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  • richardmitnick 2:20 pm on November 18, 2017 Permalink | Reply
    Tags: , , Chemistry, , Stanford University-Engineering,   

    From Stanford University – Engineering: “An advance in stem-cell development could help lead to new therapies” 

    Stanford University Name
    Stanford University – Engineering

    November 02, 2017
    Andrew Myers

    1
    Stem cells hold the promise of being able to cure ills ranging from spinal cord injuries to cancers. | Image by: luismmolina/Getty Images

    In many ways, stem cells are the divas of the biological world. On the one hand, these natural shapeshifters can transform themselves into virtually any type of cell in the body. In that regard, they hold the promise of being able to cure ills ranging from spinal cord injuries to cancers.

    On the other hand, said associate professor of materials science and engineering Sarah Heilshorn, stem cells, like divas, are also mercurial and difficult to work with.

    “We just don’t know how to efficiently and effectively grow massive numbers of stem cells and keep them in their regenerative state,” Heilshorn said. “This has prevented us from making more progress in creating therapies.”

    Until now, that is. In a recent paper in Nature Materials, Heilshorn described a solution to the dual challenges of growing and preserving neural stem cells in a state where they are still able to mature into many different cell types. The first challenge is that growing stem cells in quantity requires space. Like traditional farming, it is a two-dimensional affair. If you want more wheat, corn or stem cells, you need more surface area. Culturing stem cells, therefore, requires a lot of relatively expensive laboratory real estate, not to mention the energy and nutrients necessary to pull it all off.

    The second challenge is that once they’ve divided many times in a lab dish, stem cells do not easily remain in the ideal state of readiness to become other types of cells. Researchers refer to this quality as “stemness.” Heilshorn found that for the neural stem cells she was working with, maintaining the cells’ stemness requires the cells to be touching.

    Heilshorn’s team was working with a particular type of stem cell that matures into neurons and other cells of the nervous system. These types of cells, if produced in sufficient quantities, could generate therapies to repair spinal cord injuries, counteract traumatic brain injury or cure some of the most severe degenerative disorders of the nervous system, like Parkinson’s and Huntington’s diseases.

    Seeking stemness

    Heilshorn’s solution involves the use of better materials in which to grow stem cells. Her lab has developed new polymer-based gels that allow the cells to be grown in three dimensions instead of two. This new 3-D process takes up less than 1 percent of the lab space required by current stem cell culturing techniques. And because cells are so tiny, the 3-D gel stack is just a single millimeter tall, roughly the thickness of a dime.

    “For a 3-D culture, we need only a 4-inch-by-4-inch plot of lab space, or about 16 square inches. A 2-D culture requires a plot four feet by four feet, or about 16 square feet,” more than 100-times the space, according to first author Chris Madl, a recent doctoral graduate in bioengineering from Heilshorn’s lab

    In addition to the dramatic savings of lab space, the new process demands fewer nutrients and less energy, as well.

    The gels the team developed allow the stem cells to remodel the long molecules and maintain physical contact with one another to preserve critical communication channels between cells. “The simple act of touching is key to communication between stem cells and to maintaining stemness. If stem cells can’t remodel the gels, they can’t touch one another,” Madl explained.

    “The stem cells don’t exactly die if they can’t touch, but they lose that ability to regenerate that we really need for therapeutic success,” Heilshorn added.

    Striking results

    This need for neural stem cell to remodel their environment differs from what Heilshorn has found in working with other types of stem cells. For those cells, it is the stiffness of the gels – not the ability to remodel – that is the key factor in maintaining stemness. It is as if for these other types of stem cells, gels must mimic the rigidity of the tissue in which the cells will eventually be transplanted. Not so with neural progenitors, said Heilshorn.

    “Neural cell stemness is not sensitive to stiffness and that was a big surprise to us,” she said.

    The result was so striking and unexpected that Heilshorn, at first, didn’t believe her own results. The lab ended up testing three entirely different gels to see if their conclusion held, an unusual supplementary step in this kind of research. With each new material, they saw that those that could be remodeled produced quality stem cells; those that could not be remodeled had a negative effect on stemness.

    Next up on Heilshorn’s research agenda is to create gels that can be injected directly from the lab dish into the body. The possibilities have her feeling optimistic about stem cell therapies again. For a time, she said, it felt as if the field had hit a wall, as initial excitement for regeneration gave way to uninspiring results in the clinic. With her new finding, she said, it feels like new things may be just around the corner.

    “There’s this convergence of biological knowledge and engineering principles in stem cell research that has me hopeful we might finally actually solve some big problems,” she said.

    See the full article here .

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    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

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  • richardmitnick 12:09 pm on November 15, 2017 Permalink | Reply
    Tags: A Speed Gun for Photosynthesis, A type of optical sensor that if the science bears out will be able to estimate the rate of photosynthesis, , , Chemistry, , SIF - Solar Induced Fluorescence, Specially designed sap flow sensors, Such aDevice would revolutionize agriculture forestry and the study of Earth’s climate and ecosystems   

    From NIST: “A Speed Gun for Photosynthesis” 


    NIST

    1
    The NIST forest in Gaithersburg, Maryland. Credit: R. Press/NIST

    November 03, 2017 [NIST is not always quick to social media]
    Rich Press

    On a recent sunny afternoon, David Allen was standing by a third-floor window in a research building at the National Institute of Standards and Technology (NIST), holding in his hands a device that looked like a cross between a video camera and a telescope. The NIST campus is in suburban Gaithersburg, Maryland, but looking out the window, Allen could see 24 hectares (60 acres) of tulip tree, oak, hickory and red maple—a remnant of the northeastern hardwood forest that once dominated this landscape.

    Allen mounted the device on a tripod and pointed it out the window at the patch of forest below. The device wasn’t a camera, but a type of optical sensor that, if the science bears out, will be able to estimate the rate of photosynthesis—the chemical reaction that enables plants to convert water, carbon dioxide (CO2) and sunlight into food and fiber—from a distance.

    That measurement is possible because when plants are photosynthesizing, their leaves emit a very faint glow of infrared light. That glow is called Solar Induced Fluorescence, or SIF, and in recent years, optical sensors for measuring it have advanced dramatically. The sensor that Allen had just mounted on a tripod was one of them.

    “If SIF sensors end up working well,” Allen said, “I can imagine an instrument that stares at crops or a forest and has a digital readout on it that says how fast the plant is growing in real time.”

    Such a device would revolutionize agriculture, forestry and the study of Earth’s climate and ecosystems.

    2
    NIST scientist David Allen and Boston University Ph.D. student Julia Marrs aim a SIF sensor at a specific tree in the NIST forest.
    Credit: R. Press/NIST

    Allen is a NIST chemist whose research involves remote sensing—the technology that’s used to observe Earth from outer space. Remote sensing allows scientists to track hurricanes, map terrain, monitor population growth and produce daily weather reports. The technology is so deeply embedded in our everyday lives that it’s easy to take for granted. But each type of remote sensing had to be developed from the ground up, and the SIF project at NIST shows how that’s done.

    Some satellites are already collecting SIF data, but standards are needed to ensure that those measurements can be properly interpreted. NIST has a long history of developing standards for satellite-based measurements, and Allen’s research is aimed at developing standards for measuring SIF. Doing that requires a better understanding of the biological processes that underlie SIF, and for that, Allen teamed up with outside scientists.

    At the same time that Allen was aiming a SIF sensor through that third-floor window, a team of biologists from Boston University and Bowdoin College was in the NIST forest measuring photosynthesis up close. A pair of them spent the day climbing into the canopy on an aluminum orchard ladder. Once there, they would use a portable gas exchange analyzer to measure photosynthesis directly based on how much CO2 the leaf pulled out of the air. They also measured SIF at close range.

