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  • richardmitnick 12:31 pm on December 18, 2018 Permalink | Reply
    Tags: , Biology, , , , , Planetary HAZE (PHAZER) chamber   

    From JHU HUB: “Alien imposters: Planets with oxygen don’t necessarily have life, study finds” 

    Johns Hopkins

    From JHU HUB

    12.17.18
    Chanapa Tantibanchachai

    1
    Chao He shows off the lab’s PHAZER setup. Image credit: Chanapa Tantibanchachai

    In their search for life in solar systems near and far, researchers have often accepted the presence of oxygen in a planet’s atmosphere as the surest sign that life may be present there. A new Johns Hopkins study, however, recommends a reconsideration of that rule of thumb.

    Simulating in the lab the atmospheres of planets beyond the solar system, researchers successfully created both organic compounds and oxygen, absent of life.

    The findings, published Dec. 11 by the journal ACS Earth and Space Chemistry, serve as a cautionary tale for researchers who suggest the presence of oxygen and organics on distant worlds is evidence of life there.

    2
    A CO2-rich planetary atmosphere exposed to a plasma discharge in Sarah Hörst’s lab. Image credit: Chao He

    “Our experiments produced oxygen and organic molecules that could serve as the building blocks of life in the lab, proving that the presence of both doesn’t definitively indicate life,” says Chao He, assistant research scientist in the Johns Hopkins University Department of Earth and Planetary Sciences and the study’s first author. “Researchers need to more carefully consider how these molecules are produced.”

    Oxygen makes up 20 percent of Earth’s atmosphere and is considered one of the most robust biosignature gases in Earth’s atmosphere. In the search for life beyond Earth’s solar system, however, little is known about how different energy sources initiate chemical reactions and how those reactions can create biosignatures like oxygen. While other researchers have run photochemical models on computers to predict what exoplanet atmospheres might be able to create, no such simulations to his knowledge have before now been conducted in the lab.

    The research team performed the simulation experiments in a specially designed Planetary HAZE (PHAZER) chamber in the lab of Sarah Hörst, assistant professor of Earth and planetary sciences and the paper’s co-author. The researchers tested nine different gas mixtures, consistent with predictions for super-Earth and mini-Neptune type exoplanet atmospheres; such exoplanets are the most abundant type of planet in our Milky Way galaxy. Each mixture had a specific composition of gases such as carbon dioxide, water, ammonia, and methane, and each was heated at temperatures ranging from about 80 to 700 degrees Fahrenheit.

    He and the team allowed each gas mixture to flow into the PHAZER setup and then exposed the mixture to one of two types of energy, meant to mimic energy that triggers chemical reactions in planetary atmospheres: plasma from an alternating current glow discharge or light from an ultraviolet lamp. Plasma, an energy source stronger than UV light, can simulate electrical activities like lightning and/or energetic particles, and UV light is the main driver of chemical reactions in planetary atmospheres such as those on Earth, Saturn, and Pluto.

    After running the experiments continuously for three days, corresponding to the amount of time gas would be exposed to energy sources in space, the researchers measured and identified resulting gasses with a mass spectrometer, an instrument that sorts chemical substances by their mass to charge ratio.

    The research team found multiple scenarios that produced both oxygen and organic molecules that could build sugars and amino acids—raw materials for which life could begin—such as formaldehyde and hydrogen cyanide.

    “People used to suggest that oxygen and organics being present together indicates life, but we produced them abiotically in multiple simulations,” He says. “This suggests that even the co-presence of commonly accepted biosignatures could be a false positive for life.”

    See the full article here .


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    Please help promote STEM in your local schools.

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    About the Hub
    We’ve been doing some thinking — quite a bit, actually — about all the things that go on at Johns Hopkins. Discovering the glue that holds the universe together, for example. Or unraveling the mysteries of Alzheimer’s disease. Or studying butterflies in flight to fine-tune the construction of aerial surveillance robots. Heady stuff, and a lot of it.

    In fact, Johns Hopkins does so much, in so many places, that it’s hard to wrap your brain around it all. It’s too big, too disparate, too far-flung.

    We created the Hub to be the news center for all this diverse, decentralized activity, a place where you can see what’s new, what’s important, what Johns Hopkins is up to that’s worth sharing. It’s where smart people (like you) can learn about all the smart stuff going on here.

    At the Hub, you might read about cutting-edge cancer research or deep-trench diving vehicles or bionic arms. About the psychology of hoarders or the delicate work of restoring ancient manuscripts or the mad motor-skills brilliance of a guy who can solve a Rubik’s Cube in under eight seconds.

    There’s no telling what you’ll find here because there’s no way of knowing what Johns Hopkins will do next. But when it happens, this is where you’ll find it.

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

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  • richardmitnick 3:02 pm on December 14, 2018 Permalink | Reply
    Tags: , Biology, In the Ediacaran period complex organisms including soft-bodied animals up to a meter long sprang to life in deep ocean waters, ,   

    From Stanford University: “Stanford researchers unearth why deep oceans gave life to the first big, complex organisms” 

    Stanford University Name
    From Stanford University

    December 12, 2018
    Josie Garthwaite
    (650) 497-0947
    josieg@stanford.edu

    In the beginning, life was small.

    For billions of years, all life on Earth was microscopic, consisting mostly of single cells. Then suddenly, about 570 million years ago, complex organisms including animals with soft, sponge-like bodies up to a meter long sprang to life. And for 15 million years, life at this size and complexity existed only in deep water.

    1
    More than 570 million years ago, in the Ediacaran period, complex organisms including soft-bodied animals up to a meter long sprang to life in deep ocean waters. (Image credit: Peter Trusler)

    Scientists have long questioned why these organisms appeared when and where they did: in the deep ocean, where light and food are scarce, in a time when oxygen in Earth’s atmosphere was in particularly short supply. A new study from Stanford University, published Dec. 12 in the peer-reviewed Proceedings of the Royal Society B, suggests that the more stable temperatures of the ocean’s depths allowed the burgeoning life forms to make the best use of limited oxygen supplies.

    All of this matters in part because understanding the origins of these marine creatures from the Ediacaran period is about uncovering missing links in the evolution of life, and even our own species. “You can’t have intelligent life without complex life,” explained Tom Boag, lead author on the paper and a doctoral candidate in geological sciences at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth).

    The new research comes as part of a small but growing effort to apply knowledge of animal physiology to understand the fossil record in the context of a changing environment. The information could shed light on the kinds of organisms that will be able to survive in different environments in the future.

    “Bringing in this data from physiology, treating the organisms as living, breathing things and trying to explain how they can make it through a day or a reproductive cycle is not a way that most paleontologists and geochemists have generally approached these questions,” said Erik Sperling, senior author on the paper and an assistant professor of geological sciences.

