【Native Speaker每日综合训练—43系列】【43-16】科技 Evolution

伊蔓达

内容：伊蔓达 编辑：伊蔓达

Stay tuned to our latest post! Follow us here ---> http://weibo.com/u/3476904471

今天的主题讲与Human Evolution有关的一些发现，比如生活在青藏高原(Tibetan Plateau)的人是如何进化出对高海拔氧气稀薄地区的耐受能力，再比如人类基因测序，Illumina公司声称人类基因组测序的成本已经降到了约1000美元，是真的吗？
Please enjoy and have fun~

Part I: Speaker

Polar Bear Rapid Evolution Lets Them Be Fat Fit
May 22, 2014 |By Karen Hopkin  

A triple bacon cheeseburger seems like a heart attack on a plate. So how can polar bears thrive on their version, seal blubber? Turns out they’ve stocked up on genes that let them clear fats from their blood. That’s according to a study in the journal Cell. [Shiping Liu et al, Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears]

Polar bears are well adapted to life on the sea ice. Up to half their body weight’s fat, which gives them extra insulation and buoyancy, and provides them with a ready source of energy.

But how can an animal so fat also be so fit? Researchers compared the genomes of polar bears with those of brown bears, and found that polar bears have accumulated genetic changes that boost their heart health and fat metabolism. One gene in particular, called ApoB, helps move cholesterol out of the blood—where it causes problems in humans—and into cells.

These genomic changes happened quickly, evolutionarily speaking. Polar bears and brown bears diverged from a common ancestor less than half a million years ago. But if that seems super speedy, the ability to digest lactose didn’t spread through human populations until we domesticated cows, just 10,000 years ago. A moooving testament to the power of natural selection.

Source: Scientific America
http://www.scientificamerican.com/podcast/episode/polar-bear-rapid-evolution/

[Rephrase 1, 01:16]

伊蔓达

Part II: Speed

Human or Hobbit?
The arguments over an ancient skeleton just won’t die
Oct 14, 2014 |By Kate Wong

[Time 2]
Old debates die hard in the study of human origins. In October 2004 paleoanthropologists announced the discovery of a new human species that lived as recently as 17,000 years ago on the Indonesian island of Flores. Homo floresiensis, also known as the hobbit, was an overnight sensation. Just over a meter tall, with a brain a third the size of our own, the creature was in many ways as primitive as our 3.2-million-year-old relative, Lucy. Yet it was a contemporary of Homo sapiens and apparently made relatively advanced stone tools and hunted large animals — activities associated with brainier humans. Noting the conflicting observations, skeptics immediately countered that the bones belonged to a diseased H. sapiens individual, not a new species. And so began a battle over bones that continues to this day.

The latest attack comes from some of those same doubters. In a paper published in August in the Proceedings of the National Academy of Sciences USA, Maciej Henneberg of the University of Adelaide in South Australia and his colleagues argue that the bones of the most complete individual from the site, known as LB1, exhibit features indicative of Down syndrome. They base their argument on the small circumference of LB1’s skull, among other traits.

Hobbit team members have been quick to reject the Down syndrome claim. William Jungers of Stony Brook University notes that there is no known case of Down syndrome (ancient or modern) in which an individual had a head circumference as small as LB1’s. Nor do people with Down syndrome share LB1’s other distinctive features, such as her projecting midface and thick braincase walls.

Still, even if the new work does not prove that LB1 had Down syndrome, the possibility remains that she suffered from some other pathology that produced her strange features. Biological anthropologist Thomas Schoenemann of Indiana University Bloomington, who studies brain evolution, notes that proponents of H. floresiensis have insisted that scientists treat LB1 as representative of a new species unless a specific developmental anomaly can be matched to it. But that position “is simply not reasonable, given how odd [LB1] is with respect to the rest of the [human] fossil record,” he says. “What we really need are more specimens and some trail of fossils that shows us how LB1 got to Flores” while retaining characteristics of australopithecines for more than a million years, Schoenemann observes. Ongoing excavation of the Flores site has yet to yield more small skulls.
[429 words]