    3
    Boston University ecologist Lucy Hutyra (left) works at the forest edge alongside plant physiological ecologist Barry Logan (center) and ecologist Jaret Reblin, both of Bowdoin College in Brunswick, Maine. They measured photosynthesis directly, as well as temperature, humidity, and other environmental variables. Credit: R. Press/NIST

    Other scientists checked on specially designed sap flow sensors they had installed on the trunks of trees to measure the movement of water toward the leaves for photosynthesis.

    “We’re measuring the vital signs of the trees,” said Lucy Hutyra, the Boston University ecologist who led the team of scientists on the ground. The idea was to use those ground measurements to make sense of the SIF data collected from a distance.

    “If we measure an increase in photosynthesis at the leaf, we should see a corresponding change in the optical signal,” Hutyra said.

    4
    After directly measuring photosynthesis in an individual leaf using a field portable gas exchange analyzer, scientists preserved a small sample of leaf tissue in liquid nitrogen. They would later analyze that tissue in the lab to measure levels of chlorophyll and other pigments. Credit: R. Press/NIST

    The research was also taking place at still a higher level. That afternoon, Bruce Cook and Larry Corp, scientists with NASA’s G-LiHT project, flew over the NIST forest in a twin-turboprop plane that carried multiple sensors, including a SIF sensor and Light Detection and Ranging (LiDAR) sensors that mapped the internal structure of the forest canopy. The aircraft made six parallel passes over the forest at about 340 meters (1,100 feet, slightly above the minimum safe altitude allowed by FAA regulations), the instruments peering out from a port cut into the belly of the aircraft.

    That gave the scientists three simultaneous measurements to work with: from the ground, from the window above the forest and from the air. They’ll spend months correlating the data.

    “It’s tricky, because when you go from the leaf level to the forest level, you often get different results,” Allen said. For instance, at the forest level, the SIF signal is affected by the variations in the canopy, including its contours and density. “We’re still studying those effects.”

    5
    At the airport in Gaithersburg, Maryland, NASA earth scientist Bruce Cook (left), leader of the Goddard LiDAR, Hyperspectral, and Thermal (G-LiHT) project, shows David Allen and Julia Marrs the sensor array in the bottom of the aircraft. Credit: R. Press/NIST

    Currently, there is no reliable way to measure photosynthesis in real time over a wide area. Instead, scientists measure how green an area is to gauge how much chlorophyll is present—that’s the molecule that supports photosynthesis and gives leaves their color. But if a plant lacks water or nutrients, it may be green even if the photosynthetic machinery is switched off.

    SIF may be a much better indicator of active photosynthesis. When plants are photosynthesizing, most of the light energy absorbed by the chlorophyll molecule goes into growing the plant, but about two to five percent of that energy leaks away as SIF. The amount of leakage is not always proportional to photosynthesis, however. Environmental variables also come into play.

    The NIST forest is a test bed for understanding how all those variables interrelate. In addition to SIF data and the vital signs of trees, the scientists are collecting environmental data such as temperature, relative humidity and solar irradiance. They’re also figuring out the best ways to configure and calibrate the SIF instruments.

    “We’d like to see robust, repeatable results that make sense,” Allen said. “That will allow us to scale up from the leaf level, to the forest level, to the ecosystem level, and to estimate photosynthesis from measurements made at any of those scales.”

    Making SIF scalable is a key part of the measurement standard that Allen is working to create, and it will go from the ground level to measurements made from outer space.

    6
    A corner of the NIST forest shot by NASA scientists, and the plane that carried them and their G-LiHT airborne imaging system.
    Credit: Bruce Cook, Larry Corp/NASA (left); David Allen/NIST

    Using SIF to measure photosynthesis in real time would allow farmers to use only as much irrigation and fertilizer as their crops need, and only when they need it. Forest managers would be able to know how fast their timber is growing without having to tromp through the woods with a tape measure. Environmental managers would be able to monitor the recovery of damaged or deforested habitats after a drought or forest fire.

    And scientists would have a powerful new tool for studying how plants help regulate the amount of CO2 in the atmosphere.

    Humans add CO2 to the atmosphere when they burn fossil fuels, and land-based plants remove roughly a quarter of that CO2 through photosynthesis. But the environmental factors that affect that process are not well understood, mainly because scientists haven’t had a good way to measure the uptake of CO2 at the ecosystem level. SIF measurements, and the standards for interpreting them accurately, might help solve that problem.

    “CO2 exchange by plants is one of the most important biological processes on the planet,” Allen said, “and SIF will give us a new way to see that process in action.”

    See the full article here.

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    NIST Campus, Gaitherberg, MD, USA

    NIST Mission, Vision, Core Competencies, and Core Values

    NIST’s mission

    To promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology in ways that enhance economic security and improve our quality of life.
    NIST’s vision

    NIST will be the world’s leader in creating critical measurement solutions and promoting equitable standards. Our efforts stimulate innovation, foster industrial competitiveness, and improve the quality of life.
    NIST’s core competencies

    Measurement science
    Rigorous traceability
    Development and use of standards

    NIST’s core values

    NIST is an organization with strong values, reflected both in our history and our current work. NIST leadership and staff will uphold these values to ensure a high performing environment that is safe and respectful of all.

    Perseverance: We take the long view, planning the future with scientific knowledge and imagination to ensure continued impact and relevance for our stakeholders.
    Integrity: We are ethical, honest, independent, and provide an objective perspective.
    Inclusivity: We work collaboratively to harness the diversity of people and ideas, both inside and outside of NIST, to attain the best solutions to multidisciplinary challenges.
    Excellence: We apply rigor and critical thinking to achieve world-class results and continuous improvement in everything we do.

     
  • richardmitnick 1:01 pm on November 14, 2017 Permalink | Reply
    Tags: Advanced Biofuels and Bioproducts Process Demonstration Unit (ABPDU), , , , Chemistry, Here we’re cultivating an entire community of microbes to access enzymes that we couldn’t get from isolates, Joint BioEnergy Institute (JBEI) based at Lawrence Berkeley National Laboratory (Berkeley Lab), , Metagenomic analysis, New types of cellulases enzymes that help break down plants into ingredients that can be used to make biofuels and bioproducts   

    From LBNL: “To Find New Biofuel Enzymes, It Can Take a Microbial Village” 

    Berkeley Logo

    Berkeley Lab

    November 14, 2017
    Sarah Yang
    scyang@lbl.gov
    (510) 486-4575

    A new study led by researchers at the Department of Energy’s Joint BioEnergy Institute (JBEI), based at Lawrence Berkeley National Laboratory (Berkeley Lab), demonstrates the importance of microbial communities as a source of stable enzymes that could be used to convert plants to biofuels.

    1
    This 50-milliliter flask contains a symbiotic mix of bacteria derived from compost that was maintained for three years. (Credit: Steve Singer/JBEI)

    The study, recently published in the journal Nature Microbiology, reports on the discovery of new types of cellulases, enzymes that help break down plants into ingredients that can be used to make biofuels and bioproducts. The cellulases were cultured from a microbiome. Using a microbial community veers from the approach typically taken of using isolated organisms to obtain enzymes.

    The scientists first studied the microbial menagerie present in a few cups of municipal compost. Metagenomic analysis at the DOE Joint Genome Institute (JGI) of the microbiome helped reveal that 70 percent of the enzymatic activity originated from cellulases produced by a cluster of uncultivated bacteria in the compost. They found that the enzymes easily broke down the cellulose in plant biomass into glucose at temperatures up to 80 degrees Celsius.