    Goldilocks and temperature change

    Previously, scientists had theorized that animals have an optimum temperature at which they can thrive with the least amount of oxygen. According to the theory, oxygen requirements are higher at temperatures either colder or warmer than a happy medium. To test that theory in an animal reminiscent of those flourishing in the Ediacaran ocean depths, Boag measured the oxygen needs of sea anemones, whose gelatinous bodies and ability to breathe through the skin closely mimic the biology of fossils collected from the Ediacaran oceans.

    “We assumed that their ability to tolerate low oxygen would get worse as the temperatures increased. That had been observed in more complex animals like fish and lobsters and crabs,” Boag said. The scientists weren’t sure whether colder temperatures would also strain the animals’ tolerance. But indeed, the anemones needed more oxygen when temperatures in an experimental tank veered outside their comfort zone.

    Together, these factors made Boag and his colleagues suspect that, like the anemones, Ediacaran life would also require stable temperatures to make the most efficient use of the ocean’s limited oxygen supplies.

    Refuge at depth

    It would have been harder for Ediacaran animals to use the little oxygen present in cold, deep ocean waters than in warmer shallows because the gas diffuses into tissues more slowly in colder seawater. Animals in the cold have to expend a larger portion of their energy just to move oxygenated seawater through their bodies.

    2
    Shallow waters offered sunlight and food supplies, but the deeper waters where large, complex organisms first evolved provided a refuge from wild swings in temperature. (Image credit: Shutterstock)

    But what it lacked in useable oxygen, the deep Ediacaran ocean made up for with stability. In the shallows, the passing of the sun and seasons can deliver wild swings in temperature – as much as 10 degrees Celsius in the modern ocean, compared to seasonal variations of less than 1 degree Celsius at depths below one kilometer (.62 mile). “Temperatures change much more rapidly on a daily and annual basis in shallow water,” Sperling explained.

    In a world with low oxygen levels, animals unable to regulate their own body temperature couldn’t have withstood an environment that so regularly swung outside their Goldilocks temperature.

    The Stanford team, in collaboration with colleagues at Yale University, propose that the need for a haven from such change may have determined where larger animals could evolve. “The only place where temperatures were consistent was in the deep ocean,” Sperling said. In a world of limited oxygen, the newly evolving life needed to be as efficient as possible and that was only possible in the relatively stable depths. “That’s why animals appeared there,” he said.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus. No image credit

    Stanford University

    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

    Stanford University Seal

     
  • richardmitnick 10:45 am on December 10, 2018 Permalink | Reply
    Tags: , Biology, Calditol, , Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments, , Sulfolobus acidocaldarius   

    From Stanford University: “Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments” 

    Stanford University Name
    From Stanford University

    December 5, 2018
    Danielle Torrent Tucker
    (650) 497-9541
    dttucker@stanford.edu

    Scientists discovered a protein that modifies a microbe’s membrane and helps it survive in hot, acidic environments, proving a long-standing hypothesis that these structures have a protective effect.

    1
    The microorganism Sulfolobus acidocaldarius lives in extreme environments, such as Emerald Hot Spring in Yellowstone National Park. (Image credit: Rennett Stowe / flickr)

    Within harsh environments like hot springs, volcanic craters and deep-sea hydrothermal vents – uninhabitable by most life forms – microscopic organisms are thriving. How? It’s all in how they wrap themselves.

    Stanford University researchers have identified a protein that helps these organisms form a protective, lipid-linked cellular membrane – a key to withstanding extremely highly acidic habitats.

    Scientists had known that this group of microbes – called archaea – were surrounded by a membrane made of different chemical components than those of bacteria, plants or animals. They had long hypothesized that it could be what provides protection in extreme habitats. The team directly proved this idea by identifying the protein that creates the unusual membrane structure in the species Sulfolobus acidocaldarius.

    The structures of some organisms’ membranes are retained in the fossil record and can serve as molecular fossils or biomarkers, leaving hints of what lived in the environment long ago. Finding preserved membrane lipids, for example, could suggest when an organism evolved and how that may have been the circumstance of its environment. Being able to show how this protective membrane is created could help researchers understand other molecular fossils in the future, offering new evidence about the evolution of life on Earth. The results appeared the week of Dec. 3 in Proceedings of the National Academy of Sciences.

    “Our model is that this organism evolved the ability to make these membranes because it lives in an environment where the acidity changes,” said co-author Paula Welander, an assistant professor of Earth system science at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth). “This is the first time we’ve actually linked some part of a lipid to an environmental condition in archaea.”

    Rare chemistry

    The hot springs where S. acidocaldarius is found, such as those in Yellowstone National Park that are over 200 degrees Fahrenheit, can experience fluctuating acidity. This organism is also found in volcanic craters, deep-sea hydrothermal vents and other acidic environments with both moderate and cold temperatures.

    Welander became interested in studying this microbe because of its rare chemistry, including its unusual lipid membranes. Unlike plants and fungi, archaeal organisms do not produce protective outer walls of cellulose and their membranes do not contain the same chemicals as bacteria. Scientists had explored how the species produced its unusual membrane for about 10 years before experimentation stopped in 2006, she said.

    “I think we forget that some things just haven’t been done yet – I’ve been finding that a lot ever since I stepped into the geobiology world,” Welander said. “There are so many questions out there that we just need the basic knowledge of, such as, ‘What is the protein that’s doing this? Does this membrane structure really do what we’re saying it does?’”

    From previous research in archaea, Welander and her team knew that the organisms produce a membrane containing a ringed molecule called a calditol. The group thought this molecule might underlie the species’ ability to withstand environments where other organisms perish.

    To find out, they first went through the genome of S. acidocaldarius and identified three genes likely to be involved in making a calditol. They then mutated those genes one-by-one, eliminating any proteins the genes made. The experiments revealed one gene that, when mutated, produced S. acidocaldarius that lacked calditol in the membrane. That mutated organism was able to grow at high temperatures but withered in a highly acidic environment, suggesting that the protein is necessary to both make the unusual membrane and withstand acidity.

    The work was particularly challenging because Welander’s lab had to replicate those high temperature, acidic conditions in which the microbes thrive. Most of the incubators in her lab could only reach body temperature, so lead author Zhirui Zeng, a postdoctoral researcher in Welander’s lab, figured out how to imitate the organism’s home using a special small oven, she said.

    “That was really cool,” Welander said. “We did a lot of experimenting to try to figure out the chemistry.”

    Third domain of life

    This work is about more than just finding one protein, Welander said. Her research explores lipids found in present-day microbes with the goal of understanding Earth’s history, including ancient climatic events, mass extinctions and evolutionary transitions. But before scientists can interpret evolutionary characteristics, they need to understand the basics, like how novel lipids are created.

    Archaea are sometimes called the “third domain of life,” with one domain being bacteria and the other being a group that includes plants and animals – collectively known as eukaryotes. Archaea includes some of the oldest, most abundant lifeforms on the planet, without which the ecosystem would collapse. Archaea are particularly anomalous microbes, confused with bacteria one day and likened to plants or animals the next because of their unique molecular structures.