Source: Science American
http://www.scientificamerican.com/article/human-or-hobbit/

With Help From Extinct Humans, Tibetans Adapted To High Altitude
July 02, 2014 |By Rae Ellen Bichell

[Time 3]
At an altitude of nearly 3 miles, the Tibetan plateau is an extreme place to live. It's cold, it's hard to grow food, and there's about 40 percent less oxygen in the air than there is at sea level.
Somehow, though, native Tibetans are adapted to it. Their bodies — and their blood in particular — work differently than those of people used to lower altitudes. The Tibetans' advantage might be thanks to an ancient inheritance.

When someone used to living at low altitude travels to the oxygen-deprived Tibetan plateau, his or her body responds by producing more red blood cells to help circulate oxygen through the body.

Sounds like a good thing, right? Not quite.

"You don't want your blood to become too thick," says Rasmus Nielsen, a geneticist at University of California, Berkeley. Too many red blood cells can lead to thick blood that is harder for the heart to pump. People who aren't adapted to high altitudes have an increased risk of stroke. When pregnant women move up to high altitudes, they tend to have difficulties with high blood pressure, suffer a higher rate of infant mortality and are more likely to give birth to small babies.

Native Tibetans don't have those problems. Their blood doesn't contain extra red blood cells, yet it still manages to keep them alive and well. It's a mystery how they manage to function so well at high altitude without the extra help, but it's clear that they are able to avoid the health pitfalls that other people can encounter at high altitude.

According to Nielsen and a bunch of geneticists writing in the journal Nature, the Tibetans appear to have benefited from a genetic gift from the Denisovans, an extinct human ancestor known primarily from a little girl's tooth and pinkie bone.

Tibetans have a gene, EPAS1, that's known to help regulate how the body responds to low oxygen levels. "It's also been called the 'super athlete gene,' because we know that certain humans that have a special version of this gene have a better performance with certain types of athletics," says Nielsen.
[350 words]

[Time 4]
At first, Nielsen and his colleagues weren't sure how Tibetans had gotten the gene. But now they have an idea. "We think we have very good evidence that it came from Denisovans," he says. The DNA patterns seen around that gene match those of the Denisovans, a sister group to the Neanderthals.

He says Tibetans were able to adapt because they got the genes from another human species that was already adapted to the environment. It's a lot more efficient than waiting around for evolution to do the job.

Here's how the (very speculative) story might have gone: Modern humans evolve in Africa about 100,000 years ago and then start spreading across the globe, encountering new environments, and also other archaic human species, like Neanderthals and Denisovans. They mingle and mate, trading genetic material. Some inherit the EPAS1 gene. Eventually, some move up to high altitudes. The ones with the EPAS1 gene thrive more at high altitude than those without it. Over generations and generations, the gene becomes more common in the population.

We probably have extinct human ancestors to thank (and curse) for a lot. Denisovans and Neanderthals might have contributed to modern human immune systems and skin pigmentation, but also to diseases like lupus and Crohn's.

"I think that it's very clear from the work of the last few years that ancient archaic humans interbred with modern humans as modern humans expanded out of Africa 50,000 years ago," says David Reich, a geneticist at Harvard Medical School.

As with many studies of ancient genetics, Reich cautions against jumping to conclusions. "What these authors show is that this genetic material is of archaic human origin, and that's important," says Reich. "But whether it's of Denisovan or of Neanderthal or of some other archaic source, that's not clear."

What is clear is that the genes of modern humans have elements of human species past.

"We exchanged genes with a lot of other lineages that existed 100,000 years ago or 50,000 years ago," says Nielsen. "We are in some sense mongrels made of DNA from many many different lineages of hominins."

