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  • richardmitnick 8:58 am on March 4, 2017 Permalink | Reply
    Tags: , Harvard, Making math more Lego-like,   

    From Harvard: “Making math more Lego-like” 

    Harvard University
    Harvard University

    March 2, 2017
    Peter Reuell

    1
    “[A] picture is worth 1,000 symbols,” quips Professor Arthur Jaffe (left). Jaffe and postdoctoral fellow Zhengwei Liu have developed a pictorial mathematical language that can convey pages of algebraic equations in a single 3-D drawing. Rose Lincoln/Harvard Staff Photographer

    Galileo called mathematics the “language with which God wrote the universe.” He described a picture-language, and now that language has a new dimension.

    The Harvard trio of Arthur Jaffe, the Landon T. Clay Professor of Mathematics and Theoretical Science, postdoctoral fellow Zhengwei Liu, and researcher Alex Wozniakowski has developed a 3-D picture-language for mathematics with potential as a tool across a range of topics, from pure math to physics.

    Though not the first pictorial language of mathematics, the new one, called quon, holds promise for being able to transmit not only complex concepts, but also vast amounts of detail in relatively simple images. The language is described in a February 2017 paper published in the Proceedings of the National Academy of Sciences.

    “It’s a big deal,” said Jacob Biamonte of the Quantum Complexity Science Initiative after reading the research. “The paper will set a new foundation for a vast topic.”

    “This paper is the result of work we’ve been doing for the past year and a half, and we regard this as the start of something new and exciting,” Jaffe said. “It seems to be the tip of an iceberg. We invented our language to solve a problem in quantum information, but we have already found that this language led us to the discovery of new mathematical results in other areas of mathematics. We expect that it will also have interesting applications in physics.”

    When it comes to the “language” of mathematics, humans start with the basics — by learning their numbers. As we get older, however, things become more complex.

    “We learn to use algebra, and we use letters to represent variables or other values that might be altered,” Liu said. “Now, when we look at research work, we see fewer numbers and more letters and formulas. One of our aims is to replace ‘symbol proof’ by ‘picture proof.’”

    The new language relies on images to convey the same information that is found in traditional algebraic equations — and in some cases, even more.

    “An image can contain information that is very hard to describe algebraically,” Liu said. “It is very easy to transmit meaning through an image, and easy for people to understand what they see in an image, so we visualize these concepts and instead of words or letters can communicate via pictures.”

    “So this pictorial language for mathematics can give you insights and a way of thinking that you don’t see in the usual, algebraic way of approaching mathematics,” Jaffe said. “For centuries there has been a great deal of interaction between mathematics and physics because people were thinking about the same things, but from different points of view. When we put the two subjects together, we found many new insights, and this new language can take that into another dimension.”

    In their most recent work, the researchers moved their language into a more literal realm, creating 3-D images that, when manipulated, can trigger mathematical insights.

    “Where before we had been working in two dimensions, we now see that it’s valuable to have a language that’s Lego-like, and in three dimensions,” Jaffe said. “By pushing these pictures around, or working with them like an object you can deform, the images can have different mathematical meanings, and in that way we can create equations.”

    Among their pictorial feats, Jaffe said, are the complex equations used to describe quantum teleportation. The researchers have pictures for the Pauli matrices, which are fundamental components of quantum information protocols. This shows that the standard protocols are topological, and also leads to discovery of new protocols.

    “It turns out one picture is worth 1,000 symbols,” Jaffe said.

    “We could describe this algebraically, and it might require an entire page of equations,” Liu added. “But we can do that in one picture, so it can capture a lot of information.”

    Having found a fit with quantum information, the researchers are now exploring how their language might also be useful in a number of other subjects in mathematics and physics.

    “We don’t want to make claims at this point,” Jaffe said, “but we believe and are thinking about quite a few other areas where this picture-language could be important.”

    See the full article here .

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    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 3:52 pm on February 12, 2017 Permalink | Reply
    Tags: Gender discrimination is not just a women's issue, Harvard, ,   

    From Science Node: Women in STEM – “Continue the conversation” Very Important 

    Science Node bloc
    Science Node

    07 Feb, 2017
    Helen Patton

    1

    According to recent research conducted by the US National Science Foundation (NSF), although women comprise more than half of the U.S. workforce, only 28% are employed in STEM related fields and of that, only 11% are pursuing a career in information security.

    Similarly, when looking at workplace diversity, minorities represented 29% of STEM related fields, with approximately 6% Hispanic and 8% African-American representation in the IT sector.

    2
    Leading ladies. Participants in a gender and diversity panel at the Internet2 Technology Exchange. From left, Theresa Semmens, Helen Patton, Mary Dunker, and Kimberly Milford. Courtesy Internet2.

    When asked why women chose to leave the profession or why they might not consider a career in information security and IT, often the answers are as complex as the problem.

    Some cite stereotyping, organizational culture, and the lack of encouragement and support from management and fellow colleagues. Others cite the lack of guidance from management and uncertainty about their career trajectory.

    Moving forward, my co-panelists and I offer the following guiding principles to anyone interested in supporting gender and diversity initiatives.

    Engaging everyone in the dialogue

    Gender discrimination is not just a women’s issue – it’s a men’s issue, too. Similarly, making concerted efforts to challenge the lack of diversity in the workplace should be everyone’s concern. It’s important to include both men and women in the conversation and work collectively at solving the gender discrimination and diversity problems in the workplace.

    Building a community of allies

    Many of our male colleagues have expressed their desire to put an end to gender discrimination and make real change to improve diversity. There needs to be tools and resources, such as this one about male allies, that help our colleagues become allies for women both at work and at home.

    Sharing success stories

    It’s important to move beyond simply presenting the data on gender discrimination in the workplace. In addition to making tools accessible, we must highlight possible solutions and share success stories alongside the data. A good reference for this is the National Center for Women and Information Technology (NCWIT).


    Target practices. Building on insights from behavioral economics, Iris Bohnet argues that to overcome gender bias in organizations and society, we should focus on de-biasing systems — how we evaluate performance, hire, promote, structure tests, form groups — rather than on trying to de-bias people.

    Another great resource is Iris Bohnet’s book What Works – Gender Diversity by Design, which makes suggestions on ways we can recruit, hire, develop, and promote gender diverse talent.

    Inclusive language

    We want to be conscious of how we present the profession through the use of language. We want to avoid using terms and descriptions that may come across as biased, either consciously or unconsciously. We want to ensure the terms and language we use are gender-inclusive.