    The research is particularly interesting because the classification for archaea is still debated by taxonomists. They were only separated from the bacteria and eukaryote domains in the past two decades, following the development of genetic sequencing in the 1970s.

    “There are certain things about archaea that are different, like the lipids,” Welander said. “Archaea are a big area of research now because they are this different domain that we want to study, and understand – and they’re really cool.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus. No image credit

    Stanford University

    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 11:30 am on November 16, 2018 Permalink | Reply
    Tags: , Biology, , Shedding new light on photosynthesis, , University of Michigan researchers have developed a powerful microscope that can map how light energy migrates in photosynthetic bacteria on timescales of one-quadrillionth of a second.   

    From University of Michigan: “Shedding new light on photosynthesis” 

    U Michigan bloc

    From University of Michigan

    October 11, 2018
    Morgan Sherburne
    morganls@umich.edu

    1
    Employing a series of ultrashort laser pulses, a new microscope reveals intricate details that govern photosynthetic processes in purple bacteria. Image credit: Vivek Tiwari, Yassel Acosta and Jennifer Ogilvie

    University of Michigan researchers have developed a powerful microscope that can map how light energy migrates in photosynthetic bacteria on timescales of one-quadrillionth of a second.

    The microscope could help researchers develop more efficient organic photovoltaic materials, a type of solar cell that could provide cheaper energy than silicon-based solar cells.

    In photosynthetic plants and bacteria, light hits the leaf or bacteria and a system of tiny light-harvesting antenna shuttle it along through proteins to what’s called a reaction center. Here, light is “trapped” and turned into metabolic energy for the organisms.

    Jennifer Ogilvie, U-M professor of physics and biophysics, and her team want to capture the movement of this light energy through proteins in a cell, and the team has taken one step toward that goal in developing this microscope. Their study has been published in Nature Communications.

    Ogilvie, graduate student Yassel Acosta and postdoctoral fellow Vivek Tiwari worked together to develop the microscope, which uses a method called two-dimensional electronic spectroscopy to generate images of energy migration within proteins during photosynthesis. The microscope images an area the size of one-fifth of a human blood cell and can capture events that take a period of one-quadrillionth of a second.

    Two-dimensional spectroscopy works by reading the energy levels within a system in two ways. First, it reads the wavelength of light that’s absorbed in a photosynthetic system. Then, it reads the wavelength of light detected within the system, allowing energy to be tracked as it flows through the organism.

    The instrument combines this method with a microscope to measure a signal from nearly a million times smaller volumes than before. Previous measurements imaged samples averaged over sections that were a million times larger. Averaging over large sections obscures the different ways energy might be moving within the same system.

    “We’ve now combined both of those techniques so we can get at really fast processes as well as really detailed information about how these molecules are interacting,” Ogilvie said. “If I look at one nanoscopic region of my sample versus another, the spectroscopy can look very different. Previously, I didn’t know that, because I only got the average measurement. I couldn’t learn about the differences, which can be important for understanding how the system works.”

    In developing the microscope, Ogilvie and her team studied colonies of photosynthetic purple bacterial cells. Previously, scientists have mainly looked at purified parts of these types of cells. By looking at an intact cell system, Ogilvie and her team were able to observe how a complete system’s different components interacted.

    The team also studied bacteria that had been grown in high light conditions, low light conditions and a mixture of both. By tracking light emitted from the bacteria, the microscope enabled them to view how the energy level structure and flow of energy through the system changed depending on the bacteria’s light conditions.

    Similarly, this microscope can help scientists understand how organic photovoltaic materials work, Ogilvie says. Instead of the light-harvesting antennae complexes found in plants and bacteria, organic photovoltaic materials have what are called “donor” molecules and “acceptor” molecules. When light travels through these materials, the donor molecule sends electrons to acceptor molecules, generating electricity.

    “We might find there are regions where the excitation doesn’t produce a charge that can be harvested, and then we might find regions where it works really well,” Ogilvie said. “If we look at the interactions between these components, we might be able to correlate the material’s morphology with what’s working well and what isn’t.”

    In organisms, these zones occur because one area of the organism might not be receiving as much light as another area, and therefore is packed with light-harvesting antennae and few reaction centers. Other areas might be flooded with light, and bacteria may have fewer antennae—but more reaction centers. In photovoltaic material, the distribution of donor and receptor molecules may change depending on the material’s morphology. This could affect the material’s efficiency in converting light into electricity.

    “All of these materials have to have different components that do different things—components that will absorb the light, components that will take that the energy from the light and convert it to something that can be used, like electricity,” Ogilvie said. “It’s a holy grail to be able to map in space and time the exact flow of energy through these systems.”

    See the full article here .


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    stem

    Stem Education Coalition

    U MIchigan Campus

    The University of Michigan (U-M, UM, UMich, or U of M), frequently referred to simply as Michigan, is a public research university located in Ann Arbor, Michigan, United States. Originally, founded in 1817 in Detroit as the Catholepistemiad, or University of Michigania, 20 years before the Michigan Territory officially became a state, the University of Michigan is the state’s oldest university. The university moved to Ann Arbor in 1837 onto 40 acres (16 ha) of what is now known as Central Campus. Since its establishment in Ann Arbor, the university campus has expanded to include more than 584 major buildings with a combined area of more than 34 million gross square feet (781 acres or 3.16 km²), and has two satellite campuses located in Flint and Dearborn. The University was one of the founding members of the Association of American Universities.

    Considered one of the foremost research universities in the United States,[7] the university has very high research activity and its comprehensive graduate program offers doctoral degrees in the humanities, social sciences, and STEM fields (Science, Technology, Engineering and Mathematics) as well as professional degrees in business, medicine, law, pharmacy, nursing, social work and dentistry. Michigan’s body of living alumni (as of 2012) comprises more than 500,000. Besides academic life, Michigan’s athletic teams compete in Division I of the NCAA and are collectively known as the Wolverines. They are members of the Big Ten Conference.

     
  • richardmitnick 10:54 am on November 15, 2018 Permalink | Reply
    Tags: "Searching for ocean microbes", , Bermuda Atlantic Time Series, Biology, Cyverse, DNA Databank of Japan, European Bioinformatics Institute, Hawaiian Ocean Time Series, Hurwitz Lab-University of Arizona, iMicrobe platform, National Center for Biotechnology Information, National Microbiome Collaborative, , Planet Microbe, , The Hurwitz Lab corrals big data sets into a more searchable form to help scientists study microorganisms,   

    From Science Node: “Searching for ocean microbes” 

    Science Node bloc
    From Science Node

    07 Nov, 2018
    Susan McGinley

    How one lab is consolidating ocean data to track climate change.

    1
    Courtesy David Clode/Unsplash.

    Scientists have been making monthly observations of the physical, biological, and chemical properties of the ocean since 1988. Now, thanks to the Hurwitz Lab at the University of Arizona (UA), researchers around the world have greater access than ever before to the information collected at these remote ocean sites.