In other words, we're mutts.
[355 words]

Source: NPR
http://www.npr.org/blogs/health/2014/07/02/326947693/thanks-to-extinct-humans-tibetans-adapted-to-high-altitude

What Did Ancient Egyptians Really Eat?
Alexander Hellemans, ISNS Contributor   |   May 08, 2014

[Time 5]
Did the ancient Egyptians eat like us? If you're a vegetarian, tucking in along the Nile thousands of years ago would have felt just like home.

In fact, eating lots of meat is a recent phenomenon. In ancient cultures vegetarianism was much more common, except in nomadic populations. Most sedentary populations ate fruit and vegetables.

Although previous sources found the ancient Egyptians to be pretty much vegetarians, until this new research it wasn't possible to find out the relative amounts of the different foods they ate. Was their daily bread really daily? Did they binge on eggplants and garlic? Why didn't someone spear a fish?
A French research team figured out that by looking at the carbon atoms in mummies that had lived in Egypt between 3500 B.C. and 600 A.D. you could find out what they ate.

All carbon atoms are taken in by plants from carbon dioxide in the atmosphere by the process of photosynthesis. By eating plants, and the animals that had eaten plants, the carbon ends up in our bodies.

The sixth-lightest element on the periodic table – carbon – exists in nature as two stable isotopes: carbon-12 and carbon-13. Isotopes of the same element behave the same in chemical reactions but have slightly different atomic masses, with the carbon-13 being slightly heavier than the carbon-12. Plants are categorized into two groups. The first group, C3, is most common in plants such as garlic, eggplants, pears, lentils and wheat. The second smaller group, C4, comprises foodstuffs like millet and sorghum.

The common C3 plants take in less of the heavier isotope carbon-13, while the C4 plants take in more. By measuring the ratio of carbon-13 to carbon-12 you can distinguish between these two groups. If you eat a lot of C3 plants, the concentration of carbon-13 isotopes in your body will be lower than if your diet consisted mainly of C4 plants.

The mummies that the French researchers studied were the remains of 45 people that had been shipped to two museums in Lyon, France during the 19th century. "We had an approach that was a little different," explained Alexandra Touzeau, who led the research team at the University of Lyon. "We worked a lot with bones and teeth, while most researchers study hair, collagen and proteins. We also worked on many different periods, with not many individuals for each period, so we could cover a very long time span."
[402 words]

[Time 6]
The researchers reported their findings in the Journal of Archaeological Science. They measured carbon-13 to carbon-12 ratios (and also some other isotope ratios) in bone, enamel and hair in these remains, and compared them to similar measurements performed on pigs that had received controlled diets consisting of different proportions of C3 and C4 foodstuffs. As pigs have a similar metabolism to humans, their carbon isotope ratios could be compared to what was found in the mummies.

Hair absorbs a higher rate of animal proteins than bone or teeth, and the isotope ratios in hair of the mummies corresponded to that found in hair of modern European vegetarians, confirming that the ancient Egyptians were also mainly vegetarians. As is the case with many modern people, their diet was wheat- and barley-based. A main conclusion of the research was that C4 cereals, like millet and sorghum, were only a minor part of the diet, less than 10 percent.

But there were a few surprises.

"We found that the diet was constant over time; we had expected changes," said Touzeau. This showed that the ancient Egyptians adapted well to the environment while the Nile region became increasingly arid between 3500 B.C. and 600 A.D.

To Kate Spence, an archeologist and specialist in ancient Egypt at the U.K.'s University of Cambridge, this could be expected: "Although the area is very arid, they were cultivating crops along the river just by managing irrigation, which is very effective," she said.  When the level of the Nile decreased, farmers just came closer to the river and kept on cultivating in the same way.

The real mystery is the fish. Most people would probably expect the ancient Egyptians living along the Nile to have eaten loads of fish. However, despite considerable cultural evidence, there seems to have been little fish in their diet.

