Class Supplement, Nature Podcast Digest Mar 8 2012

The original script of this podcast: http://www.nature.com/nature/podcast/v483/n7388/nature-2012-03-08.html
The audio file of this podcast: http://www.nature.com/nature/podcast/archive.html


ゴリラはチンパンジーの次にヒトに近い。ヒトとチンパンジーの分岐（６百万年前）より４百万年前に分岐。ゲノムの３０％はヒトゲノムに近く、耳の形状と聴覚がヒトに似ている。また、種が分岐しても異種交配が起こることや、ヒトの影響を受ける以前から絶滅の危機にひんしていたことが分かっている。
Kerri Smith: Why is that important to have the gorilla as well as these other primate species then?

Magdalena Skipper: Our closest relative is of course the chimp. The gorilla is our second closest relative and we are sort of interested to know how we have evolved, how the evolution within the great apes has progressed and with every genome sequence available we're discovering more and more information, which we can compare, understand the tempo of evolution, down each of the branches of the evolutionary tree.

Magdalena Skipper: Now we can say, with quite some certainty that the chimp-human splits occurred about six million years ago and the chimp-gorilla-human about 10 million years ago. The dates themselves are not hugely different from what some other previous estimates have told us, although they push the date further back in time. What's interesting that it really is for the first time that the genetic evidence is in line with the ecological evidence there that we have found.

Magdalena Skipper: So, 30% of our genome, we're actually more similar to the gorilla than we are to the chimp. Most of these similarities lie outside the protein coding genes. You might think then that's not so important therefore, but actually it is very important because that 30% encompasses a lot of gene regulation. In other words, it's how the genes are expressed.

Magdalena Skipper: There are two notable things. So, one evolution of genes that are involved in perception; in this particular case, it's auditory perception. So, it turns out that the genes which are involved in hearing are accelerated and down the gorilla lineage, but also down the human lineage. What is also quite interesting is many of these genes, when mutated in a human, are involved in hearing associated diseases. These are quite crucial genes. Another interesting thing yet is that when you talk about the morphology of the gorilla and the human, we might indeed not look very much alike, but actually the external morphology of the ear is very, very similar between gorilla and the humans.

Magdalena Skipper: There are a number of interesting insights that emerge from this analysis. One for example is that they're able to estimate the timing for the split between these two species. They're considered to be separate species, not just separate populations and that is estimated to have happened around 1.75 million years ago. The other interesting insight is that although that's when the timing of speciation can be pulled back to, it is clear that that's not when interbreeding stopped between these species. So that's a view that's emerging from a few similar comparisons of species that there is rarely a very clear-cut species break that those individuals continue to interbreed. And the final insight in particularly from eastern gorillas which live in smaller populations, perhaps not surprisingly, they also have less genetic variation and this is a message for conservationist.

Kerri Smith: So thank you to Magdalena and to hear more about how the gorilla genome might influence conservation, we're joined by Harry Marshall, a primate researcher based here at Zoological Society of London and at Imperial College. Harry how are gorillas doing in general, I mean, they're on an endangered list right?

Harry Marshall: They are. Well, for example, these guys are part of the western gorillas and this paper has shown us that the western gorillas have potentially had quite a low population for many millennia, so well, well before humans really turned up and had an influence.

過去７年間、各地に大地震が連発。頻度は過去１１０年間の２．５倍。大地震が連鎖することや、従来のモデルを超える要因の存在が分かってきている。３．１１は大地震のかつてない綿密な記録を残した。正確な予知は無理だが警報システムは更なる改善が期待できる。
Geoff Marsh: In the last 7 years that earth has been repeatedly shaken by earthquakes of unusually massive magnitudes, there was this Sumatra earthquake in 2004, which triggered similar events nearby in 2005 and 2007. Next was Chile's great quake in 2010 and a year ago this week, the devastating earthquake and tsunami which hit northeast Japan. These events are providing humbling lessons writes geophysicist, Thorne Lay in a comment piece for Nature this week. Charlotte Stoddart called Thorne at the University of California, Santa Cruz to hear about how these mega quakes are shaking up seismology. Nature 483, 149–150 (08 March 2012); Nature 483, 147–148 (08 March 2012)

Thorne Lay: Well, it seems that way because there is an unusual concentration of activity for the past seven years and many of those events have been in the headlines. So, people are aware of them and relative to kind of the long-term behaviour of big earthquakes, they have been happening about two and half times of the frequency that we had experienced over the previous 110 years.