    U Arizona bloc

    Led by Bonnie Hurwitz, assistant professor of biosystems engineering at UA, the Hurwitz Lab corrals big data sets into a more searchable form to help scientists study microorganisms – bacteria, fungi, algae, viruses, protozoa – and how they relate to each other, their hosts and the environment.

    3
    Sample collection. Bonnie Hurwitz next to the metal pod that serves as the main chamber for the Alvin submersible that scientists operate to collect samples from the deepest parts of the ocean not accessible to people. Courtesy Stefan Sievert, Woods Hole Oceanographic Institution.

    The lab is building a data infrastructure on top of Cyverse to integrate and build information from diverse data stores in collaboration with the broader cyber community. The goal is to give people the ability to use data sets that span a range of storage servers, all in one place.

    “One of the exciting things my lab is funded for is Planet Microbe, a three-year project through the National Science Foundation (NSF), to bring together genomic and environmental data sets coming from ocean research cruises,” Hurwitz said.

    “Samples of water are taken using an instrument called a CTD that measures salinity, temperature, depth, and other features to create a scan of ocean conditions across the water column.”

    As the CTD descends into the ocean, bottles are triggered at different depths to collect water samples for a variety of experiments including sequencing the DNA/RNA of microbes. The moment each sample leaves the ship is often the last time these valuable and varied data appear together.

    The first phase of the project focuses on the Hawaiian Ocean Time Series and the Bermuda Atlantic Time Series. At both locations, samples are collected across an ocean transect at a variety of depths across the water column, from surface to deep ocean.

    4
    A CTD device that measures water conductivity (salinity), temperature and depth is mounted underneath a set of water bottles used for collecting samples at varying depths in a column of water. Courtesy Tara Clemente, University of Hawaii.

    The readings taken at each level stream out to data banks around the world. Different labs conduct the analyses, but the Hurwitz lab reunites all of the data sets, including data from these long-term ecological sites used for monitoring climate and changes in the oceans.

    “Oceanographers have different tool kits. They are collecting data on ship to observe both the ocean environment and the genetics of microbes to understand the role they play in the ocean,” Hurwitz said. “We are including these data in a very simple web-based platform where users can run their own analyses and data pipelines to use the data in new ways.”

    While still in year one of the project, the first data have just been released under the iMicrobe platform, which connects users with computational resources for analyzing and visualizing the data.

    The platform’s bioinformatics tools let researchers analyze the data in new ways that may not have originally been possible when the data were collected, or to compare these global ocean data sets with new data as it becomes available.

    “We’re plumbers, actually, creating the pipelines between the world’s oceanographic data sets. We’re trying to enable scientists to access data from the world’s oceans,” Hurwitz said.

    A larger mission

    In addition to their Planet Microbe work, Hurwitz and her team work with the three entities that store and sync all of the world’s “omics” (genomics, proteomics) data – the European Bioinformatics Institute, the National Center for Biotechnology Information and the DNA Databank of Japan, and others.

    “We are working with the National Microbiome Collaborative, a national effort to bring together the world’s data in the microbiome sciences, from human to ocean and everything in between,” Hurwitz said.

    “Having those data sets captured and searchable is great,” said Hurwitz. “They are so big they can’t be housed in any one place. The infrastructure allows you to search across these areas.”

    5
    Going deep. Hurwitz and Amy Apprill, associate scientist at Woods Hole Oceanographic Institution, in front of the human-piloted Alvin submersible. Deep-water samples are collected using the pod’s robotic arm because the pressure of the water is too intense for divers. Courtesy Stefan Sievert, Woods Hole Oceanographic Institution.

    “If we want to start looking at things together in a holistic manner, we need to be able to remotely access data that are not on our servers. We are essentially indexing the world’s data and becoming a search engine for microbiome sciences.”

    By reconnecting ‘omics data with environmental data from oceanographic cruises, Hurwitz and her team are speeding up discoveries into environmental changes affecting the marine microbes that are responsible for producing half the air that we breathe.

    These data can be used in the future to predict how our oceans respond to change and to specific environmental conditions.

    “Our researchers can not only use a $30 million supercomputer at XSEDE (Extreme Science and Engineering Discovery Environment) supported by the NSF for running analyses, they also have access to modern big data architectures through a simple computer interface.”

    “We’re trying to understand where all the data are and how we can sync them,” Hurwitz said. “How data are structured and assembled together has been like the Wild West. We’re figuring it out.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    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 7:22 pm on November 9, 2018 Permalink | Reply
    Tags: , , , , , Biology, , , , , , , , , Understanding our own backyard will be key in interpreting data from far-flung exoplanets   

    From COSMOS Magazine: “The tech we’re going to need to detect ET” 

    Cosmos Magazine bloc

    From COSMOS Magazine

    09 November 2018
    Lauren Fuge

    1
    Searching for biosignatures rather than examples of life itself is considered a prime strategy in the hunt for ET. smartboy10/Getty Images

    Move over Mars rovers, new technologies to detect alien life are on the horizon.

    A group of scientists from around the world, led by astrochemistry expert Chaitanya Giri from the Tokyo Institute of Technology in Japan, have put their heads together to plan the next 20 years’ worth of life-detection technologies. The study is currently awaiting peer review, but is freely available on the pre-print site, ArXiv.

    For decades, astrobiologists have scoured the skies and the sands of other planets for hints of extraterrestrial life. Not only are these researchers trying to find ET, but they’re also aiming to learn about the origin and evolution of life on Earth, the chemical composition of organic extraterrestrial objects, what makes a planet or satellite habitable, and more.

    But the answers to such questions are preceded by long years of planning, development, problem-solving and strategising.

    Late in 2017, 20 scientists from Japan, India, France, Germany and the USA – each with a special area of expertise – came together at a workshop run by the Earth-Life Science Institute (ELSI) at Giri’s Tokyo campus. There, they discussed the current progress and enticing possibilities of life-detection technologies.

    In particular, the boffins debated which ones should be a priority for research and development for missions within the local solar system – in other words, which instruments will be most feasible to out onto a space probe and send off to Mars or Enceladus during the next couple of decades.

    Of course, the planets and moons in the solar system are an extremely limited sample of the number of potentially habitable worlds in the universe, but understanding our own backyard will be key in interpreting data from far-flung exoplanets.

    So, according to these astrobiology experts, what’s the future plan for alien detection?

    The first step of any space mission is to study the planet or satellite from afar to determine whether it is habitable. Luckily, an array of next-generation telescopes is currently being built, from the ultra-sensitive James Webb Space Telescope, slated for launch in 2021, to the gargantuan Extremely Large Telescope in Chile, which will turn its 39-metre eye to the sky in 2024. The authors point out that observatories such as these will vastly expand our theoretical knowledge of planet habitability.