    Commitment to mentorship

    A coach, mentor, or advocate will instill in the person seeking help and advice the idea that they can make a difference and are valued for their contributions. Mentorship forms a support system that enhances a positive experience of growth and development for an individual’s career.

    Research suggests that the most beneficial mentoring is based on mutual learning, active engagement, and striving to push the leadership capabilities of mentees.

    Championing diversity

    We need to ensure that everyone who has an interest and desire to break into information security has the opportunity, comfort level, and confidence to do so.

    Diversity in the workplace contributes to an institution’s creativity and adds new perspectives to professional conversations. It creates a well-rounded team and allows for more efficiencies, diverse ideas, varied technical skill sets, broader communication forums, and business management skill sets.

    Women and minorities need champions; those who advocate, support, and recognize their efforts and contributions.

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 8:31 am on February 9, 2017 Permalink | Reply
    Tags: , Focused on developing the medical school arm of the new Free Aleppo University., Harvard, Harvard Scholar at Risk fellow Mahmoud Hariri,   

    From Harvard: “Hands of a healer, heart of a Syrian” 

    Harvard University
    Harvard University

    February 8, 2017
    Colleen Walsh

    1
    Syrian trauma surgeon and Harvard Scholar at Risk fellow Mahmoud Hariri is working on ways to improve medical training in Syria. He plans to return home when his Harvard term is up.
    Stephanie Mitchell/Harvard Staff Photographer

    Experience as a trauma surgeon drives Scholar at Risk in mission to aid medical community in war-torn homeland

    Sometimes he goes by John White. Sometimes he’s Abdulaziz Adel. At Harvard he is Mahmoud Hariri. His many names are a product of his life in Syria, where being a doctor treating the wounded is often as dangerous as being a rebel fighting the regime of Bashar al-Assad.

    There have been 400 documented attacks on medical facilities since the Syrian war began in 2011 and close to 800 medical workers killed, according to figures from the U.S.-based nongovernmental organization Physicians for Human Rights. The assaults have been executed almost entirely by the Assad government or its allies, according to the NGO, and have targeted civilians with ruthless precision.

    Hariri, a surgeon and currently a Harvard Scholars at Risk fellow, has witnessed firsthand those brutal campaigns and their horrific aftermath: bodies marred by barrel bombs (cylinders crammed with explosives and shrapnel); burned remains of medical students kidnapped and murdered for the crime of trying to aid the injured; a woman, nine months pregnant, who lost her baby when a sniper’s bullet pierced its skull.

    Tragedy dominated Hariri’s daily reality the past several years in Aleppo, the city where he was born and first devoted his life to helping others.

    “Medicine was my ambition since I was a child,” the 50-year-old physician said on a recent afternoon in his Harvard office on Story Street, thousands of miles removed from the devastation of his home city, where hundreds of thousands have died since fighting broke out in 2011. “They used to call me, since I was in the middle school, ‘How are you, doctor? Where are you going, doctor?’”

    When it was time to pick a specialty, Hariri opted for general surgery because of its “practical chance to save lives.” He didn’t imagine that his days removing gallbladders, fixing hernias, and teaching at Aleppo University would help prepare him to be a trauma surgeon saving lives on the front lines. He was wrong.

    The father of four turns to his computer to pull up a video of a group of medical personnel working feverishly in an improvised Aleppo operating room. “That’s me,” he says, pointing to blue rubber-gloved hands holding a beating heart spurting blood from a hole torn open by shrapnel. (The patient survived.)

    After shadowing and assisting David Nott, a London specialist and war surgeon who visited Aleppo in 2013 for six weeks, Hariri was on his own. Soon he was performing complex surgeries — vascular, lung, and open-heart — with lives in the balance.

    At Harvard, he is helping others gain the experience they need to become doctors in his war-ravaged country, where skilled medical professionals are increasingly rare. Hariri, who is being hosted by the Harvard Humanitarian Initiative and the Harvard T.H. Chan School of Public Health’s Department of Global Health and Population, is focused on developing the medical school arm of the new Free Aleppo University.

    “It’s accredited and registered with the World Health Organization,” said Hariri, adding, “It’s our university.”

    He is also working on building a network of doctors, medical educators, and experts who can continue to train young doctors in Syria whose postgraduate work was interrupted by civil war. Hariri and his Syrian team are connecting via the web specialists from the United States, the United Kingdom, and Saudi Arabia with Syrian students for interviews, oral exams, and online tests.

    In Aleppo, Hariri helped coordinate an underground network of physicians and makeshift hospitals, safe houses filled with supplies where doctors can perform emergency surgeries. To avoid being targeted by bombs they removed sirens and lights from their ambulances and camouflaged the trucks’ bright yellow paint with mud. They trained themselves to do everything, from patient record-keeping to preparing for and responding to chemical attacks.

    “Step by step we learned how to organize the work.”

    Harari is convinced that education is the light that will show his country the way out of conflict.

    “Fighting extremism starts from education,” he said, “not from the fight. I believe that education, education is the key for freedom, self-dignity, development, and getting rid of all extremism. For that reason I am working on this with my friends.”

    In 2014, his friends in the Syrian medical community promised to nominate him for the Harvard fellowship if the surgeon promised them something as well: he would return. Hariri chuckled as he recalled the agreement. Going back, he said, has never been in question. His response to those who ask him about seeking asylum in the United States is always the same.

    “I need to go back home,” he tells them. “I believe that my home needs me. I have to work for them.”

    In the spring, after his fellowship ends, Hariri will stay true to his promise, heading first to Turkey, where he will leave his family, and then back to Syria to continue his work.

    “I know that the future looks grim … I don’t expect that something good will be happening soon. But in spite of this, we do believe that we have to do our best.”

    See the full article here .

    Please help promote STEM in your local schools.

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    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 3:50 pm on January 26, 2017 Permalink | Reply
    Tags: Advance in high-pressure physics, Atomic metallic hydrogen, Diamond anvil cell, Harvard   

    From Harvard: “Advance in high-pressure physics” 

    Harvard University
    Harvard University

    January 26, 2017
    Peter Reuell

    Harvard scientists announce they’ve created metallic hydrogen, which has been just a theory.


    Access mp4 video here .

    Nearly a century after it was theorized, Harvard scientists report they have succeeded in creating the rarest material on the planet, which could eventually develop into one of its most valuable.

    Thomas D. Cabot Professor of the Natural Sciences Isaac Silvera and postdoctoral fellow Ranga Dias have long sought the material, called atomic metallic hydrogen. In addition to helping scientists answer some fundamental questions about the nature of matter, the material is theorized to have a wide range of applications, including as a room-temperature superconductor. Their research is described in a paper published today in Science.

