Earth Resides in Oddball Solar System, Alien Worlds Show

Original Article

Our solar system may be an oddball in the universe. A new study using data from NASA’s Kepler Space Telescope shows that in most cases, exoplanets orbiting the same star have similar sizes and regular spacing between their orbits.

By contrast, our own solar system has a range of planetary sizes and distances between neighbors. The smallest planet, Mercury, is about one-third the size of Earth — and the biggest planet, Jupiter, is roughly 11 times the diameter of Earth. There also are very different spacings between individual planets, particularly the inner planets.

This means our solar system may have formed differently than other solar systems did, the research team suggested, although more observations are needed to learn what the different mechanisms were. [The Most Intriguing Alien Planet Discoveries of 2017]

“The planets in a system tend to be the same size and regularly spaced, like peas in a pod. These patterns would not occur if the planet sizes or spacings were drawn at random,” Lauren Weiss, the study’s lead author and an astrophysicist at the University of Montreal, said in a statement.

The research team examined 355 stars that had a total of 909 planets, which periodically transit across their faces (as seen from Earth). The planets are between 1,000 and 4,000 light-years away from Earth.

After running a statistical analysis, the team found that a system with a small planet would tend to have other small planets nearby — and vice-versa, with big planets tending to have big neighbors. These extrasolar systems also had regular orbital spacing between the planets.

“The similar sizes and orbital spacing of planets have implications for how most planetary systems form,” researchers said in the statement. “In classic planet-formation theory, planets form in the protoplanetary disk that surrounds a newly formed star. The planets might form in compact configurations with similar sizes and a regular orbital spacing, in a manner similar to the newly observed pattern in exoplanetary systems.”

In our own solar system, however, the story is very different. The four terrestrial planets (Mercury, Venus, Earth and Mars) are very widely spaced apart. The team pointed to evidence from other research that Jupiter and Saturn may have disrupted the structure of the young solar system. While the statement did not specify how, several other research studies have examined the movements of these giant planets and their potential impact on the solar system.

Each of the exoplanets examined in the study was originally found by Kepler, which launched in 2009 and continues to send data today. But more-detailed information was obtained with the W.M. Keck Observatory in Hawaii; Weiss is a member of the California-Kepler Survey team there, which is examining the light signatures of thousands of planets discovered by Kepler.

Weiss said she plans a follow-up study at Keck to look for Jupiter-like planets in multiplanet systems. The aim is to better understand if the presence of a Jupiter-size planet would alter the position of other planets in the same system.

“Regardless of their outer populations, the similarity of planets in the inner regions of extrasolar systems requires an explanation,” researchers said in the statement. “If the deciding factor for planet sizes can be identified, it might help determine which stars are likely to have terrestrial planets that are suitable for life.”

The study was published Jan. 3 in The Astronomical Journal.

How DNA Testing Botched My Family’s Heritage, and Probably Yours, Too

Original Article

My grandfather was caramel-skinned with black eyes and thick, dark hair, and until he discovered that he was adopted, he had no reason to suspect that he was not the son of two poor Mexicans as he’d always been told. When he found his adoption papers, according to family lore, he pestered the nuns at the Dallas orphanage where he had lived as an infant for the name of his birth mother. Name in hand, at 10 years old, he hopped a bus to Pennsylvania, met his birth mother, and found out that he was actually Syrian.

At least that’s what we thought until my Aunt Cat mailed a tube of her spit in to AncestryDNA.

The author’s grandparents in Dallas on their wedding day. Image Courtesy the author

Genetic testing suggested that my aunt’s genetic makeup was only a tiny bit Middle Eastern—16 percent, not the 50 percent you might expect if your father was a full-blooded Syrian, as my grandfather believed himself to be. The rest of her Ancestry breakdown provided some explanation, but mostly more confusion. While we typically think of the Caucasus as countries on the Black and Caspian seas like Turkey and Armenia, Ancestry’s test also said it includes Syria. According to Ancestry, the Caucasus accounted for another 15 percent of my Aunt Cat’s DNA. What about the other 20 percent? One line-item stood out as something my aunt hadn’t expected, based on what she knew about either of her parents: She was 30 percent Italian-Greek. My mother’s test revealed similar results.

This caused a minor family scandal. My grandfather’s mother was born in Pennsylvania, but she had lived in an insular Syrian community that never really assimilated. She became pregnant as a teen by her father’s best friend. The assumption had always been that he was Syrian, too. If we weren’t who we thought we were, well, then, who were we?

“I guess we never knew the name of Dad’s father,” my aunt told me, bemused. Suddenly it seemed as though all along we had been missing a gigantic puzzle piece of information about our family tree. At least, my aunt quipped, this was a solid explanation for why she loved pasta.

It’s right there in the fine print of any consumer DNA test, if you bother to read it: DNA testing can come with identity-disrupting surprises, be it an unexpected relative, genetic condition, or, in our case, heritage. But something about this particular surprise didn’t feel quite right.

My Aunt Cat is our family’s amateur genealogist, and she has logged hundreds of hours both on Ancestry.com and in my grandmother’s attic, piecing together the story of our family tree. She’s found countless third, fourth, and fifth cousins with ties to Syria, but no one from either Italy or Greece. In her twenties, she even visited my grandfather’s biological mother and aunt. She recalled them passing around a hookah, yelling in Arabic, and expressing repulsion at the American-style cold cut platter served at a community function. Given how segregated the family was, it seemed like a stretch, she told me, to imagine that anyone had ever had so much as a friendly conversation with an Italian.

I suspected the error might lay not in my family narrative, but in the DNA test itself. So I decided to conduct an experiment. I mailed my own spit samples to AncestryDNA, as well as to 23andMe and National Geographic. For each test I got back, the story of my genetic heritage was different—in some cases, wildly so.