    2
    This chart shows the bacterial composition of the community in the bioreactor after two weeks of culturing. (Credit: Sebastian Kolinko/JBEI)

    “Here we’re cultivating an entire community of microbes to access enzymes that we couldn’t get from isolates,” said study principal investigator Steve Singer, senior scientist in Berkeley Lab’s Biological Systems and Engineering Division and director of Microbial and Enzyme Discovery at JBEI. “Some microbes are difficult to culture in a lab. We are cultivating microbes living in communities, as they occur in the wild, which allows us to see things we don’t see when they are isolated. This opens up the opportunity to discover new types of enzymes that are only produced by microbes in communities.”

    The bacterial population, Candidatus Reconcilibacillus cellulovorans, yielded cellulases that were arranged in remarkably robust carbohydrate-protein complexes, a structure never before observed in isolates. The stability of the new cellulase complexes makes them attractive for applications in biofuels production, the study authors said.

    “The enzymes persist, even after a decline in bacterial abundance,” said Singer, who compared the microbial community with sourdough starters fermented from wild yeast and friendly bacteria. “We kept the microbial community cultivation going for more than three years in the lab.”

    3
    A bioreactor at ABPDU was used to scale the growth of a mixture of bacteria from 50 milliliters to 300 liters. (Credit: Roy Kaltschmidt/Berkeley Lab).

    This stability is a key advantage over other cellulases that degrade more rapidly at high temperature, the researchers said.

    To determine whether the enzyme production can be scalable for industrial applications, JBEI scientists collaborated with researchers from the Advanced Biofuels and Bioproducts Process Demonstration Unit (ABPDU) at Berkeley Lab, a scale-up facility established by DOE to help accelerate the commercialization of biofuels research discoveries.

    Researchers at JBEI, a DOE Bioenergy Research Center, were able to produce 50-milliliter samples, but in about six weeks, the scientists at ABPDU scaled the cultures to a volume 6,000 times larger – 300 liters – in industrial bioreactors.

    The study’s lead author is Sebastian Kolinko, who worked on the study as a JBEI postdoctoral researcher.

    Other co-authors on this study include researchers from Taipei Medical University, the University of Georgia, the Manheim University of Applied Sciences, and Technical University of Braunschweig in Germany.

    JGI is a DOE Office of Science User Facility. This work was primarily supported by the DOE Office of Science and the DOE Office of Energy Efficiency and Renewable Energy.

    See the full article here .

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  • richardmitnick 1:26 pm on November 9, 2017 Permalink | Reply
    Tags: Chemistry, , , Oil and water do not mix?, , Surfactants   

    From MIT: “A new way to mix oil and water” 

    MIT News
    MIT Widget

    MIT News

    November 8, 2017
    David L. Chandler

    1
    Graduate student Ingrid Guha holds a jar containing a clear liquid that looks like water to the naked eye, but it’s actually an emulsion of oil and water at the nanoscale.
    Image: Melanie Gonick, MIT

    2
    Optical images demonstrate that when water droplets condense on an oil bath, the droplets rapidly coalesce to become larger and larger (top row of images, at 10-minute intervals). Under identical conditions but with a soap-like surfactant added (bottom row), the tiny droplets are much more stable and remain small. Courtesy of the researchers

    Condensation-based method developed at MIT could create stable nanoscale emulsions.

    The reluctance of oil and water to mix together and stay that way is so well-known that it has become a cliché for describing any two things that do not go together well. Now, a new finding from researchers at MIT might turn that expression on its head, providing a way to get the two substances to mix and remain stable for long periods — no shaking required. The process may find applications in pharmaceuticals, cosmetics, and processed foods, among other areas.

    The new process involves cooling a bath of oil containing a small amount of a surfactant (a soap-like substance), and then letting water vapor from the surrounding air condense onto the oil surface. Experiments have shown that this can produce tiny, uniform water droplets on the surface that then sink into the oil, and their size can be controlled by adjusting the proportion of surfactant. The findings, by MIT graduate student Ingrid Guha, former postdoc Sushant Anand, and associate professor Kripa Varanasi, are reported in the journal Nature Communications.

    As anyone who has ever used salad dressing knows, no matter how vigorously the mixture gets shaken, the oil and the vinegar (a water-based solution) will separate within minutes. But for many uses, including new drug-delivery systems and food-processing methods, it’s important to be able to get oil in water (or water in oil) to form tiny droplets — only a few hundred nanometers across, too small to see with the naked eye — and to have them stay tiny rather than coalescing into larger droplets and eventually separating from the other liquid.

    Typically, in industrial processes these emulsions are made by either mechanically shaking the mix or using sound waves to set up intense vibrations within the liquid, a process called sonicating. But both of these processes “require a lot of energy,” Varanasi says, “and the finer the drops, the more energy it takes.” By contrast, “our approach is very energy inexpensive,” he adds.

    “The key to overcoming that separation is to have really small, nanoscale droplets,” Guha explains. “When the drops are small, gravity can’t overcome them,” and they can remain suspended indefinitely.

    For the new process, the team set up a reservoir of oil with an added surfactant that can bind to both oil and water molecules. They placed this inside a chamber with very humid air and then cooled the oil. Like a glass of cold water on a hot summer day, the colder surface causes the water vapor to precipitate. The condensing water then forms droplets at the surface that spread through the oil-surfactant mixture, and the sizes of these droplets are quite uniform, the team found. “If you get the chemistry just right, you can get just the right dispersion,” Guha says. By adjusting the proportion of surfactant in the oil, the droplet sizes can be well-controlled.

    In the experiments, the team produced nanoscale emulsions that remained stable over periods of several months, compared to the few minutes that it takes for the same mixture of oil and water to separate without the added surfactant. “The droplets stay so small that they’re hard to see even under a microscope,” Guha says.

    Unlike the shaking or sonicating methods, which take the large, separate masses of oil and water and gradually get them to break down into smaller drops — a “top down” approach — the condensation method starts off right away with the tiny droplets condensing out from the vapor, which the researchers call a bottom-up approach. “By cloaking the freshly condensed nanoscale water droplets with oil, we are taking advantage of the inherent nature of phase-change and spreading phenomena,” Varanasi says.

    “Our bottom-up approach of creating nanoscale emulsions is highly scalable owing to the simplicity of the process,” Anand says. “We have uncovered many new phenomena during this work. We have found how the presence of surfactant can change the oil and water interactions under such conditions, promoting oil spreading on water droplets and stabilizing them at the nanoscale.”

    The team says that the approach should work with a variety of oils and surfactants, and now that the process has been identified, their findings “provide a kind of design guideline for someone to use” for a particular kind of application, Varanasi says.

    “It’s such an important thing,” he says, because “foods and pharmaceuticals always have an expiration date,” and often that has to do with the instability of the emulsions in them. The experiments used a particular surfactant that is widely used, but many other varieties are available, including some that are approved for food-grade products.

    In addition, Guha says, “we envision that you could use multiple liquids and make much more complex emulsions.” And besides being used in food, cosmetics, and drugs, the method could have other applications, such as in the oil and gas industry, where fluids such as the drilling “muds” sent down wells are also emulsions, Varanasi says.

    The work was supported by the MIT Energy Initiative, the National Science Foundation, and a Society in Science fellowship. Anand, the co-author who was a postdoc at MIT, is now an assistant professor at the University of Illinois.

    See the full article here .

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    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 12:34 pm on November 7, 2017 Permalink | Reply
    Tags: , Chemistry, Discovering detrimental leaks by developing “smart” paper that can sense the presence of water, , , Smart paper,   

    From University of Washington: “‘Smart’ paper can conduct electricity, detect water” 

    U Washington

    University of Washington

    November 6, 2017
    Michelle Ma

    1
    Anthony Dichiara, a University of Washington professor in the School of Environmental and Forest Sciences, holds a piece of “smart” paper created in his lab. Mark Stone/University of Washington

    In cities and large-scale manufacturing plants, a water leak in a complicated network of pipes can take tremendous time and effort to detect, as technicians must disassemble many pieces to locate the problem. The American Water Works Association indicates that nearly a quarter-million water line breaks occur each year in the U.S., costing public water utilities about $2.8 billion annually.