    NASA/ESA/CSA Webb Telescope annotated

    ESO/E-ELT,to be on top of Cerro Armazones in the Atacama Desert of northern Chile. located at the summit of the mountain at an altitude of 3,060 metres (10,040 ft).

    Just because a world is deemed habitable doesn’t mean life will be found all over it, though. It may exist only in limited geographical niches. To reach these inaccessible sites, the paper argues that we will require “agile robotic probes that are robust, able to seamlessly communicate with orbiters and deep space communications networks, be operationally semi-autonomous, have high-performance energy supplies, and are sterilisable to avoid forward contamination”.

    But according to Elizabeth Tasker, associate professor at the Japan Aerospace Exploration Agency (JAXA), who was not involved in the study, getting there is only half the struggle.

    “In fact, it’s the most tractable half because we can picture the problems we will face,” she says.

    The second, more pressing issue is how to recognise life unlike anything we know on Earth.

    As Tasker explains: “We only have Earth life to compare to and this is the result of huge evolutionary history on a planet whose complex past is unlikely to be replicated closely. That’s a lot of baggage to separate out.”

    According to the paper, the way forward is to equip missions with a suite of life-detection instruments that don’t look for life as we know it, but are instead able to identify the kinds of features that make organisms function.

    The authors outline a huge variety of exciting technologies that could be used for this purpose, including spectroscopy techniques (to analyse potential biological materials), quantum tunnelling [Nature Nanotechnology
    ] (to find DNA, RNA, peptides, and other small molecules), and fluorescence microscopy [ https://www.hou.usra.edu/meetings/lpsc2014/pdf/2744.pdf ](to identify the presence of cell membranes).

    They also nominate different forms of gas chromatography (to spot amino acids and sugars formed by living organisms, plus checking to see if molecules are “homochiral” [Space Science Reviews] (a suspected biosignature) using microfluidic devices and microscopes.

    High-resolution, miniaturised mass spectrometers would also be helpful, characterising biopolymers, which are created by living organisms, and measuring the elemental composition of objects to aid isotopic dating.

    Giri and colleagues also stress that exciting developments in machine learning, artificial intelligence, and pattern recognition will be useful in determining whether chemical samples are biological in origin.

    Interestingly, researchers are also developing technologies that may allow the detection of life in more unconventional places. On Earth, for example, cryotubes were recently used [International Journal of Systematic and Evolutionary Microbiology] to discover several new species of bacteria in the upper atmosphere.

    The scientists also discuss how certain technologies – such as high-powered synchrotron radiation and magnetic field facilities – are not yet compact enough to fly to other planets, and so samples must continue to be brought back for analysis.

    Several sample-and-return missions are currently underway, including JAXA’s Martian Moons exploration mission to Phobos, Hayabusa-2 to asteroid Ryugu, and NASA’s OSIRIS-rex to asteroid Bennu. What we learn from handling the organic-rich extraterrestrial materials brought back from these trips will be invaluable.

    JAXA MMX spacecraft

    JAXA/Hayabusa 2 Credit: JAXA/Akihiro Ikeshita

    NASA OSIRIS-REx Spacecraft

    What we learn from handling the organic-rich extraterrestrial materials brought back from these trips will be invaluable.

    The predictions and recommendations put forward by Giri and colleagues are the first steps in getting these technologies discussed in panel reviews, included in decadal surveys, and eventually funded.

    They complement several similar efforts, including a report prepared by US National Academies of Science, Engineering and Medicine (NASEM), calling for an expansion of the range of possible ET indicators, and a US-led exploration of how the next generation of radio telescopes will be utilised by SETI.

    Perhaps most importantly, these papers all highlight the need for collaborative work between scientists across disciplines.

    “A successful detection of life will need astrophysicists and geologists to examine possible environments on other planets, engineers and physicists to design the missions and instruments that can collect data, and chemists and biologists to determine how to classify life,” JAXA’s Tasker says.

    “But maybe that is appropriate: finding out what life really is and where it can flourish is the story of everyone on Earth. It should take all of us to unravel.”

    See the full article here .


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  • richardmitnick 1:50 pm on November 7, 2018 Permalink | Reply
    Tags: Biology, , , , , , , Researchers create most complete high-res atomic movie of photosynthesis to date, , ,   

    From SLAC National Accelerator Lab: “Researchers create most complete high-res atomic movie of photosynthesis to date” 

    From SLAC National Accelerator Lab

    November 7, 2018

    Andrew Gordon
    agordon@slac.stanford.edu
    (650) 926-2282

    In a major step forward, SLAC’s X-ray laser captures all four stable states of the process that produces the oxygen we breathe, as well as fleeting steps in between. The work opens doors to understanding the past and creating a greener future.

    1
    Using SLAC’s X-ray laser, researchers have captured the most complete high-res atomic movie to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe. (Gregory Stewart, SLAC National Accelerator Laboratory)

    Despite its role in shaping life as we know it, many aspects of photosynthesis remain a mystery. An international collaboration between scientists at SLAC National Accelerator Laboratory, Lawrence Berkeley National Laboratory and several other institutions is working to change that. The researchers used SLAC’s Linac Coherent Light Source (LCLS) X-ray laser to capture the most complete and highest-resolution picture to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe. The results were published in Nature today.

    SLAC/LCLS

    Explosion of life

    When Earth formed about 4.5 billion years ago, the planet’s landscape was almost nothing like what it is today. Junko Yano, one of the authors of the study and a senior scientist at Berkeley Lab, describes it as “hellish.” Meteors sizzled through a carbon dioxide-rich atmosphere and volcanoes flooded the surface with magmatic seas.

    Over the next 2.5 billion years, water vapor accumulating in the air started to rain down and form oceans where the very first life appeared in the form of single-celled organisms. But it wasn’t until one of those specks of life mutated and developed the ability to harness light from the sun and turn it into energy, releasing oxygen molecules from water in the process, that Earth started to evolve into the planet it is today. This process, oxygenic photosynthesis, is considered one of nature’s crown jewels and has remained relatively unchanged in the more than 2 billion years since it emerged.

    “This one reaction made us as we are, as the world. Molecule by molecule, the planet was slowly enriched until, about 540 million years ago, it exploded with life,” said co-author Uwe Bergmann, a distinguished staff scientist at SLAC. “When it comes to questions about where we come from, this is one of the biggest.”

    A greener future

    Photosystem II is the workhorse responsible for using sunlight to break water down into its atomic components, unlocking hydrogen and oxygen. Until recently, it had only been possible to measure pieces of this process at extremely low temperatures. In a previous paper, the researchers used a new method to observe two steps of this water-splitting cycle [Nature]at the temperature at which it occurs in nature.

    Now the team has imaged all four intermediate states of the process at natural temperature and the finest level of detail yet. They also captured, for the first time, transitional moments between two of the states, giving them a sequence of six images of the process.