The author’s DNA test results from AncestryDNA.

My AncestryDNA test revealed that I, too, had geographic roots in the Middle East, the Caucasus, and Southern Europe, along with the expected big dose of Scandinavian from my very Norwegian father. Weirdly, though, my percentages of Middle Eastern and Caucasus were almost as high as my mom and aunt’s, though you would expect them to be closer to half.

It got more confusing from there. My test through National Geographic (which partners with the DNA sequencing company Helix for its test) gave me even more links to the Middle East, with 16 percent of my DNA from Asia Minor, 6 percent from the Persian Gulf and 9 percent something called “Jewish Diaspora.” Unlike AncestryDNA, National Geographic’s test assigns your heritage to broad regions instead of modern nation-states. But I could infer that, according to National Geographic, I was less Scandinavian based on my percentage of Northwestern European. I was also more Southern European and, for fun, now had a good chunk of Eastern European thrown in there, too.

The author’s DNA test results from National Geographic.

23andMe’s ancestry results were the most confounding of all. It found that I was only 3 percent Scandanavian, a number that, based on my recent family history, I know is flatly wrong. It also found I was only 5.5 percent Middle Eastern and a whopping 62.6 percent Northwestern European. And no Eastern European at all.

The author’s DNA test results from 23andMe.

 I also uploaded my 23andMe data to GenCove, a small ancestry-test startup founded by scientists. Based on the exact same data that 23andMe had crunched, GenCove reported that 8 percent of my DNA was from the Indian subcontinent. 23andMe had found I had no South Asian DNA at all.

The author’s DNA test results from GenCove, using 23andMe data.

Four tests, four very different answers about where my DNA comes from—including some results that contradicted family history I felt confident was fact. What gives?

There are a few different factors at play here.

Genetics is inherently a comparative science: Data about your genes is determined by comparing them to the genes of other people.

As Adam Rutherford, a British geneticist and author of the excellent book “A Brief History of Everyone Who Ever Lived,” explained to me, we’ve got a fundamental misunderstanding of what an ancestry DNA test even does.

“They’re not telling you where your DNA comes from in the past,” he told me, “They’re telling you where on Earth your DNA is from today.”

Ancestry, for example, had determined that my Aunt Cat was 30 percent Italian by comparing her genes to other people in its database of more than six million people, and finding presumably that her genes had a lot of things in common with the present-day people of Italy.

Heritage DNA tests are more accurate for some groups of people than others, depending how many people with similar DNA to yours have already taken their test. Ancestry and 23andMe have actually bothpublished papers about how their statistical modeling works.

As Ancestry puts it: “When considering AncestryDNA estimates of genetic ethnicity it is important to remember that our estimates are, in fact, estimates. The estimates are variable and depend on the method applied, the reference panel used, and the other customer samples included during estimation.”

That the data sets are primarily made up of paying customers also skews demographics. If there’s only a small number of Middle Eastern DNA samples that your DNA has been matched against, it’s less likely you’ll get a strong Middle Eastern match.

“Different companies have different reference data sets and different algorithms, hence the variance in results,” a spokesman from 23andMe told me. “Middle Eastern reference populations are not as well represented as European, an industry-wide challenge.”

As a person of Syrian descent, the British genealogist Debbie Kennett told me, my test was simply not going to be as accurate as fellow Americans whose relatives skew more European. “The tests are mainly geared for an American audience, and they tend to not have a lot of Middle Eastern ancestry,” she said.

Likewise, Kennett said, because relatively few English people have taken tests from American companies like Ancestry or 23andMe, residents of the U.K. are likely to find less useful results.

“A lot of English people come up with a low percentage of British. My dad was only 8 percent British and most of his ancestors as far back as I can trace came back from Great Britain,” she told me. “People in America come up with much higher percentage of British, often.”

Another anecdote that stuck with me came from my friend Alexis Madrigal. Initially, he said, his Mexican family came up as Arab North African, which was surprising. As 23andMe refined its test and its data set grew, it also refined the results: Now, he was descended from Jewish people from Southern Europe. The number of Madrigals in central Spain had long led the family to suspect that their migratory path to Mexico had at some point passed through this region. As more people took the test, the picture of where his family was “from” changed. The Canadian bioethicist Timothy Caulfield shared a similar story. At first a DNA test revealed he was entirely Irish, but as the data set changed, he gradually became less Irish.

When we talk about “ancestry,” we also don’t always mean the same thing. Ancestry just implies people you’re descended from. But when? In America, we often mean whenever our relatives came to the U.S. On my dad’s side, I expected to see a lot of Scandinavian, because just a few generations ago my great grandparents came from Norway to North Dakota. On my mom’s side, my grandmother has a relative that came to America on the Mayflower. Both are what come to mind when I think of my “ancestors,” but they are separated by several generations and hundreds of years in time. Rutherford pointed out that if we went 5oo years back, my ancestors were probably from all over Europe.

“You and I are probably fifth cousins,” he said.

Where your ancestors are from depends on what period in time you’re talking about. Why don’t I instead say I’m 50 percent North Dakotan and 50 percent Texan?

Tests also differ from one another because they’re simply looking at different things. The results of ancestry tests aren’t based on a reading of your whole genome. The vast majority of every human’s DNA is identical to any other human’s. Ancestry tests look at SNPs, the places on your genome where an individual letter tends to differ between people and give us insight into characteristics like disease, ancestry, and physical appearance. When an SNP occurs within a gene, then, in science-speak, that gene has more than one allele, or alternate forms of a gene that exist in the exact same place on a chromosome. To make matters more confusing, some tests look at mitochondrial and Y chromosome DNA, while others don’t.