    A University of Washington team wants to simplify the process for discovering detrimental leaks by developing “smart” paper that can sense the presence of water. The paper, laced with conductive nanomaterials, can be employed as a switch, turning on or off an LED light or an alarm system indicating the absence or presence of water.

    The researchers described their discovery in a paper appearing in the November issue of the Journal of Materials Chemistry A.

    “Water sensing is very challenging to do due to the polar nature of water, and what is used now is very expensive and not practical to implement,” said lead author Anthony Dichiara, a UW assistant professor of bioresource science and engineering in the School of Environment and Forest Sciences. “That led to the reason to pursue this work.”

    See slide show of images at the full article.

    Along with Dichiara, a team of UW undergraduate students in the Bioresource Science and Engineering program successfully embedded nanomaterials in paper that can conduct electricity and sense the presence of water. Starting with pulp, they manipulated the wood fibers and carefully mixed in nanomaterials using a standard process for papermaking, but never before used to make sensing papers.

    Discovering that the paper could detect the presence of water came by way of a fortuitous accident. Water droplets fell onto the conductive paper the team had created, causing the LED light indicating conductivity to turn off. Though at first they thought they had ruined the paper, the researchers realized they had instead created a paper that was sensitive to water.

    When water hits the paper, its fibrous cells swell to up to three times their original size. That expansion displaces conductive nanomaterials inside the paper, which in turn disrupts the electrical connections and causes the LED indicator light to turn off.

    This process is fully reversible, and as the paper dries, the conductive network re-forms so the paper can be used multiple times.

    The researchers envision an application in which a sheet of conductive paper with a battery could be placed around a pipe or under a complex network of intersecting pipes in a manufacturing plant. If a pipe leaks, the paper would sense the presence of water, then send an electrical signal wirelessly to a central control center so a technician could quickly locate and repair the leak.
    example use around a pipe

    The paper could be wrapped around a pipe, as shown in this example, to detect leaks.Mark Stone/University of Washington

    In addition, the paper is so sensitive that it can also detect trace amounts of water in mixtures of various liquids. This ability to distinguish water from other molecules is particularly valuable for the petroleum and biofuel industries, where water is regarded as an impurity.

    “I believe that for large-scale applications, this is definitely doable,” Dichiara said. “The price for nanomaterials is going to drop, and we’re already using an established papermaking process. You just add what we developed in the right place and time in the process.”

    The nanomaterials added to the paper were engineered in such a way that they can be incorporated during conventional papermaking without having to modify the process. These materials are made of extremely conductive carbon. Because carbon is found in all living things, nearly any natural material can be burned to make charcoal, and then carbon atoms can be extracted to synthesize the materials. The team has experimented with making nanomaterials from banana peels, tree bark and even animal feces.

    They also tried making nanomaterials from wood scraps to show that the entire papermaking process can be completed with cheap, natural materials.

    “Now we have a sustainable process where everything is from pulp and paper, and we can make conductive materials from them,” Dichiara said.

    The paper, stiff and smooth in texture, is a rich black color because of the nanomaterials (carbon from charcoal). The 8-inch disks made in the lab are prototypes; the team hopes to test the process on an industrial-sized papermaking machine next, which will require more nanomaterials and paper pulp.

    Other co-authors are Sheila Goodman, a UW graduate student, and Delong He and Jinbo Bai of Universite Paris-Saclay in France. UW undergraduate students Jimeng Cui, Riley Fitzpatrick, Sydney Fry, Demi Lidorikiotis, Anna Song and Zoie Tisler completed additional lab work.

    Funding for this research came from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, McIntire Stennis project, and from the UW School of Environmental and Forest Sciences.

    ###

    For more information, contact Dichiara at abdichia@uw.edu or 206-543-1581.

    Along with Dichiara, a team of UW undergraduate students in the Bioresource Science and Engineering program successfully embedded nanomaterials in paper that can conduct electricity and sense the presence of water. Starting with pulp, they manipulated the wood fibers and carefully mixed in nanomaterials using a standard process for papermaking, but never before used to make sensing papers.

    Discovering that the paper could detect the presence of water came by way of a fortuitous accident. Water droplets fell onto the conductive paper the team had created, causing the LED light indicating conductivity to turn off. Though at first they thought they had ruined the paper, the researchers realized they had instead created a paper that was sensitive to water.

    When water hits the paper, its fibrous cells swell to up to three times their original size. That expansion displaces conductive nanomaterials inside the paper, which in turn disrupts the electrical connections and causes the LED indicator light to turn off.

    This process is fully reversible, and as the paper dries, the conductive network re-forms so the paper can be used multiple times.

    The researchers envision an application in which a sheet of conductive paper with a battery could be placed around a pipe or under a complex network of intersecting pipes in a manufacturing plant. If a pipe leaks, the paper would sense the presence of water, then send an electrical signal wirelessly to a central control center so a technician could quickly locate and repair the leak.

    3
    The paper could be wrapped around a pipe, as shown in this example, to detect leaks.Mark Stone/University of Washington

    They also tried making nanomaterials from wood scraps to show that the entire papermaking process can be completed with cheap, natural materials.

    “Now we have a sustainable process where everything is from pulp and paper, and we can make conductive materials from them,” Dichiara said.

    The paper, stiff and smooth in texture, is a rich black color because of the nanomaterials (carbon from charcoal). The 8-inch disks made in the lab are prototypes; the team hopes to test the process on an industrial-sized papermaking machine next, which will require more nanomaterials and paper pulp.

    Other co-authors are Sheila Goodman, a UW graduate student, and Delong He and Jinbo Bai of Universite Paris-Saclay in France. UW undergraduate students Jimeng Cui, Riley Fitzpatrick, Sydney Fry, Demi Lidorikiotis, Anna Song and Zoie Tisler completed additional lab work.

    Funding for this research came from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, McIntire Stennis project, and from the UW School of Environmental and Forest Sciences.

    See the full article here .

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 2:00 pm on November 2, 2017 Permalink | Reply
    Tags: , , Chemistry, , , Room for growth: Princeton’s Vertical Farming Project harvests knowledge for a budding industry   

    From Princeton University- “Room for growth: Princeton’s Vertical Farming Project harvests knowledge for a budding industry” 

    Princeton University
    Princeton University

    Nov. 2, 2017
    Morgan Kelly, Princeton Environmental Institute

    1
    Princeton University’s Vertical Farming Project was established as a model vertical farm — which involves growing food crops indoors on stacked shelves — to generate accessible and up-to-date research for the field. For her senior thesis, Princeton senior Jesenia Haynes (above) is analyzing the environmental impacts of growing kale and lettuce in a vertical farm versus a conventional farm. Haynes is one of several student researchers engaged in the Vertical Farming Project, which is part of the Campus as Lab Initiative.
    Video still from Nick Donnoli, Office of Communications

    Princeton University’s Vertical Farming Project began at a conference in 2016 when the topic turned to increasing the crop yield of hydroponic systems — wherein plants are grown indoors without soil by using only water and nutrient solutions — by pressurizing water with extra oxygen in a tank before feeding it to the plants. The idea was on everyone’s lips.

    Paul Gauthier knew it was wrong. A plant physiologist, he realized that once the water leaves the tank, it will depressurize and release more oxygen, which reduces photosynthesis.