    The goal of the project, said co-author Jan Kern, a scientist at Berkeley Lab, is to piece together an atomic movie using many frames from the entire process, including the elusive transient state at the end that bonds oxygen atoms from two water molecules to produce oxygen molecules.

    “Studying this system gives us an opportunity to see how metals and proteins work together and how light controls such kinds of reactions,” said Vittal Yachandra, one of the authors of the study and a senior scientist at Berkeley Lab who has been working on Photosystem II for more than 35 years. “In addition to opening a window on the past, a better understanding of Photosystem II could unlock the door to a greener future, providing us with inspiration for artificial photosynthetic systems that produce clean and renewable energy from sunlight and water.”

    Sample assembly line

    For their experiments, the researchers grow what Kern described as a “thick green slush” of cyanobacteria — the very same ancient organisms that first developed the ability to photosynthesize — in a large vat that is constantly illuminated. They then harvest the cells for their samples.

    At LCLS, the samples are zapped with ultrafast pulses of X-rays [Science] to collect both X-ray crystallography and spectroscopy data to map how electrons flow in the oxygen-evolving complex of photosystem II. In crystallography, researchers use the way a crystal sample scatters X-rays to map its structure; in spectroscopy, they excite the atoms in a material to uncover information about its chemistry. This approach, combined with a new assembly-line sample transportation system [Nature Methods], allowed the researchers to narrow down the proposed mechanisms put forward by the research community over the years.

    Mapping the process

    Previously, the researchers were able to determine the room-temperature structure of two of the states at a resolution of 2.25 angstroms; one angstrom is about the diameter of a hydrogen atom. This allowed them to see the position of the heavy metal atoms, but left some questions about the exact positions of the lighter atoms, like oxygen. In this paper, they were able to improve the resolution even further, to 2 angstroms, which enabled them to start seeing the position of lighter atoms more clearly, as well as draw a more detailed map of the chemical structure of the metal catalytic center in the complex where water is split.

    This center, called the oxygen-evolving complex, is a cluster of four manganese atoms and one calcium atom bridged with oxygen atoms. It cycles through the four stable oxidation states, S0-S3, when exposed to sunlight. On a baseball field, S0 would be the start of the game when a player on home base is ready to go to bat. S1-S3 would be players on first, second, and third. Every time a batter connects with a ball, or the complex absorbs a photon of sunlight, the player on the field advances one base. When the fourth ball is hit, the player slides into home, scoring a run or, in the case of Photosystem II, releasing breathable oxygen.

    The researchers were able to snap action shots of how the structure of the complex transformed at every base, which would not have been possible without their technique. A second set of data allowed them to map the exact position of the system in each image, confirming that they had in fact imaged the states they were aiming for.

    1
    In photosystem II, the water-splitting center cycles through four stable states, S0-S3. On a baseball field, S0 would be the start of the game when a batter on home base is ready to hit. S1-S3 would be players waiting on first, second, and third. The center gets bumped up to the next state every time it absorbs a photon of sunlight, just like how a player on the field advances one base every time a batter connects with a ball. When the fourth ball is hit, the player slides into home, scoring a run or, in the case of Photosystem II, releasing the oxygen we breathe. (Gregory Stewart/SLAC National Accelerator Laboratory)

    Sliding into home

    But there are many other things going on throughout this process, as well as moments between states when the player is making a break for the next base, that are a bit harder to catch. One of the most significant aspects of this paper, Yano said, is that they were able to image two moments in between S2 and S3. In upcoming experiments, the researchers hope to use the same technique to image more of these in-between states, including the mad dash for home — the transient state, or S4, where two atoms of oxygen bond together — providing information about the chemistry of the reaction that is vital to mimicking this process in artificial systems.

    “The entire cycle takes nearly two milliseconds to complete,” Kern said. “Our dream is to capture 50-microsecond steps throughout the full cycle, each of them with the highest resolution possible, to create this atomic movie of the entire process.”

    Although they still have a way to go, the researchers said that these results provide a path forward, both in unveiling the mysteries of how photosynthesis works and in offering a blueprint for artificial sources of renewable energy.

    “It’s been a learning process,” said SLAC scientist and co-author Roberto Alonso-Mori. “Over the last seven years we’ve worked with our collaborators to reinvent key aspects of our techniques. We’ve been slowly chipping away at this question and these results are a big step forward.”

    In addition to SLAC and Berkeley Lab, the collaboration includes researchers from Umeå University, Uppsala University, Humboldt University of Berlin, the University of California, Berkeley, the University of California, San Francisco and the Diamond Light Source.

    Key components of this work were carried out at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), Berkeley Lab’s Advanced Light Source (ALS) and Argonne National Laboratory’s Advanced Photon Source (APS). LCLS, SSRL, APS, and ALS are DOE Office of Science user facilities. This work was supported by the DOE Office of Science and the National Institutes of Health, among other funding agencies.

    SLAC/SSRL

    LBNL/ALS

    ANL APS

    See the full article here .


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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

     
  • richardmitnick 12:51 pm on October 19, 2018 Permalink | Reply
    Tags: , , Biology, , ,   

    From Science Magazine: “Chemists find a recipe that may have jump-started life on Earth’ 

    AAAS
    From Science Magazine

    1
    New research spells out the simple chemical steps that may have launched the RNA World. Mark Garlick/Science Source

    Oct. 18, 2018
    Robert F. Service

    In the molecular dance that gave birth to life on Earth, RNA appears to be a central player. But the origins of the molecule, which can store genetic information as DNA does and speed chemical reactions as proteins do, remain a mystery. Now, a team of researchers has shown for the first time that a set of simple starting materials, which were likely present on early Earth, can produce all four of RNA’s chemical building blocks.

    Those building blocks—cytosine, uracil, adenine, and guanine—have previously been re-created in the lab from other starting materials. In 2009, chemists led by John Sutherland at the University of Cambridge in the United Kingdom devised a set of five compounds likely present on early Earth that could give rise to cytosine and uracil, collectively known as pyrimidines. Then, 2 years ago, researchers led by Thomas Carell, a chemist at Ludwig Maximilian University in Munich, Germany, reported that his team had an equally easy way to form adenine and guanine [Nature], the building blocks known as purines. But the two sets of chemical reactions were different. No one knew how the conditions for making both pairs of building blocks could have occurred in the same place at the same time.

    Now, Carell says he may have the answer. On Tuesday, at the Origins of Life Workshop here, he reported that he and his colleagues have come up with a simple set of reactions that could have given rise to all four RNA bases.

    Carell’s story starts with only six molecular building blocks—oxygen, nitrogen, methane, ammonia, water, and hydrogen cyanide, all of which would have been present on early Earth. Other research groups had shown that these molecules could react to form somewhat more complex compounds than the ones Carell used.

    To make the pyrimidines, Carell started with compounds called cyanoacetylene and hydroxylamine, which react to form compounds called amino-isoxazoles. These, in turn, react with another simple molecule, urea, to form compounds that then react with a sugar called ribose to make one last set of intermediate compounds.