The CEO of GenCove, the company where I had uploaded my 23andMe data to get drastically different results, told me that even though he expects a fair amount of variability between algorithms, even he was surprised at how differently his company and 23andMe had interpreted my DNA data. He asked me to also upload my Ancestry data, and ran both data sets again after GenCove’s algorithm had been updated. The results were all over the map.

“To be honest I’m a little confused about what’s going on,” CEO Joseph Pickrell told me.

Each testing company is looking at different alleles from different parts of the genome, and using different algorithms to crunch that data. (You can see a list of how company tests differ here.) It’s worth mentioning that genetics is also probabilistic: just because you have the gene, doesn’t mean you have the trait.

“One British company identified an allele in me that gave me ginger hair, and 23andMe didn’t,” said Rutherford. “That’s a simple case where they just used different alleles. That’s relatively simple to explain.”

And sometimes, the algorithms might just get it wrong. Rutherford told me his 23andMe test came back with a tiny amount of Native American DNA. The finding actually linked up with one anecdote from his family lore, about a relative of his father’s that was a Native American tribesman and horse jumper in a British traveling circus.

“As a geneticist, I am absolutely convinced that they’re not related,” he told me. “It’s just statistical noise that happens to coincide with this cool story.” Statistically, it’s unlikely that such tiny amount of Native American DNA would have been enough to show up on Rutherford’s test.

A big problem is that many of us have a basic misunderstanding of what exactly we’re reading when Ancestry or 23andMe or National Geographic sends us colorful infographics about how British or Irish or Scandinavian we are. It’s not that the science is bad. It’s that it’s inherently imperfect, an estimation based on how much our DNA matches up with people in other places around the world, in a world where people have been mixing and matching and getting it on since the beginning of human history.

“You’re creating different algorithms and you’re using different data sets as your reference points, so it makes sense that you’re going to get some different responses,” the Harvard geneticist Robert Green explained to me, as I tried to make sense of my own DNA data. “It’s not that one’s wrong and one’s right. It’s that there isn’t an agreed-upon approach to pick the right number of markers and combine them mathematically. Everyone is sort of just making it up as they go along.”

At the continental level, said Kennett, ancestry testing is useful. It can tell you pretty reliably whether you are African or Asian or European. It can also reliably identify close familial relatives, as distant as third or fourth cousins. Otherwise, Kennett said, “take it with a large pinch of salt.”

Nearly everyone I interviewed for this story said that, taken with the right mindset, ancestry DNA testing can be fun. As more people take DNA tests and company data sets grow, the results from those tests will also become more detailed and accurate. Anecdotally, I saw this in my own results. Ancestry has the biggest DNA database, and its interpretation of my DNA was also most in-line with what I expected.

“The more people that take tests, the better the experience for all of us,” an Ancestry spokesman told me. “Your DNA does not change, our science does.”

But consumer genetic testing companies have also fueled the misunderstanding of their products, suggesting that those colorful results reveal something profound about what makes you, you.

Take this AncestryDNA ad about Kyle Merker, who, the ads explains, grew up German, wearing a lederhosen and performing traditional German dances. Then an AncestryDNA test revealed he was actually Scottish and Irish. He bought a kilt.

Ancestry.com is suggesting—quite heavy-handedly—that your DNA can define your identity. A few changes to those As, Gs, Ts, and Cs, and all of the sudden you’re river dancing.

“Your culture is not your genes,” said Caulfield. “But the message these companies send is somehow where your genes are from matters. That’s not necessarily constructive. The role of genes in who we are is very complex. If anything, as genetic research moves forward we’re learning that it’s even more complex than we thought.”

In truth, your specific ancestors actually have relatively little impact on your DNA. Some 99.99 percent of your DNA is identical to every other human’s. We’re mostly just all the same. But instead of embracing our genetic similarities, we cling to those differences as symbols of what makes us unique. Consumer DNA testing tends to reinforce that—even though the difference that one test reveals might not even exist in another.

“These companies are asking people to pay for something that is at best trivial and at worst astrology,” said Rutherford. “The biggest lesson we can teach people is that DNA is probabilistic and not deterministic.”

Your DNA is only part of what determines who you are, even if the analysis of it is correct. Plenty of people love pasta, with or without Italian DNA.

If the messaging of consumer DNA companies more accurately reflected the science, though, it might be a lot less compelling: Spit in a tube and find out where on the planet it’s statistically probable that you share ancestry with today.

Learning he was Syrian did not seem to impact my grandfather’s identity as a Mexican man. And how could it? His life story was the story of so many children of immigrants. His father, Manuel, had swum the Rio Grande from Mexico to America in hopes of a better future. He worked as a waiter, and my great-grandmother as a seamstress. At age 10, my grandfather was sent to work at a Coca-Cola bottling plant to help the family make ends meet. He lost a finger. Eventually, he met my blonde-haired, blue-eyed grandmother and moved to California, hoping to raise their children somewhere it would matter less that one of their parents spoke Spanish as a first language.

But me, I don’t even look the part. I’m fair with blue eyes. As a kid, I remember wincing when my friend’s mom made xenophobic comments directed at Mexicans, never suspecting her daughter’s fair friend had some Mexican ties, even if they were not by blood but by heart. As an adult, I learned Arabic and perfected my tamale-making, all in search of some sort of an identity fit. When my grandfather was dying, I struggled with the relationship between DNA and cultural identity. I wondered what would become of my Mexican heritage, once my last living link to it was gone.

In the end, I finally found the same wisdom my grandfather never seemed to question. Sometimes your heritage doesn’t have anything at all to do with your genetics—and I didn’t even have to spit in a test tube to figure it out.

Half the Universe’s Missing Matter Has Just Been Finally Found

Original Article

By Leah Crane

The missing links between galaxies have finally been found. This is the first detection of the roughly half of the normal matter in our universe – protons, neutrons and electrons – unaccounted for by previous observations of stars, galaxies and other bright objects in space.