    “This is the Holy Grail of high-pressure physics,” Silvera said of the quest to find the material. “It’s the first-ever sample of metallic hydrogen on Earth, so when you’re looking at it, you’re looking at something that’s never existed before.”

    In their experiments, Silvera and Dias squeezed a tiny hydrogen sample at 495 gigapascal (GPa), or more than 71.7 million pounds per square inch, which is greater than the pressure at the center of the Earth. At such extreme pressures, Silvera explained, solid molecular hydrogen, which consists of molecules on the lattice sites of the solid, breaks down, and the tightly bound molecules dissociate to transforms into atomic hydrogen, which is a metal.

    While the work creates an important window into understanding the general properties of hydrogen, it also offers tantalizing hints at potentially revolutionary new materials.

    “One prediction that’s very important is metallic hydrogen is predicted to be meta-stable,” Silvera said. “That means if you take the pressure off, it will stay metallic, similar to the way diamonds form from graphite under intense heat and pressure, but remain diamonds when that pressure and heat are removed.”

    Understanding whether the material is stable is important, Silvera said, because predictions suggest metallic hydrogen could act as a superconductor at room temperatures.

    “As much as 15 percent of energy is lost to dissipation during transmission,” he said, “so if you could make wires from this material and use them in the electrical grid, it could change that story.”

    A room temperature superconductor, Dias said, could change our transportation system, making magnetic levitation of high-speed trains possible, as well as making electric cars more efficient and improving the performance of many electronic devices. The material could also provide major improvements in energy production and storage. Because superconductors have zero resistance, superconducting coils could be used to store excess energy, which could then be used whenever it is needed.

    Metallic hydrogen could also play a key role in helping humans explore the far reaches of space, as a more powerful rocket propellant.

    2
    Microscopic images of the stages in the creation of atomic molecular hydrogen: Transparent molecular hydrogen (left) at about 200 GPa, which is converted into black molecular hydrogen, and finally reflective atomic metallic hydrogen at 495 GPa. Courtesy of Isaac Silvera.

    “It takes a tremendous amount of energy to make metallic hydrogen,” Silvera explained. “And if you convert it back to molecular hydrogen, all that energy is released, so that would make it the most powerful rocket propellant known to man, and could revolutionize rocketry.”

    The most powerful fuels in use today are characterized by a “specific impulse” (a measure, in seconds, of how fast a propellant is fired from the back of a rocket) of 450 seconds. The specific impulse for metallic hydrogen, by comparison, is theorized to be 1,700 seconds.

    “That would easily allow you to explore the outer planets,” Silvera said. “We would be able to put rockets into orbit with only one stage, versus two, and could send up larger payloads, so it could be very important.”

    In their experiments, Silvera and Dias turned to one of the hardest materials on Earth, diamond. But rather than natural diamond, Silvera and Dias used two small pieces of carefully polished synthetic diamond and treated them to make them even tougher. Then they mounted them opposite each other in a device known as a diamond anvil cell.

    “Diamonds are polished with diamond powder, and that can gouge out carbon from the surface,” Silvera said. “When we looked at the diamond using atomic force microscopy, we found defects, which could cause it to weaken and break.”

    The solution, he said, was to use a reactive ion etching process to shave a tiny layer — just five microns thick, or about a tenth the thickness of a human hair — from the diamond’s surface. The diamond was then coated with a thin layer of alumina to prevent the hydrogen from diffusing into the crystal structure and embrittling it.

    After more than four decades of work on metallic hydrogen, and nearly a century after it was first theorized, it was thrilling to see the results, Silvera said.

    “It was really exciting,” he said. “Ranga was running the experiment, and we thought we might get there, but when he called me and said, ‘The sample is shining,’ I went running down there, and it was metallic hydrogen.”

    “I immediately said we have to make the measurements to confirm it, so we rearranged the lab … and that’s what we did.”

    See the full article here .

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    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 1:31 pm on January 19, 2017 Permalink | Reply
    Tags: , , Harvard, , ,   

    From Harvard: Women in STEM – “Strengthening ties among women in physics” 

    Harvard University

    Harvard University

    January 18, 2017
    Alvin Powell

    1
    An attendee at the Conference for Undergraduate Women in Physics examines equipment in the lab of Michael J. Aziz, the Gene and Tracy Sykes Professor of Materials and Energy Technologies. Photo by Silvia Mazzocchin

    When Margaret Morris looks around her physics class, sometimes she is the only woman there.

    Morris, a senior at Brandeis University, is living the reality for physics in the United States. At a time when women make up the majority of the country’s college students, their numbers still trail male peers in certain fields. And in some disciplines, like physics, women remain a small minority.

    Last weekend, 250 physics majors gathered at Harvard to take a collective step toward a new reality.

    The Conference for Undergraduate Women in Physics included lab tours, lectures, personal stories, and practical discussions about research, graduate school applications, how to deal with discrimination and implicit bias, and finding mentors.

    2
    Margaret Morris, a senior at Brandeis University, listens to a presentation at the Conference for Undergraduate Women in Physics. Morris was one of 250 physics majors in attendance. Photo by Silvia Mazzocchin

    Organizer Anne Hebert, a Harvard grad student, said the conference was designed to connect participants with a support network that will help them move ahead in the field.

    “As an undergraduate, obviously I noticed there weren’t many girls around,” Hebert said. “Every girl in physics has a moment when they turn their head and realize they’re the only girl in the room.”

    One of her fellow organizers, Ellen Klein, a Harvard doctoral student, said that as an undergrad at Yale University, she felt supported by faculty members and never experienced blatant gender discrimination. But she has noticed that there have been fewer women as she’s advanced through different academic levels.

    3
    Ellen Klein (not pictured), a Harvard Graduate School of Arts and Sciences doctoral student, said she’s noticed fewer women as she’s advanced through different academic levels. Photo by Silvia Mazzocchin

    Delilah Gates, also an organizing committee member and Harvard doctoral student, agreed with Klein and Hebert that bias, though often subtle, is still a problem. All three have heard male classmates joke about women and understood in a visceral way that, though real progress has been made, plenty of work remains.

    Gates added that as a black woman, she felt a lot of pressure in college to show that her opportunities weren’t handed to her because of race, leaving her temporarily conflicted about applying to graduate school.

    “In college, I kind of didn’t anticipate it. I was struck by the pressure I felt because of being an African-American woman and [proving] that no one was handing it to me because I check off a diversity box,” Gates said.