Thorne Lay: We're certainly learning about the nature of interactions between earthquakes and how one giant earthquake can change the stress in the rock and produce the conditions for subsequent giant earthquakes and that has happened in several configurations that sometimes surprised us to where the big earthquakes would occur and how quickly they could trigger adjacent activity. So, each of them has been a learning experience.

Thorne Lay: Well, in a general sense we understand what causes earthquakes but the precise locations and the environments in which the earth can produce really huge earthquakes has been expanded by the recent occurrences. They've happened in places where we didn't fully expect them based on earlier ideas that had evolved when we were just developing the ideas of plate tectonics. So, we now recognize they can happen a bit more extensively in the plate boundaries than we had thought.

Thorne Lay: Well, the Japan earthquake a year ago was certainly the best recorded earthquake ever for a giant earthquake because of the huge number of instruments that the Japanese had deployed around their country. So by studying the processes prior to the earthquake there were very active foreshock behaviour for two months in advance of the earthquake and apparent migration of slow sliding as part of the fault toward the area that initially ruptured for the big earthquake and then studying the broad region and the extensive aftershocks that occurred around the fault after it occurred. All those aspects are better constrained than we've ever been able to do before because of the tremendous instrumentation available in Japan.

Thorne Lay: Fairly little progress has been made toward earthquake prediction per se, but what we're getting much better out is quickly after an earthquake begins to get warning about shaking, to get warning about tsunami that might be excited. So for the great earthquake in Japan we did have early warning of the tsunami and the methods could have been more robust than they were and they could have anticipated the size of tsunami better but today I think we would be able to do much better.

震災後の再建が遅れている理由：　がれき処理、再建関連の規制・費用、政府と民間の考え方の違い。津波の記憶保持の努力と困難。
There are several reasons for the delay and rebuilding. Government restrictions and payment for building contracts scare construction companies away. And there is a lot of mess to be cleaned up before building can even start, 22000 tons of debris which will take three years to clear and even when that's out of the way, it won't necessarily mean full steam ahead. Proposals on how to rebuild offered by the central or local governments don't always match with what people want. Governments want to rebuild sea walls, replant tsunami control forests and raise roads as embankments to keep tsunamis at bay, but this time the walls and the forests largely failed. Engineers are confident that they can build them better even to withstand the most massive potential tsunami. But that is neither economically feasible nor desirable for those who appreciate their sea views. And this is is instead is placed on softer solutions, meant to keep people out of harms way. New zoning laws for example prevents schools, hospitals and houses from being built in areas that might get thrashed in a tsunami. But city officials are having a difficult time explaining to people that they can't build a house on their property because a massive tsunami might come in a thousand years time. Perhaps that's understandable. That is the distant future after all, meanwhile some lessons on tsunami planning could be learned from the distant past. Towns throughout Japan have memorial stones or shrines 200 or 300 years old showing the record of inundation of past tsunami and learning to people not to live any closer to the coast. Sendai has one too. It sits in a busy residential area that adjoins other neighbourhoods stretching all the way to the sea. A new research centre is putting together a hi-tech version. A database of images showing what the area look like at the time of the recent disaster. Let's hope this hi-tech memorial map does its job reminding people what disaster might befall them but behind the hope invested in the new plans, I suspect and many of the town planners and scientists seem to suspect as well that there will always be people who ignore warnings and end up scampering up muddy embankments at the last minute.

忘れるのにはエネルギーがいる。【メモリー消去時に消費するエネルギー　＞　得られるエネルギー】が実験で示された。これにより、　１）思考実験マックスウェルの魔物は熱力学の第２法則（エネルギーを増やすにはエネルギーを消費しなければならない）に反しない（仕事をせずにエネルギー大の原子ばかりを集めることはできても、原子選別関連の古い記憶を消す際にエネルギーを使ってしまうので、エントロピー（エネルギー減少の方向性）には勝てない）ということが証明された。　２）　この最小限の熱放出がコンピュータ小型化の限界となることが分かる。
Geoff Brumfiel: Imagine two boxes with gas molecules bumping around inside and they're connected by a little door and atop this door sits a mischievous demon who can open and close it at will, now this little demon, he sees exactly what the gas molecules are doing inside the box and so it's not too hard maybe to imagine that by opening the door just the right time he can let the fast moving molecules fly into one box and the slow moving molecules creep into the other and eventually you could imagine a box that sort of full of very hot fast moving gas on one side and very cold slow moving gas on the other.

Kerri Smith: Okay, I can imagine that but it sounds like quite a lot of work just to separate a gas.