You have probably heard about the hunt for dark matter, a mysterious substance thought to permeate the universe, the effects of which we can see through its gravitational pull. But our models of the universe also say there should be about twice as much ordinary matter out there, compared with what we have observed so far.

Two separate teams found the missing matter – made of particles called baryons rather than dark matter – linking galaxies together through filaments of hot, diffuse gas.

“The missing baryon problem is solved,” says Hideki Tanimura at the Institute of Space Astrophysics in Orsay, France, leader of one of the groups. The other team was led by Anna de Graaff at the University of Edinburgh, UK.

Because the gas is so tenuous and not quite hot enough for X-ray telescopes to pick up, nobody had been able to see it before.

“There’s no sweet spot – no sweet instrument that we’ve invented yet that can directly observe this gas,” says Richard Ellis at University College London. “It’s been purely speculation until now.”

So the two groups had to find another way to definitively show that these threads of gas are really there.

Both teams took advantage of a phenomenon called the Sunyaev-Zel’dovich effect that occurs when light left over from the big bang passes through hot gas. As the light travels, some of it scatters off the electrons in the gas, leaving a dim patch in the cosmic microwave background – our snapshot of the remnants from the birth of the cosmos.

Stack ‘em up

In 2015, the Planck satellite created a map of this effect throughout the observable universe. Because the tendrils of gas between galaxies are so diffuse, the dim blotches they cause are far too slight to be seen directly on Planck’s map.

Both teams selected pairs of galaxies from the Sloan Digital Sky Survey that were expected to be connected by a strand of baryons. They stacked the Planck signals for the areas between the galaxies, making the individually faint strands detectable en masse.

Tanimura’s team stacked data on 260,000 pairs of galaxies, and de Graaff’s group used over a million pairs. Both teams found definitive evidence of gas filaments between the galaxies. Tanimura’s group found they were almost three times denser than the mean for normal matter in the universe, and de Graaf’s group found they were six times denser – confirmation that the gas in these areas is dense enough to form filaments.

“We expect some differences because we are looking at filaments at different distances,” says Tanimura. “If this factor is included, our findings are very consistent with the other group.”

Finally finding the extra baryons that have been predicted by decades of simulations validates some of our assumptions about the universe.

“Everybody sort of knows that it has to be there, but this is the first time that somebody – two different groups, no less – has come up with a definitive detection,” says Ralph Kraft at the Harvard-Smithsonian Center for Astrophysics in Massachusetts.

“This goes a long way toward showing that many of our ideas of how galaxies form and how structures form over the history of the universe are pretty much correct,” he says.

Different Meditation Practices Reshape Brain in Different Ways

Original Article

By Tereza Pultarova

Credit: Mooshny/Shutterstock

Different types of meditation change the brain in different ways, a new study finds.

In one of the largest studies on meditation and the human brain to date, a team of neuroscience researchers at the Max Planck Institute of Human Cognitive and Brain Sciences in Germany examined 300 participants in a nine-month meditation program. The project, called ReSource, consisted of three periods of three months each. During this program, the participants each practiced different three types of meditation focused on improving attention, compassion or cognitive skills.

At the beginning of the program, and then again at the end of each three-month period, the researchers took measurements of the participants’ brains using a variety of techniques, including magnetic resonance imaging (MRI). The researchers found that not only did certain brain regions change substantially within the three-month periods, but these regions also changed differently based on the type of meditation the participants had practiced. [Mind Games: 7 Reasons You Should Meditation]

“We were surprised [by] how much can actually happen in three months, because three months isn’t that long,” said Veronika Engert, a neuroscience researcher at Max Planck. Engert was the lead author of one of two papers published on Oct. 4 by the research group in the journal Science Advances.

Engert told LiveScience that while changes in brain structure after intensive meditation programs have been observed before, this is the first time that researchers could clearly see the changes that followed a period of practicing a specific type of meditation.

The participants were divided into three groups, and practiced each type of meditation in a different order. This allowed the researchers to more reliably link the changes in the brain to the type of meditation that was being practiced.

For example, in one part of the study, a group of participants was asked to practice mindfulness-based attention for 30 minutes daily six days a week for three months. During this type of meditation, the participants were taught to focus on their breath with their eyes closed or to monitor tension in their bodies. At the end of the three-month period, the participants showed thickening in the prefrontal cortex of the brain, an area involved in complex thinking, decision-making and attention, Engert said.

After the three-month session that focused on mindfulness, that group moved on to types of mediation focused on developing social skills such as compassion and understanding a situation from a perspective of another person. As with the first session, the researchers observed different changes in the people’s brains after each of the next two sessions.

“If people train [in the skill of] perspective-taking, we see changes in brain regions that are important for these cognitive processes” Engert said. Or, if people focus on affect, or emotion, “then we see changes in brain regions that are important for emotional regulation,” she said.

But the participants’ brains weren’t the only things that were changing. The researchers also observed changes in the behavior of the participants, and these changes matched up with the changes in their brains.

In another part of the study, the researchers measured how the participants responded to a stressful situation similar to a job interview or an exam. The scientists found that all respondents who were practicing meditation reported feeling less stressed than people who were not meditating. However, only those participants practicing compassion and perspective-taking showed consistently lower levels of the stress hormone cortisol in their saliva after the stressful situation, according to Engert.

“After this type of a stress test we usually see that cortisol rises after about 20 minutes,” said Engert. “This rise in cortisol was lower by 51 percent in those subjects who had the social training.”

One limitation of the study was that the participants included only healthy people who did not have any type of mental health condition. Engert said the researchers haven’t looked at whether meditation could be used to, for example, help people suffering from depressionor anxiety. However, Engert said, considering the fact that stress is a major contributor to a wide range of diseases that plague the modern world, the findings could help tailor approaches that could be used as preventive measures. Stress, according to Engert contributes not only to the development of depression but also cardiovascular or metabolic diseases.