    The campus conference, organized through the American Physical Society, was one of 10 that took place across the United States and Canada and the first to be hosted by Harvard.

    4
    Suela Restelica, a sophomore at Orange County Community College in New York state, joined her fellow physics majors. Photo by Silvia Mazzocchin

    Some 1,500 women attended a session somewhere, Hebert said. A workshop titled SPIN UP, for Supporting Inclusion for Underrepresented Peoples, preceded the Harvard conference. The event was aimed at other underrepresented groups in the field, including minorities, students with disabilities, and students from low-income families.

    Physics helps solve problems facing humanity, said Masahiro Morii, chair of Harvard’s Physics Department, which provided logistical support for the student-run conference. And, though women make up half the population, they still make up less than 25 percent of physics graduate students.

    “Until it’s 50 percent, we’re still wasting a lot of talent that’s out there,” Morii said.

    See the full article here .

    Please help promote STEM in your local schools.

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    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 10:23 am on January 13, 2017 Permalink | Reply
    Tags: , , Harvard, , , Sugar stands accused   

    From Harvard: “Sugar stands accused” This Is Important for All 

    Harvard University

    Harvard University

    Sugar was in the dock at Harvard Law School this week, accused of a prime role in the twin epidemics of obesity and diabetes sweeping the country.

    1
    Gary Taubes signs copies of his book “The Case Against Sugar” following his talk for the Food Law and Policy Clinic. The acclaimed science writer hypothesizes that sugar “has deleterious effects on the human body that lead to obesity and diabetes, and that it should be considered a prime suspect [in the national dietary epidemic].” Stephanie Mitchell/Harvard Staff Photographer

    Science journalist and author Gary Taubes ’77 made his case that sugar consumption — which has risen dramatically over the last century — drives metabolic dysfunction that makes people sick. The hour-long talk was sponsored by the Food Law and Policy Clinic and drawn from Taubes’ new book, The Case Against Sugar.

    A reputation for “empty calories” — devoid of vitamins and nutrients but otherwise no different from other foods containing an equal number of calories — has allowed sugar to maintain a prominent place in the U.S. diet. Taubes is dubious. First, all calories are not equal because the body metabolizes different foods in different ways. More specifically, there may be something about eating too much sugar — in particular fructose, which is metabolized in the liver — that implicates it in metabolic disease.

    “I’m making an argument that sugar is uniquely toxic,” said Taubes. “It has deleterious effects on the human body that lead to obesity and diabetes.”

    Taubes laid out a case that he admitted was “largely circumstantial,” though one he considers compelling enough that it would gain at least an indictment from an impartial jury. The problem with the evidence, he said, is that public health researchers haven’t focused enough attention on sugar.

    “The research doesn’t exist beyond reasonable doubt that sugar is to blame,” Taubes said.

    Diabetes, Taubes noted, was once a rare disease. He traced its rise through the 1800s and 1900s from just a fraction of 1 percent of the cases seen at Massachusetts General Hospital to a condition that afflicts nearly 10 percent of the U.S. population, according to the Centers for Disease Control and Prevention. That increase, he said, coincides with an increase in sugar in the American diet.

    He tied today’s problems to both the sugar industry and some of the scientists responsible for informing the public about diet. Two researchers prominent in Harvard’s history didn’t escape blame: Elliott Joslin, the founder of the Harvard-affiliated Joslin Diabetes Center, and Frederick Stare, the founder of the Harvard T.H. Chan School of Public Health’s Nutrition Department.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 10:46 am on January 5, 2017 Permalink | Reply
    Tags: , , Harvard, , , , The Search for Extraterrestrial Genomes or SETG   

    From Many Worlds: “In Search of Panspermia” 

    NASA NExSS bloc

    NASA NExSS

    Many Worlds

    Many Words icon

    2017-01-05
    Marc Kaufman

    1
    This image is from the NASA Remote Sensing Tutorial. NASA

    When scientists approach the question of how life began on Earth, or elsewhere, their efforts generally involve attempts to understand how non-biological molecules bonded, became increasingly complex, and eventually reached the point where they could replicate or could use sources of energy to make things happen. Ultimately, of course, life needed both.

    Researchers have been working for some time to understand this very long and winding process, and some have sought to make synthetic life out of selected components and energy. Some startling progress has been made in both of these endeavors, but many unexplained mysteries remain at the heart of the processes. And nobody is expecting the origin of life on Earth (or elsewhere) to be fully understood anytime soon.

    To further complicate the picture, the history of early Earth is one of extreme heat caused by meteorite bombardment and, most important, the enormous impact some 4.5 billion years of the Mars-sized planet that became our moon. As a result, many early Earth researchers think the planet was uninhabitable until about 4 billion years ago.

    Yet some argue that signs of Earth life 3.8 billion years ago have been detected in the rock record, and lifeforms were certainly present 3.5 billion years ago. Considering the painfully slow pace of early evolution — the planet, after all, supported only single-cell life for several billion years before multicellular life emerged — some researchers are skeptical about the likelihood of DNA-based life evolving in the relatively short window between when Earth became cool enough to support life and the earliest evidence of actual life.

    1
    A DNA helix animation. Life on Earth is based on DNA, and some researchers have been working on ways to determine whether DNA life also exists on Mars or elsewhere in the solar system. No image credit.

    So what else, from a scientific as opposed to a religious perspective, might have set into motion the process that made life out of non-life?

    A team of prominent scientists at MIT and Harvard are sufficiently convinced in the plausibility of panspermia that they have spent a decade, and a fair amount of NASA and other funding, to design and produce an instrument that can be sent to Mars and potentially detect DNA or more primitive RNA.

    In other words, life not only similar to that on Earth, but actually delivered long ago from Earth. It’s called the The Search for Extraterrestrial Genomes, or SETG.

    Gary Ruvkun is one of those researchers, a pioneering molecular biologist at Massachusetts General Hospital and professor of genetics at Harvard Medical School.

    I heard him speaking recently at a Space Sciences Board workshop on biosignatures, where he described the real (if slim) possibility that DNA or RNA-based life exists now on Mars, and the instrument that the SETG group is developing to detect it should it be there.

    The logic of panspermia — or perhaps “dispermia” if between but two planets — is pretty straight-forward, though with some significant question marks. Both Earth and Mars, it is well known, were pummeled by incoming meteorites in their earlier epochs, and those impacts are known to have sufficient force to send rock from the crash site into orbit.

    Mars meteorites have been found on Earth, and Earth meteorites no doubt have landed on Mars. Ruvkun said that recent work on the capacity of dormant microbes to survive the long, frigid and irradiated trip from planet to planet has been increasingly supportive.

