you know, few sort of genome sequences and other scientific analysis of this virus out this year. Is 2009 going to be the end of this story as well, or we are likely to see it being next year's story?

Daniel Cressey: Well, as we moved in to the later half of the year, it has kind of calmed down a bit, things have not been quite as bad as people thought and the vaccination campaigns have picked up but there is still the chance of this to go very nasty.

Kerri Smith: Alright, so swine flu was perhaps a bit of surprise this year, but CERN and the LHC was not. You know, we were hearing about this last year, what has been going on in 2009, we were looking forward to some results?

Geoff Brumfiel: Well, I mean we ended up getting some results in 2009 and actually I would say it has been a pretty good year for the LHC. You may remember in 2008 it had this massive breakdown blew out a whole sector of the machine took a long time to fix and they really hopefully got it right this time, they took a lot of time putting in new relief valves, putting in new safety systems, make sure this cannot happen again and by the end of this year, just before Christmas they actually started taking data.

Kerri Smith: Are you looking forward to 2010 then?

Geoff Brumfiel: Yeah, I think this time 2010 could be a pretty good year for the LHC, they are hoping to run at some relatively high energies, though not as high as it has been designed for probably, but they will accumulate quite a bit of data, there is some tantalizing stuff they might see like dark matter or super symmetric particles. So there is a really good chance we might get something good in 2010.

Kerri Smith: So sticking with physics then and dark matter what has 2009 revealed about this elusive substance?

Geoff Brumfiel: Well, we have had a lot of hints in 2009 that could lead to a dark matter discovery. I do not think anyone has claimed to see anything conclusive, but basically there have been a series of measurements by satellites that have shown there could be dark matter flying around our Milky Way galaxy. Astronomers think there is and then just way last week we had some data unveiled from a very precise underground detector that showed two events that may be dark matter particles interacting with the detector. There is just no way to tell, we only have two events but the LHC should be able to see a similar sort of particle that should create them in its collisions and we may see it in 2010.

Kerri Smith: Now you will forgive me for not having paid much attention to those two events just highlighted last week, because the world was converging on Copenhagen at the same time and we were all a bit concerned about the climate negotiations done. Climate has been a really big theme in 2009, hasn't it?

Daniel Cressey: It has and unfortunately for the Copenhagen negotiations, the build-up to them were slightly overshadowed by what is now rather unfortunately being called climate-gate, where a whole bunch of e-mails were hacked and distributed all around the world and various people took some of the, maybe slightly inopportune language in some of these e-mails as being evidenced for a vast global conspiracy where people such as us in Nature were conspiring to convince the world that climate change was real.

Kerri Smith: So how did these e-mails and climate-gate impact on what happened in Copenhagen?

Daniel Cressey: Well, everyone it seems in the entire world actually went to Copenhagen and tried to get in to the meeting. So there was a huge amount of debate that went on and actually the impact that the climate-gate e-mails was probably rather small but there was still no really impressive deal that came out of this meeting and we are probably going to see ongoing raving about Copenhagen and what they have did and did not achieve over the coming months.

Kerri Smith: And incidentally you can check out Nature's four videos on the subject of COP15 and the Climate Conference on our YouTube channel, Now this year 2009 has also been a massive year for Darwin, I have to say I have never quite heard this word so much in one year. Dan, tell us what was going on, how was that people celebrating?

Daniel Cressey: That is right. Well, the physicists were busy trying to stand up the theories they currently hold, the biologists were busy celebrating a work that is now 150 years old and Darwin and his publication of On the Origin of Species.

Kerri Smith: Now we heard about quite a few quite impressive fossils which Darwin would have loved to hear about, had he been with us for this celebration?

Daniel Cressey: That is right, although Darwin's rather questioning mind, you might hope that he may be would not have got caught up in some of the more extreme hullabaloo over the first of these fossils, which was a primate called Ida and this was discovered unveiled to huge fan fair hailed as a missing link and one of the most important fossils ever made and it was very impressive and it looked very nice but subsequently some people have been suggesting that may be it was not quite as big a deal as was made out at that time.

Kerri Smith: But it was nonetheless a complete and a very beautiful fossil. And Ardi was the second of these fossils that we were excited about this year.

Daniel Cressey: That is right, it has been a good year for fossils of primates and people who like to throw words like missing link around. Now the second one of these fossils was arguably more impressive and more important and it is probably going to be of great interest to people writing textbooks in future.

Kerri Smith: So Ardi is likely to make it into the textbooks, just clarify for us exactly what is so important about this fossil?

Daniel Cressey: Well, Ardi is likely to be a human ancestor and it is older than Lucy which has been one of the kind of keystone fossil so far. Well, follow-up research showed that Ida probably was not a human ancestor.

Kerri Smith: All right, so that was 2009 all wrapped up and as we prepare to wrap some presents under the tree, let us think about what might happen next year. What are your predictions Geoff?

Geoff Brumfiel: Well, next year NASA will stop flying the space shuttle and the US will stop having access to space, I mean, this is a pretty big deal, I should say access to man space flight. Of course, yes, astronauts will continue to fly on Russian vehicles but there would be no follow-on for several years to come if at all and I think that is a pretty big development in the world of space.

Kerri Smith: But it is not the end of I suppose what we might still call the space race, I mean, other countries are jumping to the fore.

Geoff Brumfiel: Other countries, yes, but actually I think what is interesting is private companies are jumping to the fore. We have Virgin Galactic which is going to be flying its spacecraft in 2010, it is a suborbital craft but nonetheless that is a big step and there is a pretty good chance that SpaceX, a California based company is going to fly a large vehicle called Falcon 9 that could potentially end up carrying US astronauts to the space stations, so this could be the start of private space.

Kerri Smith: So all I have to do is round up my 200,000 dollars and I can be part of this endeavour.

Geoff Brumfiel: That is right!

Kerri Smith: And Dan, any favourite predictions for next year?

Daniel Cressey: Well, I would think that the two biggest stories of this year will continue to roll on into next year which is swine flu, it is going to continue at a rather low level and then will either have to deal with the fact that it has got really nasty or that a lot of people got it wrong and predicted it was going to be nastier than it was. We will also going to see an increasingly shrill debate over climate change and possibly with what some might consider the failure of an international agreement in Copenhagen may be, hopefully will see more countries being willing to go alone and unilaterally decide they are going to take action.

Kerri Smith: Okay and on that optimistic note thanks guys for coming in.

Adam Rutherford: That is all from us in 2009. Join us in the New Year with all the biggest, best and bold busting science from Nature and beyond with all the shenanigans from your team of dedicated pod people. You have been listening to the Nature podcast produced as ever by Charlotte Stoddart, I am Adam Rutherford.

Kerri Smith: And I am Kerri Smith. Happy holidays science fans.