In addition, the findings could help researchers develop tailored training programs for specific areas of the brain to help people perform better in various areas of their lives, she said, however, more research is needed to understand exactly how such programs affect the brain.

The team will now focus on studying the effects of the three mind-training techniques on children and people working in highly stressful professions, Engert said.

Originally publishedon Live Science.

Nobel Prize Awarded for Biological Clock Discoveries

Original Article

By Jordana Cepelewicz

 

Ninety minutes before dawn in the eastern United States, the Nobel committee announced that it was awarding this year’s Nobel Prize in Physiology or Medicine to three American biologists for their research on the control of circadian rhythms. Jeffrey C. Hallat the University of Maine, Michael Rosbash at Brandeis University and Michael W. Young at the Rockefeller University share the prize for their discoveries of the genetic and biomolecular mechanisms that help the cells of plants and animals (including humans) mark the 24-hour cycle of day and night. That research became a cornerstone of the science of chronobiology, the study of how organisms track time and adapt to its cycles.

“It’s a really beautiful example of basic research that has led to incredible discoveries,” commented Paul Hardin, who studies chronobiology at Texas A&M University. “Almost every aspect of physiology and metabolism will be controlled by the circadian clock.” For example, in the case of mammals, he said, 20–30 percent of the genes in any given tissue may be under the control of an internal clock. “But if you take all the tissues of the body, the vast majority of genes are under clock control in one tissue or another.”

Josephine Arendt, an emeritus professor of endocrinology at Surrey University who studies circadian rhythms, agreed about the importance of the work winning this year’s prize. Health and fitness can be profoundly affected by disorders that throw off that 24-hour timekeeping mechanism or any of the neurological and hormonal systems that rely on it. “Their work underpins [that of] people like me who are interested in applying circadian principles to human health,” she said.

Jeffrey C. Hall, Michael Rosbash and Michael W. Young (left to right) are new Nobel laureates in celebration of their discoveries about the genetic and biomolecular mechanism that governs the circadian rhythm.

Jeffrey C. Hall, Michael Rosbash and Michael W. Young (left to right) are new Nobel laureates in celebration of their discoveries about the genetic and biomolecular mechanism that governs the circadian rhythm.

Jeffrey C. Hall, Michael Rosbash and Michael W. Young (left to right) are new Nobel laureates in celebration of their discoveries about the genetic and biomolecular mechanism that governs the circadian rhythm.

Jeffrey C. Hall, Michael Rosbash and Michael W. Young (left to right) are new Nobel laureates in celebration of their discoveries about the genetic and biomolecular mechanism that governs the circadian rhythm.

The Gairdner Foundation (Hall and Young); Mike Lovett/Brandeis University (Rosbash)

The study of circadian rhythms goes back to at least the 18th century, when scientists noticed that certain plants would open their leaves at sunrise and close them at sunset even in the absence of lighting cues. Later evidence showed that essentially all organisms had some internal biological clock that allowed them to match their physiology to the day-night cycle. Work in the 1970s by Ronald Konopka and Seymour Benzer showed that this clock was under genetic control because mutations could disrupt it. The name period was given to that gene but little else was known about it. Indeed, how a gene could allow cells to keep time remained a mystery.

Answers began to fall into place in 1984, when Hall and Rosbash working at Brandeis and Young at Rockefeller independently isolated the period gene in fruit flies. Hall and Rosbash showed that the cellular concentrations of the protein made by period, PER, were high during the day and then dropped at night, befitting a 24-hour timekeeping gene.

The Brandeis researchers hypothesized that a feedback loop might be governing this gene-protein system: When concentrations of PER climbed high enough, they shut down the activity of period. When PER degraded, period could start up again. PER could thereby inhibit its own synthesis. The hitch in this scheme was that for it to work, something had to transport PER from the cell’s cytoplasm, where it was made, into the nucleus where period dwelled. Hall and Rosbash showed that PER was getting into the nucleus but it was unclear how until 1994, when Young discovered the timeless gene, which was also essential for proper circadian rhythms. The protein made by timeless, TIM, latches on to cytoplasmic PER and escorts it into the nucleus to inhibit period. Young later identified a third gene, doubletime, that also delays the build-up of PER in cells to further improve the linkage of this circadian mechanism to the time of day.

Lucy Reading-Ikkanda/Quanta Magazine

Andrew Millar, the chair of systems biology at the University of Edinburgh and an expert on plant circadian rhythms, noted that the precise genetic clock mechanism that Hall, Rosbash and Young identified was specific to animals, but that conceptually similar mechanisms built around analogous genes were soon identified in plants, fungi, bacteria and other organisms by other researchers. “It’s the breadth of application of biological rhythm research that makes it so fascinating,” he said.

Chronobiology is consequently a field in its early days. Researchers are still trying to fully understand the connection between the circadian rhythm within cells and animals’ need for sleep. Not only do diverse organisms use a variety of mechanisms to maintain circadian rhythms and other temporal cycles, some cells of the body may use specialized timekeeping systems for specialized functions. New biological rhythms — and their influence on organisms — continue to be discovered. Nevertheless, the dissection of this circadian timekeeping system by these scientists already stands as a landmark achievement.

This post was updated on October 2 with additional comments from

DNA Surgery on Embryos Removes Disease

Original Article

By James Gallagher

Precise “chemical surgery” has been performed on human embryos to remove disease in a world first, Chinese researchers have told the BBC.

The team at Sun Yat-sen University used a technique called base editing to correct a single error out of the three billion “letters” of our genetic code.

They altered lab-made embryos to remove the disease beta-thalassemia. The embryos were not implanted.

The team says the approach may one day treat a range of inherited diseases.

Base editing alters the fundamental building blocks of DNA: the four bases adenine, cytosine, guanine and thymine.