    “They wanted to provide more oxygen to the roots to increase the yield, but they were doing the opposite of that,” said Gauthier, an associate research scholar in geosciences and the Princeton Environmental Institute. “That’s when I decided to get into the game.”

    In April, Gauthier launched the Vertical Farming Project with support from a High Meadows Foundation Sustainability Fund grant obtained through the Office of Sustainability. The project includes a number of student researchers and is part of the Campus as Lab Initiative. Vertical farming involves growing food crops indoors on stacked shelves. Hydroponics is the most popular form of vertical farming, but the concept is always the same. Sheltered from pests, frost and the scorching sun, plants can grow rapidly, with harvests taking place several times a year. The Princeton farm can produce mature basil in one month, month after month.

    Located in a small windowless room in Moffett Laboratory, Princeton’s vertical farm is used to identify the optimal conditions for growing food indoors. The farm contains about 80 plants. (No tomatoes, for space considerations: “If you give them the right conditions, they’ll grow and grow and grow and never stop,” Gauthier said.) The most successful plants are herbs and leafy greens, which allow for the occasional feast. The project has partnered with an eating club, the Terrace F. Club, which has incorporated the project’s bounty into meals. An Oct. 24 event at Forbes College featured dishes made with lettuce and herbs from the vertical farm and the Princeton Garden Project served alongside produce from a commercial food distributor.

    Gauthier, who has been at the University since 2012 and focuses his research on plant resilience to environmental stress, envisions the Princeton project as an open-source model for vertical farming. Free from having to turn a profit, he and the students involved in the project can experiment with various crops, techniques, technologies and nutrient solutions. Their focus is getting the best harvest with the least amount of resource consumption, then making those data publicly available. They grow less common crops such as edible flowers and wheat. Wheat from the Princeton vertical farm is ready for harvest in 65 days. One of Gauthier’s side projects is to see how much and how economically he can produce flour from a single wheat harvest. He would like to eventually grow citrus and fruit shrubs.

    “We want to create new knowledge in the field,” Gauthier said. “We want to prove that this is sustainable. All the research strengths of Princeton can be combined into this project: sustainability, environmental science, biology and engineering. We hope Princeton will start leading the field by providing new technologies and training students for consulting in this new industry.”

    Paul Gauthier (left), a plant physiologist and an associate research scholar in geosciences and the Princeton Environmental Institute, launched the project in April to identify the optimal conditions for growing various crops with the least amount of water and energy, then make those data publicly available to potential growers. In this video, Gauthier, Haynes and sophomore Seth Lovelace (right) discuss the project’s aims and their individual research interests.
    Video by [not named].

    A field ripe for cultivation

    In recent years, vertical farming has gained traction as a method for producing food for a growing global population that is running short on arable land. Reducing the need for new — or even existing — farmland would go a long way toward preserving natural ecosystems and restoring the ones ravaged by agriculture, according to Dickson Despommier, the Columbia University microbiologist whose 2010 book, The Vertical Farm, helped popularize the topic. Vertical farms reportedly consume up to 95 percent less water than conventional farming by recycling water and they also eliminate the chemical-laden runoff that poisons waterbodies and aquifers.

    The technique also has potential for bringing locally sourced and readily available food to arid and urban areas, which would reduce shipping-related carbon emissions. Several vertical farms are now based in and around New York City, including the world’s largest vertical farm, Newark-based AeroFarms, which produces up to 2 million pounds of produce annually and is headquartered in an old steel mill.

    Gauthier discovered, however, that the industry overall suffers a lack of accessible and up-to-date research on everything from leaf physics to a breakdown of the market. He found very little or outdated peer-reviewed data on nutrient efficiency, automation or sustainable energy and water use. The hydroponic farmers Gauthier has met largely rely on trial-and-error and information from the 1980s. Commercial vertical farms are private businesses that keep their research results to themselves, he said.

    “In science, we know very well how to grow plants hydroponically,” Gauthier said. “The problem is that the public doesn’t know that.”

    Admittedly, vertical farming is not a booming research area, Gauthier said. For instance, there’s little data on growing herbs and leafy greens, which are high-demand crops, he said. Plant and agricultural scientists largely focus on optimizing traditional farming, particularly through the use of genetically modified crops.

    “There’s a difference between what science is doing and what vertical farmers need to know,” Gauthier said.

    3
    The Princeton vertical farm contains about 80 plants. The most successful are herbs and leafy greens, which have been distributed on campus. The Terrace F. Club eating club has incorporated the vertical farm’s harvests into meals. An Oct. 24 event at Forbes College (above) featured salads made with lettuce from the vertical farm (foreground) versus lettuce from a commercial food distributor. Photo by Nick Donnoli, Office of Communications

    Questions keep cropping up

    For her senior thesis, Princeton student Jesenia Haynes is analyzing the environmental impacts of growing kale and lettuce in a vertical farm versus a conventional farm. Her focus is on water and electricity use, the energy costs of producing fertilizer, and the resources that go into shipping and delivering produce to consumers.

    Haynes, who is majoring in ecology and evolutionary biology with a certificate in environmental studies, has been working with Gauthier nearly since the project began. She has gardened since childhood, but her interest in sustainable agricultural was piqued by lectures and classes at Princeton such as ENV 200: “The Environmental Nexus.” While she enjoys growing food, she also is now aware of the obstacles vertical farming poses.

    “The maintenance of the farm for me has been the most challenging part. The biggest problem if you want to reproduce this system on a local scale is having the people to maintain it,” Haynes said. “But with any new initiative, you need to keep improving it. It takes time and effort. We have to keep working to make the process better.”

    In August, Manolya Adan, a graduate student of Gauthier’s based at Imperial College London, visited vertical farms around the United States. Her goal is to build a carbon-footprint model of the entire vertical-farm supply chain. Vertical farms are expanding rapidly, she said — in the past five years, the number in Asia has increased from 23 to 130. (A driving force is the advancement of light-emitting diode, or LED, technology that can provide ample light more efficiently than incandescent lightbulbs. In particular, Gauthier explained, LEDs now incorporate green light, which is essential for secondary plant metabolism.)

    Vertical farms frequently tout the environmental benefits of their trade, but there’s no publicly available information with which anyone can objectively verify those claims, Adan said. “Vertical farming holds a lot of promise, but I want to see what the actual benefit is in terms of reducing our environmental impact,” Adan said. “We want the industry to do well and we need to be sustainable. It’s about helping companies see what they themselves are doing and what they could do better.”

    Operational costs are a significant obstacle facing vertical, Gauthier said — more than 85 percent of vertical farms fail within two years. LEDs, labor and space are expensive, but there is no hard data on what drives these operations to close. Senior Rozalie Czesana, a Woodrow Wilson School of Public and International Affairs major, is preparing to examine the costs associated with running a small vertical farm, together with the feasibility of scaling them up to the community level. Her focus will be on “food deserts,” or areas such as low-income urban neighborhoods that often lack sufficient access to fresh, healthy food.

    Czesana, who established the project’s partnership with the Terrace F. Club, previously conducted a comparative study that examined the speed of growth and average water use of herbs and lettuce in the vertical farm versus a greenhouse. She found that the vertical farm is much more resilient to New Jersey weather — the heat wave in May 2016 killed most of the greenhouse produce despite constant care. She also found that while basil, lettuce and kale do much better in the vertical farm under a certain nutrient concentration, cilantro preferred the greenhouse.

    Sophomore Seth Lovelace, a prospective mathematics major, works with Gauthier to analyze the level of individual nutrients in the solution they feed the plants using a technique called inductively coupled plasma mass spectrometry (ICP-MS). They can then adjust the amount of a certain nutrient based on what a plant uses most, as well as adjust the micronutrients that influence flavor, Lovelace said.