    Finally, in the presence of sulfur-containing compounds called thiols and trace amounts of iron or nickel salts, these intermediates transform into the pyrimidines cytosine and uracil. As a bonus, this last reaction is triggered when the metals in the salts harbor extra positive charges, which is precisely what occurs in the final step in a similar molecular cascade that produces the purines, adenine and guanine. Even better, the step that leads to all four nucleotides works in one pot, Carell says, offering for the first time a plausible explanation of how all of RNA’s building blocks could have arisen side by side.

    “It looks pretty good to me,” says Steven Benner, a chemist with the Foundation for Applied Molecular Evolution in Alachua, Florida. The process provides a simple way to produce all four bases under conditions consistent with those believed present on early Earth, he says.

    The process doesn’t solve all of RNA’s mysteries. For example, another chemical step still needs to “activate” each of RNA’s four building blocks to link them into the long chains that form genetic material and carry out chemical reactions. But making RNA under conditions like those present on early Earth now appears within reach.

    See the full article here .


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    • stewarthoughblog 11:31 pm on October 19, 2018 Permalink | Reply

      Some interesting science here, but mostly wildly speculative naturalism. The “molecular dance” is a myth, like Darwin’s “warm little ponds,” Oparin-Haldane primordial soup or Miller-Urey test tube goo. There are no naturalistic processes capable of any appreciable assembly of abiotic chemicals at any level that approach the basic, elemental level of assembly required for the origin of life.

      RNA, in particular, is an intermediate molecule that is easily mutated, easily contaminated, highly reactive, composed of homochiral AGCU that does not develop naturalistically and does not function at any level that produces metabolic processes or reproduce.

      The intelligently designed, highly orchestrated lab experiments are biogeochemically irrelevant to primordial Earth conditions and do no demonstrate any significant achievement relative to the origin of life.

      Like

  • richardmitnick 5:13 pm on October 5, 2018 Permalink | Reply
    Tags: , Biology, , Rutgers Researchers Discover Possible Cause for Alzheimer's and Traumatic Brain Injury,   

    From Rutgers University: “Rutgers Researchers Discover Possible Cause for Alzheimer’s and Traumatic Brain Injury” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University

    September 26, 2018

    Jennifer Forbes Mullenhard
    732-788-8301
    mullenjf@rwjms.rutgers.edu

    Caitlin Coyle
    848-445-1955
    caitlin.coyle@rutgers.edu

    The new mechanism may have also led to the discovery of an effective treatment.

    1
    Federico Sesti, a professor of neuroscience and cell biology at Rutgers Robert Wood Johnson Medical School discovered possible cause for Alzheimer’s which may have also led to the discovery of an effective treatment.
    Photo: Kim Sokoloff

    Rutgers researchers have discovered a new mechanism that may contribute to Alzheimer’s disease and traumatic brain injury. They now hope to launch a clinical trial to test the treatment in humans.

    What causes Alzheimer’s is unknown, but a popular theory suggests a protein known as amyloid-beta slowly builds up a plaque in the brains of people with Alzheimer’s. But in a recent study in the journal Cell Death & Disease, Federico Sesti, a professor of neuroscience and cell biology at Rutgers Robert Wood Johnson Medical School, looked at a new mechanism, which involves a non-amyloid-beta protein, a potassium channel referred to as KCNB1.

    Under conditions of stress in a brain affected by Alzheimer’s, KCNB1 builds up and becomes toxic to neurons and then promotes the production of amyloid-beta. The build-up of KCNB1 channels is caused by a chemical process commonly known as oxidation.

    “Indeed, scientists have known for a long time that during aging or in neurodegenerative disease cells produce free radicals,” said Sesti. “Free radicals are toxic molecules that can cause a reaction that results in lost electrons in important cellular components, including the channels.”

    The study found that in brains affected by Alzheimer’s, the build-up of KCNB1 was much higher compared to normal brains.

    “The discovery of KCNB1’s oxidation/build-up was found through observation of both mouse and human brains, which is significant as most scientific studies do not usually go beyond observing animals,” said Sesti. “Further, KCBB1 channels may not only contribute to Alzheimer’s but also to other conditions of stress as it was found in a recent study that they are formed following brain trauma.”

    In the cases of Alzheimer’s and traumatic brain injury, the build-up of KCNB1 is associated with severe damage of mental function. As a result of this discovery, Sesti successfully tested a drug called Sprycel in mice. The drug is used to treat patients with leukemia.

    “Our study shows that this drug and similar ones could potentially be used to treat Alzheimer’s, a discovery that leads the way to launching a clinical trial to test this drug in humans.”

    See the full article here .


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    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

     
  • richardmitnick 1:39 pm on September 30, 2018 Permalink | Reply
    Tags: , , Biology, , Top 10 Design Flaws in the Human Body   

    From Nautilus: “Top 10 Design Flaws in the Human Body” 

    Nautilus

    From Nautilus

    May 14, 2015 [Just now in social media]
    By Chip Rowe Illustrations by Len Small

    From our knees to our eyeballs, our bodies are full of hack solutions [Did G-d do a bad job?].

    1

    The Greeks were obsessed with the mathematically perfect body. But unfortunately for anyone chasing that ideal, we were designed not by Pygmalion, the mythical sculptor who carved a flawless woman, but by MacGyver. Evolution constructed our bodies with the biological equivalent of duct tape and lumber scraps. And the only way to refine the form (short of an asteroid strike or nuclear detonation to wipe clean the slate) is to jerry-rig the current model. “Evolution doesn’t produce perfection,” explains Alan Mann, a physical anthropologist at Princeton University. “It produces function.”

    With that in mind, I surveyed anatomists and biologists to compile a punch list for the human body, just as you’d do before buying a house. Get out your checkbook. This one’s a fixer-upper.

    1. An unsound spine

    Problem: Our spines are a mess. It’s a wonder we can even walk, says Bruce Latimer, director of the Center for Human Origins at Case Western Reserve University, in Cleveland. When our ancestors walked on all fours, their spines arched, like a bow, to withstand the weight of the organs suspended below. But then we stood up. That threw the system out of whack by 90 degrees, and the spine was forced to become a column. Next, to allow for bipedalism, it curved forward at the lower back. And to keep the head in balance—so that we didn’t all walk around as if doing the limbo—the upper spine curved in the opposite direction. This change put tremendous pressure on the lower vertebrae, sticking about 80 percent of adults, according to one estimate, with lower back pain.
    Fix: Go back to the arch. “Think of your dog,” Latimer says. “From the sacrum to the neck, it’s a single bow curve. That’s a great system.” Simple. Strong. Pain-free. There’s only one catch: To keep the weight of our heads from pitching us forward, we’d need to return to all fours.