    “Earth is filled with life in every nook and cranny, and that life is wildly diverse,” he told the workshop. “So if you’re looking for life on Mars, surely the first thing to look for is life like we find on Earth. Frankly, it would be kind of stupid not to.”

    The instrument being developed by the group, which is led by Ruvkun and Maria Zuber, MIT vice president for research and head of the Department of Earth, Atmospheric and Planetary Sciences. It would potentially be part of a lander or rover science package and would search DNA or RNA, using techniques based on the exploding knowledge of earthly genomics.

    The job is made easier, Ruvkun said, by the fact that the basic structure of DNA is the same throughout biology. What’s more, he said, there about 400 specific genes sequences “that make up the core of biology — they’re found in everything from extremeophiles and bacteria to worms and humans.”

    Those ubiquitous gene sequences, he said, were present more than 3 billion years ago in seemingly primitive lifeforms that were, in fact, not primitive at all. Rather, they had perfected some genetic pathways that were so good that they still used by most everything alive today.

    And how was it that these sophisticated life processes emerged not all that long (in astronomical or geological terms) after Earth cooled enough to be habitable? “Either life developed here super-fast or it came full-on as DNA life from afar,” Ruvkun said. It’s pretty clear which option he supports.

    Ruvkun said that the rest of the SETG team sees that kind of inter-planetary transfer — to Mars and from Mars — as entirely plausible, and that he takes panspermia a step forward. He thinks it’s possible, though certainly not likely nor remotely provable today, that life has been around in the cosmos for as long as 10 billion years, jumping from one solar system and planet to another. Not likely, but at idea worth entertaining.

    Maria Zuber of MIT, who was the PI for the recent NASA GRAIL mission to the moon, has been part of the SETG team since near its inception, and MIT research scientist Christopher Carr is the project manager. Zuber said it was a rather low-profile effort at the start, but over the years has attracted many students and has won NASA funding three times including the currently running Maturation of Instruments for Solar System Exploration (MatISSE) grant.

    “I have made my career out of doing simple experiments. if want to look for life beyond earth helps to know what you’re looking for.

    “We happen to know what life on Earth is like– DNA based or possibly RNA-based as Gary is looking for as well. The point is that we know what to look for. There are so many possibilities of what life beyond Earth could be like that we might as well test the hypothesis that it, also, is DNA based. It’s a low probability result, but potentially very high value.”

    DNA sequencing instruments like the one her team is developing are taken to the field regularly by thousands of researchers, including some working with with SETG. The technology has advanced so quickly that they can pick up a sample in a marsh or desert or any extreme locale and on the spot determine what DNA is present. That’s quite a change from the pain-staking sequencing done painstakingly by graduate students not that long ago.

    Panspermia, Zuber acknowledged, is a rather improbable idea. But when nature is concerned, she said “I’m reticent to say anything is impossible. After all, the universe is made up of the same elements as those on Earth, and so there’s a basic commonality.”

    Zuber said the instrument was not ready to compete for a spot on the 2020 mission to Mars, but she expects to have a sufficiently developed one ready to compete for a spot on the next Mars mission. Or perhaps on missions to Europa or the plumes of Enceladus.

    he possibility of life skipping from planet to planet clearly fascinates both scientists and the public. You may recall the excitement in the mid 1990s over the Martian meteorite ALH84001, which NASA researchers concluded contained remnants of Martian life. (That claim has since been largely refuted.)

    Of the roughly 61,000 meteorites found on Earth, only 134 were deemed to be Martian as of two years ago. But how many have sunk into oceans or lakes, or been lost in the omnipresence of life on Earth? Not surprisingly, the two spots that have yielded the most meteorites from Mars are Antarctica and the deserts of north Africa.

    And when thinking of panspermia, it’s worthwhile to consider the enormous amount of money and time put into keeping Earthly microbes from inadvertently hitching a ride to Mars or other planets and moons as part of a NASA mission.

    The NASA office of planetary protection has the goal of ensuring, as much as possible, that other celestial bodies don’t get contaminated with our biology. Inherent in that concern is the conclusion that our microbes could survive in deep space, could survive the scalding entry to another planet, and could possibly survive on the planet’s surface today. In other words, that panspermia (or dispermia) is in some circumstances possible.

    Testing whether a spacecraft has brought Earth life to Mars is actually another role that the SETG instrument could play. If a sample tested on Mars comes back with a DNA signature result exactly like one on Earth–rather one that might have come initially from Earth and then evolved over billions of years– then scientists will know that particular bit of biology was indeed a stowaway from Earth.

    Rather like how a very hardy microbe inside a meteorite might have possibly traveled long ago.

    See the full article here .

    Please help promote STEM in your local schools.

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    About Many Worlds

    There are many worlds out there waiting to fire your imagination.

    Marc Kaufman is an experienced journalist, having spent three decades at The Washington Post and The Philadelphia Inquirer, and is the author of two books on searching for life and planetary habitability. While the “Many Worlds” column is supported by the Lunar Planetary Institute/USRA and informed by NASA’s NExSS initiative, any opinions expressed are the author’s alone.

    This site is for everyone interested in the burgeoning field of exoplanet detection and research, from the general public to scientists in the field. It will present columns, news stories and in-depth features, as well as the work of guest writers.

    About NExSS

    The Nexus for Exoplanet System Science (NExSS) is a NASA research coordination network dedicated to the study of planetary habitability. The goals of NExSS are to investigate the diversity of exoplanets and to learn how their history, geology, and climate interact to create the conditions for life. NExSS investigators also strive to put planets into an architectural context — as solar systems built over the eons through dynamical processes and sculpted by stars. Based on our understanding of our own solar system and habitable planet Earth, researchers in the network aim to identify where habitable niches are most likely to occur, which planets are most likely to be habitable. Leveraging current NASA investments in research and missions, NExSS will accelerate the discovery and characterization of other potentially life-bearing worlds in the galaxy, using a systems science approach.
    The National Aeronautics and Space Administration (NASA) is the agency of the United States government that is responsible for the nation’s civilian space program and for aeronautics and aerospace research.

    President Dwight D. Eisenhower established the National Aeronautics and Space Administration (NASA) in 1958 with a distinctly civilian (rather than military) orientation encouraging peaceful applications in space science. The National Aeronautics and Space Act was passed on July 29, 1958, disestablishing NASA’s predecessor, the National Advisory Committee for Aeronautics (NACA). The new agency became operational on October 1, 1958.