"There is abundant evidence for fishing in Egyptian wall reliefs and models (both spear and net fishing), and fish shows up in offering lists.  There is also a lot of archeological evidence for fish consumption from sites such as Gaza and Amama," said Spence, who added that some texts indicated that a few fish species were not consumed due to religious associations. "All this makes it a bit surprising that the isotopes should suggest that fish was not widely consumed."
[385 words]

Source: Live Science
http://www.livescience.com/45450-what-did-ancient-egyptians-really-eat.html

伊蔓达

Part III: Obstacle

Illumina Says 228,000 Human Genomes Will Be Sequenced This Year
Record number of genomes being decoded, but cost of DNA sequencing might not fall much further, says Illumina president.

By Antonio Regalado on September 24, 2014

Henry Ford kept lowering the price of cars, and more people kept buying them. The San Diego–based gene sequencing company Illumina has been doing something similar with the tools needed to interpret the human genetic code.

As of this year, an estimated 228,000 human genomes have been completely sequenced by researchers around the globe, said Francis de Souza, president of Illumina, the maker of machines for DNA sequencing, during MIT Technology Review’s EmTech conference in Cambridge, Massachusetts.

De Souza said Illumina’s estimates suggest that the number will double about every 12 months, reaching 1.6 million genomes by 2017, as the technology shifts from a phase of collapsing prices to expanding use in medicine.

The price of sequencing a single genome has dropped from the $3 billion spent by the original Human Genome Project 13 years ago to as little as $1,000, he said.

During an interview, De Souza questioned whether the price would keep falling at that rate. “It’s not clear you can get another order of magnitude out of this,” he said. Instead, he said, his company’s focus is now on making DNA studies more widespread in hospitals, police labs, and other industries.

“The bottleneck now is not the cost—it’s going from a sample to an answer,” De Souza said. “People are saying the price is not the issue.”

Illumina’s sequencing machines, which cost as much as $1 million each, are unmatched in their speed and accuracy. But the company’s growth has rested sometimes precariously on two curves. One has been the collapsing price of sequencing. The other is the soaring demand from genome scientists and funding agencies.

During the EmTech conference, De Souza said Illumina’s success was due to a “hard pivot” the company made in 2006, when it got into the DNA sequencing business by acquiring Solexa, a U.K. startup, and bet its fortunes “on a technology with no sales, that no one knew if it would work.”

That bet succeeded spectacularly, with Illumina machines now accounting for more than 90 percent of all DNA data produced. Last year, Illumina sold $1.4 billion worth of equipment, chemicals, and tests, about 25 percent more than the year before.

But De Souza says Illumina is now pivoting again. This time, its big bet is that DNA sequencing will become routine in medicine, not just in research labs. To make sure that happens, he said, the company is investing in simplifying its technology, winning FDA approval for more diagnostic tests doctors could order directly, developing ways to store DNA data in the cloud, and even launching a DNA app store. “The big pivot now is to the clinic. Getting there will change everything that we do,” he said.

For now, most DNA sequencing is still done by science labs. Of the 228,000 genomes Illumina estimates have been sequenced so far, more than 80 percent are part of scientific research projects, De Souza said. Those include a plan that the U.K.’s government is undertaking to decode 100,000 genomes over several years.

But Illumina’s future business will look different, De Souza said. Sequencing is becoming common in hospitals, particularly for guiding the treatment of cancer patients. Illumina has said it thinks the total possible market for high-speed DNA studies is about $20 billion a year, of which half is connected to studying the DNA of people fighting malignancies like melanoma, lung cancer, or brain tumors, the company estimates.

Recently, many smaller companies and labs have launched DNA tests to scan tumor tissue for mutations. These tests, which largely use Illumina machines, are designed to detect the “driver mutations” of a person’s cancer and help doctors pick the drug that could work best. However, the tests are only lightly regulated, and scientific findings have been rushed into commercial use. Often, doctors are picking drugs on the strength of slim evidence.

“There is a cacophony that is not serving patients well,” Rick Klausner, Illumina’s chief medical officer, said earlier this year. “We think these tests need to be regulated.”