    2. An inflexible knee

    Problem: As Latimer says, “You take the most complex joint in the body and put it between two huge levers—the femur and the tibia—and you’re looking for trouble.” The upshot is your knee only rotates in two directions: forward and back. “That’s why every major sport, except maybe rugby, makes it illegal to clip, or hit an opponent’s knee from the side.”

    2

    Fix: Replace this hinge with a ball and socket, like in your shoulders and hips. We never developed this type of joint at the knee “because we didn’t need it,” Latimer says. “We didn’t know about football.”

    3. A too-narrow pelvis

    Problem: Childbirth hurts. And to add insult to injury, the width of a woman’s pelvis hasn’t changed for some 200,000 years, keeping our brains from growing larger.
    Fix: Sure, you could stretch out the pelvis, Latimer says, but technologists may already be onto a better solution. “I would bet that in 10,000 years, or even in 1,000 years, no woman in the developed world will deliver naturally. A clinic will combine the sperm and egg, and you’ll come by and pick up the kid.”

    4. Exposed testicles

    Problem: A man’s life-giving organs hang vulnerably outside the body.
    Fix: Moving the testicles indoors would save men the pain of getting hit in the nuts. To accomplish this, first you’d need to tweak the sperm, says Gordon Gallup, an evolutionary psychologist at the State University of New York at Albany. Apparently the testicles (unlike the ovaries) get thrown out in the cold because sperm must be kept at 2.5 to 3 degrees Fahrenheit below the body’s internal temperature. Gallup hypothesizes that these lower temperatures keep sperm relatively inactive until they enter the warm confines of a vagina, at which point they go racing off to fertilize the egg.1 This evolutionary hack prevents sperm from wearing themselves out too early. So change the algorithm, Gallup says. Keep the sperm at body temperature and make the vagina hotter. (And, by the way, there’s no need to draw up new blueprints: Elephants offer a pretty good prototype.)

    5. Crowded teeth

    Problem: Humans typically have three molars on each side of the upper and lower jaws near the back of the mouth. When our brain drastically expanded in size, the jaw grew wider and shorter, leaving no room for the third, farthest back molars. These cusped grinders may have been useful before we learned to cook and process food. But now the “wisdom teeth” mostly just get painfully impacted in the gums.
    Fix: Get rid of them. At one point, they appeared to be on their way out—about 25 percent of people today (most commonly Eskimos) are born without some or all of their third molars. In the meantime, we’ve figured out how to safely extract these teeth with dental tools, which, Mann notes, we probably wouldn’t have invented without the bigger brains. So you could call it a wash.

    6. Meandering arteries

    Problem: Blood flows into each of your arms and legs via one main artery, which enters the limb on the front side of the body, by the biceps or hip flexors. To supply blood to tissues at a limb’s back side, such as the triceps and hamstrings, the artery branches out, taking circuitous routes around bones and bundling itself with nerves. This roundabout plumbing can make for some rather annoying glitches. At the elbow, for instance, an artery branch meets up with the ulnar nerve, which animates your little finger, just under the skin. That’s why your arm goes numb when the lower tip of your upper arm bone, called the humerus or “funny bone,” takes a sharp blow.
    The Fix: Feed a second artery into the back side of each arm and leg, by the shoulder blades or buttock, says Rui Diogo, an assistant professor of anatomy at Howard University, in Washington, DC, who studies the evolution of primate muscles. This extra pipe would provide a more direct route from the shoulder to the back of the hand, preventing vessels and nerves from wandering too close to the skin.

    7. A backward retina

    Problem: The photoreceptor cells in the retina of the eye are like microphones facing backward, writes Nathan Lents, an associate professor of molecular biology at the City University of New York. This design forces light to travel the length of each cell, as well as through blood and tissue, to reach the equivalent of a receiver on the cell’s backside. The setup may encourage the retina to detach from its supporting tissue—a leading cause of blindness. It also creates a blind spot where cell fibers, akin to microphone cables, converge at the optic nerve—making the brain refill the hole.
    Fix: Poach the obvious solution from the octopus or the squid: Just flip the retina.

    3

    8. A misrouted nerve

    Problem: The recurrent laryngeal nerve (RLN) plays a vital role in our ability to speak and swallow. It feeds instructions from the brain to the muscles of the voice box, or larynx, below the vocal cords. Theoretically, the trip should be a quick one. But during fetal development, the RLN gets entwined in a tiny lump of tissue in the neck, which descends to become blood vessels near the heart. That drop causes the nerve to loop around the aorta before traveling back up the larynx. Having this nerve in your chest makes it vulnerable during surgery—or a fist fight.
    Fix: “This one’s easy,” says Rebecca Z. German, a professor of anatomy and neurobiology at Northeast Ohio Medical University, in Rootstown. While a baby is in utero, develop the RCN after sending that irksome neck lump of vessel tissue to the chest. That way, the nerve won’t get dragged down with it.

    9. A misplaced voice box

    Problem: The trachea (windpipe) and esophagus (food pipe) open into the same space, the pharynx, which extends from the nose and mouth to the larynx (voice box). To keep food out of the trachea, a leaf-shaped flap called the epiglottis reflexively covers the opening to the larynx whenever you swallow. But sometimes, the epiglottis isn’t fast enough. If you’re talking and laughing while eating, food may slip down and get lodged in your airway, causing you to choke.
    Fix: Take a cue from whales, whose larynx is located in their blowholes. If we moved the larynx into our nose, says German, we could have two independent tubes. Sure, we’d lose the ability to talk. But we could still communicate in song, as whales do, through vibrations in our nostrils.

    10. A klugey brain

    Problem: The human brain evolved in stages. As new additions were being built, older parts had to remain online to keep us up and running, explains psychologist Gary Marcus in his book Kluge: The Haphazard Evolution of the Mind.2 And that live-in construction project led to slapdash workarounds. It’s as if the brain were a dysfunctional workplace, where young employees (the forebrain) handled newfangled technologies like language while the old guard (the midbrain and hindbrain) oversaw the institutional memory—and the fuse box in the basement. A few outcomes: depression, madness, unreliable memories, and confirmation bias.
    Fix: We’re screwed.

    6

    References

    1. Gallup, G.G., Finn, M.M., & Sammis, B. On the origin of descended scrotal testicles: The activation hypothesis. Evolutionary Psychology 7, 517-526 (2009).

    2. Marcus, G. Kluge: The Haphazard Evolution of the Human Mind Houghton Mifflin, Boston, MA (2008).

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Welcome to Nautilus. We are delighted you joined us. We are here to tell you about science and its endless connections to our lives. Each month we choose a single topic. And each Thursday we publish a new chapter on that topic online. Each issue combines the sciences, culture and philosophy into a single story told by the world’s leading thinkers and writers. We follow the story wherever it leads us. Read our essays, investigative reports, and blogs. Fiction, too. Take in our games, videos, and graphic stories. Stop in for a minute, or an hour. Nautilus lets science spill over its usual borders. We are science, connected.

     
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