    “We’re really trying to bring metrics to the vertical-farming game. All of our team members are trying to get data so we can make the farm grow better, to help these plants thrive,” Lovelace said. “Interdisciplinary research, when applied to any project, really enhances how the project moves forward. I think the access to this kind of research as an undergrad is amazing.”

    Gauthier welcomes the student interest. “I want undergrads involved because they are the next generation and the big burden of saving the planet will be on them,” he said. “When they are familiar with this system and know it, they can start thinking outside of the box.

    “The industry is growing for sure and it will be part of our lives in the future,” he said. “That’s what this project is about — understanding this system well enough to expand it.”

    4
    The Oct. 24 “Meet What You Eat” event featured the harvests from Princeton Garden and Vertical Farming projects. From left to right: sophomore Anna Marsh, Garden Project leader; junior Emmy Bender, Garden Project leader; sophomore Laurie Zielinkski; sophomore Natalie Grayson, vertical farm manager; Violette Chamoun, Campus Dining operations manager; Alex Trimble, Campus Dining chef du cuisine; senior Rozalie Czesana, who is conducting an economic analysis for the Vertical Farming Project; Gauthier; and Patrick Caddeau, dean of Forbes College.
    Photo by
    Nick Donnoli, Office of Communications

    See the full article here .

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    About Princeton: Overview

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    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

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  • richardmitnick 1:35 pm on November 2, 2017 Permalink | Reply
    Tags: , , Chemistry, Earth Microbiome Project, , Mapping the Microbiome of … Everything, Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale,   

    From UCSD: “Mapping the Microbiome of … Everything” 

    UC San Diego bloc

    UC San Diego

    November 01, 2017
    Heather Buschman

    Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale.

    1
    From left, Berkeley Lab researchers Eric Dubinsky, Shi Wang (on left), and Neslihan Tas contributed to the Earth Microbiome Project. LBNL.

    ​In the Earth Microbiome Project, an extensive global team co-led by researchers at University of California San Diego, Pacific Northwest National Laboratory, University of Chicago and Argonne National Laboratory collected more than 27,000 samples from numerous, diverse environments around the globe. They analyzed the unique collections of microbes — the microbiomes — living in each sample to generate the first reference database of bacteria colonizing the planet. Thanks to newly standardized protocols, original analytical methods and open data-sharing, the project will continue to grow and improve as new data are added.

    The paper describing this effort, published November 1 in Nature, was co-authored by more than 300 researchers at more than 160 institutions worldwide.

    2
    Earth Microbiome Project collaborators collect and analyze samples from diverse environments around the world. Top left: Hiking through the rain forest of Puerto Rico to sample soils with students (credit: Krista McGuire, University of Oregon). Top middle: Colobine monkeys in China, whose fecal microbiomes were sampled for this study (credit: Kefeng Niu). Top right: Bat in Belize, whose fecal microbiome was sampled for this study (credit: Angelique Corthals and Liliana Davalos). Bottom Left: Researcher sampling a stream in the Brooks Mountain Range, Alaska (credit: Byron Crump). Bottom middle: Swabbing bird eggshells from Spain (credit: Juan Peralta-Sanchez). Bottom right: Researcher sampling the southernmost geothermal soils on the planet, at summit of Mt. Erebus, Ross Island, Antarctica (credit: S. Craig Cary, Univ. of Waikato, New Zealand).

    The Earth Microbiome Project was founded in 2010 by Rob Knight, PhD, professor at UC San Diego School of Medicine and director of the Center for Microbiome Innovation at UC San Diego; Jack Gilbert, PhD, professor and faculty director of The Microbiome Center at University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory; Rick Stevens, PhD, associate laboratory director at Argonne National Laboratory and professor and senior fellow at University of Chicago; and Janet Jansson, PhD, chief scientist for biology and laboratory fellow at Pacific Northwest National Laboratory. Knight, Gilbert and Jansson are also co-senior authors of the Nature paper and Stevens is a co-author.

    “The potential applications for this database and the types of research questions we can now ask are almost limitless,” Knight said. “Here’s just one example — we can now identify what kind of environment a sample came from in more than 90 percent of cases, just by knowing its microbiome, or the types and relative quantities of microbes living in it. That could be useful forensic information at a crime scene … think ‘CSI.’”

    The goal of the Earth Microbiome Project is to sample as many of the Earth’s microbial communities as possible in order to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. This task requires the help of scientists from all over the globe. So far, the project has spanned seven continents and 43 countries, from the Arctic to the Antarctic, and more than 500 researchers have contributed to the sample and data collection. Project members are using this information as part of approximately 100 studies, half of which have been published in peer-reviewed journals.

    “Microbes are everywhere,” said first author Luke Thompson, PhD, who took on the role of project manager while a postdoctoral researcher in Knight’s lab and is currently a research associate at the National Oceanic and Atmospheric Administration (NOAA). “Yet prior to this massive undertaking, changes in microbial community composition were identified mainly by focusing on one sample type, one region at a time. This made it difficult to identify patterns across environments and geography to infer generalized principles.”

    Project members analyze bacterial diversity among various environments, geographies and chemistries by sequencing the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve as “barcodes” to identify different types of bacteria, allowing researchers to track them across samples from around the world. Earth Microbiome Project researchers also used a new method to remove sequencing errors in the data, allowing them to get a more accurate picture of the number of unique sequences in the microbiomes.

    Within this first release of data, the Earth Microbiome Project team identified around 300,000 unique microbial 16S rRNA sequences, almost 90 percent of which don’t have exact matches in pre-existing databases.

    Pre-existing 16S rRNA sequences are limited because they were not designed to allow researchers to add data in a way that’s useful for the future. Project co-author Jon Sanders, PhD, a postdoctoral researcher in Knight’s lab, compares the difference between these other databases and the Earth Microbiome Project to the difference between a phone book and Facebook. “Before, you had to write in to get your sequence listed, and the listing would contain very little information about where the sequence came from or what other sequences it was found with,” he said. “Now, we have a framework that supports all that additional context, and which can grow organically to support new kinds of questions and insights.”

    “There are large swaths of microbial diversity left to catalogue. And yet we’ve ‘recaptured’ about half of all known bacterial sequences,” Gilbert said. “With this information, patterns in the distribution of the Earth’s microbes are already emerging.”

    According to Gilbert, one of the most surprising observations is that unique 16S sequences are far more specific to individual environments than are the typical units of species used by scientists. The diversity of environments sampled by the Earth Microbiome Project helps demonstrate just how much local environment shapes the microbiome. For example, the skin microbiomes of cetaceans (whales and dolphins) and fish are more similar to each other than they are to the water they swim in; conversely, the salt in saltwater microbiomes makes them distinct from freshwater, but they are still more similar to each other than to aquatic animal skin. Overall, the microbiomes of a host, such as a human or animal, were quite distinct from free-living microbiomes, such as those found in water and soil. For example, the free-living microbiomes were far more diverse, in general, than host-associated microbiomes.

    “These global ecological patterns offer just a glimpse of what is possible with coordinated and cumulative sampling,” Jansson said. “More sampling is needed to account for factors such as latitude and elevation, and to track environmental changes over time. The Earth Microbiome Project provides both a resource for the exploration of myriad questions, and a starting point for the guided acquisition of new data to answer them.”

    For more about the Earth Microbiome Project, visit earthmicrobiome.org and follow @earthmicrobiome on Twitter. For the complete list of co-authors and institutions participating in the Earth Microbiome Project, view the full Nature paper .

    The project was funded, in part, by the John Templeton Foundation, W. M. Keck Foundation, Argonne National Laboratory, Australian Research Council, and Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation (ACI-1053575).