In cancer clinics, Illumina thinks its job is to reduce confusion and offer simplified, and standardized, tests. This year it announced collaborations with several drug companies and academic centers to develop “panels” that would decode the 100 or so most important cancer genes. Those panels would be sold as FDA-approved kits.

De Souza said such cancer diagnostics would be a test of Illumina’s effort to transform itself from a seller of complex instruments to an everyday brand in hospitals. “Researchers can roll their own, but a lot of customers just want the answer,” he said. “For a lot of uses, the technology needs to be pre-packaged to be accessible.”
[815 words]

Source:Technology Review
http://www.technologyreview.com/news/531091/emtech-illumina-says-228000-human-genomes-will-be-sequenced-this-year/

ZOEYZHANG114

thank you zoo much

Cassidy大洁洁

辛苦啦~

time 2 - 00:02:43

2004 announced a discovery of new species, small brain. but countered that is caused by disease

some argue LB1 has feature of Down syndrome. this claim is then rejected.

scientist need more specimen to study the LB1

time 3 - 00:01:58

Tibetans adapted to live at high altitude. when people used to live at low altitude move to high altitude, their body produce more red blood cell to circulate oxygen, which seems good but actually it is not. thick blood leads to higher possibility of stroke. pregnant women move up to high altitude may suffer infant mortality and give birth to small babies. tibetans can live well because inheritance of ancestor, they have EPAS1 to help regulate response of body to low oxygen level.

time 4 - 00:01:27

nielsen and his crew guessed that tibetans’ gene came from denisovans.

time 5 - 00:02:09

do egyptians only eat vegetarians? a franch researcher team figured out the answer by looking at the carbon atoms in mummies. plants are categorized into 2 groups, c3 plants(which take less carbon-13)and c4 plants (which take more carbon-13).

time 6 - 00:02:02

the team compared carbon-13 to carbon-12 ratios of mummies with pigs (which have similar metabolism to humans). evidence (hair) showed that egyptians were mainly vegetarians. few surprises: the diet was constant over time even the environment was arid during a period; many evidence for fishing but the isotopes results didn’t agree with that.

time 7 - 00:04:29

number of gene sequencing will increase. price decreased.  two pivot: collapsing price; turning gene sequencing to medical use. to help fight cancer and diseases. tests need to be regulated to offer simplified and standardized test.

cyndichiang

Speaker
Polar bear thrives in ice ares and how it adapt to this environment.
Polar bear has fat that can provide isulation and energy source while keeping fit.
Compared with brown bear,which has the same ancester as polar bear's, polar bear genetically changed quickly and evolved a particular gene called A-B that can move cholesterol out of blood.

Obstacle: 4'51''
Illumina ,a gene sequencing company has increased its number of genomes but has decreased its price to 1000
It plans to use its data or equipmeng into practice that is in clinics instead of comfining to research
The sequencing test is increasingly popular among hospitals and I thinks that the current job is to reduce confusion and offer simplified, and standardized tests.

MAGGIEHE1993

time2: 2min 52"
       Paleoanthropologists have conflicts about the origins of bones recently found. Some thinks the bones belong to a
       diseased H. sapiens individual but doubters thinks that the bones exhibit features indicative of Down syndrome. A
       paleoanthropologist said more specimens and some trail of fossils are needed to know the origin exactly.
time3: 1min 42"
       For ordinary people, the Tibetan plateau is an extreme to live. Some people will suffer some health problem when move
       there. But native Tibetans do not have those problems. Their blood doesn't contain extra red blood cells.
time4: 1min 33"
       Tibetans' well adaptation to the extreme environment is due to their genes from another human species that was already
       adapted to the environment. Scientists have found new evidence to support the claim.
time5: 2min 27"
       Scientists have found that ancient Egyptians were pretty much vegetarians and they used the test of carbon to find out
       the relative amounts of the different foods they ate. Different kinds of vegetables contain different components of
       carbon isotopes.
time6: 1min 54"
       The researchers measured carbon-13 to carbon-12 ratios in some parts of the body and have found that ancitent Egyptians
       were mainly vegetarians. But there were a few surprises. First the ratio was rather constant although the Nile became
       arid over the years. Second the ancient Egyptians seem to consume little fish although they live close to the Nile.
Obstacle: President of Illumina said an estimated 228000 human genemes have been completely sequenced by researchers around the
          globe. The company hopes that the technology would become a regular procedure in the hospital rather than just an
          experiment in the science lab.