They are commonly known by their respective letters, A, C, G and T.

All the instructions for building and running the human body are encoded in combinations of those four bases.

DNAImage copyrightGETTY IMAGES

The potentially life-threatening blood disorder beta-thalassemia is caused by a change to a single base in the genetic code – known as a point mutation.

The team in China edited it back.

They scanned DNA for the error then converted a G to an A, correcting the fault.

Junjiu Huang, one of the researchers, told the BBC News website: “We are the first to demonstrate the feasibility of curing genetic disease in human embryos by base editor system.”

He said their study opens new avenues for treating patients and preventing babies being born with beta-thalassemia, “and even other inherited diseases”.

The experiments were performed in tissues taken from a patient with the blood disorder and in human embryos made through cloning.

Genetics revolution

Base editing is an advance on a form of gene-editing known as Crispr, that is already revolutionising science.

Crispr breaks DNA. When the body tries to repair the break, it deactivates a set of instructions called a gene. It is also an opportunity to insert new genetic information.

Base editing works on the DNA bases themselves to convert one into another.

Prof David Liu, who pioneered base editing at Harvard University, describes the approach as “chemical surgery”.

He says the technique is more efficient and has fewer unwanted side-effects than Crispr.

He told the BBC: “About two-thirds of known human genetic variants associated with disease are point mutations.

“So base editing has the potential to directly correct, or reproduce for research purposes, many pathogenic [mutations].”

EmbryoImage copyrightGETTY IMAGES

The research group at Sun Yat-sen University in Guangzhou hit the headlines before when they were the first to use Crispr on human embryos.

Prof Robin Lovell-Badge, from the Francis Crick Institute in London, described parts of their latest study as “ingenious”.

But he also questioned why they did not do more animal research before jumping to human embryos and said the rules on embryo research in other countries would have been “more exacting”.

The study, published in Protein and Cell, is the latest example of the rapidly growing ability of scientists to manipulate human DNA.

It is provoking deep ethical and societal debate about what is and is not acceptable in efforts to prevent disease.

Prof Lovell-Badge said these approaches are unlikely to be used clinically anytime soon.

“There would need to be far more debate, covering the ethics, and how these approaches should be regulated.

“And in many countries, including China, there needs to be more robust mechanisms established for regulation, oversight, and long-term follow-up.”

Poliovirus Kills Off Cancer Cells Stops Tumor Regrowth

Original Article

By Ana Sandoiu

Researchers from Duke University in Durham, NC, may have discovered a new way of killing off cancer cells.

The team was jointly led by Dr. Matthias Gromeier, a professor in the Department of Neurosurgery, and Prof. Smita Nair, who is an immunologist in the Department of Surgery.

The new research – which is published in the journal Science Translational Medicine – shows how a modified poliovirus enables the body to use its own resources to fight off cancer. The modified virus bears the name of recombinant oncolytic poliovirus (PVS-RIPO).

PVS-RIPO has been in clinical trials since 2011 and preliminary results have offered hope to patients with one of the most aggressive forms of brain tumor: recurrent glioblastoma. So, the researchers set out to investigate more deeply how exactly PVS-RIPO works.

Explaining the rationale behind their research endeavor, Dr. Gromeier says, “Knowing the steps that occur to generate an immune response will enable us to rationally decide whether and what other therapies make sense in combination with poliovirus to improve patient survival.”

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Poliovirus attacks tumors, inhibits regrowth

The researchers examined the behavior of the poliovirus in two human cell lines: melanomaand triple-negative breast cancer. They observed that the poliovirus attaches itself to cancerous cells. These cells have an excess of the CD155 protein, which acts as a receptor for the poliovirus.

Then, the poliovirus starts to attack the malignant cells, triggering the release of antigens from the tumorAntigens are toxic substances that the body does not recognize, therefore setting off an immune attack against them.

So, when the tumor cells release antigens, this alerts the body’s immune system to start attacking. At the same time, the poliovirus infects the dendritic cells and macrophages.

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Dendritic cells are cells whose role it is to process antigens and “present” them to T cells, which are a type of immune cell. Macrophages are another type of immune cell – namely, large white blood cells whose main role is to rid our bodies of debris and toxic substances.

The cell culture results – which the researchers then verified in mouse models – showed that once PVS-RIPO infects the dendritic cells, these cells “tell” T cells to start the immune attack.

Once started, this process seems to be continuously successful. The cancer cells continue to be vulnerable to the immune system’s attack over a longer period of time, which appears to stop the tumor from regrowing.

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As Prof. Nair explains, “Not only is poliovirus killing tumor cells, it is also infecting the antigen-presenting cells, which allows them to function in such a way that they can now raise a T cell response that can recognize and infiltrate a tumor.”

“This is an encouraging finding, because it means the poliovirus stimulates an innate inflammatory response.”

Prof. Smita Nair

Speaking to Medical News Today about the clinical implications of the findings and the scientists’ directions for future research, Dr. Gromeier said, “Our findings provide clear rationales for moving forward with clinical trials in breast cancer, prostate cancer, and malignant melanoma.”

“This includes novel combination treatments that we will pursue,” he added.

More specifically, he explains, because the study revealed that after treatment with the poliovirus “immune checkpoints are increased on immune cells,” a future strategy the researchers plan to explore is “[oncolytic] poliovirus combined with immune checkpoint blockade.”

Scientists Just Discovered the First Brainless Animal That Sleeps

Original Article

By Sarah Kaplan


Cassiopea jellyfish rests upside-down on black sand and pulses, rhythmically contracting and relaxing its bell. At night, Cassiopea jellies pulse less frequently — a clue that they’re sleeping, researchers report. (Photo by JanEaster.com)

It was well past midnight when Michael Abrams, Claire Bedbrook and Ravi Nath crept into the Caltech lab where they were keeping their jellyfish. They didn’t bother switching on the lights, opting instead to navigate the maze of desks and equipment by the pale blue glow of their cellphones. The students hadn’t told anyone that they were doing this. It wasn’t forbidden, exactly, but they wanted a chance to conduct their research without their PhD advisers breathing down their necks.