    Since that time, most U.S. space exploration efforts have been led by NASA, including the Apollo moon-landing missions, the Skylab space station, and later the Space Shuttle. Currently, NASA is supporting the International Space Station and is overseeing the development of the Orion Multi-Purpose Crew Vehicle and Commercial Crew vehicles. The agency is also responsible for the Launch Services Program (LSP) which provides oversight of launch operations and countdown management for unmanned NASA launches. Most recently, NASA announced a new Space Launch System that it said would take the agency’s astronauts farther into space than ever before and lay the cornerstone for future human space exploration efforts by the U.S.

    NASA science is focused on better understanding Earth through the Earth Observing System, advancing heliophysics through the efforts of the Science Mission Directorate’s Heliophysics Research Program, exploring bodies throughout the Solar System with advanced robotic missions such as New Horizons, and researching astrophysics topics, such as the Big Bang, through the Great Observatories [Hubble, Chandra, Spitzer, and associated programs. NASA shares data with various national and international organizations such as from the [JAXA]Greenhouse Gases Observing Satellite.

     
  • richardmitnick 9:36 am on December 22, 2016 Permalink | Reply
    Tags: , Diamonds are a lab’s best friend, Harvard, Tracking neural signals in the brain   

    From Harvard: “Diamonds are a lab’s best friend” 

    Harvard University
    Harvard University

    1
    PH.D. candidates Jenny Schloss (left) and Matthew Turner are co-authors of a recent paper on using nitrogen vacancy centers — atomic-scale impurities in diamond — to track neural activity. “We want to understand the brain from the single-neuron level all the way up, so we envision that this could become a tool useful both in biophysics labs and in medical studies,” said Schloss.
    Rose Lincoln/Harvard Staff Photographer

    Harvard researchers trace neural activity by using quantum sensors

    December 19, 2016
    Peter Reuell

    It’s one of the purest and most versatile materials in the world, with uses in everything from jewelry to industrial abrasives to quantum science. But a group of Harvard scientists has uncovered a new use for diamonds: tracking neural signals in the brain.

    Using atomic-scale quantum defects in diamonds known as nitrogen-vacancy (NV) centers to detect the magnetic field generated by neural signals, scientists working in the lab of Ronald Walsworth, a faculty member in Harvard’s Center for Brain Science and Physics Department, demonstrated a noninvasive technique that can image the activity of neurons.

    The work was described in a recent paper in the Proceedings of the National Academy of Sciences, and was performed in collaboration with Harvard faculty members Mikhail (Misha) Lukin and Hongkun Park.

    “The idea of using NV centers for sensing neuron magnetic fields began with the initial work of Ron Walsworth and Misha Lukin about 10 years ago, but for a long time our back-of-the-envelope calculations made it seem that the fields would be too small to detect, and the technology wasn’t there yet,” said Jennifer Schloss, a Ph.D. student and co-author of the study.

    “This paper is really the first step to show that measuring magnetic fields from individual neurons can be done in a scalable way,” said Ph.D. student and fellow co-author Matthew Turner. “We wanted to be able to model the signal characteristics, and say, based on theory, ‘This is what we expect to see.’ Our experimental results were consistent with these expectations. This predictive ability is important for understanding more complicated neuronal networks.”

    At the heart of the system developed by Schloss and Turner, together with postdoctoral scientist John Barry, is a tiny — just 4-by-4 millimeters square and half a millimeter thick — wafer of diamond impregnated with trillions of NV centers.

    The system works, Schloss and Turner explained, because the magnetic fields generated by signals traveling in a neuron interact with the electrons in the NV centers, subtly changing their quantum “spin” state. The diamond wafer is bathed in microwaves, which put the NV electrons in a mixture of two spin states. A neuron magnetic field then causes a change in the fraction of spins in one of the two states. Using a laser constrained to the diamond, the researchers can detect this fraction, reading out the neural signal as an optical image, without light entering the biological sample.

    In addition to demonstrating that the system works for dissected neurons, Schloss, Turner, and Barry showed that NV sensors could be used to sense neural activity in live, intact marine worms.

    “We realized we could just put the whole animal on the sensor and still detect the signal, so it’s completely noninvasive,” Turner said. “That’s one reason using magnetic fields offers an advantage over other methods. If you measure voltage- or light-based signals in traditional ways, biological tissue can distort those signals. With magnetic fields, though the signal gets smaller with stand-off distance, the information is preserved.”

    Schloss, Turner, and Barry were also able to show that the neural signals traveled more slowly from the worm’s tail to its head than from head to tail, and their magnetic field measurements matched predictions of this difference in conduction velocity.

    While the study proves that NV centers can be used to detect neural signals, Turner said the initial experiments were designed to tackle the most accessible approach to the problem, using robust neurons that produce especially large magnetic fields. The team is already working to further refine the system, with an eye toward improving its sensitivity and pursuing applications to frontier problems in neuroscience. To sense signals from smaller mammalian neurons, Schloss explained, they intend to implement a pulsed magnetometry scheme to realize up to 300 times better sensitivity per volume. The next step, said Turner, is implementing a high-resolution imaging system in hopes of producing real-time, optical images of neurons as they fire.

    “We’re looking at imaging networks of neurons over long durations, up to days,” said Schloss. “We hope to use this to understand not just the physical connectivity between neurons, but the functional connectivity — how the signals actually propagate to inform how neural circuits operate over the long term.”

    “No tool that exists today can tell us everything we want to know about neuronal activity or be applied to all systems of interest,” Turner said. “This quantum diamond technology lays out a new direction for addressing some of these challenges. Imaging neuron magnetic fields is a largely unexplored area due to previous technological limitations.”

    The hope, Schloss said, is that the tool might one day find a home in the labs of biomedical researchers or anyone interested in understanding brain activity.

    “We want to understand the brain from the single-neuron level all the way up, so we envision that this could become a tool useful both in biophysics labs and in medical studies,” she said. “It’s noninvasive and fast, and the optical readout could allow for a variety of applications, from studying neurodegenerative diseases to monitoring drug delivery in real time.”

    Walsworth credits the leadership of Josh Sanes, the Paul J. Finnegan Family Director of the center, and Kenneth Blum, executive director, for enabling this biological application of quantum diamond technology. “Center for Brain Science leadership provided the essential lab space and a welcoming, interdisciplinary community,” he said. “This special environment allows physical scientists and engineers to translate quantum technology into neuroscience.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 1:33 pm on December 8, 2016 Permalink | Reply
    Tags: , Harvard, ,   

    From Harvard: “Colorful clones track stem cells” 

    Harvard University

    Harvard University

    November 23, 2016 {Just found this in social media.]
    Hannah Robbins, HSCI Communications

    1

    Harvard Stem Cell Institute (HSCI) researchers have used a colorful cell-labeling technique to track the development of the blood system and trace the lineage of adult blood cells traveling through the vast networks of veins, arteries, and capillaries back to their parent stem cells in the marrow.

