Class Supplement, Nature Podcast Digest Mar 1 2012

The original script of this podcast: http://www.nature.com/nature/podcast/v483/n7387/nature-2012-03-01.html
The audio file of this podcast: http://www.nature.com/nature/podcast/archive.html


医者兼物理学者で博学なトマス・ヤングはロゼッタストーン解読の突破口を開いた（アルファベットとしての絵文字の使用法に気付いた）人物でもあった。
Andrew Robinson: Well, that was based on the oval shapes in the hieroglyphic script known as cartouche, and people had suggested well may be it's the name of a king, or maybe it's the name of a God and that was one suggestion and that turned out to be right. Then somebody else said well, maybe therefore it's not written in the normal Egyptian hieroglyphic script that nobody can understand maybe it's written in an alphabet and that sounds a bit odd but the fact is all languages write foreign names differently and that was really the key that you could match the hieroglyphs symbols inside a cartouche, with a name of a Greek king, in this case Ptolemy who was king of Egypt at that time of Rosetta stone and the Rosetta stone is in fact about Ptolemy, it's about his carnation.

Kerri Smith: You're arguing that a helping hand was given to Champollion in the form of Thomas Young.

Andrew Robinson: Well, yes Thomas Young started the process and Champollion for various reasons was never really willing to admit that and the reason is of course that the first steps are the hardest in really any problem any scientific problem and though therefore the inventor doesn't really want to concede that it was the credit for the first steps even if everything else was done by him and in fact in Champollion's case he did do pretty well everything except the Crucial opening idea of the cartouche being spelt as an alphabet which was really Young's contribution and he was the one who first with the concept of a hieroglyphic “alphabet” and Champollion took that idea without much credit from Young.

人口分布が分かれば通勤等による人の流れを予測できることが分かった。これは都市部ほど近場に通勤する人が多くなるため。事例別の変数が複数含まれる従来の計算法、重力モデル（都市を天体、人を物体に見立てて計算）より普遍性があり正確。
Geoff Marsh: When you're packed on to a train platform or stuck in a traffic jam it's hard not to wonder where on earth everyone could possibly be heading. Our next guest may have the answer. Filippo Simini of North-eastern University in Boston and his team have come up with a new way of predicting large scale mobility patterns. To determine where people are going it turns out that all you need to know is how they are first spread out. Ewen Callaway who does his commuting by bicycle gave Filippo a call. Nature (2012)

Ewen Callaway: Why would we want to be able to know where people are going to go?

Filippo Simini: Yeah, I think this is a fascinating problem. There are many phenomena of major societal and scientific interest that are affected by the mobility patterns of a large number of individuals. The accuracy at predicting the number of travellers or commuters between two locations like two cities or counties is of primary importance when it comes to the design of a convenient and efficient transportation system and its poor or high quality has the potential to hamper or enhance a country's economy.

Filippo Simini: So, at first our go was to have a model to predict commuting trips; so we started by trying to imagine how people would look for a new job. In fact while the home to work trip is a daily process it is determined by a one time choice which is the job selection. The main idea behind our model is that an individual would accept a closer job with a better pay. What we found is that the salary distribution and the density of job offers do not affect the trip distribution, whereas the population distribution is what ended up being the most important factor. Since the only needed information is the population density, our model is parameter free opposed to the gravity law that usually contains from 3 to 9 parameters and this means that our radiation model is a universal formula that can be applied to regions without the need for previous traffic data.

Ewen Callaway: So, does this mean that all you have to know is how people are spread around to predict where they're going to go?

Filippo Simini: Yes, the population density is related to the number of employment opportunities you will find, so if you live in a highly populated area you would probably find a good job closer to home, while if you live in a low populated area you will have to travel farther to find comparable employment opportunities.


昨年まで14年間続いた南西オーストラリアの干ばつは同地域だけでなく、北西部の干ばつと連動して過去8年間オーストラリア全土に干ばつを起こしていた可能性がある。
Corie Lok: Southeast Australia was devastated by a 14-year long drought that ended just last year. It turns out though that the drought affected not just this region but the entire continent during most of this period. Researchers found evidence of decreased rainfall, water storage and plant growth throughout the country between 2002 and 2010. They linked the drought in the southeast to irregular patterns in Indian Ocean circulation but in the northwest the drought there was associated with reduced tropical cyclone activity. The author suggests that distinct climatic factors can combine to create a continental scale drought. The research was published in the Journal Geophysical Research Letters. Nature 483, 8 (01 March 2012).