“When you start working on something totally crazy, it’s good to get data before you tell anybody,” Abrams said.

The “totally crazy” undertaking in question: an experiment to determine whether jellyfish sleep.

It had all started when Bedbrook, a graduate student in neurobiology, overheard Nath and Abrams mulling the question over coffee. The topic was weird enough to make her stop at their table and argue.

“Of course not,” she said. Scientists still don’t fully know why animals need to snooze, but research has found that sleep is a complex behavior associated with memory consolidation and REM cycles in the brain. Jellyfish are so primitive they don’t even have a brain — how could they possibly share this mysterious trait?

Her friends weren’t so sure. “I guess we’re going to have to test it,” Nath said, half-joking.

Bedbrook was dead serious: “Yeah. Yeah, we are.”

After months of late-night research, Bedbrook has changed her mind. In a paper published Thursday in the journal Current Biology, she, Nath and Abrams report that the upside-down jellyfish Cassiopea exhibit sleeplike behavior — the first animals without a brain known to do so. The results suggest that sleep is deeply rooted in our biology, a behavior that evolved early in the history of animal life and has stuck with us ever since.

Further study of jellyfish slumber might bring scientists closer to resolving what Nath called “the paradox of sleep.”

Think about it, he urged. If you’re asleep in the wild when a predator comes along, you’re dead. If a food source strolls past, you go hungry. If a potential mate walks by, you miss the chance to pass on your genetic material.

“Sleep is this period where animals are not doing the things that benefit from a natural selection perspective,” Nath said.

Abrams chimed in: “Except for sleep.” Nath laughed.

“We know it must be very important. Otherwise, we would just lose it,” Bedbrook said. If animals could evolve a way to live without sleep, surely they would have. But many experiments suggest that when creatures such as mice are deprived of sleep for too long, they die. Scientists have shown that animals as simple as the roundworm C. elegans, with a brain of just 302 neurons, need sleep to survive.

Cassiopea has no brain to speak of — just a diffuse “net” of nerve cells distributed across their small, squishy bodies. These jellyfish barely even behave like animals. Instead of mouths, they suck in food through pores in their tentacles. They also get energy via a symbiotic relationship with tiny photosynthetic organisms that live inside their cells.

“They’re like weird plant animals,” Bedbrook said.

They’re also ancient: Cnidarians, the phylogenetic group that includes jellies, first arose some 700 million years ago, making them some of Earth’s first animals. These traits make Cassiopea an ideal organism to test for the evolutionary origins of sleep. Fortuitously, Abrams already had some on hand.

So the trio designed an experiment. At night, when the jellies were resting and their professors were safely out of the picture, the students would test for three behavioral criteria associated with sleep.

First: Reversible quiescence. In other words, the jellyfish become inactive but are not paralyzed or in a coma. The researchers counted the jellyfish’s movements and found they were 30 percent less active at night. But when food was dropped into the tank, the creatures perked right up. Clearly not paralyzed.

Second: An increased arousal threshold. This means it’s more difficult to get the animals’ attention; they have to be “woken up.” For this, the researchers placed sleeping jellies in containers with removable bottoms, lifted the containers to the top of their tank, then pulled out the bottom. If the jellyfish were awake, they’d immediately swim to the floor of the tank. But if they were asleep, “they’d kind of strangely float around in the water,” Abrams said.

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Watch a magnificent jellyfish at a depth of more than 12,000 feet
This jellyfish was seen during a dive on April 24, while exploring Enigma Seamount at a depth of more than 12,000 feet. (NOAA)

“You know how you wake up with vertigo? I pretend that maybe there’s possible chance that the jellyfish feel this,” Nath added. “They’re sleeping and then they wake up and they’re like, ‘Ahhhh!’ ”

And third: The quiescent state must be homeostatically regulated. That is, the jellyfish must feel a biological drive to sleep. When they don’t, they suffer.

“This is really equivalent to how we feel when we pull an all-nighter,” Bedbrook said. She’s all too familiar with the feeling — getting your PhD requires more late nights than she’s willing to count.

The jellyfish have no research papers to keep them awake past their bedtimes, so the scientists prevented them from sleeping by “poking” them with pulses of water every 20 minutes for an entire night. The following day, the poor creatures swam around in a daze, and the next night they slept especially deeply to make up for lost slumber.


Jellyfish in their tank. (Caltech)

Realizing they really had something here, the students clued their professors in on what they were doing. The head of the lab where Nath worked, Caltech and Howard Hughes Medical Institute biologist Paul Sternberg, offered the trio a closet in which they could to continue their experiments.

“It’s important,” Sternberg said, “because it’s [an organism] with what we think of as a more primitive nervous system. … It raises the possibility of an early evolved fundamental process.”

Sternberg, along with Abram and Bedbrook’s advisers, is a co-author on the Current Biology paper.

Allan Pack, the director of the Center for Sleep and Respiratory Neurobiology at the University of Pennsylvania, was not involved in the jellyfish research, but he’s not surprised by the finding, given how prevalent sleep is in other species.

“Every model that has been looked at … shows a sleep-like state,” he said.

But the revelations about jellyfish sleep are important, he said, because they show how basic sleep is. It appears to be a “conserved” behavior, one that arose relatively early in life’s history and has persisted for millions of years. If the behavior is conserved, then perhaps the biological mechanism is too. Understanding why jellyfish, with their simple nerve nets, need sleep could lead scientists to the function of sleep in humans.