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    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

     
  • richardmitnick 7:02 am on October 25, 2017 Permalink | Reply
    Tags: A new theory that cast the origin of life as an inevitable outcome of thermodynamics, , , Chemistry, , First Support for a Physics Theory of Life, Jeremy England, ,   

    From Quanta: “First Support for a Physics Theory of Life” 

    Quanta Magazine
    Quanta Magazine

    July 26, 2017 [Where has this been hiding?]
    Natalie Wolchover

    Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

    1
    Shayla Fish for Quanta Magazine

    The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of “entropy” or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and “should be as unsurprising as rocks rolling downhill.”

    Since then, England, a 35-year-old associate professor at the Massachusetts Institute of Technology, has been testing aspects of his idea in computer simulations. The two most significant of these studies were published this month — the more striking result in the Proceedings of the National Academy of Sciences (PNAS) and the other in Physical Review Letters (PRL). The outcomes of both computer experiments appear to back England’s general thesis about dissipation-driven adaptation, though the implications for real life remain speculative.

    “This is obviously a pioneering study,” Michael Lässig, a statistical physicist and quantitative biologist at the University of Cologne in Germany, said of the PNAS paper written by England and an MIT postdoctoral fellow, Jordan Horowitz. It’s “a case study about a given set of rules on a relatively small system, so it’s maybe a bit early to say whether it generalizes,” Lässig said. “But the obvious interest is to ask what this means for life.”

    The paper strips away the nitty-gritty details of cells and biology and describes a simpler, simulated system of chemicals in which it is nonetheless possible for exceptional structure to spontaneously arise — the phenomenon that England sees as the driving force behind the origin of life. “That doesn’t mean you’re guaranteed to acquire that structure,” England explained. The dynamics of the system are too complicated and nonlinear to predict what will happen.

    The simulation involved a soup of 25 chemicals that react with one another in myriad ways. Energy sources in the soup’s environment facilitate or “force” some of these chemical reactions, just as sunlight triggers the production of ozone in the atmosphere and the chemical fuel ATP drives processes in the cell. Starting with random initial chemical concentrations, reaction rates and “forcing landscapes” — rules that dictate which reactions get a boost from outside forces and by how much — the simulated chemical reaction network evolves until it reaches its final, steady state, or “fixed point.”

    3
    eremy England, an associate professor of physics at the Massachusetts Institute of Technology, thinks he has found the physical mechanism underlying the origin of life. Katherine Taylor for Quanta Magazine

    Often, the system settles into an equilibrium state, where it has a balanced concentration of chemicals and reactions that just as often go one way as the reverse. This tendency to equilibrate, like a cup of coffee cooling to room temperature, is the most familiar outcome of the second law of thermodynamics, which says that energy constantly spreads and the entropy of the universe always increases. (The second law is true because there are more ways for energy to be spread out among particles than to be concentrated, so as particles move around and interact, the odds favor their energy becoming increasingly shared.)

    But for some initial settings, the chemical reaction network in the simulation goes in a wildly different direction: In these cases, it evolves to fixed points far from equilibrium, where it vigorously cycles through reactions by harvesting the maximum energy possible from the environment. These cases “might be recognized as examples of apparent fine-tuning” between the system and its environment, Horowitz and England write, in which the system finds “rare states of extremal thermodynamic forcing.”

    Living creatures also maintain steady states of extreme forcing: We are super-consumers who burn through enormous amounts of chemical energy, degrading it and increasing the entropy of the universe, as we power the reactions in our cells. The simulation emulates this steady-state behavior in a simpler, more abstract chemical system and shows that it can arise “basically right away, without enormous wait times,” Lässig said — indicating that such fixed points can be easily reached in practice.

    Many biophysicists think something like what England is suggesting may well be at least part of life’s story. But whether England has identified the most crucial step in the origin of life depends to some extent on the question: What’s the essence of life? Opinions differ.

    Form and Function

    England, a prodigy by many accounts who spent time at Harvard, Oxford, Stanford and Princeton universities before landing on the faculty at MIT at 29, sees the essence of living things as the exceptional arrangement of their component atoms. “If I imagine randomly rearranging the atoms of the bacterium — so I just take them, I label them all, I permute them in space — I’m presumably going to get something that is garbage,” he said earlier this month. “Most arrangements [of atomic building blocks] are not going to be the metabolic powerhouses that a bacterium is.”

    It’s not easy for a group of atoms to unlock and burn chemical energy. To perform this function, the atoms must be arranged in a highly unusual form. According to England, the very existence of a form-function relationship “implies that there’s a challenge presented by the environment that we see the structure of the system as meeting.”

    But how and why do atoms acquire the particular form and function of a bacterium, with its optimal configuration for consuming chemical energy? England hypothesizes that it’s a natural outcome of thermodynamics in far-from-equilibrium systems.

    The Nobel-Prize-winning physical chemist Ilya Prigogine pursued similar ideas in the 1960s, but his methods were limited. Traditional thermodynamic equations work well only for studying near-equilibrium systems like a gas that is slowly being heated or cooled. Systems driven by powerful external energy sources have much more complicated dynamics and are far harder to study.

    The situation changed in the late 1990s, when the physicists Gavin Crooks and Chris Jarzynski derived “fluctuation theorems” that can be used to quantify how much more often certain physical processes happen than reverse processes. These theorems allow researchers to study how systems evolve — even far from equilibrium. England’s “novel angle,” said Sara Walker, a theoretical physicist and origins-of-life specialist at Arizona State University, has been to apply the fluctuation theorems “to problems relevant to the origins of life. I think he’s probably the only person doing that in any kind of rigorous way.”

    Coffee cools down because nothing is heating it up, but England’s calculations [PhysRevX] suggested that groups of atoms that are driven by external energy sources can behave differently: They tend to start tapping into those energy sources, aligning and rearranging so as to better absorb the energy and dissipate it as heat. He further showed that this statistical tendency to dissipate energy might foster self-replication [The Journal of Chemical Physics]. (As he explained it in 2014, “A great way of dissipating more is to make more copies of yourself.”) England sees life, and its extraordinary confluence of form and function, as the ultimate outcome of dissipation-driven adaptation and self-replication.

    However, even with the fluctuation theorems in hand, the conditions on early Earth or inside a cell are far too complex to predict from first principles. That’s why the ideas have to be tested in simplified, computer-simulated environments that aim to capture the flavor of reality.

    In the PRL paper, England and his coauthors Tal Kachman and Jeremy Owen of MIT simulated a system of interacting particles. They found that the system increases its energy absorption over time by forming and breaking bonds in order to better resonate with a driving frequency. “This is in some sense a little bit more basic as a result” than the PNAS findings involving the chemical reaction network, England said.

    Crucially, in the latter work, he and Horowitz created a challenging environment where special configurations would be required to tap into the available energy sources, just as the special atomic arrangement of a bacterium enables it to metabolize energy. In the simulated environment, external energy sources boosted (or “forced”) certain chemical reactions in the reaction network. The extent of this forcing depended on the concentrations of the different chemical species. As the reactions progressed and the concentrations evolved, the amount of forcing would change abruptly. Such a rugged forcing landscape made it difficult for the system “to find combinations of reactions which are capable of extracting free energy optimally,” explained Jeremy Gunawardena, a mathematician and systems biologist at Harvard Medical School.

    Yet when the researchers let the chemical reaction networks play out in such an environment, the networks seemed to become fine-tuned to the landscape. A randomized set of starting points went on to achieve rare states of vigorous chemical activity and extreme forcing four times more often than would be expected. And when these outcomes happened, they happened dramatically: These chemical networks ended up in the 99th percentile in terms of how much forcing they experienced compared with all possible outcomes. As these systems churned through reaction cycles and dissipated energy in the process, the basic form-function relationship that England sees as essential to life set in.