yinghua9122

原来有首页呢，从新开始小分队，坚持。

Speaker
why the polar bear so fat but also so fit? because of the gene.
Researchers compared the genes of polar bear with those of brown bear, and the results indicate that polar bear has special gene which helps it absore fat from blood and doesn't cause problems.

Stefan00

Time 2: The new discovered fossil is a new specie or just one we already know.
Time 3: People who live in lower altitude would increase their red cell to adapt to a plateau. But too many red cells do harm to those people, Tibetans don’t have a similar problem. That thanks to their ancestors who bequeathed Tibetans a special “super athlete genes”.
Time 4:1’54 a hypothesis that how the super athlete genes are preserved and passed to modern human.
Time 5: 2’15 how to test out what did the ancient Egypt people eat. By using differences between carbon 12 and carbon 13.
Time 6: 1’49  The test shows that the diet of Egyptians was quiet constant. And they rarely ate fish.That discovery is surprising.

Obstacle : 4'23 Introduction to a company do something about sequencing the genomes. What’s the bottleneck of their development.

成成儿

坚持就会有变化～～
【Speaker】 3'
this post talks about an evolution developed by the polar bear.
The polar bear is fat but also fit. researches discovered that a special material in polar bear's blood can clear fat which could be harmful in human's blood.
bears cost less than half million years to develop this adaptation; however human would spend 10 thousand million years.

【time2】 4'48''
the article is about the argument whether the LB1 species is a new specious and is the human origins.
the proponents point out that the skull of LB1 is biger than others and LB1 could hunt biger anmials than others. Also, their fossil dated to older years. Therefore, they think LB1, also called hobit is a new specious.
While, the opponents argue that only one kind of difference could identify the new specious. Although there have many differences between LB1 and others, LB1 cannot be a new specious without the special difference.
In sum, more information should be excavated, such as samll skull of LB1.

【time 3】 2'45''
the situation in the tibetan plateau is tough. nonnative people will suffer from less oxgen and there will be more red cell in the blood.
but much red cells in blood is dangerous. for example-pergnent...
while, the native people have a special gene which could help them possess less red cell, thus adapting the tough situation. for example, athlethe...

【time 4】 3'10''
this paragraph talks about how the native people get the gene. the idea is that people from african hold some genes and then they spread to all around the world.
those who went to Tibet develop certain kind of gene to adapt to the situation.

【time 5】3'58''
this paragraph talks about the diet of ancient egyptians. new research studys this topic through the analysis of carbon atoms.
the basic principle is that different food contains different carbon atoms and these atoms will acumulate in human's body such as bones, hairs.
therefore, studying the difference of carbon atoms in human's body could help to learn the diet of ancient people.

【time 6】2'36''
this paragraph talks about the results, showing that the ancient people's staple food is vegetable. they ate more wheat but less C4.
although the area is arid, their diet shows they are good at irrigation.
however, there is a surprise. they live near the river and theie paintings show the scenario of fishing, but they eat less fish. the possible reason is religion.

【part III】 7'25''
this article talks about the perspective of DS of the commercial gene market.
DS points out a trend that the price of DNA sequence will decrease and the demand will increase.
He talks two pivots of his company. the first one is that several years ago, the company worry about the demand of their business because of unknown results of the DNA research.
The second pivot they encounter now is that whether the clinic could be allowed to buy their products like scientific lab which account for 80 percent of DNA sequence research now.
The company have predicted that the demand of DNA sequence research appling to medicine must be huge. and they begin to study DNA sequence of cancer cell.