日本の蚊がわずか20年でアメリカ全土に適応。冬の開始時期の変動に素早く適応したため。
And from the world of Evolutionary Biology comes this paper from the Journal American Naturalist about the Asian tiger mosquito. This aggressive biter arrived in the United States in 1985 on a shipment of used tires from Japan and has since spread across much of the eastern part of the country. Biologists have found that in just 20 years the insect has quickly adapted to differences in the timing of winter onset from Florida in the South all the way north to New Jersey. This adaptation was among the fastest documented in nature. Other traits such as body size did not appear to be evolving during this time suggesting that in the changing climate animals evolved mainly by adapting to changes in seasonal shifts. Nature 483, 8-9 (01 March 2012)

通常ありえない速さで重度の遺伝子異常障害の特定・治療を可能にしたのは、研究所と同じ検査機器のある病院と、遺伝関連の同じ症例を見つけやすいアーミッシュ社会だった。地域に即した医療のモデルとしても参考になる。（アーミッシュ：　18世紀初頭とほぼ変わらない生活を続けるキリスト教徒の一派で近親者同志が比較的近距離で生活している。共同体の結束強化に役立つ場合に限り科学技術を歓迎する。）
Geoff Marsh: Tests eventually gave a tentative diagnosis, a genetic disorder called SCID, severe combined immunodeficiency, but pending further tests Raylon again was sent home with his parents. At the end of his tether Leon contacted Kevin Strauss a paediatrician at the clinic for special children in Strasburg Pennsylvania.

Trisha Gura: What the clinic does is in beds in the middle of a cornfield all the high tech tools of genomics and it actually puts them to work in real everyday clinical care.

Trisha Gura: The two doctors of the clinic start with the genetic diagnosis of DNA sample that they used at lab to try to come up with a diagnosis but they keep ongoing trying to find any sort of a cure or treatment that will help these kids. It is probably the only clinic in the world that has both a hitching post and an Ion Torrent sequencer and the clinic uses both because the Amish and Mennonite, many of them eschew technology such as cars or cell phones and drive horses and buggies.

Geoff Marsh: Strauss immediately set about organising a bone marrow transplant for Raylon but it's all came too late and he passed away just over six months of age. Then in 2011 the Hoover family had another child Kendra and the nightmare seemed to be recurring.

Leon Hoover: So, I called Kevin back and I really think we have a SCID baby. He said well come on Leon whatever we can, we will have to, do this together, when he said we'll have to do this together it did really matter.

Geoff Marsh: So with Kendra there was much more rapid response which meant that she was able to be diagnosed and treated very quickly. Why was this clinic especially placed to do that?

Trisha Gura: Kendra was diagnosed within 12 hours of birth, within another 24 hours Kevin Strauss was in the car in order to find a bone marrow donor from 16 relatives. They had a match within 48 hours and Kendra received her bone marrow transplant within 16 days of birth that is completely unheard of in a regular traditional medical system.

Geoff Marsh: And let's just expand on how this clinic does differ from the normal model of genomic medicine.
Trisha Gura: More often than not genomics tools reside in a laboratory. Laboratories are not allowed to do work for clinic unless they have special clearance and so it takes a long time to get these sorts of diagnoses and often the only way one can do so is that the patient is involved in a research study. This clinic is with beds in it, its laboratory so therefore Dr.

Strauss or Dr. Puffenberger can order a test in the same way that a regular physician could order a cholesterol test.

Trisha Gura: Mennonites and Amish are almost a throw back, they immigrated here at the beginning of the 18th century. They were a small group of founder families, so families know of each other so when a child comes into the clinic with a specific illness and no one knows what it is, more often than not there is another family residing somewhere nearby that everybody knows about with the same disease and that sort of connection helps the researchers out immensely when they're trying to hunt down the causes for various illnesses.

Geoff Marsh: Does it all seem a bit strange to you that these you know essentially technology shunning people are embracing these very high-tech facilities.

Trisha Gura: One would thinks so but if it's something that separates or divides from each other like a television set or a cell phone then the communities or the churches tend to shoo the technology but if it's something that brings them together like medical technology that helps children then the communities unanimously embrace it.

Geoff Marsh: Does it serve as a model for you know places outside of these communities or is this community really very unique?

Trisha Gura: It depends on who you talk to, but the community can be a model for clinics elsewhere for a lot of reasons. The main one is there is no such thing as one general population. It's actually sub population of different groups so if you're dealing with these sub populations then the clinic provides a better smaller model of what genetics might be rather than trying to look at the whole world as one general population and then sort to the genes that way.

知られている中では最古の森林跡は3億８千万年前のものでＮＹ州にある。大きな竹か木生シダの様な「木」（木質無し）や巨大なツタ類で裸子植物の祖とつながる植物が茂っていた。当時の生態系が分かるだけでなく、（現在の生態系よりも単純なので）生態系自体の理解に役立つ。
Kerri Smith: But this week we've got fossil trees. A whole forest of in fact because researchers have uncovered over a thousand square meters of ancient forest floor at Riverside Quarry near Gilboa in New York State. Some years ago researchers excavating this site found specimens that turned out to be the oldest known trees on Earth and now they've gone back and found a whole lot more. When these trees were alive 380 million years ago, plants were relatively new on land and the only animals crawling around were arthropods.

William Stein: For the first time in my career I was able to actually walk an ancient forest floor. I know many of the players, many of the actual individual members of this flora to some extent, it's a very long time ago and they're very different than today, but actually walk that floor and see the spacing of the trees, see the fact that the trees were different in size indicating presumably different aged trees, saying that they were actually part of a community that consisted of not just one type of tree but three and it was just a big thrill.