“I think it’s one of the major biological questions of our time,” Pack said. “We spend a third of a life sleeping. Why are we doing it? What’s the point?”

 

New Research Suggest Climate Change Not As Threatening As Previously Thought

Original Article

By Henry Bodkin

the planet than previously thought because scientists got their modelling wrong, a new study has found. New research by British scientists reveals the world is being polluted and warming up less quickly than 10-year-old forecasts predicted, giving countries more time to get a grip on their carbon output.

An unexpected “revolution” in affordable renewable energy has also contributed to the more positive outlook.

Experts now say there is a two-in-three chance of keeping global temperatures within 1.5 degrees above pre-industrial levels, the ultimate goal of the 2015 Paris Agreement.

Paris climate change deal: Moment agreement announcedParis climate change deal: Moment agreement announced

They also condemned the “overreaction” to the US’s withdrawal from the Paris Climate Accord, announced by Donald Trump in June, saying it is unlikely to make a significant difference.

According to the models used to draw up the agreement, the world ought now to be 1.3 degrees above the mid-19th-Century average, whereas the most recent observations suggest it is actually between 0.9 and 1 degree above.

We’re in the midst of an energy revolution and it’s happening faster than we thoughtProfessor Michael Grubb, University College London

The discrepancy means nations could continue emitting carbon dioxide at the current rate for another 20 years before the target was breached, instead of the three to five predicted by the previous model.

“When you are talking about a budget of 1.5 degrees, then a 0.3 degree difference is a big deal”, said Professor Myles Allen, of Oxford University and one of the authors of the new study.

Published in the journal Nature Geoscience, it suggests that if polluting peaks and then declines to below current levels before 2030 and then continue to drop more sharply, there is a 66 per cent chance of global average temperatures staying below 1.5 degrees.

The goal was yesterday described as “very ambitious” but “physically possible”.

Another reason the climate outlook is less bleak than previously thought is stabilising emissions, particularly in China.

Renewable energy has also enjoyed more use than was predicted.

China has now acquired more than 100 gigawatts of solar cells, 25 per cent of which in the last six months, and in the UK, offshore wind has turned out to cost far less than expected.

Professor Michael Grubb, from University College London, had previously described the goals agreed at Paris in 2015 as “incompatible with democracy”.

Outrage at Trump's withdrawal from Paris climate agreementOutrage at Trump’s withdrawal from Paris climate agreement

But yesterday he said: “We’re in the midst of an energy revolution and it’s happening faster than we thought, which makes it much more credible for governments to tighten the offer they put on the table at Paris.”

He added that President Trump’s withdrawal from the agreement would not be significant because “The White House’s position doesn’t have much impact on US emissions”.

“The smaller constituencies – cities, businesses, states – are just saying they’re getting on with it, partly for carbon reduction, but partly because there’s this energy revolution and they don’t want to be left behind.”

The new research was published as the Met Office announced that a “slowdown” in the rate of global temperature rises reported over roughly the first decade of this century was now over.

The organisation said the slowdown in rising air temperatures between 1999 and 2014 happened as a result of a natural cycle in the Pacific, which led to the ocean circulation speeding up, causing it to pull heat down in the deeper ocean away from the atmosphere.

However, that cycle has now ended.

Claire Perry, the climate change and industry minister, claimed Britain had already demonstrated that tackling climate change and running a strong economy could go “hand in hand”.

“How is the time to build on our strengths and cement our position as a global hub for investment in clean growth,” she said.

 

Neil DeGrasse Tyson Says It Is ‘Too Late’ To Recover From Climate Change

Original Article

By Alexandra King

Scientist and astrophysicist Neil deGrasse Tyson said Sunday that, in the wake of devastating floods and damage caused by Hurricanes Harvey and Irma, climate change had become so severe that the country “might not be able to recover.”

In an interview on CNN’s “GPS,” Tyson got emotional when Fareed Zakaria asked what he made of Homeland Security Adviser Tom Bossert’s refusal to say whether climate change had been a factor in Hurricanes Harvey or Irma’s strength — despite scientific evidence pointing to the fact that it had made the storms more destructive.
“Fifty inches of rain in Houston!” Tyson exclaimed, adding, “This is a shot across our bow, a hurricane the width of Florida going up the center of Florida!”
“What will it take for people to recognize that a community of scientists are learning objective truths about the natural world and that you can benefit from knowing about it?” he said.
Tyson told Zakaria that he had no patience for those who, as he put it, “cherry pick” scientific studies according to their belief system.
“The press will sometimes find a single paper, and say, ‘Oh here’s a new truth, if this study holds it.’ But an emergent scientific truth, for it to become an objective truth, a truth that is true whether or not you believe in it, it requires more than one scientific paper,” he said.
“It requires a whole system of people’s research all leaning in the same direction, all pointing to the same consequences,” he added. “That’s what we have with climate change, as induced by human conduct.”
Tyson said he was gravely concerned that by engaging in debates over the existence of climate change, as opposed to discussions on how best to tackle it, the country was wasting valuable time and resources.
“The day two politicians are arguing about whether science is true, it means nothing gets done. Nothing,” he said. “It’s the beginning of the end of an informed democracy, as I’ve said many times. What I’d rather happen is you recognize what is scientifically truth, then you have your political debate.”
Tyson told Zakaria that he believed that the longer the delay when it comes to responding to the ongoing threat of climate change, the bleaker the outcome. And perhaps, he hazarded, it was already even too late.
“I worry that we might not be able to recover from this because all our greatest cities are on the oceans and water’s edges, historically for commerce and transportation,” he said.
“And as storms kick in, as water levels rise, they are the first to go,” he said. “And we don’t have a system — we don’t have a civilization with the capacity to pick up a city and move it inland 20 miles. That’s — this is happening faster than our ability to respond. That could have huge economic consequences.”