Geoff Brumfiel: Well, actually in the funny world of theoretical physics it's not. The physicist James Clerk Maxwell came up with this imaginary demon in the mid 1800s and according to his calculations manipulating that door very, very carefully would allow the devil to separate the gas without doing any work and that would violate the second law of thermodynamics, which as I am sure you remember, is that rule that says you got to do work if you want to go against entropy.

Geoff Brumfiel: Yeah, and Maxwell's demon really bothered physicists for decades until a guy named Landauer came along and he figured out that to really understand this experiment you have to look inside the demon's head. It turns out that the demon does the work by measuring all these little gas molecules and sort of recording in its mind where they are and where they're going. For various abstruse mathematical reasons, the work is actually done when the information is erased when the demon raises its knowledge and replaces it with new knowledge in the molecules but it doesn't really matter. This Landauer limit is the minimal amount of heat you need to erase information in a computer or in this case the demon's brain and it's always greater than whatever work you can extract by separating the gas. So, basically this means you can't build a perpetual motion machine using a clever computer or demon. Now the thing is that the Landauer limit has never been tested because the amount of heat you need to erase information is very small that is until now. Eric Lutz a physicist at the University of Augsburg in Germany has measured this limit for the very first time.

Geoff Brumfiel: And that's exactly what you have done right; you've managed to create a single particle test of Landauer principle. In this case we should say you're using a glass bead and the trick is to be able to measure exactly how much heat it took to make that move. So how are you able to do that?

Eric Lutz: We do not actually measure the heat, we measure the trajectory of the particle by using some camera that follows the dynamics of the glass bead and from the knowledge of the trajectory meaning the position of the particle we will have each time we can actually calculate the heat. The only thing we actually have to do is to photo this position of the particle while you manipulate to trap and what we did was to show that this heat is always larger than the Landauer bound and that's for very long erasure cycles we do approach the Landauer limit but we never exceeded confirming the initial prediction by Landauer.

Geoff Brumfiel: Right, so this is the first time that anyone has actually ever been able to show the heat that it takes to erase information, I guess first of all it shows that the second law of thermodynamics holds.

Eric Lutz: I would say that the Landauer's principle is important for two main reasons, the first reason, the fundamental reason and this is indeed the fact that the Maxwell's demon does not violate the second law of thermodynamics. The second reason is more practical and is linked to miniaturization process in the computer industry. When chips are getting smaller and smaller and when you try to dissipate less and less heat while doing some binary calculations , logical calculations and the limit actually today is about the actual dissipation right today by the factor of one thousand above the Landauer limit but decreases by the factor of two every five years. So people predict that in the next twenty to thirty years this Landauer bound might actually be achieved or attained and the Landauer bound is the fundamental limit and you cannot go below that. So once you reach it you have a problem, you can't continue building smaller and smaller chips. This is one of the main factors limiting this miniaturization process.

規模が世界第２位のアルバータ油田は、今後１０年間原油採掘が続くが、既に中規模都市か大規模火力発電所相当の汚染が確認されている。
Corie Lok: The oil sands in Alberta, Canada are the second largest crude oil reserves in the world. Extracting the oil from the sand, clay and water it's mixed with requires mining and other methods. So researchers took a look at the air pollution generated by oil sands operations. They analyzed satellite data and found high atmospheric levels of two major pollutants, nitrogen dioxide and sulphur dioxide. The amount of pollution was comparable to what you would find over mid size cities or near large coal burning power plants. We at Nature like this paper because it's one of the first to assess air quality over the Canadian oil sands where production is expected to grow over the next decade. The study was published in the Journal Geophysical Research Letters. Nature 483, 126 (08 March 2012)

ＨＩＶウイルスに破壊される前にＣＤ４Ｔ細胞が感染した細胞を破壊しようとする段階がある。これはＡＩＤＳ進行の目安になる。
Moving on to the topic of Immunology here's an interesting story that I like to call, kill or be killed. That's the challenge that a type of immune cell faces when confronted with HIV. This virus infects and destroys mainly this group of cells called CD4 T cells. But new research shows that these cells can also directly kill infected cells in the earlier states of the disease. Researchers took a look at the responses of these T-cells in patients who had just been diagnosed but had not yet begun treatment. After following these patients for a year, the scientists found that some of the patients had lower viral loads than the others. These patients also had more of the CD4 T cells and a greater proportion of these cells made proteins that kill other cells. This was an interesting paper to us because it suggests that doctors might be able to predict how HIV infection will progress in a patient by measuring the responses of their T cells early on. The paper can be found in the Journal Science Translational Medicine. Nature 483, 126 (08 March 2012)