    Developed at Harvard’s Center for Brain Science, the technique involves coding multiple colors of fluorescent protein into a cell’s DNA. As genes recombine inside the cell, the cell elaborates a color unique to its genetic code. For blood stem cells, that color becomes a genetic signature passed down to daughter cells; purple stem cells, for example, will only make purple blood cells.

    Two independent research teams, one led by David Scadden, HSCI co-director and Gerald and Darlene Jordan Professor of Medicine at Harvard University, and the other by his colleague Leonard Zon, HSCI Executive Committee member and director of the Stem Cell Program at Boston Children’s Hospital, adapted the color-based labeling to the blood system to better understand how blood stem cells behave.

    In a study recently published in Cell, a research team led by Scadden found that in mice individual blood stem cells had a specific and restricted blood production repertoire.

    “We used to think of stem cells as the mother cell that gives rise to all these other cells in the system on an as-needed basis,” said Vionnie Yu, first author of the study and, at the time of the research, a postdoctoral fellow in Scadden’s lab. But their results suggest that stem cells have a scripted set of responses and cannot make just any blood cell type.

    When transplanted into a new environment, each cell not only consistently made the same mature blood cell types but also the same number of those cells. Additionally, clones responded similarly to inflammatory and chemotoxic stress, suggesting the cells had a hardwired memory dictating their behavior. They found that this memory was written into the stem cell epigenome.

    Blood stem cells, said Scadden, may be more like chess pieces with a fixed way they can behave within the system.

    “When you are young and have a full chess set you can mount a vigorous and multilayered defense to an attack on your system,” Scadden said, “but if you lose chess pieces with age or you don’t receive a full suite of players during a bone marrow transplant, the pieces you have left could determine your ability to protect yourself.”

    In addition to looking at blood stem cells in adult mice, color tagging also allows researchers to explore the blood system as a zebrafish embryo develops.

    “We’ve been working with David Scadden for years as part of the HSCI. Initially, we presented our work at a joint lab meeting and realized we could study stem cell clones with this multicolor system,” said Zon, who is also a professor in Harvard’s Stem Cell and Regenerative Biology department. “We shared ideas and results, and even wrote a grant together on the topic. It is wonderful that studying clonal dynamics in two different animals could provide such complementary information.”

    In a study published Monday in Nature Cell Biology, the researcher team led by Zon used the color-tagging system to find the origin and number of stem cells that contribute to lifelong blood production.

    About 24 to 30 hours after fertilization, dozens of stem cells budded off from the dorsal side of the aorta. Only 20 made it to a secondary site before heading to the kidney marrow, the zebrafish equivalent to human and mouse bone marrow.

    After transplanting the multicolored marrow into fish that had received sublethal doses of radiation, the researchers found that some blood stem cell lineages supplied a greater proportion of blood than they had before and that certain lineages could survive harsher conditions than others.

    Knowing which cells are responsible for blood production could have implications for understanding the development of blood cancers, explained Jonathan Henninger, a graduate student in Zon’s lab at Boston Children’s Hospital and first author in the study.

    For example, one cell could develop a mutation that gives it a competitive edge, allowing it to take over the blood system.

    “If that cell starts behaving badly, it could lead to blood disorders, such as myeloid dysplasia and leukemia,” Henninger said.

    Researchers know these disorders come from a single stem cell or a downstream progenitor cell, said Henninger, but right now they are looking at populations of stem cells in bulk. “To be able to identify that single cell that went awry could help us better understand these diseases.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 9:22 am on December 7, 2016 Permalink | Reply
    Tags: , , Harvard, Professor Pier Paolo Pandolfi   

    From Harvard: “Fresh ways to fight cancer” 

    Harvard University
    Harvard University

    December 6, 2016
    Alvin Powell

    1
    Professor Pier Paolo Pandolfi speaks about revolutionary developments in cancer care and how he sees treatment evolving. “We will defeat cancer. Conceptually, we can. But it will take time.”
    Stephanie Mitchell/Harvard Staff Photographer

    In recent years, cancer patients have benefited from a new array of weapons to fight the disease. Traditional chemotherapy and radiation therapy — blunt clubs aimed at any fast-growing cell in the body — have been augmented by “targeted therapy” drugs that interfere with specific cellular functions in an attempt to block cancer growth.

    More recently, therapies that unleash the body’s immune system on cancer have been making their way to the clinic, offering new “immunotherapy” weapons in what has become an expanding clinical arsenal.

    Researchers came to Boston in November for a daylong symposium on curing cancer. The session at Beth Israel Deaconess Medical Center (BIDMC) was hosted by Pier Paolo Pandolfi, George C. Reisman Professor of Medicine at Harvard Medical School and director of BIDMC’s Cancer Center and Cancer Research Institute.

    Pandolfi talked to the Gazette about the encouraging progress in the fight against cancer and about a promising new avenue of investigation opened by the discovery of another type of RNA.

    GAZETTE: You wrote in 2013 that we’re in a period of unprecedented opportunity in cancer research. Do you still believe that, and, if so, why?

    PANDOLFI: Absolutely. … I haven’t changed my mind a bit. Actually, there is more enthusiasm now, and our symposium was a testament to the enthusiasm. It was well attended because everyone is [asking] about the revolution in immune therapy. … But there is a second aspect, which is the noncoding RNA revolution. I don’t know if you’ve heard about it?

    GAZETTE: What can you tell me about it?

    PANDOLFI: This eye-opening, almost inconvenient truth emerged that our genome is a bit more complex than anticipated.

    We are [now] able to not only sequence the genome, but to sequence the transcriptome, the RNA that comes from the DNA.

    We realized that our protein-coding genome is only 2 percent of the [entire genome], [but] the rest of the genome — the other 98 percent — is not silent and does more than regulate protein-coding gene expression. In fact, it’s heavily transcribed and … at last count, we may have as many as 100,000 RNAs in our cells that don’t code for proteins.

    These include circular RNAs, circRNAs, which we didn’t see until now because we didn’t have the bioinformatics tools. Now, we appreciate that this species is one of the most abundant RNAs in our cells.

    We discovered that these RNAs are functional or profoundly dysfunctional, driving disease as well as protein-coding genes. This new knowledge will allow us to find new disease genes, to develop new drugs and new medicines. We are talking about RNA medicine. In our Cancer Center, we launched the Institute for RNA Medicine, a research initiative [that] is expected soon to become Harvard-wide.