    Information Processors

    Experts said an important next step for England and his collaborators would be to scale up their chemical reaction network and to see if it still dynamically evolves to rare fixed points of extreme forcing. They might also try to make the simulation less abstract by basing the chemical concentrations, reaction rates and forcing landscapes on conditions that might have existed in tidal pools or near volcanic vents in early Earth’s primordial soup (but replicating the conditions that actually gave rise to life is guesswork). Rahul Sarpeshkar, a professor of engineering, physics and microbiology at Dartmouth College, said, “It would be nice to have some concrete physical instantiation of these abstract constructs.” He hopes to see the simulations re-created in real experiments, perhaps using biologically relevant chemicals and energy sources such as glucose.

    But even if the fine-tuned fixed points can be observed in settings that are increasingly evocative of life and its putative beginnings, some researchers see England’s overarching thesis as “necessary but not sufficient” to explain life, as Walker put it, because it cannot account for what many see as the true hallmark of biological systems: their information-processing capacity. From simple chemotaxis (the ability of bacteria to move toward nutrient concentrations or away from poisons) to human communication, life-forms take in and respond to information about their environment.

    To Walker’s mind, this distinguishes us from other systems that fall under the umbrella of England’s dissipation-driven adaptation theory, such as Jupiter’s Great Red Spot. “That’s a highly non-equilibrium dissipative structure that’s existed for at least 300 years, and it’s quite different from the non-equilibrium dissipative structures that are existing on Earth right now that have been evolving for billions of years,” she said. Understanding what distinguishes life, she added, “requires some explicit notion of information that takes it beyond the non-equilibrium dissipative structures-type process.” In her view, the ability to respond to information is key: “We need chemical reaction networks that can get up and walk away from the environment where they originated.”

    Gunawardena noted that aside from the thermodynamic properties and information-processing abilities of life-forms, they also store and pass down genetic information about themselves to their progeny. The origin of life, Gunawardena said, “is not just emergence of structure, it’s the emergence of a particular kind of dynamics, which is Darwinian. It’s the emergence of structures that reproduce. And the ability for the properties of those objects to influence their reproductive rates. Once you have those two conditions, you’re basically in a situation where Darwinian evolution kicks in, and to biologists, that’s what it’s all about.”

    Eugene Shakhnovich, a professor of chemistry and chemical biology at Harvard who supervised England’s undergraduate research, sharply emphasized the divide between his former student’s work and questions in biology. “He started his scientific career in my lab and I really know how capable he is,” Shakhnovich said, but “Jeremy’s work represents potentially interesting exercises in non-equilibrium statistical mechanics of simple abstract systems.” Any claims that it has to do with biology or the origins of life, he added, are “pure and shameless speculations.”

    Even if England is on the right track about the physics, biologists want more particulars — such as a theory of what the primitive “protocells” were that evolved into the first living cells, and how the genetic code arose. England completely agrees that his findings are mute on such topics. “In the short term, I’m not saying this tells me a lot about what’s going in a biological system, nor even claiming that this is necessarily telling us where life as we know it came from,” he said. Both questions are “a fraught mess” based on “fragmentary evidence,” that, he said, “I am inclined to steer clear of for now.” He is rather suggesting that in the tool kit of the first life- or proto-life-forms, “maybe there’s more that you can get for free, and then you can optimize it using the Darwinian mechanism.”

    Sarpeshkar seemed to see dissipation-driven adaptation as the opening act of life’s origin story. “What Jeremy is showing is that as long as you can harvest energy from your environment, order will spontaneously arise and self-tune,” he said. Living things have gone on to do a lot more than England and Horowitz’s chemical reaction network does, he noted. “But this is about how did life first arise, perhaps — how do you get order from nothing.”

    See the full article here .

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    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
    • stewarthoughblog 12:29 am on October 27, 2017 Permalink | Reply

      This is intellectually insulting as none of this “new physics” resolves the intractable problems of homochirality, homopolymerization, cell membranes, and nucleotide coding, nor does it give any viability to correct the myths of chemical evolution.

      Like

    • richardmitnick 12:47 pm on October 27, 2017 Permalink | Reply

      I only approved this comment so as to not deny freedom of speech. This does not mean that I agree or disagree, only that you have freedom of speech for your opinions.

      Like

  • richardmitnick 8:39 am on October 24, 2017 Permalink | Reply
    Tags: , Chemistry, ,   

    From Manu Garcia: “Our atoms” 


    Manu Garcia, a friend from IAC.

    The universe around us.
    Astronomy, everything you wanted to know about our local universe and never dared to ask.

    10/24/17
    Manu Astrologus

    Where do our atoms?
    1
    The hydrogen that is in your body, present in every molecule of water came from the Big Bang. No other significant sources of hydrogen in the universe. The carbon body formed by nuclear fusion within the stars, like oxygen. Much of the iron body formed during supernovae stars, stellar explosions that occurred long ago and far away. Gold in their jewelery was probably made of neutron stars during collisions that may have been visible as gamma-ray bursts short or events of gravitational waves. Elements such as phosphorus and copper are present in our bodies in small amounts but are essential for the functioning of all known life. It presented the periodic table is color-coded to indicate the best estimate of humanity in terms of nuclear origin of all known elements. Nuclear sites creating some elements, such as copper, are not well known and remain topics of observational and computational research.

    Image Credit & License: Wikipedia : Cmglee ; Data: Jennifer Johnson (OSU) .

    Posted in Astronomy Picture of the Day, APOD on 24 October 2017

    The periodic table.
    2
    Modern periodic table with 18 columns.

    Of Tximitx – Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=52698867

    The periodic table is an arrangement of the chemical elements in a table, ordered by their atomic number (number of protons), its electron configuration and chemical properties. This arrangement shows periodic trends, as elements with similar behavior in the same column.

    In the words of Theodor Benfey, table and periodic law “are the heart of chemistry, comparable to the theory of evolution in biology (which happened to the concept of the Great Chain of Being), and the laws of thermodynamics in classical physics. ”

    The rows of the table are called periods and columns groups. Some groups have names. For example group 17 is the halogens and the group 18 of the noble gases. The table also is divided into four blocks with some similar chemical properties. Because the positions are ordered, the table can be used to obtain relationships between the properties of the elements, or predict properties of new elements yet discovered or synthesized. The periodic table provides a useful tool for analyzing the chemical behavior and is widely used in chemistry and other science framework.

    Dmitri Mendeléyev in 1869 published the first version of the periodic table was widely recognized. The developed to illustrate periodic trends in the properties of the then known elements, to sort the items based on its chemical properties, although Julius Lothar Meyer, working separately conducted an order from the physical properties of atoms . Mendeleev also predicted some properties of then unknown elements anticipated that occupy the empty places in your table. Subsequently it showed that most of his predictions were correct when the items in question were discovered.

    Mendeleev periodic table has since been expanded and enhanced with the discovery or synthesis of new elements and development of new theoretical models to explain the chemical behavior. The current structure was designed by Alfred Werner from the version of Mendeleev. There are also other newspapers arrangements according to different properties and use it as you want to give (didactics, geology, etc.).

    Have been discovered or synthesized all elements of atomic number 1 (hydrogen) to 118 (oganesón); IUPAC confirmed the elements 113, 115, 117 and 118 on December 30, 2015, and their names and official symbols were made public on November 28, 2016. The first 94 exist naturally, although some only found in small amounts and were synthesized in the laboratory before being found in nature. the elements with atomic numbers 95 to 118 only they have been synthesized in laboratories. There were also produced numerous synthetic radioisotopes of elements present in nature. Elements of 95-100 existed in nature in the past but is currently not. The research to find new elements for synthesis of higher atomic numbers continues.

    See the full article here .

    Please help promote STEM in your local schools.

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