福島第１原発は、１２月以降原子炉が１００度を下回り安定している（２０１２年３月８日現在の報道）一方でまた大地震が起こる可能性もある。炉心溶融から１年たち、環境への影響はチェルノブイリ程ではないと言われているが、政府への不信感が大きな傷跡として残っている。避難命令の出た地域の放射能レベルは２０ミリシーベルトでがん発病の可能性は非常に低い数値であり、従来から人口の４０％が癌を発病するので原発事故が原因かどうか特定するのは難しい。帰宅はできても米作は風評の問題がある。政府の対応は問題もあったが及第と言える点もある。
Geoff Brumfiel: Well, the situation at the plant has in many ways changed and in some ways it's still very much the same one year later, as you recall a year ago a tsunami struck the plant and it triggered meltdowns in three reactors there. And initially there was basically a rush to cool the reactors by any means necessary, they were flooded with sea water and boric acid to try and stop any further meltdowns. And subsequently that sea water was replaced by fresh water and the reactors were somewhat stabilized. And really since about September not much has changed. The reactors continued to be flooded with fresh water that is recycled and put back in and they'd been growing gradually cooler and so in December they dropped below a 100 degrees Centigrade which means that they've now officially reached what they call a cold shutdown condition. This just basically means it's slightly less dangerous than it was before. However risks remain in the plant, the big one is that an earthquake could strike again and could cause more leaks or further discharges of radioactivity. So, the situation is fragile but stable and it's likely to remain this way possibly for a few years to come until the radioactivity is cooled still further.

Geoff Brumfiel: The human impact I think is really in many ways the most important part of this disaster. I spoke to a lot of scientists who were studying the environmental fallout and the various contamination issues and the consensus seems to be that in the area around the plant it's very serious but further away it appears that a lot of the radioactivity has been dispersed and the environmental impact long term is not going to be as bad as say Chernobyl. The psychological impact, the human impact on the other hand is very real and very present for the people of Japan. Over a 100,000 people have voluntarily evacuated or been forced to leave their homes as a result of the accident and many of those people have not yet returned home. They're living in temporary housing and they're really living in a state of constant fear. They are afraid of radiation which they can't see or taste or touch and obviously that leads to a lot of paranoia.

Geoff Brumfiel: Yeah, I did some reporting with Ichiko Fuyuno, who is a Japanese speaker and she talked to a lot of people who are working in the Fukushima area. What she found was that people are deeply, deeply mistrustful of the government. The government has been slow to respond to the crisis in certain ways, they've delivered inconsistent information. They've upped the radiation limits and people just don't believe them anymore. They think that anything that involves the government is a lie , probably covering up some greater health hazard that Fukushima poses. What is interesting is the independent scientists I spoke to from the International community really don't think that's the case and some of them are looking quite hard at this through an UN organization. They believe that actually today the information the government releases is pretty good but clearly the trust has been lost.

Geoff Brumfiel: Well, that's a very good question. Our current understanding of the situation is that in most parts of the evacuation zone, residents that have moved back would probably receive below 20 millisievert of radiation a year. Now 20 millisievert is a fair bit, there's no reason to deny that but it's well below the 100 millisievert level that most people link to a slight, a very slight increase in the chances of getting cancer later in life. So, for the most part and I should say that you know low dose radiation science is not a 100% clear because 40% of the population gets cancer anyway, so you know it's very hard to tell, if these low doses increase that risk. But with what we know it's probably pretty safe for people to move back into that area. You know, whether they could continue doing the things that they were doing, Fukushima was a major centre for rice production, even though the radiation levels are relatively low and the contamination levels are going to be relatively low in rice, they'll still be detectable if anyone really going to buy radioactive rice.

Geoff Brumfiel: Well, we have a leader in Nature this week that sort of goes into this a little bit and I think the first thing to say is that whenever you have a catastrophe of this magnitude it's easy to point a finger. And in the case of the tsunami, the earthquake tsunami and subsequent meltdown, there's plenty of finger pointing that's going on in the past year. That being said there are things that the Japanese government got right. It did have advanced tsunami warning systems, so warning did not work as well as they could have but they did work and they probably saved lives. Similarly the response to Fukushima, the nuclear crisis, left a lot to be desired but at the end of the day they did manage to evacuate nearly everyone in very short time and the health studies we have today seem to indicate that almost no one received a significant dose of radiation. So it's really a mixed bag.