William Stein: In the Devonian we are seeing at the very beginning our plant forms and plant architecture on land. They start out as being extremely small moss-like plants and by the end of the Devonian we actually have the establishment of forests of modern scale. In the middle of the Devonian which is where the river side quarry site resides in time we see the very beginning of trees like forms, however they're not related to modern trees at all. The largest of the trees is Eospermatopteris. These plants were bamboo like perhaps hollow weedy, they did not have wood. They had an overall form that was perhaps very much like a tree-fern or a modern palm but they were not anywhere closely related. They are kind of like dinosaurs of that period. So, very different and perhaps related to more modern forms but they were much more primitive and quite a larger.

William Stein: Very interesting period. You know this is Eospermatopteris we have the oldest evidence we found of plants that actually aren't woody. They are not the trees and not the largest of the trees of that site, but they seem to have the most amount of tissues.

Charlotte Stoddart: The other thing that I read in your paper is that you found a gigantic creeping plant.

William Stein: We found a creeping plant say they are like large vine-like plants or perhaps ground running fern like things, perhaps climbing up onto the top of these trees. They came as a big surprise. We didn't have any idea that there will be a plant of that type at this locality. Equally a big surprise is the fact that we were able to identify them belonging to an early progymnosperm group which is the ancestor of the sea plant assemblies that dominate modern landscapes.

William Stein: The most important thing that's emerging from this is the fact that we now can study ancient ecology and we can now not just talk about the systematics and relationships of individual groups or individual species but we can now talk about how ecosystems became established in land and this is very important for we're going to ever understand how ecosystems work, and one thing is nice about this early forms is that the plants, plant morphology is not that complicated yet plant ecology is probably nowhere near complicated as modern systems. We have a real opportunity to actually understand the assemblage of our forest systems.

患者の幹細胞に手を加えて本人の体内に戻す治療（無認可）に中止命令。
Mark Peplow: We've been looking closely at a company called Celltex which is based in Texas, it's a very young company and it's a company which has benefited from a huge infusion of cash in the state to try and push forward the development of adult stem cell treatment but in the state of Texas doctors are sort of leaping ahead if you like and actually administering these treatments before they've gone through all the usual clinical trials that one would expect to prove that they work.

Kerri Smith: So, let's just talk a little bit more about what Celltex are doing and let's be clear we're not talking here about embryonic stem cells. These are adult stem cells.

Mark Peplow: Well, Celltex says that it multiplies and banks stem cells that are derived from people's abdominal fat and that its official line on this and if that was it was doing then that will be absolutely fine but Nature has uncovered a number of different lines of evidence suggesting that it is involved with the clinical use of the cells in Texas which in other cases of other companies the FDA has viewed as illegal. The FDA in 2010 ordered a company called Regenerative Sciences in Colorado to stop administering the very same sort of cells to patients arguing that they haven't authorized their use. The company and FDA are now involved in a legal dispute over that.

Kerri Smith: So, it's fine to bank them and you can get Celltex your cells if you like and pay them to keep hold of them but as far as the FDA, the Food and Drug Administration are concerned it's not okay to actually do anything medical with these.

Mark Peplow: Yeah that's right. Because they're unproven treatments. We don't really understand the implications for their safety. Certainly don't know about their efficacy. It seems certainly all the researchers that we contacted far too soon in the developments of these therapies to be charging patients up to 25000 dollars to undergo a series of injections of these sorts of cells to treat their conditions.

Kerri Smith: What kinds of conditions?

Mark Peplow: Well, we spoke to a doctor called Jamshid Lotfi who Celltex pays to inject cells into patients cells that have been cultured and expanded in number at Celltex and he says that he has administered these cells to more than 20 patients, some patients have multiple sclerosis, some have Parkinson's disease and he also mentioned Alzheimer's disease, so those sorts of things.

Kerri Smith: The company Regenerative Science that you mentioned in Colorado was stopped from doing this, what's going to happen with Celltex.

Mark Peplow: Well we don't know and the FDA won't comment on future or ongoing cases of these kinds, so we don't know. At the moment Texas Medical Board which recollects physicians in the state is aware that those growing concern about doctors administering these procedures and earlier this month drafted rules that were trying to increase the oversight on physicians, those rules stipulated that physicians have to get approval from an independent review committee before choosing patient and they're expected to become a law in April.

Kerri Smith: But in all of these proposed treatments basically what's happening is you're just injecting someone's own cells back into them so it's not a drug, right?

Mark Peplow: Well that's what lot of advocates of the treatments argue that if you're just re-injecting a patient's' own cells that shouldn't be a drug, it's little more than a skin graft for example, it doesn't fall under the FDA's jurisdiction. Now the FDA argues that any cells that have been more than minimally manipulated, that is the phrase that they use does fall in to their jurisdiction, because you're not just re-injecting the patient's cell, you know, you're doing stuff to them in the lab and then putting them back so it's clearly not the direct replacement. In Celltex 's case they take a sample of about 100,000 of a patient's stem cells and culture them over them about three weeks to produce 800 million cells and those are then injected back into the patient in batches of about 200 millions cells at a time.