    GAZETTE: What about treatments in the mainstream today or moving into the mainstream?

    PANDOLFI: There are two major breakthroughs. One is the targeted therapy revolution.

    Conceptually, we’ve moved from chemotherapy and radiotherapy, which are based on the only thing that we [once] knew about cancer: that it is characterized by proliferation.

    The idea was that if you block proliferation, the cancer will suffer. [But] resistance ensues, and toxicity is huge because our body also has [noncancer] cells that proliferate.

    Then we discovered cancer is driven by protein-coding genes. … We could develop drugs that do not necessarily kill the cancer cell, but rather fix the molecular problem [within the cell].

    This approach led to great success. The reason why I’m here and director of this Cancer Center is … the story of a leukemia, APL [acute promyelocytic leukemia], which we cured.

    We developed a combinatorial treatment, which eradicated the disease. We found two drugs that go after the oncogene. Now this concept is accepted, with hundreds of targets, hundreds of oncogenes or tumor suppressors. The pharmaceutical industry is working hard in that space.

    The second new weapon is immune therapy. Cancer cells shut down the immune response in many ways. Cancer basically develops a shield to protect itself from the immune system. Now scientists have cracked this shield with approaches that go after it and break it down.

    The fruition of this new approach is what we are experiencing now. There are immune therapies that can really cure, meaning you can deploy the drug that breaks the shield and the immune system wipes the cancer out. The beauty of all this is … you can develop vaccines.

    You can create vaccines whereby the immune system remembers … so if there’s residual disease, as soon as the cancer tries to resurface, it will be again attacked by the immune system.

    GAZETTE: We know a lot more about cancer than we did before, but part of what we know is that even within different types of cancer — lung cancer, liver cancer, breast cancer — there are different genetic profiles …

    PANDOLFI: We already know that cancer is not one disease, but many. Complexity is very high.

    So the challenge is twofold. We have hundreds of new [drug candidate] molecules, for each and every pathway of cancer. The first hurdle is to understand very rapidly which cancer they may work on, which cancer they may not, and why.

    Then, say the cancer [has] many mutations. Which mutation would confer resistance to that drug, and which combination of drugs will overcome that resistance? How can we combine them with immune therapies? The challenge now is how do we test all these things because if we did it in a human being, it would take forever.

    We came up with this idea of the “mouse hospital,” which is one of the signatures of our Cancer Center. We re-created the complexity of human cancer at three levels.

    First, we made mice that are genetically engineered to harbor all these genes that we are talking about, and now the noncoding RNAs. So the idea is to make a mouse which is a phenocopy of the cancer of Mr. Smith, who is treated at the Cancer Center, by engineering the mouse to express the genes of Mr. Smith.

    The second way is that you take the tumor of Mr. Smith, a biopsy, and you put it in a mouse. This is called an “avatar approach” or “patient-derived xenograft.” So you put the tumor in a mouse, and then you retransplant it in many mice. You have 100 mice, then you treat them with several drugs to very quickly understand which [drug] would work and which one would not.

    Meanwhile, Mr. Smith gets his standard therapy. They offer him drug X, then he fails and they offer him drug Y. As soon as he fails everything standard, there is what I call the panic phase. If you have the [mouse] avatar, while the patient is given the standard treatment, you can find a new drug or new drug combination that you can offer.

    The third approach is even faster. Again, Mr. Smith comes to the center, we biopsy his tumor or we take a leukemia sample and we put it in a [lab] dish. We grow mini tumors — organoids — and again test with several drugs. The organoid has the advantage that it is much less expensive and much faster. You can go from biopsy to drug testing in a matter of weeks.

    The next hurdle is very simple: Who pays for it? Maybe we’ll convince the insurers to pay for organoids. You don’t want to spend a huge amount of money to give Mr. Smith a drug that doesn’t work. So … why don’t you give us a little more money to do genotyping analysis and organoids? This prescreening allows you to know if the drug is needed.

    But we are not yet there. [Now] this approach is funded by government through grants, by philanthropy, and by the cancer center.

    GAZETTE:: How long until these new therapies become the standard of care? People are still getting chemo and radiation therapy …

    PANDOLFI: This is a big ongoing argument. We still offer a standard of care that is oftentimes obsolete. We know it doesn’t work. Why don’t we flip the approach? Why don’t we offer the targeted therapies first and then maybe we follow with the standard of care?

    The other thing happening now is the need to deliver combination therapy. But the FDA still doesn’t allow you to try a combination or cocktail of drugs in [clinical trials]. You have to do it one at a time, which is never-ending. There are a number of people who are pushing to do a cocktail of drugs up front. You would combine them all and do phase 1 and phase 2 and phase 3 [trials].

    At the moment all this is done, almost invariably, at the end of the journey when the panic phase ensues.

    GAZETTE: And when the person is much sicker.

    PANDOLFI: And when the patient is much sicker, when the cancer is much more complex because it has evolved in your body.

    The last point I would make is that there is only one way to fight the complexity of cancer, which is to diagnose it earlier and earlier and earlier. We will defeat cancer. Conceptually, we can. But it will take time.

    We need to push the envelope [of] early diagnosis. [If] you have three nanoparticles in your body that signal there is something wrong, you go in and take them out. If you can do that, you’re treating a cancer which is simpler … the genetic complexity is smaller, the size is smaller, and the targeted therapy and immune therapy will be much easier to deploy.

    I think the noncoding RNA will help. We need to find biomarkers that we can use and can monitor on almost a regular basis. We will probably introduce a panel of genes or RNAs that you can detect in your blood that will spy for possible cancer development.

    GAZETTE: Would you do that every year at your annual checkup?

    PANDOLFI: Why not? Men over 50 have the PSA [prostate specific antigen] test … and the PSA is one marker. Imagine that you can test 100 markers and increase the accuracy. You have a test that is all cancer, “pan-cancer,” you have 50 genes, and you are sure that if one of them is regulated, it’s either prostate or colon. You follow up with imaging and if you find something wrong, you get it out.

    GAZETTE: Which cancers do you think are most likely to be cured?

    PANDOLFI: The ones for which we have more knowledge. Although leukemia is not entirely cured, the first successes that we experienced were in leukemias, the first real cures were in leukemias.

    The other factor is that you need to have some time to play the game, so I think slowly developing cancers that give time to the operators to use this panoply of drugs, such as prostate cancer or cancers that are already impacted by current therapies, will be cured first.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
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